Microbiology Research doi: 10.3390/microbiolres17080155

Authors: Marta Gonçalves Joana Campos Inês C. Rodrigues Nuno Vale Paulo Martins da Costa Paula Silva

Campylobacter spp. are common commensals in broiler chickens and certain species are major causes of foodborne illness in humans. However, their on-farm dynamics and environmental dissemination remain poorly understood. This study investigated the occurrence and temporal dynamics of Campylobacter spp. in commercial broiler production systems by integrating faecal and airborne monitoring across three consecutive production cycles in two farms with contrasting productive historical performance. Faecal (n = 24) and air samples (n = 24) were analysed using culture-based methods, quantitative polymerase chain reaction (qPCR), and 16S rRNA gene amplicon sequencing, which were subsequently compared to assess concordance. In faecal samples, Campylobacter spp. colonisation generally occurred from mid-cycle onwards, with earlier and more consistent detection in the farm with suboptimal growth performance. In the optimal growth-performing farm, colonisation was not detected in the first cycle but emerged in subsequent cycles, coinciding with declining productive parameters, which include mortality, average weight at slaughter, Feed Conversion Ratio (FCR), and European Production Efficiency Factor (EPEF). Airborne Campylobacter DNA was intermittently detected by qPCR, in some cases preceding or occurring independently of faecal detection, whereas culture-based methods consistently failed to recover viable Campylobacter from air samples. Microbiome sequencing detected Campylobacter sporadically and at low relative abundances, yielding fewer positive detections across the monitored sampling timepoints than the targeted methods. Overall, qPCR proved to be the most sensitive approach across matrices, while faecal culture provided biologically meaningful data on viable loads. This study also documented temporal changes in Campylobacter detection patterns alongside productive performance indicators under commercial production conditions. These findings highlight the complementary value of faecal and airborne monitoring and underscore the importance of combining targeted molecular and culture-based approaches to characterise Campylobacter dynamics under commercial production conditions.

Microbiology Research doi: 10.3390/microbiolres17080154

Authors: Ana R. Miljković

Candida infections represent a major global public health challenge and remain among the most common opportunistic fungal infections worldwide. Although Candida albicans remains the predominant pathogen, the incidence of infections caused by non-albicans species, particularly Candidozyma auris, has increased substantially in recent years. Candida infections range from superficial mucocutaneous disease to invasive life-threatening infections associated with high morbidity and mortality. In addition to clinical burden, growing evidence indicates a substantial negative impact on health-related quality of life, particularly among patients with recurrent vulvovaginal candidiasis and chronic fungal infections.

Microbiology Research doi: 10.3390/microbiolres17080153

Authors: Rodrigo Costa Ainhoa Ferreira Cordero Francisco Ferreira João Metello Carina Santos João Belo Patrícia Coelho Sónia Mateus Miguel Castelo Branco Francisco Rodrigues

Staphylococcus aureus is one of the leading causes of both community- and healthcare-associated infections. Nasal colonization constitutes the primary reservoir for subsequent infection and transmission, while methicillin-resistant Staphylococcus aureus (MRSA) remains a major public health concern because of its resistance to multiple antimicrobial agents. However, data regarding community nasal colonization in rural Portuguese populations remain scarce. The BI-STAPH Project was established to address this knowledge gap through systematic surveillance of rural communities in inland Portugal. To estimate the prevalence of presumptive nasal colonization by Staphylococcus aureus and MRSA among adults living in the municipality of Fundão, Portugal, and to explore potential associations between colonization and demographic, behavioural, occupational, and environmental characteristics. A prospective community-based cross-sectional study was conducted as the second phase of the BI-STAPH Project. A total of 200 adults were recruited from different parishes of the municipality of Fundão. Bilateral nasal swabs were collected and processed using standardized microbiological methods for the presumptive identification of S. aureus. Presumptive MRSA isolates were investigated using a PBP2′ latex agglutination assay. Sociodemographic and exposure-related information was obtained through structured questionnaires. Associations between presumptive colonization and participant characteristics were evaluated using Pearson’s chi-square or Fisher’s exact tests, as appropriate. Presumptive S. aureus nasal colonization was identified in 56 of 200 participants, corresponding to a prevalence of 28.0% (95% CI: 21.8–34.2%). No presumptive MRSA-positive isolates were identified, corresponding to an observed prevalence of 0% (95% CI: 0.0–1.8%). Colonization prevalence was 29.5% among females and 26.8% among males, and ranged from 25.8% to 31.1% across age groups; neither sex nor age was significantly associated with colonization. Participants reporting daily animal contact had a colonization prevalence of 32.3%, compared with 20.5% among those without animal contact, but this difference was not statistically significant (p = 0.075). Overall, no statistically significant associations were identified between presumptive S. aureus colonization and the demographic, behavioural, occupational, or environmental variables evaluated. Presumptive S. aureus nasal colonization was common among adults living in the rural municipality of Fundão, Portugal, whereas no presumptive MRSA-positive isolates were identified in this study population. No statistically significant associations were observed between colonization and the characteristics evaluated. These findings expand the epidemiological evidence generated by the BI-STAPH Project and support continued community-based surveillance of S. aureus in rural Portugal. Future multicentre studies incorporating molecular confirmation, antimicrobial susceptibility testing, and larger populations will be important to better characterize circulating strains and transmission patterns within a One Health framework.

Microbiology Research doi: 10.3390/microbiolres17080152

Authors: Teodora Tihomirova Dimitar Parvanov Margarita Ruseva Rumiana Ganeva Maria Handzhiyska Jinahn Safir Ivan Pavlov Sofia Koristashevskaya Dimitar Metodiev Blaga Rukova Georgi Stamenov Savina Hadjidekova

The role of the endometrial microbiome in embryo implantation remains incompletely understood. While most studies have focused on taxonomic composition and Lactobacillus dominance, the ecological organization of microbial communities associated with implantation success has received limited attention. The aim of this study was to investigate whether implantation outcome following euploid embryo transfer is associated with differences in endometrial microbial network structure and community organization. Endometrial biopsies collected during the window of implantation from 95 women undergoing subsequent euploid embryo transfer were analyzed using 16S rRNA gene sequencing. Microbial diversity, co-occurrence networks, community structure, hub taxa, network robustness, and microbial association patterns were evaluated. The Pregnant group demonstrated a more interconnected microbial network with a greater number of significant associations, larger ecological modules, and increased network integration than the Non-pregnant group. Seventeen microbial associations were unique to the Pregnant network, whereas eleven were unique to the Non-pregnant network, indicating implantation-associated ecological rewiring. Lactobacillus-centered association patterns also differed between groups. These findings suggest that successful implantation is associated with coordinated endometrial microbial community organization rather than changes in individual taxa. Microbial network structure may represent a novel dimension of endometrial receptivity assessment.

Microbiology Research doi: 10.3390/microbiolres17080151

Authors: Hongbo Yuan Yanyan Liu Xu Li Jiaping Lv Xiaoyang Pang Shuwen Zhang Lizhi Ma Hui Zhang Yunna Wang

Short stature is a common pediatric endocrine–metabolic disorder characterized by impaired linear growth and increased risks of adverse health outcomes. Although previous reviews have summarized associations between gut microbiota and childhood health, few have focused on the mechanistic links among microbial composition, microbial-derived metabolites, endocrine regulation, and skeletal growth in short stature. This review provides an integrated framework exploring the potential interactions among gut microbiota composition, microbial-derived metabolites, endocrine regulation, and skeletal development in short stature. We summarize the clinical characteristics and epidemiological features of major short stature subtypes and discuss emerging evidence demonstrating the involvement of gut microbiota alterations and metabolite dysregulation in growth regulation. Particular attention is given to the bidirectional interactions between the gut microbiota and the growth hormone/insulin-like growth factor-1 (GH/IGF-1) axis, as well as the potential role of the gut–liver–bone axis in skeletal growth. Furthermore, this review integrates evidence from metabolomics studies, experimental animal models, and microbiota-targeted interventions to provide mechanistic insights into microbiota-mediated growth regulation. Dietary factors, physical activity, sleep, antibiotic exposure, probiotic interventions, and current clinical treatments are also discussed from the perspective of microbiota modulation. Despite increasing interest in microbiota-based strategies, clinical translation remains limited by insufficient functional validation, unclear causal relationships, and a lack of well-designed intervention trials. Future integration of functional microbiology, multi-omics approaches, and human-based validation platforms may facilitate the development of microbiome-based precision interventions for improving growth outcomes in children with short stature, particularly those with ISS.

Microbiology Research doi: 10.3390/microbiolres17080150

Authors: Alice Caramaschi Marianna Farotto Marta Mellai Francesco Favero Davide Corà Paolo Bottino Christian Leli Lidia Ferrara Chiara Bazzano Silvio Collani Valeria Bonato Andrea Rocchetti Marinella Bertolotti Annalisa Roveta Antonio Maconi Elisa Bona

During the COVID-19 pandemic, healthcare systems experienced significant disruption, increasing the risk of multidrug-resistant (MDR) pathogen transmission. Acinetobacter baumannii, a critical-priority MDR pathogen, is known for its ability to persist in hospital environments and rapidly acquire resistance. To investigate the genomic characteristics, antimicrobial resistance determinants, and phylogenetic relationships of outbreak-associated Acinetobacter baumannii isolates, whole-genome sequencing (WGS) and comparative genomic analyses on 24 clinical and environmental strains collected during the COVID-19 period were performed. Twenty-four A. baumannii isolates collected between August 2020 and February 2021 from clinical and environmental samples were analyzed by WGS. All isolates displayed an MDR phenotype, with uniform resistance to carbapenems and aminoglycosides, and preserved colistin susceptibility. One environmental strain showed extreme drug resistance. WGS confirmed medium-quality genome assemblies and the clonal spread of a single A. baumannii lineage. Most resistance genes, including OXA-23, ADC-type β-lactamases, and ade efflux pumps, were chromosomally encoded and shared across all isolates. Plasmid-mediated resistance genes were variably distributed. This outbreak of MDR A. baumannii was driven by the clonal dissemination of a genomically stable lineage. Combined genomic and epidemiological analyses underscore the importance of integrated surveillance and environmental decontamination to prevent the spread of MDR pathogens.

Microbiology Research doi: 10.3390/microbiolres17080149

Authors: Koycho Koev

Raw-milk and raw dairy products remain a high-sensitivity One Health interface because they bypass a major microbial control step and may carry viable foodborne pathogens, bacteria exhibiting antimicrobial resistance (AMR), and AMR genes from dairy animals, farm environments, milking equipment, handlers, storage systems, and informal or direct-sale chains. This narrative review synthesizes verified scientific evidence on raw milk as a potential vehicle pathway for resistant foodborne pathogens, clinically relevant opportunistic bacteria, indicator organisms, and AMR determinants, and evaluates AMR-related emerging public health risks through a One Health perspective. The review integrates evidence from outbreak investigations, raw milk and raw dairy surveillance, culture-based antimicrobial susceptibility testing, polymerase chain reaction (PCR), whole-genome sequencing (WGS), metagenomics, metaproteomics, risk assessment, and the consumer-risk literature. The synthesis shows that raw-milk-associated AMR evidence should be interpreted by inference level rather than by a single organism or global prevalence estimate. Public health concern becomes stronger when detection or occurrence is supported by viable recovery, plausible consumer exposure, transmission linkage, infection or colonization evidence, source-attribution data, or quantified burden estimates. Evidence is strongest for exposure pathways involving Campylobacter, extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales, methicillin-resistant Staphylococcus aureus (MRSA), Salmonella, Listeria, Enterococcus, Yersinia, and raw-milk resistomes, although causal strength differs across organism groups and study designs. The review distinguishes detection or occurrence, viable recovery, potential exposure, transmission, infection or colonization, source attribution, and attributable AMR burden. One Health control requires mastitis prevention, prudent antimicrobial use, milking hygiene, environmental monitoring, pasteurization or equivalent exposure barriers, WGS-supported outbreak investigation, integrated surveillance, and targeted risk communication.

Microbiology Research doi: 10.3390/microbiolres17080148

Authors: Chae Yeon Hwang Murugesan Chandrasekaran Se Chul Chun

Pepper (Capsicum annuum L.) is a major vegetable cultivated for seasoning in Korea. Peppers are typically grown as seedlings and transplanted into fields. Infection with Rhizoctonia solani immediately before transplantation can cause significant damage and loss during cultivation. The effectiveness of chemical fungicides is becoming increasingly limited owing to pesticide resistance, emphasizing the need for sustainable agricultural practices. This study aimed to identify a novel biocontrol agent by investigating tidal flat microorganisms capable of controlling damping-off disease in pepper caused by Rhizoctonia solani. Furthermore, we studied the inhibitory effects of different Bacillus species on the mycelial growth of R. solani AG-4 (KACC 40141) for the biological control of damping-off disease. Of the 116 bacterial strains from the tidal flats tested, five (including Bacillus sp. JB005) showed strong inhibitory activity in dual-culture assays against R. solani AG-4. These strains also demonstrated siderophore production, suggesting their potential to suppress damping-off in pepper. We screened useful agricultural traits (e.g., biofilm formation, IAA production, and phosphate solubilizing activity); the most promising strains were used for greenhouse experiments. The results indicated that Bacillus sp. JB005 strongly inhibited damping-off in pepper, suggesting that Bacillus sp. JB005 could serve as a biocontrol agent against R. solani infections.

Microbiology Research doi: 10.3390/microbiolres17080147

Authors: Audrius Kačergius

Replacing chemical compounds with biologically derived bioproducts in agriculture can make a comprehensive contribution to achieving the goals of both the Paris Agreement and the Green Deal. Scientific literature contains a significant amount of data on the use of probiotics in agriculture, which facilitate the supply of nutrients to plants, stimulate physiological processes, and inhibit the development of pathogens. These products do not have a negative impact on the surrounding environment and can therefore be used in sustainable land management. This article analyzes the microbiological composition of a bio-input made from fermented nettle extract and the species diversity of the cultivable bacteria. It was found that this input is rich in bacteria beneficial to plants and soil (Clostridium, Paenibacillus, Frankia, Rhizobium, Bradyrhizobium, Azospirillum, Azotobacter, and others), some of which can be cultured under artificial conditions. Among the cultivable bacteria grown from the tested input, the majority were representatives of the Pseudomonadota (92%), and a small proportion were Bacillota (6%). Among them were a great many different bacteria beneficial to the soil ecosystem. Thus, there is considerable potential here for the use of these bacteria in the production of biological products.

Microbiology Research doi: 10.3390/microbiolres17080146

Authors: Faten Ben Chehida Wafa Tombari Haythem Gharsa Youssef Rabia Sana Ferhi Maha Jrad Lilia Messadi

In the published paper [...]

Microbiology Research doi: 10.3390/microbiolres17080145

Authors: Alana Oswaldina Gavioli Meira dos Santos Botega Ellen Cristina Gaetti-Jardim Christiane Marie Schweitzer Elerson Gaetti-Jardim Júnior Anamaria Mello Miranda Paniago

The spread of antimicrobial-resistant bacteria in aquatic environments is a public health concern, especially in areas with anthropogenic activity. Hydroelectric reservoirs may act as interfaces facilitating the dissemination of resistance. Escherichia coli is used as an indicator of environmental contamination and antimicrobial resistance. To investigate the occurrence of E. coli in reservoirs of the Urubupungá Hydroelectric Complex (Paraná River basin, Brazil) and to characterize antimicrobial resistance profiles and ESBL/AmpC-related genes. Methods: Water samples were collected during rainy and dry seasons (2022–2024). A total of 200 E. coli isolates were analyzed by broth microdilution (EUCAST). ESBL and AmpC production were phenotypically assessed, and resistance genes (blaCTX-M, blaTEM, blaSHV, and ampC) were detected by PCR. 26% of isolates showed resistance to at least one antimicrobial, mainly tetracycline (18%), amoxicillin (15%), and ampicillin (15%). All isolates were susceptible to imipenem, meropenem, and norfloxacin. Among the investigated resistance markers, ampC was the most frequently detected gene, whereas blaCTX-M was the predominant ESBL-associated determinant. Significant associations were observed between blaCTX-M and resistance to cefotaxime, ceftazidime, and cefepime, whereas the presence of ampC was significantly associated with cefoxitin resistance. Significant associations were observed between β-lactam resistance and ESBL genes. Hydroelectric reservoirs under anthropogenic influence may serve as environmental reservoirs of antimicrobial-resistant E. coli, particularly ESBL producers. These findings highlight the role of aquatic environments in the dissemination of clinically relevant resistance genes.

Microbiology Research doi: 10.3390/microbiolres17080144

Authors: Silvia Preziuso Anna-Rita Attili Chiara Storoni Lorenza Di Perna Yubao Li Vincenzo Cuteri

In the original publication [...]

Microbiology Research doi: 10.3390/microbiolres17080143

Authors: Catherine W. Y. Wong Isai Salas Gonzalez Laura M. Carroll Joelle K. Salazar Thomas F. Rau Max Teplitski Wei Zhang

The transition toward reusable food packaging driven by European circular economy regulations introduces new food safety challenges related to microbial persistence and cross-contamination. GS-2 is a novel, food-safe antimicrobial formulation developed for use as a coating on reusable packaging materials. In the present study, the intrinsic antimicrobial activity of GS-2 was evaluated in liquid suspension against foodborne bacterial (Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella enterica Agona) and fungal pathogens (Aspergillus flavus and Aspergillus niger), and the transcriptomic response of L. monocytogenes following sublethal GS-2 exposure was investigated. GS-2 exhibited concentration-dependent microbicidal activity, with strong reductions observed at ≥2.8–3.0% against bacterial strains and A. flavus, while A. niger demonstrated resistance. Among bacteria, L. monocytogenes showed the greatest sensitivity, with populations reduced below detection limits at 3% GS-2. To elucidate mechanistic responses, RNA sequencing was performed on L. monocytogenes exposed to sublethal GS-2 concentrations (0.1–1.0%). Transcriptomic analyses using discrete and continuous models revealed a pronounced adaptive stress response at 0.5% GS-2, characterized by coordinated upregulation of pathways involved in carbon, nitrogen, and nucleotide metabolism. At higher sublethal concentrations (1%), transcriptional profiles shifted toward growth arrest and cellular damage management. These findings support GS-2 as a promising antimicrobial for enhancing the microbial safety of reusable food packaging systems.

Microbiology Research doi: 10.3390/microbiolres17080142

Authors: Georgiana-Denisa Gavriliţă Ştefania Ungureanu Paul-Cosmin Tirla Cristian Pop Alexandra Enache

Nosocomial bronchopneumonia is a severe lung infection that develops more than 48 h after hospital admission and is frequently caused by antibiotic-resistant bacteria. It is often identified postmortem in forensic practice, particularly in patients with severe traumatic injuries requiring prolonged hospitalization and immobilization. Diagnosis is typically based on macroscopic findings and histopathological examination of lung tissue. This study aimed to evaluate the diagnostic value of postmortem microbiological testing by comparison with antemortem microbiological data. Ten patients with a clinical diagnosis of nosocomial bronchopneumonia were selected from forensic cases. During autopsy, tracheal swabs and lung tissue samples were collected and subjected to culture-based and molecular analyses. The results were compared with those obtained from antemortem microbiological investigations. Pathogens characteristic of nosocomial infections were identified; however, concordance with in-hospital microbiological data was highest when using next-generation sequencing (NGS) metagenomic analysis. Tracheal swab culture appears to have limited reliability for postmortem identification of bacterial agents in healthcare-associated bronchopneumonia. In contrast, metagenomic next-generation sequencing (mNGS) of lung tissue obtained at autopsy showed the highest concordance with antemortem microbiological findings and may provide valuable complementary diagnostic information, particularly in polymicrobial infections.

Microbiology Research doi: 10.3390/microbiolres17080141

Authors: David Montes-Moreno Verónica Alacid Antonio V. Sanz-Ros Pedro Palazón Inmaculada Garrido-Jurado

The growing demand for sustainable crop protection has intensified interest in biological control agents. This study characterized a Trichoderma asperellum strain (IDE-10) to assess its suitability for integrated pest and disease management. Key ecophysiological traits, including temperature, pH, and ultraviolet (UV) tolerance, were evaluated, along with compatibility with commonly used fungicides and insecticides. The strain exhibited optimal growth at 28.28 °C and sustained high growth rates up to 35 °C, with a maximum threshold of 39.21 °C, indicating strong adaptation to warm climates. Sporulation was enhanced between 25 and 35 °C, with no growth at 5 °C, and soil viability remained stable from 7 to 21 °C. The IDE-10 strain demonstrated broad pH tolerance (3–7) and high resistance to UV-A and UV-B radiation, distinguishing it from commercial strains. Insecticides had no significant adverse effects, while fungicide compatibility varied, with IDE-10 being compatible with metalaxyl- and copper-based formulations. These findings highlight the robustness and adaptability of T. asperellum IDE-10, supporting its potential as a biocontrol agent for sustainable crop protection strategies, particularly in Mediterranean agricultural systems.

Microbiology Research doi: 10.3390/microbiolres17070140

Authors: Yassir Chiguer Jamila Bahhou

Tomato leaf mold, caused by Passalora fulva, is one of the most destructive fungal diseases affecting greenhouse tomato production and can cause substantial yield losses under conditions of high relative humidity and moderate temperatures that favor pathogen infection and disease development. This study evaluated the in vitro antifungal activity of a commercial fungicide formulation, Priori Top® (azoxystrobin + difenoconazole), and three essential oils derived from Eucalyptus globulus, Artemisia herba-alba, and Mentha pulegium against two monoconidial isolates of P. fulva. Unlike previous studies, which have mainly focused on mycelial growth, the present work simultaneously evaluated the effects of the tested products on mycelial growth, sporulation, and conidial germination, providing a comprehensive assessment of antifungal efficacy across three key developmental stages of the pathogen. Antifungal activity was quantified by estimating IC50 and IC90 values using Probit regression analysis. The azoxystrobin–difenoconazole formulation consistently exhibited the highest antifungal activity across all evaluated parameters and showed the lowest estimated IC50 and IC90 values for both fungal isolates. Among the tested essential oils, Artemisia herba-alba exhibited the greatest antifungal activity, reducing mycelial growth by 83% and 78% at 500 ppm for isolates 1 and 2, respectively, and consistently outperforming Mentha pulegium and Eucalyptus globulus. Differences in sensitivity were observed between the two fungal isolates, indicating intraspecific variability in their response to the tested treatments. These findings demonstrate the strong antifungal efficacy of the azoxystrobin–difenoconazole formulation against P. fulva and identify A. herba-alba essential oil as the most promising botanical treatment for integrated management of tomato leaf mold. Further greenhouse and field studies are required to validate these findings, optimize formulation strategies, and evaluate the practical application of A. herba-alba essential oil under commercial production conditions.

Microbiology Research doi: 10.3390/microbiolres17070139

Authors: Karim Zaher Halima Kholaiq Jalila El Bakkouri Naïma Amenzoui Samira Kalouch Ahmed Rguig Assiya El Kettani Sayeh Ezzikouri Ahd Ouladlahsen Ahmed Aziz Bousfiha

Acute bronchiolitis is the leading cause of infant hospitalization worldwide, with respiratory syncytial virus (RSV) historically predominating. Prospective virological data for the 2025–2026 epidemic season in Morocco were lacking. A prospective observational cohort study was conducted at the Department of Pediatric Infectious Diseases and Clinical Immunology, Casablanca Mother-Child Hospital, from August 2025 through March 2026. Consecutive infants aged 1–24 months hospitalized with acute viral bronchiolitis underwent nasopharyngeal sampling and multiplex rapid antigen testing for RSV, influenza A, influenza B, and SARS-CoV-2. A total of 131 infants were enrolled (median age 4.8 months; male-to-female ratio 0.84:1). At least one virus was identified in 63 patients (48.1%; 95% CI 39.1–57.3%). RSV predominated: 49 sole infections and 2 co-infections with influenza A, totaling 51 positives (80.9% of virus-positive cases; 38.9% of the cohort). Influenza A totaled 8 cases (12.7%), including the 2 co-infections; influenza B accounted for 2 further cases (3.2%). SARS-CoV-2 was not detected. Epidemic activity peaked in January 2026 (65 admissions), declining through February (34) and March (12). All detected pathogens have licensed preventive options, supporting the introduction of nirsevimab, maternal RSV vaccination, and seasonal influenza vaccination as public health priorities in Morocco.

Microbiology Research doi: 10.3390/microbiolres17070138

Authors: Joseph Nyombe Tshimbuka Marie Noelle Uwineza Yao Selom Atrah Wazih Nji Cho Yap Boum Muambangu Jean Paul Milambo

Mpox remains an important public health threat in several African countries, with recurrent outbreaks highlighting the need for decentralized and scalable diagnostic systems. During the 2024–2025 Mpox outbreak in Burundi, reliance on a single National Reference Laboratory limited timely diagnosis, reduced surveillance efficiency, and delayed outbreak response activities. This study describes and evaluates the implementation of a national strategy for decentralizing and expanding Mpox diagnostic capacity across Burundi. A descriptive implementation study was conducted between August 2024 and July 2025. Burundi implemented a four-phase diagnostic scale-up strategy that expanded Mpox testing services from one centralized laboratory to 56 decentralized GeneXpert-equipped laboratories, including mobile laboratory units. The implementation phases comprised strategic planning and risk mapping, pilot deployment at the national level, regional expansion, and extension to peripheral district laboratories. Key interventions included healthcare workforce training, strengthening laboratory supply chains, deployment of mobile diagnostic units, and integration of laboratory information into the national surveillance system. Program performance was assessed using indicators of laboratory network expansion, testing coverage, diagnostic turnaround time, and confirmed case detection. Following implementation, the number of operational Mpox diagnostic sites increased from 1 to 56, representing a 5500% expansion in testing capacity. National testing coverage approached 100%, substantially improving geographical access to diagnostic services. Weekly confirmed Mpox case detection increased by 496%, reflecting enhanced surveillance sensitivity and improved case identification. Diagnostic turnaround time decreased from 24–72 h under the centralized model to 2–4 h following decentralization. The expanded diagnostic network facilitated earlier case confirmation, more rapid isolation of infected individuals, strengthened surveillance activities, and accelerated implementation of outbreak control measures. The phased decentralization of Mpox diagnostics using existing GeneXpert infrastructure and mobile laboratories substantially improved testing access, reduced diagnostic delays, and strengthened outbreak response capacity in Burundi. This approach demonstrates a practical, scalable, and cost-effective model for enhancing epidemic preparedness and building resilient diagnostic systems in resource-constrained settings. Similar strategies could support improved detection and control of Mpox and other emerging infectious diseases across Africa and comparable low-resource environments.

Microbiology Research doi: 10.3390/microbiolres17070137

Authors: Hafsa Mguild Idrissa Diawara Ihssane Benzaarate Asma Er-Regragui Amine Aiddi Aboubakr Khazaz Siham El Machrafi Malak Snoussi Abdelfattah Chakib Nouzha Dini Kaotar Nayme

Pseudomonas aeruginosa is an important opportunistic pathogen increasingly associated with multidrug resistance (MDR) and therapeutic failure. Data on MDR community-associated P. aeruginosa in southern Morocco remain limited. This study evaluated the contribution of urban diagnostic laboratories to the surveillance of MDR P. aeruginosa in this underrepresented region. A retrospective multicenter study was conducted between January and December 2024 using data collected from urban medical diagnostic laboratories in southern Morocco. Clinical isolates of P. aeruginosa recovered from community-associated patients were identified using standard microbiological methods, and antimicrobial susceptibility testing was performed according to EUCAST guidelines. MDR was defined as non-susceptibility to at least one agent in three or more antimicrobial classes according to the international criteria. Associations between MDR status and demographic variables were assessed using Chi-square and Fisher’s exact tests, with statistical significance set at p < 0.05. Among the 49 P. aeruginosa isolates included, 29 (59.2%, 95% CI: 45.4–72.0%) were classified as MDR. High resistance rates were observed for several β-lactams, whereas most isolates remained susceptible to amikacin and selected β-lactam/β-lactamase inhibitor combinations. No statistically significant association was found between MDR status and demographic variables. These findings highlight the circulation of MDR P. aeruginosa in southern Morocco and suggest that urban diagnostic laboratories may provide valuable complementary data for community-level antimicrobial resistance surveillance.

Microbiology Research doi: 10.3390/microbiolres17070136

Authors: Evrard Mayombo Ngoussou Rolande Mabika Mabika Annicet Clotaire Dikoumba Florian Mbadinga Mackanga Ornella Zong Minko Léonce Fauster Ondjiangui Mundunge Mambu Fred Stecy Litchangou Bouka Franck Mounioko Jean Fabrice Yala

Urinary tract infections (UTIs) are a significant global health concern, with women being disproportionately affected. As the clinical importance of Klebsiella spp. as uropathogens continues to rise, this study aimed to determine their prevalence and associated factors among women attending a tertiary hospital in Libreville, Gabon. Bacteriological urine analyses were conducted on 791 women (inpatients and outpatients) at the Omar Bongo Ondimba Army Instruction Hospital between April and December 2024. Bacterial identification was performed using Analytical Profile Index (API 20E) strips and the VITEK® 2 Compact system. The overall UTI prevalence was 43.6% (345/791). Klebsiella spp. accounted for 14.4% (114/791) of all cases, representing an isolation rate of 33.0% (114/345) among infected participants. Klebsiella pneumoniae species complex (KpSC) was the predominant species (84.2%), followed by K. aerogenes (9.6%) and K. oxytoca (6.1%). Marital status was significantly associated with Klebsiella spp. UTIs; compared to single/divorced women, widows (OR = 2.1; 95% CI: 1.0–4.5) and those in married or cohabiting unions (OR = 1.7; 95% CI: 1.1–2.6) exhibited a significantly higher risk of infection. These findings highlight a substantial proportion of UTIs caused by Klebsiella spp. in Libreville and underscore the influence of sociodemographic factors on infection risk, emphasizing the need for targeted preventive measures in at-risk populations.

Microbiology Research doi: 10.3390/microbiolres17070135

Authors: Farhana Haider Himaxi Patel Agata J. Pacuła-Miszewska Magdalena Obieziurska-Fabisiak Jacek Ścianowski Ketan Patel Blase Billack

Vulvovaginal candidiasis (VVC) is a common mucosal infection that predominantly affects reproductive-aged women. Although conventional antifungal agents remain the primary treatment option, there is growing interest in developing alternative therapeutic approaches that can enhance antifungal efficacy while potentially reducing treatment burden. Natural products have emerged as valuable sources of bioactive compounds with antifungal potential, offering opportunities for novel combination-based therapies. Ebselen (EB), an organoselenium compound with potent redox-modulating and antifungal properties, and its structurally related analogs represent promising candidates for such strategies. Likewise, black seed oil (BSO), derived from Nigella sativa, and its major active constituent, thymoquinone (TQ), have demonstrated antifungal activity against Candida species, supporting their investigation as natural product-based partners in synergistic antifungal combinations. Commercially prepared BSO and purified TQ were tested across a range of concentrations in a broth microdilution assay in combination with EB and novel organoselenium analogs, including Ebselen Oxide (EB-Ox) and N-octyl-1,2-benzisoselenazol-3(2H)-one (APM C6). Minimum inhibitory concentrations (MICs) for single agents and combinations were determined, and the resulting datasets were analyzed using the web-based Synergy Finder platform. EB, EB-Ox, and APM C6 showed consistent synergy with BSO and TQ against C. albicans (clinical isolate S1), as indicated by positive synergy scores relative to monotherapies.

Microbiology Research doi: 10.3390/microbiolres17070134

Authors: Neptu Islamy Raharja Mohammad Amzad Hossain

Nitrogen and phosphorus are essential macronutrients that often limit plant growth due to their low bioavailability in soil. Beneficial microorganisms, including nitrogen-fixing and phosphate-solubilizing bacteria, play important roles in improving nutrient availability and supporting plant productivity. This study investigated the populations of nitrogen-fixing and phosphate-solubilizing bacteria associated with different Curcuma species. Samples were collected during the vegetative stage from rhizosphere soil, rhizomes, stems, and leaves. Plant tissues were surface-sterilized to isolate endophytic bacteria, and microbial populations were enumerated using nitrogen-free agar and Pikovskaya agar at 28 °C for 7–14 days. The results revealed clear differences in bacterial populations among plant compartments and Curcuma species. Nitrogen-fixing bacteria were most abundant in the rhizosphere, reaching 3.0–23.3 × 104 CFU/g in field conditions and 3.3–18.3 × 104 CFU/g in the plastic house, followed by rhizomes, stems, and leaves. Similarly, phosphate-solubilizing bacteria showed the highest populations in the rhizosphere (11.3–29.7 × 104 CFU/g in the field and 4.3–25.5 × 104 CFU/g in the plastic house). These findings suggest that Curcuma-associated nitrogen-fixing and phosphate-solubilizing bacteria may contribute to nutrient cycling and potentially enhance plant adaptation to environmental stresses through improved nutrient acquisition, providing a basis for future studies and biofertilizer development in sustainable agriculture.

Microbiology Research doi: 10.3390/microbiolres17070133

Authors: João Gabriel Lira de Carvalho Carmelo José Albanez Bastos Filho Qiang-Sheng Wu Aline Costa da Mota Fábio Sérgio Barbosa da Silva

Arbuscular mycorrhizal fungi positively modulate the production of plant bioactive compounds under greenhouse conditions and in experimental fields; however, their role in naturally occurring trees is poorly understood. This research aimed to verify the relationship between mycorrhizal activity and the concentration of foliar biomolecules in a natural population of Anadenanthera colubrina. Leaves and rhizosphere soil were collected from ten individuals of two fragments during the dry and rainy seasons. Foliar metabolite concentrations were quantified, while the soil was used to evaluate mycorrhizal colonization and glomalin-related soil proteins (GRSPs). Mycorrhizal colonization showed a positive correlation (p ≤ 0.05) with metabolite production only during the dry season. GRSPs has higher deposition during the dry season, but has a positive correlation (p ≤ 0.05) with metabolite production only in the rainy season. Both seasons influenced metabolite concentration, with the highest accumulation occurring during the rainy season. Therefore, mycorrhizal colonization and GRSPs deposition are related to the production of foliar metabolites of A. colubrina in a natural environment, but this relationship is strongly modulated by local rainfall.

Microbiology Research doi: 10.3390/microbiolres17070132

Authors: Maria Pandova Ralitsa Petrova Yoana Kizheva Sergei Ivanov Petya Hristova

Influent wastewater, characterized by a diverse bacterial composition of human and animal origin, is a suitable source for studying the spread of antibiotic resistance and virulence genes, particularly in Enterococcus faecalis and Enterococcus faecium. This study aimed to evaluate the potential of these two species as reservoirs and indicators of antibiotic resistance and virulence genes. Wastewater treatment plants near the three largest cities of Bulgaria (Sofia, Varna and Burgas) were selected for sampling. Influent wastewater samples were collected for a period of 3 months (February, March and May) and used in the analyses. Overall, 34 bacterial isolates (E. faecalis, n = 13 and E. faecium, n = 21) were isolated and identified by MALDI-ToF. Phenotypic and genotypic methods were used to evaluate their antibiotic resistance profiles (focusing on clinically relevant antibiotics) and virulence potential. High dissemination of phenotypic ampicillin and quinupristin-dalfoprisin resistance (97% of all tested strains and 81% of all E. faecium strains, respectively) was established. In March, the highest number of antibiotic-resistant profiles was observed, including the emergence of MDR strains, primarily among E. faecium strains. Molecular analyses revealed a dissemination of genes encoding resistance to aminoglycosides and β-lactam antibiotics. The most prevalent virulence genes were gelE and ace, found only in E. faecalis strains. All gelE-positive strains also exhibited phenotypic gelatinase activity. In this study, E. faecium shows greater antibiotic resistance potential, whereas E. faecalis exhibits increased virulence capacity. These exploratory findings support the usefulness of influent wastewater as a matrix for monitoring antibiotic-resistant and potentially virulent enterococcal isolates, while larger-scale and seasonally representative studies are needed to confirm temporal and geographic patterns.

Microbiology Research doi: 10.3390/microbiolres17070131

Authors: Océane Bonadei Célia Fortuna Rodrigues José Carlos Andrade

The skin microbiome plays a central role in maintaining cutaneous homeostasis, and its disruption has been implicated in a wide range of inflammatory and degenerative skin disorders. This review critically evaluates the current evidence on topical probiotics in dermatology, integrating microbiological mechanisms, formulation strategies, and translational and regulatory challenges within a single framework—an angle that remains insufficiently addressed in previous reviews. A targeted search of PubMed and ScienceDirect (2009–2025) was conducted to identify relevant original studies. The results suggest that topical probiotics may promote skin health through three broad, interconnected axes: (i) modulation of host responses (e.g., inflammation, immune signaling, and oxidative stress); (ii) microbial ecology and pathogen control (e.g., competition, acidification, and antimicrobial metabolite production); and (iii) support of barrier function and tissue repair (e.g., lipid metabolism, re-epithelialization, and extracellular matrix remodeling). Efficacy appears to depend strongly on strain specificity, formulation design, and microbial viability during storage and application. In addition to conventional dosage forms, advanced platforms—hydrogels, microgels, microparticles, and microneedle-based systems—have been investigated to improve stability and local delivery. Promising preclinical and clinical results have been reported for acne, wound healing, skin barrier repair, and anti-aging applications. Nevertheless, major translational challenges remain, including limited standardization, instability of live microorganisms, insufficiently representative experimental models, and regulatory uncertainty. Overall, topical probiotics represent a promising microbiome-based strategy in dermatology, but robust clinical validation and formulation optimization are still needed to support broader clinical implementation.

Microbiology Research doi: 10.3390/microbiolres17070130

Authors: Irán Suárez-González Adina Howe Julio A. Hernández-González Pablo Misael Arce Amézquita Mario Rojas Arzaluz Ricardo Vázquez-Juárez Maurilia Rojas-Contreras

Coral-associated microbial communities play a critical role in the health and resilience of reef ecosystems; however, the relative importance of host identity and environmental factors in shaping these communities remains unclear, particularly in understudied regions such as the Gulf of California. In this study, we characterized the taxonomic composition, diversity patterns, persistent taxa (core bacteriome), and predicted functional potential of bacterial communities associated with three coral genera (Pocillopora, Porites, and Pavona) and surrounding seawater using 16S rRNA gene amplicon sequencing and PICRUSt2-based functional inference. Bacterial community structure differed significantly among coral hosts (PERMANOVA, p < 0.01), whereas geographic location and measured physicochemical parameters had no detectable effect. Coral-associated bacterial communities exhibited lower alpha diversity than seawater and formed distinct host-specific clusters in beta-diversity analyses. Core bacteriome analysis revealed a combination of conserved and host-specific taxa, with Acinetobacter consistently present across hosts, while genera such as Pseudovibrio and Ruegeria showed host-specific associations. Differential abundance analyses further confirmed distinct bacterial signatures among coral genera. Predicted functional profiles were dominated by central metabolic pathways and exhibited significant differences among hosts, although overall functional composition remained relatively conserved. Stratified analyses indicated that similar metabolic pathways were supported by different taxonomic assemblages, suggesting functional redundancy. Overall, our results demonstrate that host identity is the primary driver of both taxonomic composition and predicted functional potential in coral-associated bacterial communities in the Gulf of California, highlighting the coexistence of stability and host-specific differentiation within the coral holobiont.

Microbiology Research doi: 10.3390/microbiolres17070129

Authors: Morales-Paczka Ivonne Michele Naranjo-Bravo Jaquelin Escalera-López Melanie Alicia García-Ángeles José de Jesús Parra-Ortega Berenice Contreras-Rodríguez Araceli Rivera-González Gibrán José Félix Aguirre-Garrido Ma. Guadalupe Aguilera-Arreola

Sexually transmitted infections remain a major public health concern among men who have sex with men (MSM), particularly due to the high frequency of coinfections and the limitations of syndromic management. This study aimed to describe the frequency of bacterial sexually transmitted and urogenital pathogens among symptomatic MSM attending two specialized sexual health clinics in Mexico City. A prospective cross-sectional study was conducted with 150 adult MSM presenting symptoms suggestive of urethritis. Urethral swab samples were analyzed using a multiplex real-time polymerase chain reaction (PCR) assay for the detection of Neisseria gonorrhoeae, Chlamydia trachomatis, Mycoplasma genitalium, Mycoplasma hominis, Ureaplasma urealyticum, Ureaplasma parvum, and Trichomonas vaginalis. At least one pathogen was detected in 91/150 participants (60.7%). N. gonorrhoeae was the most frequent pathogen (33.3%), followed by U. urealyticum (15.3%), M. genitalium (9.3%), and C. trachomatis (9.3%). Coinfections were identified in 15 participants, representing 10.0% of the total population and 16.5% of those with a positive PCR result. Most coinfections involved N. gonorrhoeae, particularly with C. trachomatis. These findings provide descriptive microbiological evidence on the frequency and coinfection patterns of bacterial sexually transmitted infections (STIs) associated pathogens among symptomatic MSM attending specialized sexual health clinics in Mexico City. The high detection rate and occurrence of concurrent infections highlight the limitations of syndromic management and support the value of timely multiplex molecular diagnostics to improve etiological characterization, antimicrobial stewardship, and clinical decision-making in this population.

Microbiology Research doi: 10.3390/microbiolres17070128

Authors: Mariana de Resende Damas Cardoso-Miguel Pedro Henrique Bürgel Raffael Júnio Araújo de Castro Clara Luna Marina Stephan Alberto de Oliveira Patrícia Albuquerque Ildinete Silva-Pereira Anamélia Lorenzetti Bocca Aldo Henrique Tavares

C-type lectin receptors (CLRs) play central roles in sensing fungal pathogens and coordinating Syk-CARD9-dependent inflammatory responses. While Dectin-3 contributes to antifungal immunity against several clinically relevant fungi, its role in host defense against Paracoccidioides brasiliensis remains unknown. Here, we investigated the impact of Dectin-3 deficiency using Clec4d−/− mice and primary phagocytes during experimental Paracoccidioidomycosis. Dectin-3-deficient macrophages and dendritic cells displayed unaltered cytokine production, phagocytic capacity, fungicidal activity, and maturation following P. brasiliensis challenge. Consistently, the absence of Dectin-3 did not impact survival or pulmonary fungal burden during long-term systemic infection. These findings are consistent with functional redundancy among CLRs, potentially involving Dectin-1, Dectin-2, or other Syk-coupled receptors rendering Dectin 3 dispensable for immunity to systemic experimental P. brasiliensis infection.

Microbiology Research doi: 10.3390/microbiolres17070127

Authors: Jorge Luis Cortinas-Salazar Marissa Y. Díaz-Aguilera Cristina García-De la Peña Quetzaly K. Siller-Rodríguez Sergio I. Barraza-Guerrero Juan Carlos Ontiveros-Chacón Verónica Ávila-Rodríguez Jesús Vásquez-Arroyo Luis M. Valenzuela-Núñez Annely Zamudio-López Irene Pacheco-Torres

Urban pigeons (Columba livia) are widely distributed synanthropic birds closely associated with environments of intense human activity, raising interest in their role in urban microbial dynamics. Here, we characterized the fecal bacterial microbiota of urban pigeons from northern Mexico using 16S rRNA gene amplicon sequencing (V3–V4). A total of 1479 amplicon sequence variants (ASVs) were identified across five pooled samples. Alpha diversity varied among pools, with observed richness ranging from 228 to 514 ASVs. The bacterial community was dominated by Proteobacteria and Firmicutes, particularly Escherichia–Shigella and Enterococcus. PICRUSt2-based functional predictions suggested a predominance of predicted metabolic pathways related to carbohydrate degradation and energy acquisition. Conservative taxonomic screening identified 58 gut-associated taxa, including 15 bacteria previously reported in association with humans; however, only three (Clostridium perfringens, Enterococcus faecalis, and Proteus mirabilis) showed reported zoonotic associations, all at very low relative abundances (<0.07%). These findings indicate that the fecal bacterial communities characterized in this study were dominated by taxa commonly associated with the avian gastrointestinal tract, whereas taxa that could be conservatively linked to documented zoonotic reports represented only a minor fraction of the detected microbiota. Overall, the results contribute to a more ecologically informed understanding of urban pigeon-associated microbiota within a One Health framework.

Microbiology Research doi: 10.3390/microbiolres17070126

Authors: Syed Ammar Hussain Majher I. Sarker Brajendra K. Sharma Tony Z. Jin

This study evaluates the effects of seven biochemical stimulants, ferulic acid, malic acid, L-carnitine, ergothioneine, magnesium sulfate, trehalose, and betaine, on biomass accumulation, total lipid content, and docosahexaenoic acid (DHA) production in Aurantiochytrium sp. ATCC PRA-276 under controlled fermentation conditions. The compounds were selected based on their reported roles in antioxidant defense, carbon flux regulation, osmoprotection, or methyl group donation, with the aim of assessing whether targeted, non-GMO supplementation could modestly enhance microbial productivity. Compared with the control, supplementation with L-carnitine and ferulic acid resulted in the greatest enhancement of DHA production, increasing DHA concentration by 31.7% and 29.2%, respectively. These treatments were also associated with statistically significant, albeit moderate, increases in total lipid accumulation and biomass production. These responses indicate correlated improvements in overall cellular productivity rather than isolated effects on lipid biosynthesis. DHA concentrations were quantified following lipid extraction and transesterification using GC-based analysis; however, comprehensive fatty acid compositional profiling (e.g., saturated, monounsaturated, and polyunsaturated fatty acid distributions or DHA-to-total lipid ratios) was not performed. Although direct mechanistic assays were not performed, the observed trends are consistent with known biochemical functions related to redox balance, cofactor availability, and stress adaptation. A preliminary cost-efficiency analysis identified malic acid as the most economical stimulant for DHA enhancement, whereas ergothioneine was the least cost-effective despite measurable biological effects. Collectively, these findings demonstrate that biochemical stimulation can provide incremental yet reproducible gains in DHA production and lipid accumulation. This work supports the use of targeted biochemical supplementation as a scalable, non-GMO strategy for microbial omega-3 production and establishes a foundation for future optimization through combinatorial supplementation, multi-omics validation, and process engineering.

Microbiology Research doi: 10.3390/microbiolres17070125

Authors: Fatoumata Kontao Ibrehima Guindo Assiya Elkettani Cheickna Hamallah Dicko Brehima Zerbo Hawa Sanogo Néhémie Nzoyikorea Klema Marcel Koné Alou Sanogo Demba Koita Mahamadou Abdou Zahra Aadam Jalila El Bakkouri Idrissa Diawara Ahmed Aziz Bousfiha

Invasive bacterial infections caused by Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis remain a major public health concern. This study aimed to perform the molecular characterization of bacterial strains responsible for meningitis in patients of all ages who met the World Health Organization case definition for meningitis and had cerebrospinal fluid samples collected between January 2021 and December 2022 at the Clinical Bacteriology Laboratory of the National Public Health Institute of Mali. We conducted a surveillance-based observational study using national surveillance data collected between January 2021 and December 2022. Data were collected continuously and in real time throughout the study. The analysis was cross-sectional and descriptive. Data were obtained from samples received at the laboratory, accompanied by individual clinical notification forms. For each sample, demographic data and additional clinical information, including vaccination status, were collected. Infection was diagnosed by isolating invasive strains through culture, confirmed by real-time triplex PCR, and positive cases were further characterized by real-time triplex PCR for serotyping. Overall, 103 infections were confirmed among the 1000 samples received, corresponding to a positivity rate of 10.3%. S. pneumoniae predominated with 62%, followed by H. influenzae type b with 36% and N. meningitidis serogroup X with 2%. The identified serotypes of pneumococcus were predominantly not covered by existing vaccines, particularly serotype 23A (38.30%), while others, including serotypes 1 (17.02%) and 3 (10.63%), are included in the PCV13 vaccine. The distribution of cases by age and gender shows a predominance of males, accounting for 60.2% of cases (62/103). The 0–5 age group is by far the largest, accounting for 76.7% of cases (79/103), with males representing 58. 22% (46 cases). These findings highlight the importance and the need for continuous monitoring surveillance of circulating strains and strengthening vaccination efforts to improve prevention.

Microbiology Research doi: 10.3390/microbiolres17070124

Authors: Veroslava V. Stankovic Dragana P. Jovic Natasa K. Rancic

Attention-deficit/hyperactivity disorder (ADHD) is a complex neurodevelopmental disorder increasingly discussed within the microbiota-gut–brain axis. This narrative review synthesizes evidence on bacterial and fungal dysbiosis in ADHD, with emphasis on Candida spp., diet, probiotics, synbiotics, and health-related quality of life. A structured narrative search of PubMed/MEDLINE, Scopus, and KoBSON-accessible sources was performed for studies addressing ADHD, gut microbiota, mycobiome, Candida, nutrition, microbiome-targeted interventions, and quality of life. Evidence was synthesized thematically because of methodological heterogeneity. Available studies suggest that ADHD may be associated with altered gut microbial diversity, changes in taxa such as Faecalibacterium, Blautia, Odoribacter, and Enterococcus, and immune–metabolic alterations. However, findings are heterogeneous and do not support a single ADHD-specific microbial signature. The fungal component remains insufficiently investigated, although evidence indicates increased Candida, particularly Candida albicans, in children with ADHD and a possible link with intestinal permeability. Dietary quality, micronutrient status, probiotics, and synbiotics may modulate microbiota–gut–brain pathways, but should be considered complementary and individualized, particularly in patients with gastrointestinal, dietary, immune, or metabolic vulnerability. Bacterial and fungal dysbiosis may represent biologically plausible, primarily associative components of ADHD-related pathophysiology. Evidence remains preliminary, exploratory, non-causal, and requires cautious interpretation in future research and clinical settings.

Microbiology Research doi: 10.3390/microbiolres17070123

Authors: Jian Zhang Weina Liu Huaiyu Zhang Jinquan Wang Ruiyang Zhang Xiumin Wang Hui Tao Zhenlong Wang Yongli Zhang Bing Han

With the development of the pet industry, public attention to pet food safety and nutritional health has been continuously increasing. Postbiotics were initially defined as inactivated microorganisms or microbial cellular components that confer health benefits to the host. Compared with probiotics, postbiotics possess superior safety and stability. They can effectively eliminate the potential risk of horizontal transfer of drug-resistant genes carried by live bacteria, and also feature better manufacturability and storage performance. At present, most research on postbiotics has focused on humans and large domestic animals, with relatively few applications in dogs and cats. This indicates that further research on postbiotics in canines and felines is still needed to better promote their practical application in promoting pet food health. This article provides a comprehensive review of the current research status of postbiotics, focusing on their potential benefits and mechanisms for pet health. It proposes that future studies should concentrate on in vivo experimental validation to clarify the safety, optimal dosage, and specific functions of postbiotics in companion animals. Such research will offer a scientific basis for the application of postbiotics in pet food formulations, ultimately promoting the health and welfare of pets.

Microbiology Research doi: 10.3390/microbiolres17070122

Authors: Mariana da Silva Marques Beatriz Martins Machado Juliana Torres Tomazi Fritzen Geovana Depieri Yoshitani Elis Lorenzetti Alice Fernandes Alfieri Amauri Alcindo Alfieri

Neonatal diarrhea remains a significant threat to piglet health, resulting in substantial economic losses worldwide. Among the viral pathogens associated with this condition, rotavirus (RV) has been extensively reported in Brazil; however, lineage-level classification of circulating strains remains limited. This study aimed to characterize G and P genotypes of porcine RV field strains associated with diarrhea in piglets in Southern Brazil. A total of 10 fecal samples were collected by field veterinarian from diarrheic suckling piglets aged 1 to 14 days and analyzed by RT-PCR for the detection of RV species A, B, C, and H. RV species A (RVA) was detected in 90% (9/10) of the samples, while no other RV species were identified. Genotyping based on the VP7 and VP4 genes revealed a single G3P[6] genotype combination in all RVA-positive samples. Nucleotide (nt) and deduced amino acid (aa) sequence analysis revealed high genetic similarity among strains, with values of up to 99.3% for nt and 98.0% for aa of the VP7 gene and 100% for the VP4 gene (nt and aa). Phylogenetic analysis indicated that the VP7 sequences clustered with Brazilian G3 strains, forming a distinct group consistent with a novel lineage (putative G3-XII), whereas VP4 sequences supported a new sublineage (putative P[6]-Ig). These findings demonstrate low genetic variability of RVA field strains in this neonatal diarrhea outbreak, suggesting the circulation of a single viral population. They also emphasize the importance of continuous molecular surveillance to gain a deeper understanding of viral evolution and transmission dynamics in swine populations.

Microbiology Research doi: 10.3390/microbiolres17070121

Authors: Priscila de Moraes Sanches Renata Bacila Morais dos Santos Souza Heloísa Lara Silva Eduarda Lorena Fernandes Lorenna Nicole Araújo Santos Laiane Silva Lima Laís de Moraes Antunes Adriana Dausen Meyer Ananda Portella Felix

Stressful situations can negatively affect the intestinal microbiota and contribute to gastrointestinal disorders. This study investigated the effects of a synbiotic (SYN) on fecal characteristics and ammonia concentrations, selected fecal bacterial groups, and dysbiosis index (DI) of healthy adult Beagles undergoing an abrupt dietary change. Sixteen adult dogs were divided into two groups: a placebo (PLA, no supplementation, n = 8) and a SYN supplementation group (n = 8). Dogs from both groups were fed a highly digestible diet for 20 days. On day 21, all dogs underwent an abrupt transition to a less digestible diet, which they continued to receive for an additional 20 days. Fecal samples were collected on days 20, 22, and 40 to analyze fecal dry matter, score, ammonia, pH, microbiota, and DI. The SYN supplementation did not affect fecal characteristics or DI of dogs (p > 0.05). After dietary change, an increase in fecal Bifidobacterium and universal bacteria was observed only in the PLA group (p < 0.05). In addition, dietary transition increased DI and fecal Escherichia coli regardless of the SYN supplementation (p < 0.05). Dogs fed the highly digestible diet presented greater fecal Peptacetobacter hiranonis and lower Streptococcus, Bifidobacterium, Lactobacillus, and Bacteroides (p < 0.05). Dogs supplemented with SYN presented lower fecal Clostridium perfringens than the PLA group when fed the less digestible diet (p < 0.05). These results suggest that abrupt dietary change may promote alterations associated with intestinal dysbiosis in dogs. Moreover, SYN supplementation was associated with lower fecal C. perfringens abundance in dogs fed the less digestible diet.

Microbiology Research doi: 10.3390/microbiolres17070120

Authors: Yusuke Tanaka Daiki Miki C. Nelson Hayes Yusuke Johira Ryoichi Miura Hatsue Fujino Atsushi Ono Eisuke Murakami Tomokazu Kawaoka Masataka Tsuge Shiro Oka

There have been reports of an association between the gut microbiota and the development of chronic liver disease, fibrosis, and carcinogenesis; however, it is not yet possible to reach a definite conclusion. In this cross-sectional study, we examined the association between the presence or absence of hepatocellular carcinoma (HCC) and the gut microbiota in patients with chronic hepatitis B virus (HBV) infection. The study subjects consisted of 62 consecutive HBV patients admitted to our hospital who provided informed consent to participate in the study. We performed 16S rRNA analysis using DNA extracted from fecal pellets. The sequencing depth per sample was 80,000 to 90,000 reads. We calculated the proportion of each bacterial genus so that the total for each sample added up to 100%. The male-to-female ratio was 49/13, the median age was 67 years, and 46 of the patients had HCC. Twenty microbial phyla spanning 41 classes, 79 orders, 163 families, and 431 genera were identified. Receiver operating characteristic (ROC) analysis was performed on the identified bacterial taxa, from the level of phylum down to genus, to assess their ability to distinguish between patients with and without HCC. Several bacteria with an area under the curve (AUC) > 0.65 were identified as follows: TM7 phylum TM7-3 class (AUC = 0.700); Firmicutes phylum Clostridiales class Lachnobacterium genus, Dialister genus, Ruminococcus genus, and Roseburia genus (AUC = 0.670, 0.668, 0.667, and 0.660, respectively); and Firmicutes phylum Erysipelotrichi class (AUC = 0.656). Combining three of these taxa resulted in high discriminative power (p = 0.000585) with a sensitivity and specificity of 0.761 and 0.750, respectively. A similar trend was observed in the subgroup analysis based on liver reserve capacity. Even after adjusting for factors related to liver reserve capacity in the multivariate analysis, an association between these bacterial genera and HCC was confirmed. Our results suggest that gut microbiota may be associated with the prevalence of HCC in HBV patients.

Microbiology Research doi: 10.3390/microbiolres17070119

Authors: Koycho Koev Gabriela Goujgoulova

Wesselsbron disease remains an underrecognized mosquito-borne flaviviral disease despite long-standing evidence of ruminant reproductive loss, neonatal disease, hepatic pathology, zoonotic infection, and mosquito-associated circulation. This narrative review critically synthesizes verified evidence on Wesselsbron virus (WSLV) at the animal–human–vector–environment interface, with the specific aim of clarifying why the virus should be considered a surveillance-sensitive One Health pathogen rather than a rare veterinary curiosity. The review integrates classical veterinary pathology, experimental infection studies, human case reports, serological and molecular evidence, mosquito surveillance, ecological suitability modelling, diagnostic-development studies, and recent evidence from molecular epidemiology, camel investigations, and digital histopathology. The review uses an evidence-weighted synthesis to distinguish experimentally and pathologically supported animal disease, confirmed but poorly quantified human infection, mosquito-associated detection, ecological suitability, diagnostic under-recognition, and unresolved reservoir or transmission questions before integrating these domains into a qualitative One Health risk-assessment framework. The evidence supports WSLV as a cause of ruminant abortion, neonatal disease, and hepatic lesions, confirms zoonotic potential, and indicates repeated detection in ecologically relevant mosquito and multi-host contexts. However, current data remain insufficient for robust estimates of animal burden, human incidence, reservoir competence, natural route frequency, or climate-driven expansion. WSLV should therefore be incorporated into targeted differential diagnosis, laboratory readiness, and One Health surveillance where ruminant abortion events, unexplained neonatal disease, compatible mosquito ecology, undiagnosed febrile illness, diagnostic ambiguity, or ecological suitability indicate plausible risk.

Microbiology Research doi: 10.3390/microbiolres17060118

Authors: Xiang Zhang Wenjuan Zhai Shijuan Gao

The utilization of sugarcane molasses as a low-cost carbon source for riboflavin production is hindered by the reactive oxygen species (ROS) stress induced by its complex components, which suppresses microbial metabolism. To address this, we employed adaptive laboratory evolution (ALE) under progressively increasing stress to develop a sugarcane molasses-tolerant and high-yielding Ashbya gossypii. The adapted strain achieved a riboflavin titer of 298.39 ± 2.01 mg/L, representing a 99.4% increase over the parental strain (149.66 ± 4.97 mg/L), accompanied by a 96% increase in biomass (dry cell weight). Notably, the specific riboflavin production per unit biomass showed no significant difference between the two strains, indicating that the improved total yield was primarily driven by enhanced biomass accumulation. Transcriptomic analysis revealed the molecular basis for this enhanced biomass accumulation—the elevated expression of antioxidant enzymes (SOD1, PRDX5) mitigated ROS levels to support cellular growth, while the coordinated upregulation of the pentose phosphate pathway (E2.2.1.1) and purine metabolism genes (PPAT, ADE5, PFAS, ADSL) enhanced the supply of biosynthetic precursors, ribulose-5-phosphate (Ru5P) and GTP, for nucleotide biosynthesis and cell proliferation. These metabolic adjustments collectively enabled the adapted strain to achieve robust growth under sugarcane molasses stress, thereby driving the overall increase in riboflavin production. This study elucidates the molecular mechanism underlying ALE-improved riboflavin production and provides a promising strategy for its industrial fermentation using sugarcane molasses.

Microbiology Research doi: 10.3390/microbiolres17060117

Authors: Fatma Benlekhal Ouahiba Moumen Widad Hadjab Adam Grzywaczyk Wojciech Smułek Urszula Guzik Omar Kharoubi

Antimicrobial resistance represents a major global health challenge, highlighting the urgent need for alternative bioactive compounds from natural sources. This study investigated the phytochemical composition and antimicrobial potential of saponin-enriched extracts from the trunk bark of Argania spinosa (L.) Skeels, collected from two contrasting Algerian regions: the coastal area of Stidia (ES) and the Saharan region of Tindouf (ET). Extraction yields were comparable (approximately 12.6%). UHPLC-MS analysis revealed distinct phytochemical profiles, with ES enriched in oleanane-type saponins and flavonoids, whereas ET showed a higher abundance of bayogenin-type derivatives. Key compounds included arganine C, E, and J, as well as catechin and quercetin. Antimicrobial activity was evaluated using agar well diffusion and broth microdilution assays against clinically relevant microorganisms, including the reference strains Staphylococcus aureus and Listeria innocua, together with Staphylococcus epidermidis, Escherichia coli, Klebsiella pneumoniae, Serratia marcescens, Proteus mirabilis, and Candida albicans. Both extracts exhibited broad-spectrum antimicrobial activity, although ES consistently showed lower Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal, Fungicidal Concentration (MBC)/(MFC) values than ET. MIC values ranged from 25 to 50 mg/mL for ES and from 50 to 100 mg/mL for ET. Synergistic interactions were observed between ES and gentamicin against S. aureus and between both extracts and kanamycin against K. pneumoniae. Membrane permeability assays demonstrated that both extracts increased bacterial membrane permeability, with ET producing a stronger permeabilizing effect. Atomic force microscopy of ES-treated cells revealed marked alterations in bacterial surface morphology, while molecular docking supported strong interactions of mi-saponin B and arganine derivatives with key bacterial targets. Collectively, these findings highlight the potential of A. spinosa bark saponins as natural antimicrobial agents and promising antibiotic adjuvants against multidrug-resistant pathogens.

Microbiology Research doi: 10.3390/microbiolres17060116

Authors: Yuri Song Hee Sam Na

Background: The upper gastrointestinal (GI) tract is a complex environment characterized by sharp physicochemical gradients. While the oral microbiome is a major source of microbial seeding for downstream organs, it remains unclear how these communities correlate and diverge across different anatomical sites. This study provides a high-resolution re-analysis of a comprehensive multi-site dataset to delineate the microbial architecture and ecological signatures along the oral–upper GI axis. Method: Human oral, esophageal, gastric mucosal, and gastric juice microbiome sequencing data were retrieved from the publicly available National Center for Biotechnology Information (NCBI) BioProject PRJNA1049979 database. Using these publicly available 16S rRNA sequencing data, we performed an integrated ecological analysis. Microbial diversity, taxonomic composition, and niche-specific community structures were evaluated using Quantitative Insights Into Microbial Ecology 2 (QIIME2) and R-based tools, including linear discriminant analysis effect size (LEfSe) and phylogenetic mapping. Results: The esophageal microbiome showed significantly greater richness and evenness than the oral cavity and stomach. Beta diversity analysis demonstrated clear compositional separation between oral and downstream upper GI communities, whereas gastric samples, particularly gastric juice, showed greater heterogeneity. Although major phyla were shared across sites, their relative abundances differed markedly. Oral samples were enriched with periodontal-associated taxa, including Porphyromonas, Prevotella, Alloprevotella, and Fusobacterium. In contrast, gastric mucosal samples were enriched with Akkermansia muciniphila and Helicobacter pylori, whereas gastric juice was characterized by Sarcina ventriculi, Fusobacterium periodonticum, and Clostridium perfringens. These findings indicate both taxonomic continuity and pronounced site-specific ecological divergence along the oral–upper GI axis. Conclusion: The oral cavity, esophagus, stomach, and gastric juice share a common microbial framework but exhibit distinct community restructuring driven by local environmental selection. This study provides a detailed ecological view of the oral–upper GI microbiome and highlights the importance of site-specific microbial organization in upper GI health and disease.

Microbiology Research doi: 10.3390/microbiolres17060115

Authors: Samira Islas-Valdez Robert Rubiano Ryan L. Peterson Nicole Wagner

Bretziella fagacearum (formerly Ceratocystis fagacearum (Bretz)) Hunt is a vascular pathogen responsible for oak wilt disease, which affects various oak species in North America. Once established, management options include root disruption, removal of infected wood, and fungicide application, each with variable efficacy. This is the first study to assess three commercial biofertilizers against B. fagacearum in vitro, using Spectrum supplemented with Pepzyme Clear (SPC), EM-1, and Power Gelatinase and Chitinase-producing Microorganism (PGCM), as no biological methods currently exist. These biofertilizers were chosen for microbes associated with improved nutrient uptake and for their potential biocontrol activity. We conducted dual-culture plate assays, volatile organic compounds (VOCs) assays, and non-volatile metabolite assays. EM-1 and PGCM exhibited the strongest antagonistic effects for dual-culture plate assays (56% and 68%, respectively) and for VOCs assays (62% and 47%, respectively). After 15 days of exposure to non-volatile metabolites, microscopic analysis revealed severe hyphal distortions from EM-1 and PGCM. These preliminary in vitro findings suggest that PGCM and EM-1 suppressed mycelial growth of B. fagacearum and may be used as biological control. Further field studies are needed to understand how environmental factors and soil–tree–microbe interactions can affect their efficacy against oak wilt disease.

Microbiology Research doi: 10.3390/microbiolres17060114

Authors: Xuebing Han Lingling Feng Wenli Xin Shanshan Lu Jialian Li Tao Zhang Wencong Long Ximeng Xiao Jiafeng Li Xianting Yin Xi Wang Hanyu Wang

Chromium is an environmental pollutant with high toxicity and carcinogenicity. It can induce severe oxidative stress and DNA damage after entering the human body through the food chain. As a plant growth-promoting rhizobacterium (PGPR) with both heavy metal tolerance and plant growth-promoting properties, Klebsiella variicola has considerable potential for the remediation of chromium contamination. In this study, chicory served as the experimental plant to explore the mitigating impacts of K. variicola on stress induced by hexavalent chromium (Cr(VI)) at a concentration of 400 mg/kg. The results showed that chromium severely inhibited the growth of chicory. In contrast, K. variicola significantly reduced the soil chromium content. As the chromium content decreased, the activities of soil urease, sucrase, catalase, and alkaline phosphatase were restored, increasing by 32.60–53.69%. Accordingly, the contents of total phosphorus, available phosphorus, total nitrogen, available nitrogen, soil organic carbon, and available potassium also increased by 34.71–51.81%. In addition, K. variicola reversed the decline in microbial diversity induced by chromium stress, promoted the growth of beneficial bacteria such as Acidobacteriota and Chloroflexota, and enhanced the stability of soil ecosystem functions. Ultimately, the growth inhibition of chicory caused by chromium stress was alleviated, with fresh weight, root length, maximum leaf width, maximum leaf length, plant height, and stem diameter significantly increasing by 21.89–61.60%. This study enhances our comprehension of the various functions of PGPR when exposed to heavy metal stress, and provides support for the development of microbe–plant combined strategies in the remediation of chromium-contaminated soils.

Microbiology Research doi: 10.3390/microbiolres17060113

Authors: Silvia Preziuso Anna-Rita Attili Chiara Storoni Lorenza Di Perna Yubao Li Vincenzo Cuteri

Schmallenberg virus (SBV) has evolved from an emergent Orthobunyavirus identified in Europe in 2011 into an endemic pathogen with complex epidemiological dynamics. This review focuses on three key aspects: pathogenesis and fetal neurotropism, diagnostic limitations within the Simbu serogroup, and challenges in disease control. SBV pathogenesis is characterized by immune evasion mediated by the NSs protein and a marked tropism for the developing central nervous system, resulting in congenital malformations when infection occurs during critical gestational stages. Similar mechanisms are shared with other Simbu serogroup viruses, contributing to overlapping clinical presentations and complicating differential diagnosis. Diagnostic approaches are constrained by the short duration of viraemia and significant serological cross-reactivity among related viruses. While RT-qPCR is effective for detecting acute infections, its utility is limited for retrospective diagnosis, where fetal tissues and pre-colostral serology are required. Widely used ELISAs lack serogroup specificity, raising concerns about the potential under-recognition of co-circulating or emerging viruses. Despite advances in vaccine development, implementation remains limited, and vector control strategies provide only partial mitigation. SBV therefore represents a valuable model for understanding arbovirus persistence in temperate regions. Addressing current challenges will require improved diagnostic specificity, sustainable vaccination strategies, and integrated surveillance systems.

Microbiology Research doi: 10.3390/microbiolres17060112

Authors: Parima Boontanom Praphaphorn Prasertsit Sukitta Kosol Taweesak Srithong Aiya Chantarasiri

Fusarium solani is an emerging pathogen responsible for Fusarium-related diseases in durian trees in Thailand. Several chemical fungicides and biocontrol agents are ineffective in controlling these diseases, which affects durian trees and reduces yields. This study aimed to identify soil-derived bacteria with biocontrol activity against F. solani that surpasses traditional biocontrol bacteria. The characteristics and biocontrol efficacy of effective isolates were analyzed. Four isolates from 107 bacterial isolates were identified as effective biocontrol agents against F. solani. Isolate S301 exhibited the highest inhibition at 74.31%, exceeding that of the traditional biocontrol bacterium Bacillus subtilis. These isolates antagonized F. solani by producing siderophores, fungal cell wall lytic enzymes, and hydrogen cyanide, and by promoting plant growth. Molecular and phylogenetic analyses identified the four isolates as members of the Bacillus genus, specifically B. safensis, B. thuringiensis, B. subtilis, and B. cereus. The application of B. safensis strain S101 and B. subtilis strain S301 showed potential to reduce fungal disease symptoms on Monthong durian leaves. These findings are the first to demonstrate the potential of B. safensis and B. subtilis as promising bacterial biocontrol agents for managing F. solani-related diseases in durian trees in Thailand.

Microbiology Research doi: 10.3390/microbiolres17060111

Authors: Evgeniy Aleksiev Zornitsa Mihaylova Dimitar Kosturkov

Oral squamous cell carcinoma (OSCC) represents a major global health burden, characterized by poor prognosis and limited improvement in survival over recent decades. Increasing evidence indicates that oral carcinogenesis is not solely driven by host genetic alterations but is significantly influenced by the oral microbiome through complex bidirectional interactions. This narrative review synthesizes current knowledge on the crosstalk between oral microbial communities and host genomic instability, with a specific focus on mutation-driven mechanisms. We discuss how microbial dysbiosis contributes to DNA damage, mutational signatures, epigenetic reprogramming, and immune modulation, thereby facilitating malignant transformation. Unlike previous reviews that address microbiome–cancer associations broadly, this work explicitly maps the mechanistic chain from microbial genotoxins through specific DNA repair pathway disruption to mutation accumulation in OSCC, and devotes substantial attention to the underexplored reverse direction—how host immune gene polymorphisms, DNA repair defects, and metabolic reprogramming shape the microbial niche. A comparative analysis with recent high-impact reviews is included. Finally, we outline emerging research directions, including multi-omics integration, single-cell and spatial transcriptomics, microbiome-targeted therapeutics, and artificial intelligence-assisted precision oncology approaches.

Microbiology Research doi: 10.3390/microbiolres17060110

Authors: Lidiane da Silva Nascimento Caroline da Silva Moraes Rod James Dillon Viv Maureen Dillon Gisela Lara da Costa Manoel Marques Evangelista Oliveira Fernando Ariel Genta

Leishmaniases are vector-borne diseases transmitted by phlebotomine sand flies. While bacterial associations in sand fly microbiota are well studied, fungal communities remain poorly characterized, despite their potential role in insect biology and parasite transmission. This study aimed to isolate and characterize yeast-like and filamentous fungi from different developmental stages of Lutzomyia longipalpis, the main vector of visceral leishmaniasis in the Americas, to expand knowledge on fungal microbiota and its possible relevance to vector–parasite interactions. Sand fly eggs, larvae, pupae, and adults were sampled from a laboratory colony. Fungi were isolated from insect tissues and diets using culture-based methods. Morphological identification was complemented by partial sequencing of the ITS1-5.8S-ITS2 rDNA region to identify the species. Four fungi were consistently recovered: Candida guilliermondii, Cutaneotrichosporon dermatis, Penicillium sp., and Aspergillus sp. Their presence varied across developmental stages. Presence in the gut was observed for Cu. dermatis, Penicillium sp. and Aspergillus sp. in larvae and C. guilliermondii in adult females. Evidence suggested their presence in different stages from larvae to pupae, and sex-specific differences in adults, with fungi detected only in females. This work documented the mycobiota that may be associated with L. longipalpis, including the first report of Cutaneotrichosporon in sand flies. These findings highlight fungi that may be potential modulators of sand fly biology and Leishmania development, warranting further investigation into their ecological and epidemiological roles.

Microbiology Research doi: 10.3390/microbiolres17060109

Authors: Sueptrakool Wisessombat Malatee Tayeh Sirada Naruephan Wipawadee Sianglum

Mucormycosis is a devastating invasive fungal infection primarily caused by Mucor and Rhizopus species, presenting significant clinical challenges due to limited therapeutic options and emerging drug resistance in opportunistic yeasts such as Candida albicans. This study explores foliar endophytic fungi from Thai medicinal plants as potential reservoirs for novel bioactive metabolites targeting both fungal growth and virulence factors. We report the first isolation of Fusarium proliferatum as an endophyte from Lantana camara L. foliage (voucher number 01562), with its identity confirmed through morphological characterization and sequencing of the fungal ITS4/ITS5 regions. Antifungal susceptibility testing showed potent activity against a panel of environmental Mucorales, with minimum inhibitory concentrations (MICs) ranging from 0.3 to 1 mg/L. In dual-culture assays, F. proliferatum demonstrated significant mycelial inhibition rates of 93.30% to 93.67% against Mucor spp. and 88.67% to 93.67% against Rhizopus spp. Furthermore, the crude extract exhibited a potent anti-virulence effect by suppressing the C. albicans yeast-to-hyphal transition, achieving up to 68% germination inhibition in resistant strains. Liquid chromatography–mass spectrometry (LC-MS) analysis identified 51 secondary metabolites, including the cyclic peptide beauvericin and various polyketides and indole derivatives. These findings suggest that F. proliferatum utilizes metabolic mimicry and adaptive synergy with its host plant to produce a diverse chemical arsenal. This study positions foliar endophytes of L. camara as promising candidates for the development of dual-action therapeutics to combat invasive and resistant mycoses.

Microbiology Research doi: 10.3390/microbiolres17060108

Authors: Juan Antonio Arreguin Cano Grissel Guadalupe Orozco-Molina Florencio Rueda-Gordillo Sandra Elena Hernández-Solís Abigailt Flores-Ledesma Arelly Carrillo Avila Víctor Manuel Martinez Aguilar

Periodontitis (P) and Type 2 Diabetes Mellitus (T2DM) are chronic inflammatory diseases that share pathophysiological pathways involving immune dysregulation and oxidative stress. Both conditions have been associated with increased susceptibility to viral infections, including SARS-CoV-2. In this regard, molecules associated with viral infection include angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2). This study aimed to evaluate the clinical periodontal status, oral microbiota composition, and the expression of ACE2 and TMPRSS2 in the oral epithelium and gingival tissue of patients with and without T2DM and P. Methods: This cross-sectional study enrolled 120 participants allocated into four groups based on periodontal and glycemic status: periodontally healthy non-diabetic individuals (PH non-T2DM), periodontitis without diabetes (P non-T2DM), periodontally healthy individuals with type 2 diabetes mellitus (PH T2DM), and periodontitis with T2DM (P T2DM), with 30 participants per group. Full-mouth clinical periodontal parameters were recorded by a calibrated examiner. Oral microbiota was assessed from unstimulated whole saliva, labial swab samples, and subgingival biofilm by selective culture and checkerboard DNA-DNA hybridization. Gingival exfoliative cytology and full-thickness gingival biopsies were obtained for immunohistochemical evaluation of ACE2 and TMPRSS2 expression. Cytomorphometric analysis and polymorphonuclear cell counts were performed on epithelial smears. Additionally, primary human gingival fibroblasts (HGFs) isolated from each group were stimulated with bacterial ligands (LPS, LTA, and PGN) to assess ACE2 and TMPRSS2 modulation by Western blot. Intergroup comparisons were performed using one-way ANOVA with Bonferroni post hoc correction and the Mann–Whitney U test, with statistical significance set at p < 0.05. Results: Diabetic patients exhibited higher plaque accumulation, clinical attachment loss, and bleeding on probing compared with non-diabetic individuals (p < 0.05). The diabetic groups showed significantly higher levels of Actinomyces, Fusobacterium, and Streptococcus spp., with decreased Staphylococcus counts. ACE2 and TMPRSS2 expression were markedly elevated in gingival epithelial cells of P T2DM patients, predominantly in basal and suprabasal layers. The nuclear-to-cytoplasmic ratio and polymorphonuclear cell counts were also increased in diabetic subjects. Conclusions: T2DM and P synergistically upregulate ACE2 and TMPRSS2 expression and alter the oral microbiota.

Microbiology Research doi: 10.3390/microbiolres17060107

Authors: Paulo Roberto Dall Cortivo Ueric José Borges de Souza Talyta Galafassi Zarpelon Norton Borges Junior Evgeni Evgeniev Gabev Fabrício Souza Campos Roberto Lanna-Filho

Soil microbiomes play a central role in nutrient cycling and ecosystem stability in forestry ecosystems. Here, we present an exploratory analysis of rhizosphere bacterial communities from eucalyptus plantations in two ecologically distinct Brazilian regions. Using 16S rRNA amplicon sequencing followed by ASV inference and phylogenetic reconstruction, we observed distinct taxonomic composition pattern between samples. Dominant phyla across both samples were Actinomycetota, Pseudomonadota, Acidobacteriota, and Bacillota, with Actinomycetota more abundant in TL (44.0%) than in ES (26.5%), and Acidobacteriota and Verrucomicrobiota more represented in ES. The family Streptomycetaceae and the genus Streptantibioticus were strongly enriched in ES (19.6% and 18.6%, respectively), whereas Solirubrobacteraceae, Pseudonocardiaceae, and Nocardiaceae were preferentially associated with TL. The Eldorado do Sul (ES) sample was characterized by higher observed richness and phylogenetic diversity, whereas Três Lagoas (TL) sample displayed relatively greater community evenness. Beta diversity metrics were consistent with high compositional dissimilarity between samples, with a limited fraction of ASVs forming a shared core microbiome. Despite this taxonomic variation, PICRUSt2-based predictions suggested a broadly conserved set of dominant metabolic pathways across samples. Predicted MetaCyc pathways were largely associated with central carbon metabolism, amino acid biosynthesis, and energy production. At the same time, variation in predicted metabolic profiles was observed between samples. The ES sample showed higher relative representation of pathways related to chitin degradation, purine metabolism, and nitrifier denitrification, whereas the TL sample displayed higher relative representation of pathways associated with alternative TCA variants, glyoxylate metabolism, menaquinol biosynthesis, and aromatic compound degradation. Overall, this exploratory analysis suggests that substantial taxonomic variation may coexist with a relatively conserved predicted functional framework across contrasting eucalyptus plantation systems. These observations should be interpreted as hypothesis-generating and highlight the need for future studies incorporating replicated sampling and direct functional measurements.

Microbiology Research doi: 10.3390/microbiolres17060106

Authors: María Mormeneo Ismaïl Moukadiri Jesús Zueco

The alkaline pectate lyase A from Paenibacillus barcinonensis, encoded by pelA (GenBank accession no. CAB40884), is an enzyme with high activity on pectin and potential application in sustainable industrial biotechnology. In this study, pelA was expressed in Saccharomyces cerevisiae by using different domains of the cell wall protein Pir4 as translational fusion partners. Given the presence of five potential N-glycosylation sites in the amino acid sequence coded by pelA, and two of them in conserved regions of class III pectate lyases, the effect of glycosylation on the enzymatic activity of the recombinant enzyme was investigated by expressing the recombinant fusion proteins in both standard and glycosylation deficient strains of S. cerevisiae. The correct targeting of the recombinant fusion proteins was confirmed by Western blot analysis using Pir-specific antibodies, whilst enzymatic activity on polygalacturonic acid was demonstrated on both plate assays and colorimetric assays. Maximum activities were over two and a half times higher when the enzyme was expressed in the glycosylation deficient strain, suggesting a better adaptation of this strain to the secretion of the functional enzyme.

Microbiology Research doi: 10.3390/microbiolres17060105

Authors: Martin Paul Heimböck Kine Østnes Hansen Yngve Guttormsen Sunil Kumar Pandey Endre Johnsen Bengt Erik Haug Annette Bayer Pilar Sanchez Guillaume Axel Petit Espen Holst Hansen Jeanette Hammer Andersen

Bacterial biofilms pose a major public health challenge by increasing the antimicrobial tolerance in pathogenic bacteria, thereby limiting the effect of medication-based treatment and promoting the development of antimicrobial resistance. Hence, there is a need to discover new molecules with the ability to prevent biofilm formation. We screened seven synthetic analogues of the breitfussin family of natural products for antimicrobial and antibiofilm activity using a broth microdilution and crystal violet method, respectively. Two compounds inhibited the growth of Gram-positive bacteria in their planktonic state at concentrations of 50 µM, of which one compound (2) demonstrated the ability to inhibit the biofilm formation of Staphylococcus epidermidis at sub-growth-inhibitory, low micromolar concentrations. Compound 2 did not inhibit biofilm growth in Staphylococcus aureus or Listeria monocytogenes, or the ability to eradicate pre-established biofilms. Initial Mode of Action (MoA) studies with compound 2 against S. epidermidis showed a modest impact on the cell surface hydrophobicity and early-stage adhesion to polystyrene. These findings highlight the breitfussin framework as a promising scaffold for the development of new antimicrobial and antibiofilm agents.

Microbiology Research doi: 10.3390/microbiolres17060104

Authors: Sadia Isfat Ara Rahman Farhana Khanam Fahad Khokhar Zoe Dyson Derek J. Pickard Gordon Dougan Ankur Mutreja Firdausi Qadri

The diagnosis of enteric fever has become difficult due to the nonspecific and overlapping clinical syndrome of typhoid and paratyphoid infections with other febrile illnesses. Moreover, the rapid emergence of fluoroquinolone-resistant typhoidal Salmonella and the lack of robust diagnostic methods highlight the urgent need for highly sensitive molecular techniques. Here, we evaluated the performance of a rapid, reliable, and cost-effective molecular diagnostic approach for detecting Salmonella Typhi, including the globally dominant haplotype H58 lineage (H58), and Salmonella Paratyphi A. An in-house-built conventional polymerase chain reaction (PCR) was performed on a collection of blood-culture-positive strains, and the sensitivity and specificity were compared with those of the standard blood culture results. H58 and non-H58 Typhi lineages with distinct resistance patterns were confirmed from the previously reported sequencing data. Our PCR result showed that target genes SSPA2308, STY2513, and STY0307 demonstrated 100% sensitivity and specificity for Salmonella Paratyphi A, Salmonella Typhi, and H58 Salmonella Typhi, respectively. The PCR assay reliably detected bacterial DNA at 5.2 × 104 colony-forming units (CFUs), with consistent amplification observed up to 10−1 dilution. This single-nucleotide polymorphism (SNP)-based diagnostic approach has added a new dimension to designing unique markers for multidrug-resistant (MDR)-associated H58 lineage detection and has the potential to inform local treatment algorithms.

Microbiology Research doi: 10.3390/microbiolres17060103

Authors: Tomoya Shintani

Background: This study examined potential associations between daily glucosamine (GlcN) use and the gut microbiota. Methods: In a cross-sectional sample of 200 Japanese adults aged 50–59 (100 regular GlcN users; 100 age- and sex-matched non-users), fecal 16S rRNA profiles were analyzed. α-diversity (richness, Shannon index) and β-diversity were compared; predominant genera (>1% mean abundance) were evaluated, and differential abundance was tested using ANCOM and LEfSe. A subgroup analysis assessed normal-BMI participants (18.5–25.0). Results: Overall α-diversity and β-diversity did not differ between users and non-users. Of the >150 genera detected, 22 exceeded 1% mean abundance, and their profiles were virtually identical across groups; neither ANCOM nor LEfSe identified taxa with significant differential abundance. In the normal-BMI subgroup, GlcN users showed lower species richness and a reduced prevalence of rare taxa (<10,000 total reads), with a decrease in Christensenella, which is consistent with prior intervention studies. Given reports linking Christensenella to lower frailty in specific contexts, these findings suggest a potential GlcN-related effect relevant to joint health. Conclusions: Habitual GlcN use was not strongly associated with broad changes in gut microbial diversity or common taxa in middle-aged adults, although it might have some effect on minor taxa. Longitudinal, controlled studies are warranted to confirm these findings and clarify mechanisms.

Microbiology Research doi: 10.3390/microbiolres17060102

Authors: Ibrahim S. Al Nasr Ismail Daoud Waleed S. Koko Tariq A. Khan Rainer Schobert Ridha Ben Said Noureddine Amdouni Ali O. Al-Ghamdi Bernhard Biersack

Resistance formation and considerable toxicities limit the application of currently available antiparasitic drugs. Thus, new drug candidates are required. Piperlongumine-based cinnamides are promising antiparasitic compounds. In this study, new synthetic cinnamide derivatives with variable halogen substituents (F, Cl, and Br) were prepared and analyzed. They were tested for activity against Toxoplasma gondii and Leishmania major parasites. Considerable activities against T. gondii parasites were observed for certain chloro- and bromo-substituted cinnamides (IC50 = 1.88–2.72 µM), while activities against L. major were less pronounced. Structure–activity relationships were investigated, which revealed notable relations of anti-toxoplasmal activity with the nature of the applied halogen substituents and a preference for chloro- and bromo-substituents in active compounds. In contrast to piperlongumine, the new active compounds have no methoxy substituents anymore and appear to be suitable for advanced antiparasitic studies. Successful docking of selected derivatives into the colchicine binding site of tubulin provided a strong hint at a possible mode of action for these cinnamides (S-scores of −6.075 and −5.993 kcal/mol). In addition, considerable drug-like properties were determined by ADME-T calculations. Thus, in conclusion, new halo-substituted cinnamides with promising activity against Toxoplasma gondii were identified. The selectivity for Toxoplasma parasites can lead to better drugs for the therapy of toxoplasmosis.

Microbiology Research doi: 10.3390/microbiolres17060101

Authors: Gergana Krumova-Valcheva Eva Gyurova Gergana Mateva Mihail Milanov Magdalena Baymakova Ilia Tsachev

Bivalve mollusks efficiently bioaccumulate human enteric viruses, posing significant food safety risks. This study assessed the prevalence of Norovirus (NoV GI and NoV GII), Hepatitis A virus (HAV), and Hepatitis E virus (HEV) in 59 samples of live mussels (Mytilus galloprovincialis) collected from the Bulgarian Black Sea coast between July 2022 and July 2023. Viral detection was performed using one-step real-time reverse transcription-polymerase chain reaction (RT-qPCR) following ISO 15216-2 standards, with a mean extraction efficiency of 4.06%. Norovirus GII was the most prevalent pathogen, with detection peaks following intense rainfall events in July 2023. In contrast, all samples tested negative for HAV and HEV. The analysis showed no significant correlation between E. coli contamination levels and the presence of NoV (Mann–Whitney U test, p = 0.565). The viral RNA was detected in several samples that otherwise complied with regulatory bacterial standards for direct consumption (≤230 MPN/100 g). In conclusion, within the limitations of the evaluated sample size and the specific geographically unbalanced sampling design, NoV GII was the predominant genogroup detected. These results suggest that current bacterial indicators may be insufficient to ensure viral safety in these products. In this regard, national control authorities need to undertake timely policies and measures for better and adequate surveillance, control and prevention of viruses in the different parts of the food chain.

Microbiology Research doi: 10.3390/microbiolres17050100

Authors: Rafael Martínez-Miranda Fernando A. Solis-Dominguez Aseneth Herrera-Martínez Conrado Garcia-Gonzalez Jonathan Isaac Arauz Cabrera Rafael Iván Ayala Figueroa Carlos Vidal Montiel Castañeda

Antibiotic resistance remains a major public health concern, particularly in regions with high rates of hospital- and community-acquired infections. This study aimed to quantify multidrug-resistant (MDR) bacterial strains in northern Mexico and to identify the most prevalent resistance phenotypes, the antibiotic classes with the highest resistance and susceptibility rates, the predominant MDR species, and the specimen types yielding the greatest number of isolates. Clinically relevant strains were collected from patients with confirmed infections. Microorganism identification and antimicrobial susceptibility test-ing were performed using the Vitek 2 Compact system (bioMérieux), and the results were analyzed descriptively. Of the 1544 strains analyzed, 761 (49.29%) exhibited multidrug resistance. Escherichia coli was the most frequently isolated MDR species, followed by Pseudomonas aeruginosa. Acinetobacter baumannii showed the highest resistance rate, with 95.55% of its strains classified as MDR, whereas P. aeruginosa had the lowest MDR proportion at 30.73%. These findings underscore the urgent need for rational antibiotic use and the development of new therapeutic agents, particularly those targeting Gram-negative bacilli, to mitigate the growing threat of antimicrobial resistance in this region.

Microbiology Research doi: 10.3390/microbiolres17050099

Authors: Teodora Bolyarova Pavel Stanimirov Ivo Sirakov Emilia Naseva Bilyana Sirakova Konstantin Stamatov Samuil Dzhenkov

Background and Objectives: This study aimed to detect and genotype human papillomavirus (HPV) in tissues from oral squamous cell carcinoma (OSCC), oral potentially malignant disorders (OPMD), and healthy individuals. Materials and Methods: The study included 60 patients (31 men and 29 women; median age 60 years, IQR 41.5–69.8) admitted to the Department of Dental, Oral and Maxillofacial Surgery, Medical University of Sofia. Patients were divided into three groups: healthy oral mucosa (n = 20), OPMD (n = 20), and OSCC (n = 20). HPV was tested using punch biopsies with nested PCR and chip technology. Results: Low-risk HPV was found in four (20%) healthy individuals (types 6/11, 43), seven (35%) OPMD patients (types 6/11, 42, 43), and eleven (55%) OSCC patients (types 6/11, 42, 43). Pairwise comparison showed a significant difference in HPV positivity between healthy individuals and OSCC patients (p = 0.022). Among all HPV-positive OPMDs, the virus was detected in two leukoplakia cases (28.6%), three lichen planus cases (42.9%), one lichenoid lesion case (14.3%), and one proliferative verrucous leukoplakia case (14.3%). According to binary logistic regression, OSCC patients were 4.9 times more likely to be HPV-positive compared to healthy individuals (p = 0.027). Conclusions: HPV infection may play a potential role in the pathogenesis of OPMD and OSCC.

Microbiology Research doi: 10.3390/microbiolres17050098

Authors: Nadia Habeeb Sarhan Maroua Gdoura-Ben Amor Saif Jabbar Yasir Radhouane Gdoura

Human herpesvirus 6 (HHV-6) typically remains latent but can reactivate during immunosuppression caused by chemotherapy, potentially driving immune dysregulation. The NLRP3 inflammasome is a critical innate immune complex mediating pro-inflammatory signaling implicated in tumor progression and treatment toxicity. This study investigated the association between HHV-6 antigenemia and NLRP3 inflammasome activation in 193 chemotherapy-treated cancer patients at the Oncology Hospital in Al-Najaf, Iraq. Serological markers for HHV-6 IgG, IgM, and circulating viral antigen, along with serum NLRP3 levels, were quantified using ELISA. Active HHV-6 antigenemia was observed in over half the cohort, with 56.5% positive for IgM and 42.5% exhibiting antigenemia. Elevated serum NLRP3 levels were detected in 65.8% of patients and correlated significantly with HHV-6 antigen presence, particularly in hematological and genitourinary cancers. Viral antigenemia and inflammasome activity were more prominent in females and older patients. Host gene analysis revealed Hepcidin (HAMP) polymorphisms and altered expression compared to healthy controls, suggesting links between iron metabolism, viral antigenemia, and inflammasome activity. These findings highlight a potential mechanistic connection between HHV-6 antigenemia and inflammasome-driven inflammation, which may contribute to chemotherapy-associated immune dysregulation. Monitoring HHV-6 antigenemia and NLRP3 activation may offer valuable insight into the inflammatory status of cancer patients undergoing chemotherapy.

Microbiology Research doi: 10.3390/microbiolres17050097

Authors: Jesús Andres Morales-López Teodulfo Aquino-Bolaños Angélica Bautista-Cruz Tamara Aquino-Aguilar Edgar García-Sánchez Tlacaelel Aquino-López Keyla Cruz-García

Guaje (Leucaena leucocephala), mezquite (Prosopis laevigata), and guamuchil (Pithecellobium dulce) are leguminous trees distributed throughout southeastern Mexico. Their pods and seeds constitute the main agroecological residues and represent a natural source of secondary metabolites with high biotechnological potential. The aim of this study was to determine the chemical composition, antimicrobial and antioxidant activities, and toxicity of the pods and seeds of L. leucocephala, P. laevigata, and P. dulce. It was found that pod extracts contained higher concentrations of phenolic compounds, flavonoids, and terpenes than seed extracts. Antimicrobial assays showed inhibition zones ranging from 8.1–14.7 mm (E. coli), 8.8–15.1 mm (S. aureus), 11.3–15.4 mm (E. faecalis), 8.9–24.1 mm (C. albicans), and 8.5–22.6 mm (C. krusei). The ethyl acetate (AVPD) and ethanolic (EVPD) extracts from P. dulce pods showed the highest antimicrobial activity, with MIC values ranging from 0.03 to 0.15 mg/mL, MBC values of 0.07 mg/mL (S. aureus and E. faecalis), and MFC values of 1.25 mg/mL (C. albicans) and 0.62 mg/mL (C. krusei). Antioxidant activity was higher in pod extracts, with AVPD and EVPD showing IC50 values of 0.257 and 0.320 mg/mL, respectively. Consistently, EVPD exhibited the highest phenolic content (133.24 mg GAE/g) and flavonoid content (50.90 mg QE/g), followed by AVPD (87.29 mg GAE/g and 42.40 mg QE/g, respectively). The results indicate that pod extracts of L. leucocephala and P. dulce contain secondary metabolites with broad antimicrobial and antioxidant potential and low toxicity.

Microbiology Research doi: 10.3390/microbiolres17050096

Authors: Guangle Zhang Lixue Yuan Yongxin Zhang Xiaohang Wang Li Zhang Xinyuan Zhang Ruxue Chen Zhuangzhuang Wang Bo Yu Yonghua Wang

Arbuscular mycorrhizal (AM) fungi form mutualistic symbioses with about 80% of land plants and play a key role in improving host inorganic phosphate (Pi), nitrogen, and water acquisition. Traditional AM fungi research relies on field trials, compartmented cultivation, and pot cultures—methods that are time-consuming (taking months to years) and unable to monitor dynamic transport, thus limiting efficient strain screening. We developed a real-time fluorescence imaging platform integrating sterile symbiotic microchambers with photodiode array detection. This system enables the non-invasive, quantitative tracking of hyphal cytoplasmic streaming and transport kinetics at the plant–fungal interface. Distinct AM fungi strains exhibit significant differences in fluorescence kinetics—such as accumulation rate and peak intensity—providing measurable indicators of transport efficiency. Our method overcomes the temporal and technical limitations of conventional AM fungi screening approaches. By enabling simultaneous real-time monitoring, it shortens screening cycles and provides new insights for the (1) precise screening of AM fungi strains for efficient nutrient transport; (2) investigation of nutrient exchange mechanisms; (3) development of sustainable microbial inoculants.

Microbiology Research doi: 10.3390/microbiolres17050095

Authors: Dilbar Tursun Zulhumar Yakup Huifang Bao Faqiang Zhan Yingwu Shi Hongmei Yang Jiusheng Sun Shijie Fang Ning Wang

Soil salinization is a significant environmental factor limiting agricultural production. Developing salt–alkali-tolerant microbial resources is important for the improvement of saline–alkali land. Plant growth-promoting rhizobacteria stimulate crop growth by producing the plant growth hormone indole-3-acetic acid (IAA), but their fermentation process under salt stress still needs optimization. Single-factor experiments and response surface methodology (RSM) were used to systematically optimize the fermentation conditions of the salt–alkali-tolerant Vreelandella titanicae J113. Key influencing factors were screened using the single-factor experiment design, and optimal process parameters were determined using the Box–Behnken design. IAA production and cell biomass were used as evaluation indicators to study the interactions of carbon sources, nitrogen sources, inorganic salts, temperature, cultivation time, and inoculum size. The optimal fermentation process was obtained: starch concentration 17.5 g/L, NaCl concentration 32.5 g/L, yeast extract 5 g/L, cultivation temperature 30 °C, inoculum size 3%, and cultivation time 144 h. After optimization, IAA production reached 23.02 μg/mL, an increase of 115% compared with before optimization. Salt stress experiments showed that the strain could still maintain high IAA production under 3% NaCl, demonstrating good salt tolerance. Maize seed germination experiments demonstrated that the optimized fermentation broth significantly promoted seed germination and seedling growth under salt stress conditions, with root length, fibrous root number, and fresh weight increasing by 61–86%, 137–200%, and 25–57%, respectively, compared to the control group. This study established an efficient IAA fermentation process for the salt–alkali-tolerant Vreelandella titanicae J113, providing technical support for developing microbial plant growth regulators suitable for saline–alkali land. The optimized strain exhibits excellent growth-promoting potential under salt stress conditions, offering favorable application prospects.

Microbiology Research doi: 10.3390/microbiolres17050094

Authors: Silvana M. Tapia-Cabrera Adelfo Escalante Francisco Bolívar

Aromatic compounds derived from the shikimate (SHK) pathway constitute a diverse class of high-value molecules with applications in the pharmaceutical, food, cosmetic, and chemical industries. In microbial systems, particularly Escherichia coli, this pathway links central carbon metabolism (CCM) to the biosynthesis of L-tyrosine (L-Tyr), L-phenylalanine (L-Phe), and L-tryptophan (L-Trp), which serve as key precursors for structurally diverse metabolites. Over the past decades, metabolic engineering strategies have focused on increasing precursor availability, relieving feedback inhibition, and eliminating competing pathways. More recently, advances in synthetic biology have enabled dynamic control of metabolic flux through pathway modularization, genome-scale interventions, and regulatory circuit design. In this review, we provide a comprehensive overview of the engineering of E. coli for aromatic compound biosynthesis, highlighting key developments in the optimization of the SHK pathway and its major metabolic nodes chorismate, L-Tyr, L-Phe, and L-Trp. We examine emerging approaches, including CRISPR-based regulation, biosensor-driven dynamic control, membrane engineering, and synthetic microbial consortia. Despite significant progress, challenges related to pathway regulation, cofactor balance, metabolic burden, and product toxicity remain critical bottlenecks. Integrating metabolic engineering with synthetic biology is driving the development of programmable, scalable microbial platforms for the efficient bioproduction of aromatic compounds.

Microbiology Research doi: 10.3390/microbiolres17050093

Authors: Mandlenkosi Manika Lindiwe Modest Faye Ntandazo Dlatu Mojisola Clara Hosu

Background: The global burden of drug-resistant Mycobacterium tuberculosis continues to threaten tuberculosis control efforts, largely due to the emergence and transmission of resistance-associated genetic mutations. Molecular epidemiology provides critical insights into mutation profiles and resistance associations, yet the interplay among key mutations and their contributions to complex resistance patterns remains poorly understood, particularly in high-burden settings. Methods: A retrospective, cross-sectional, laboratory-based design was used to analyze 111 phenotypically confirmed drug-resistant isolates. Molecular drug susceptibility testing (DST) for first- and second-line anti-tuberculosis drugs was performed at the National Health Laboratory Service (NHLS) TB reference laboratory. Drug-resistance profiles were classified according to World Health Organization (WHO) definitions. Descriptive and inferential statistical analyses were conducted to determine mutation frequencies, co-occurrence patterns, and associations with resistance profiles. Results: rpoB (D435V 38.7%; S450L 36.0%) and katG (S315T 80.2%) mutations predominated, forming the core molecular basis of MDR-TB, while 15% harbored inhA promoter mutations associated with low-level isoniazid resistance. The most frequent combinations included rpoB S450L with katG S315T and rpoB D435V with katG S315T, consistent with multidrug-resistant tuberculosis (MDR-TB) profiles. Nearly 48% showed dual resistance to fluoroquinolones and second-line injectables. Conclusion: This study highlights the predominance of resistance-associated mutations and their co-occurrence patterns in shaping MDR-TB profiles in the study setting. The observed burden of second-line drug resistance underscores the importance of comprehensive resistance testing. These findings support the use of mutation profiling for rapid diagnosis and informed treatment decisions, while emphasizing the need for ongoing local surveillance to guide TB control efforts.

Microbiology Research doi: 10.3390/microbiolres17050092

Authors: Jessy T. Santana Berenice González-Rete Elia Torres-Gutiérrez Juliana Cordeiro Cardoso Cláudia Moura Melo Paz M. S. Salazar-Schettino

Trypanosoma cruzi exhibits complex genetic diversity, organized into seven distinct typing units. To complete its life cycle, the parasite must adapt to the digestive tract of various species of triatomine bugs. This systematic review aimed to understand the molecular adaptation mechanisms of T. cruzi in relation to different vector species, systematizing knowledge on vector competence. Following PRISMA guidelines, 18 experimental studies (published between 1995 and 2025) were selected from the ScienceDirect, PubMed, Scopus, and Web of Science databases, focusing on the parasite–vector interface and proteomic analyses. There was a predominance of studies conducted in Brazil (66.67%), using the Rhodnius prolixus model (72.22%) and the TcI strain (clone Dm28c). The evolution of methodological approaches reflects a transition from classical techniques, such as SDS-PAGE, to high-throughput omics strategies, including LC-MS/MS and gene editing tools such as CRISPR. The findings were organized into key biological processes, including parasite adhesion mediated by perimicrovillar membrane components, glycoinositolphospholipids (GIPLs), and mucins; the influence of the metabolic and nutritional microenvironment, particularly hemoglobin-derived peptides and glucose availability; and the role of intestinal redox conditions in triggering metacyclogenesis. Overall, the available evidence suggests that T. cruzi adaptation within triatomine vectors is a multifactorial process driven by proteomic reprogramming and post-transcriptional regulation in response to environmental signals within the vector gut. However, this understanding is largely derived from studies based on Rhodnius prolixus and TcI strains, which limits the generalization of these mechanisms across other triatomine species and parasite lineages.

Microbiology Research doi: 10.3390/microbiolres17050091

Authors: Nilton Luis Murga Valderrama Gleni T. Segura Jakson Ch Del Solar Hugo Frias Ana C. Romani Deiner J. Gongora-Bardales Ulises S. Quispe-Gutierrez Carla Maria Ordinola-Ramirez Richard C. Polveiro Dielson da S. Vieira Jorge Luis Maicelo Quintana Rainer M. Lopez Lapa

The uterine microbiome plays a critical role in maintaining pH balance, modulating the immune system, and influencing fertility, especially in artificial breeding contexts. This study examined the impact of uterine microbiota on pregnancy success in cows following embryo transfer (ET), using Illumina 16S rRNA gene sequencing of the V4 hypervariable region of samples collected from the uterine horn (UH) and the uterine body (UB) of cows during the estrous cycle preceding synchronization for ET in the Amazon region. Microbiomes from the uterine horn (UH) and the uterine body (UB) were analyzed before embryo transfer. Cows that became pregnant (UH-P and UB-P) and those that did not (UH-NP and UB-NP) were compared. Fifteen cows were grouped as follows: UB-P (three), UB-NP (five), UH-P (three), and UH-NP (four). Linear discriminant analysis effect size and heat tree analyses identified Sphingobacterium and Stenotrophomonas spp. as significantly enriched in the UB-P and UH-NP groups, respectively. Additionally, non-pregnant cows exhibited more distinctive genera than pregnant ones. These findings suggest that cows achieving pregnancy have lower microbial diversity and fewer potentially pathogenic genera. This study contributes to the emerging field of pre-pregnancy uterine microbiome research in cattle, offering evidence that microbial composition may influence reproductive success, and highlights specific taxa as potential biomarkers for pregnancy outcomes following embryo transfer.

Microbiology Research doi: 10.3390/microbiolres17050089

Authors: Egidia Costanzi Giovanna Traina Marco Misuraca Donia Msakni Giada Sgaravizzi Musafiri Karama Ebtesam Al-Olayan Saeed El-Ashram Marcelo Martinez-Barbitta Massimo Zerani Beniamino T. Cenci-Goga

The present study examined the effect of Enterococcus durans cell-free supernatant (CFS) on interleukin (IL)-8, -10 and -1β gene expressions in the intestinal cell line HT-29 treated with Staphylococcus aureus CFS. HT-29 cells were incubated with E. durans CFS or S. aureus CFS, or S. aureus CFS plus E. durans CFS. All concentrations of E. durans CFS did not show cytotoxicity, while the highest treatment (44.9 μg/mL) with S. aureus CFS induced significant cell death. S. aureus CFS did not modify IL-1β gene expression, while E. durans CFS alone or in combination with S. aureus CFS reduced it. Treatment with S. aureus CFS induced greater expression of the IL-8 gene compared to S. aureus CFS plus E. durans CFS. S. aureus CFS alone or in combination with E. durans CFS increased the expression of the IL-10 gene, while E. durans CFS alone did not modify it. These results suggest a potential protective role of the E. durans secretome in mitigating the inflammatory environment in intestinal cells. This treatment could be useful to protect against possible contact with dangerous soluble microbial products present in food.

Microbiology Research doi: 10.3390/microbiolres17050090

Authors: Petya Koeva Christova

Phytopythium species are water molds that have been divided as a separate group of oomycetes about 10 years ago. They are associated with diverse environments worldwide, but the ecological function of most of the species is still under investigation. In the present study, isolation and characterization of Pp. helicoides and Pp. palingenes are described. Both Phytopythium isolates originate from an aquatic environment and were derived from infected leaves. A host range of Pp. helicoides and Pp. palingenes using pathogenicity tests with leaves and cuttings from trees, bushes, perennial and herbaceous plants that belong to 15 different families was studied. Out of 21 tested plants, 18 were susceptible to infection with Pp. helicoides and nine were negatively affected by Pp. palingenes. Pp. helicoides is distinguished by higher aggressiveness and a wider range of potential host species. These results indicate that the impact of pathogenic species from the genus Phytopythium on forests and other natural ecosystems could be much more significant than is currently known.

Microbiology Research doi: 10.3390/microbiolres17050088

Authors: Stefano Petrini Mohamed Methnani Cecilia Righi Khaled El Hicheri Cristina Casciari Aida Tatli Ben Smida Boubaker Elena Tinelli Sana Kacem Claudia Pellegrini Roberto Sabato Francesco Feliziani Giovanni Pezzotti

Livestock farming represents a key economic activity in the Tataouine Governorate of southern Tunisia, where cattle and dromedary camels coexist. Varicellovirus bovinealpha1 (BoAHV-1), the etiological agent of infectious bovine rhinotracheitis (IBR), primarily affects cattle, while its circulation in camelids remains poorly understood. Following recent European Union regulations requiring BoAHV-1 surveillance in multiple animal species, this short communication reports serological findings from dairy cattle and dromedary herds in southern Tunisia. In March 2024, serum samples were collected from four non-vaccinated farms, including two intensive Friesian dairy cattle herds and two extensive dromedary herds (50 animals each). Serum samples from all animals were tested for BoAHV-1 antibodies using competitive commercial gB- and gE-based enzyme-linked immunosorbent assays (c-ELISA) and confirmed by virus neutralization test (VNT). Antibodies against BoAHV-1 were detected in cattle from both dairy farms, with low seroprevalence and neutralizing antibody titers, indicating past or ongoing exposure. In contrast, all dromedary samples tested seronegative by both c-ELISA and VNT. These findings confirm BoAHV-1 circulation in cattle in the Tataouine region and its absence in dromedaries at sampling. Further studies involving larger sample sizes and molecular investigations are required to clarify the potential role of camelids in BoAHV-1 epidemiology in southern Tunisia.

Microbiology Research doi: 10.3390/microbiolres17050087

Authors: Giorgia Piccinini Antonio Curtoni Alessandro Bondi Mattia Genco Fabio Longo Carlotta Polizzi Paolo Valesella Silvia Corcione Francesco Giuseppe De Rosa Cristina Costa

Antimicrobial resistance (AMR) represents one of the most urgent global health threats, significantly impacting patient outcomes, healthcare systems, and economic sustainability. Rapid and accurate antimicrobial susceptibility testing (AST) are essential to guide targeted therapy, reduce inappropriate antimicrobial use, and support antimicrobial stewardship programs. However, conventional phenotypic AST methods, including broth microdilution, disk diffusion, agar dilution, and gradient strip tests, remain labor-intensive and require prolonged turnaround times, often delaying optimal therapeutic decisions. Although automated commercial platforms such as VITEK 2, BD Phoenix, MicroScan WalkAway, and Sensititre ARIS have improved laboratory workflow and standardization, they still rely on culture-based approaches and typically require 16–36 h to generate minimum inhibitory concentration (MIC) results. In recent years, several innovative rapid phenotypic AST technologies have emerged, aiming to significantly shorten the time to susceptibility results while maintaining high accuracy. This review provides an overview of currently available rapid automated phenotypic platforms for MIC determination, including VITEK® Reveal™, ASTar, FASTinov®AST, QuickMIC®, and the Accelerate Pheno® system. These systems employ advanced technologies such as volatile organic compound detection, flow cytometry, microfluidics, real-time imaging, and morphokinetic cellular analysis to deliver susceptibility results within a few hours directly from positive blood cultures. We summarize their technical principles, antibiotics and pathogens included, performances, and current limitations. Overall, the implementation of rapid phenotypic AST tools has the potential to substantially improve clinical decisions, optimize antimicrobial therapy, and contribute to fight AMR.

Microbiology Research doi: 10.3390/microbiolres17050086

Authors: Waqas Ahmad Naeem Rasool Qurat ul Ain Usama Bin Naeem Muhammad Azeem Umbreen Anwar Tehreem Fayyaz Zeba Amjad Muhammad Yasin Tipu Mehmood Ahmad

Trypanosoma evansi (T. evansi) infection poses a significant health threat to equines. This study was aimed to assess the prevalence, risk factors, hematobiochemical alterations, and oxidative stress-mediated genotoxicity associated with equine trypanosomiasis in the Rahim Yar Khan District. This cross-sectional study was conducted on 384 equines from October 2024 to September 2025. Blood samples were collected for thin blood film microscopy and PCR assay using RoTat 1.2 primers. Hematological indices were analyzed with an automated hematology analyzer; serum biochemical parameters were quantified via standard assays. Oxidative stress markers, including malondialdehyde (MDA), catalase (CAT), superoxide dismutase (SOD), and reduced glutathione (GSH), were also measured. Genotoxicity was evaluated using the alkaline comet assay. Statistical analyses included the chi-square test, logistic regression, and independent t-tests. T. evansi was detected in 5.99% of samples by microscopy and 10.16% by PCR, with no significant association with species, age, or sex. Infected equines exhibited significant reductions in hemoglobin (5.4 ± 0.6 vs. 10.8 ± 0.5 g/dL; p < 0.0001), total serum protein (2.1 ± 0.3 vs. 5.8 ± 0.2 g/dL; p < 0.0001), albumin, and globulin, alongside elevated hepatic enzymes, blood urea nitrogen, and creatinine (all p < 0.01). Oxidative stress was confirmed by increased MDA (p < 0.0001) and decreased CAT activity (p < 0.001). Genotoxicity was significantly higher in infected animals (genetic damage index; 1.12 ± 0.08 vs. 0.40 ± 0.01; p < 0.01). This study provides the first integrated assessment of molecular epidemiology and oxidative stress-mediated genotoxicity in equines in this region, suggesting the pathogenic impact of the infection and targeted diagnostics for disease management strategies.

Microbiology Research doi: 10.3390/microbiolres17050085

Authors: Jun Iwahashi Akiko Shimizu Akinobu Togo Hiroshi Fuketa Kenji Gotoh Keisuke Ohta Norihiro Shinkai Naohisa Kawamura Hiroshi Watanabe

Background: Many of the pathogenic bacteria and fungi found in hospital environments form biofilms, which allow them to persist in the environment for long periods, posing a risk of hospital-acquired infections. Although the pathogens within biofilms often have reduced levels of drug susceptibility, the efficacy of disinfectants routinely applied against planktonic pathogens must be evaluated against biofilms as well. Our objective in this study was to determine the efficacy of treatment using slightly acidic hypochlorous acid water and to compare the results with sodium hypochlorite when both were used to disinfect Candida parapsilosis biofilms. Methods: C. parapsilosis in the planktonic or biofilm state was treated with each disinfectant. The number of viable cells that remained was determined, and scanning electron microscopy (SEM) of the disinfectant-treated biofilms was performed. Results: Compared with sodium hypochlorite, in a shorter period of time, hypochlorous acid water completely killed not only planktonic C. parapsilosis but also C. parapsilosis in a biofilm that had been formed for 72 h. SEM showed that both disinfectants were effective in removing the C. parapsilosis biofilm to some extent. Conclusions: Slightly acidic hypochlorous acid water appears to be an effective disinfectant against C. parapsilosis both in suspension and in biofilms.

Microbiology Research doi: 10.3390/microbiolres17040084

Authors: Linglin Tao Alessandro Ruan Shu Quan

Komagataella phaffii (formerly Pichia pastoris) is a prominent platform for recombinant protein production, yet secretion efficiency often remains a critical bottleneck. In this study, we validated three candidate genes—WHI3, CLPP, and PMP20—previously identified through genome-wide CRISPR activation screening, for their potential to enhance heterologous protein secretion. Overexpression of these factors under the control of the methanol-inducible AOX1 promoter increased the secretion of human serum albumin (HSA), with WHI3 and CLPP yielding improvements of 18.3% and 17.9%, respectively. Furthermore, applying this strategy to human lactoferrin (hLF) revealed that WHI3 overexpression robustly enhanced hLF secretion by approximately 70%. Comparative analysis of different promoters (AOX1, GAP, and CAT) indicated that the AOX1 promoter remains the most effective driver for these enhancers, suggesting a threshold-dependent regulatory mechanism. These results demonstrate the protein-dependent nature of secretion optimization and identify WHI3, CLPP, and PMP20 as novel, effective co-expression factors for improving recombinant protein yields in K. phaffii.

Microbiology Research doi: 10.3390/microbiolres17040083

Authors: Natália Cristina de Melo Santos Evandro Neves Silva Leonardo Pereira de Araújo Carlos Roberto Prudêncio Rômulo Dias Novaes Patrícia Paiva Corsetti Leonardo Augusto de Almeida

Differences in the gut microbiota are directly reflected in lung–gut axis crosstalk, which may increase susceptibility to pulmonary infections, such as those caused by the bacterium Pseudomonas aeruginosa. Deficiency of the cytokine IL-10 leads to gut inflammation, and this pro-inflammatory environment is partly due to changes in the gut microbiota. To better understand the effects of IL-10 deficiency on the gut microbiota, the intestinal microbial composition of IL-10 KO mice was assessed, and an increase in the phyla Bacteroidetes and Proteobacteria and a decrease in the phylum Firmicutes were observed in the faeces compared with the wild-type group (WT). Additionally, IL-10 KO mice had a higher pro-inflammatory immunostimulatory caecal content. Furthermore, it was found that heterologous faecal microbiota transplantation (FMT) between groups reversed this gut imbalance. IL-10 KO mice showed greater susceptibility to acute pulmonary infection by P. aeruginosa, with a higher recovery of viable bacteria in the lung and spleen, greater tissue damage and increased expression of genes encoding pro-inflammatory cytokines in the lungs. This greater susceptibility was reversed after FMT. Taken together, these results demonstrate the role of endogenous IL-10 in the gut microbiota constitution and its importance in the pulmonary immune response against P. aeruginosa infection.

Microbiology Research doi: 10.3390/microbiolres17040082

Authors: Eleni Alaverntian Eugenia Papadaki

The gut microbiome plays a central role in human health, and probiotics are widely used to support microbial balance, though their efficacy depends on multiple factors. This study assessed the potential of commercial probiotics Saccharomyces cerevisiae var. boulardii, Weizmannia coagulans and Lacticaseibacillus rhamnosus by evaluating in vitro gastrointestinal kinetics, pharmaceutical stability, and antioxidant effects in chamomile tea. Growth across a broad pH range was modeled kinetically, while survival and inactivation were quantified in simulated gastric and intestinal fluids. Antibiotic and antifungal susceptibility was determined using disk diffusion, and antioxidant activity of fortified chamomile tea was assessed via DPPH radical scavenging. Results revealed distinct strain-dependent responses. S. cerevisiae var. boulardii and W. coagulans showed the highest gastrointestinal tolerance. The increase in fluid volume reduced survival during the gastric phase but improved survival in the intestinal phase, reflecting different stress responses. Antimicrobial susceptibility also varied, with S. cerevisiae var. boulardii exhibiting the highest resistance. Probiotic fortification enhanced chamomile tea’s antioxidant capacity, particularly for S. cerevisiae var. boulardii and L. rhamnosus. These findings provide quantitative insight into strain- and volume-dependent gastrointestinal performance, guiding the optimization of capsule formulations and the development of clean-label products combining probiotic and antioxidant benefits.

Microbiology Research doi: 10.3390/microbiolres17040081

Authors: Fatma A. Abo Nouh Ahmed M. Abdel-Azeem Tamer S. Abdelmoneim Nivien A. Nafady Saeed Mohammadi Najeeb Ur Rehman Hassan Moghtaderi Moosa Al Hamadani Saif Al-Housni Usama Qayum Abdullah M. S. Al-Hatmi

The emergence of antimicrobial resistance and the increasing incidence of cancer have highlighted the urgent need to develop new drugs; therefore, the discovery of new bioactive molecules is an important goal for future research. In this study, freshwater fungi isolated from submerged Phragmites australis from Egypt were screened for antimicrobial and cytotoxic activities. Using ITS1 and ITS4 primers, eight frequently occurring Sordariomycetes taxa were identified and were then selected for further evaluation of bioactivity. Ethyl acetate crude extracts (A–H) were evaluated for antimicrobial activity using the agar disk-diffusion method. Extracts A and E, derived from Chaetomium globosum SCUF0000404 (PX596738) and Chaetomium madrasense SCUF0000401 (PX596735), respectively, showed broad-spectrum activity at 100 mg/mL against bacterial pathogens, including Staphylococcus aureus ATCC 29213 (15.33 and 18.00 mm), Streptococcus pyogenes ATCC 19615 (11.00 mm), Escherichia coli ATCC 35218 (10.33 and 10.67 mm), Klebsiella pneumoniae ATCC 700603 (14.00 and 16.67 mm), and Pseudomonas aeruginosa ATCC 27853 (13.33 and 16.33 mm), and show antifungal activity against Candida albicans ATCC 14053 (20.33 mm), Candida krusei ATCC 6258 (15.67 and 15.33 mm), Trichosporon asahii AMS 187 (17.00 and 17.67 mm), Exserohilum rostratum AMS 1077 (34.00 and 33.67 mm), and Trichophyton indotineae AMS 180 (38.33 and 34.00 mm). Selective cytotoxic effects on the breast cancer cell line MDA-MB-231 were observed by extracts A and E at IC50 = 309 and 277 μg/mL, while non-selective cytotoxic effects on the normal HUVEC cell line were found with IC50 = 919 and 796 μg/mL, respectively. Characterization of the most effective extracts A and E by high-resolution electrospray ionization mass spectrometry (HR-ESI-MS) shows that they have a wide range of secondary metabolites, including cytochalasans, azaphilone alkaloids, steroids, terpenoids, flavonoids, and phenols. These findings underscore the chemical diversity and therapeutic potential of freshwater fungi from Egypt.

Microbiology Research doi: 10.3390/microbiolres17040080

Authors: Claudia Berenice Tinoco-Cabral Luis Alfonso Muñoz-Miranda Manuel R. Kirchmayr Vianeth Martínez-Rodríguez Miguel Padilla-Rosas Maricarmen Iñiguez-Moreno Suchiquil Rangel-Velázquez Fabiola Berenice Hernández-Reyes Claudia Lisette Charles-Niño Cesar Arturo Nava-Valdivia

Candida species can shift from commensal organisms to opportunistic pathogens. Both Candida albicans and non-albicans Candida (NAC) species colonize oral biofilms and periodontal pockets, where they may contribute to inflammation and the progression of periodontal disease. This study aimed to determine the prevalence and antifungal susceptibility profiles of Candida species in individuals with different stages of periodontal disease. A cross-sectional study was conducted in 100 participants whose periodontal status was clinically evaluated. Saliva samples were cultured on chromogenic agar for yeast isolation, species identification was confirmed by MALDI-TOF MS, and antifungal susceptibility to fluconazole, clotrimazole, nystatin, and amphotericin B was assessed. Candida spp. was detected in 35% of participants, where C. albicans was the most prevalent species, followed by Nakaseomyces glabratus (formerly Candida glabrata), Candida parapsilosis, Candida dubliniensis, and Candida tropicalis. Species distribution varied according to periodontal status, with N. glabratus predominating in early periodontitis and C. albicans appeared more frequently in higher severe stages of periodontitis. Susceptibility testing showed resistance of C. albicans to clotrimazole (63.6%) and nystatin (22.7%), whereas amphotericin B and fluconazole remained effective. NAC species, particularly N. glabratus, exhibited resistance to nystatin and variable resistance to clotrimazole but remained susceptible to amphotericin B. These findings underscore the importance of early detection and personalized antifungal strategies for managing periodontal disease complicated by Candida colonization.

Microbiology Research doi: 10.3390/microbiolres17040079

Authors: Armando Navarro-Ocaña Armando Navarro-Cid del Prado Ricardo Ernesto Ahumada-Cota Ulises Hernández-Chiñas

Intestinal infections caused by Salmonella enterica serovar Typhi (S. Typhi) remain a global health concern, making preventive strategies and diagnostic tools essential. This study aimed to identify mimotope peptides of the Vi antigen using phage display and assess their recognition by rabbit and 46 human sera, as well as their potential for diagnosis and immunogen design. Rabbits were immunized with the Vi antigen (AgVi) from S. Typhi ATCC 6539, and sera-derived IgG was used for phage biopanning. DNA sequences from selected phagotopes were synthesized as Salmonella mimotope peptides (SMPs), either linear or KLH-conjugated. Their reactivity was tested with ELISAs against AgVi and SMPs, using both rabbit sera and 46 human serum samples. Ten phagotopes were identified, with a consensus motif (D/G–A/V–x–P–x–x–G–x–x–x–x–x), suggesting α-helix structures. Immunization with KLH-conjugated peptides generated specific antibodies, particularly SMPVi/5 and SMPVi/10, which recognized AgVi and their respective peptides. Competitive inhibition assays confirmed that SMPVi/5 reduced the anti-AgVi binding in a dose-dependent manner. In human sera, AgVi recognition occurred in 52% of samples, while SMPVi/5 and SMPVi/10 were recognized in 45%. Overall, SMPVi/5 demonstrated immunogenicity and functional mimicry, supporting its use as a synthetic reagent for serological assays and as a candidate for immunogen design.

Microbiology Research doi: 10.3390/microbiolres17040078

Authors: Shubhangi Kansal Kavita Gupta Shubhneet Kaur Mamik Neelam Taneja Archana Angrup

The rise in multidrug resistance in Klebsiella pneumoniae is an alarming issue, especially in invasive infections among patients with co-morbidities. With the gain of hypervirulence traits, multidrug-resistant K. pneumoniae has led to a significant increase in chronic infections and associated mortality. This study aims to explore the distribution of multidrug-resistant and hypervirulent (hv) K. pneumoniae in invasive infections in a tertiary care hospital. A total of 231 K. pneumoniae isolates were collected over a period of six months from invasive infections. These isolates were tested phenotypically and genotypically for the presence of antimicrobial resistance, along with molecular detection of hypervirulence determinants (iucA, rmpA, rmpA2, peg344, iroB). High levels of resistance to β-lactams, fluoroquinolones, and aminoglycosides were observed. Carbapenemase-encoding genes were widely distributed, and 22% showed the presence of at least one hypervirulence gene, most commonly iucA and rmpA. Co-carriage of resistance and hypervirulence determinants in K. pneumoniae was observed in nearly 20% of the isolates, indicating the emergence of MDR-hvKP phenotypes in the hospital setting. Mortality was significantly higher among patients infected with MDR isolates, whereas hypervirulence markers were not independently associated with mortality. The presence of MDR–hypervirulent strains remains clinically concerning and underscores the need for continued genomic surveillance.

Microbiology Research doi: 10.3390/microbiolres17040077

Authors: Edmar Gonçalves Pereira Filho Stéfanne Rodrigues Rezende Ferreira Amanda Veiga Paiva Simões Eli Júnior Pereira Rodrigues Iorrana Morais de Oliveira Marillia Lima Costa Adeliane Castro da Costa Berendina Elsina Bouwman Hanstter Hallison Alves Rezende

The objective of this study is to evaluate the efficiency of surgical instruments’ manual cleaning versus automated cleaning in an ultrasonic cleaner for the removal of biofilms on surgical forceps contaminated with Staphylococcus epidermidis and Pseudomonas aeruginosa. Subsequently, the residual microbial load was quantified through microbiological culture, aiming to evaluate the effectiveness of biofilm removal under different reprocessing conditions. Cleaning is an essential step in the processing of surgical instruments to ensure the effective removal of dirt and microorganisms. Through adhesion, microorganisms can attach to surfaces and form biofilms, organized structures surrounded by an extracellular matrix consisting of various components, which favor metabolic exchanges, adaptation, resistance, and bacterial dispersion. These biofilms increase the pathogenic potential of microorganisms, contributing to the occurrence of Healthcare-Associated Infections, and to avoid these, it is essential that preventive measures aimed at microbial reduction are adopted. Automated cleaning proved more effective than manual cleaning, and the combined approach achieved the greatest microbial reduction, though persistent contamination was still observed. The ability of adhesion and biofilm formation on the surfaces of surgical instruments is regarded as a challenge for complete microbial removal. These findings enhance the need for more rigorous reprocessing protocols and complementary strategies to ensure greater safety in the use of reusable instruments in clinical practice.

Microbiology Research doi: 10.3390/microbiolres17040076

Authors: Eugenia Guadalupe Ortiz-Lechuga Verónica Almaguer-Cantú Hiram Herrera-Barquín Karla Katiushka Solís-Arévalo Ramón Alberto Batista-García Katiushka Arévalo-Niño

Biosurfactant-producing microorganisms play an important ecological role in soils impacted by hydrophobic contaminants by enhancing substrate bioavailability and influencing microbial interactions. In this study, we critically evaluated the reliability of commonly used screening methods for biosurfactant detection. A total of 71 microbial isolates (16 bacteria and 55 fungi) were obtained from vegetable oil-contaminated soil and screened using a multi-step approach combining enzymatic assays (lipolytic and hemolytic activity) and physicochemical methods, including drop-collapse, oil spreading, emulsification index (E24), and surface tension reduction. Although 21 isolates exhibited lipolytic activity and 9 showed hemolysis, inconsistent responses among assays revealed significant limitations of individual screening methods. Only two bacterial isolates consistently tested positive across all criteria. When cultivated in mineral salt medium supplemented with hydrophobic substrates, both isolates produced stable emulsions and significantly reduced surface tension (from 54.26 mN/m to 31.46 mN/m). Substrate-dependent variation was observed for isolate C3, which showed reduced surface tension (39.63 mN/m) when grown with biodiesel. These findings highlight the risk of relying on single assays and emphasize the need for integrated screening strategies to ensure reliable detection of biosurfactant-producing microorganisms.

Microbiology Research doi: 10.3390/microbiolres17040075

Authors: Doris Evelyn Yah Hui Jong Siang Yin Lee Yun Khoon Liew Phyu Synn Oo Amar Harris Arifin Zi Ni Ngai Beek Yoke Chin Shamala Salvamani Rhun Yian Koh

In the original publication [...]

Microbiology Research doi: 10.3390/microbiolres17040074

Authors: Ajran Kabir Rosbelly Rios Mohamed Saleh Daniel Mallal Barbara L. Whitt Jaden Thompson Beatrice T. Sponseller Nathan M. Slovis Mats H. T. Troedsson Hossam El-Sheikh Ali Yosra A. Helmy

Klebsiella pneumoniae has been associated with reproductive infections in equines. The detection of β-lactam resistance determinants, especially extended-spectrum β-lactamase (ESBL) genes, within genomic regions linked to horizontal gene transfer (HGT), is of a particular concern. In this study, we characterize the whole-genome sequences (WGS) of three K. pneumoniae equine isolates harboring multiple antimicrobial resistance genes. Two isolates were recovered from uterine washes of mares: one with endometritis (YAH-KPEM1) and one clinically normal (YAH-KPSE1), and a third from the feces of a diarrheic foal (YAH-KPF132). WGS was performed using the Illumina MiSeq platform, and the reads were subsequently processed through hybrid assembly in Unicycler v0.5.1. Genome annotation was completed using PROKKA v1.14.5. Strain YAH-KPEM1 was classified as ST127, whereas YAH-KPSE1 and YAH-KPF132 belonged to ST1630 and ST224, respectively. Notably, K. pneumoniae ST1630 and ST224 have not been reported before in equines. All three genomes encoded multiple antimicrobial resistance (AMR) determinants, including two encoding ESBL genes (CTX-M-15), as well as virulence factors and regions associated with HGT. Additionally, two (YAH-KPEM1 and YAH-KPSE1) isolates were found to be multidrug resistant (MDR), harboring an IncFIB(K) plasmid replicon, and another isolate, YAH-KPF132, carried an IncFII replicon. The detection of AMR and virulence genes in equine Klebsiella isolates has important clinical implications for guiding antimicrobial selection and improving treatment success.

Microbiology Research doi: 10.3390/microbiolres17040073

Authors: Zhuliang Jiang Yukai Zeng Dingping Liu Yuanjing Li

Castanopsis hystrix (C. hystrix) is one of the most dominant and ecologically important species in subtropical evergreen broad-leaved forests of China. Interactions between its root and rhizosphere microorganisms play a pivotal role in nutrient acquisition and in mediating plant response s to environmental stresses. In this study, high-throughput 16S ribosomal RNA (16S rRNA) sequencing combined with untargeted metabolomics was employed to systematically characterize the rhizosphere microbial community and root exudates in C. hystrix. The results showed that, compared with non-rhizosphere soil, bacterial diversity in the rhizosphere of C. hystrix was significantly reduced, while several specialized and potentially efficient taxa were selectively enriched, particularly Candidatus_Solibacter, Candidatus_Xiphinematobacter, and Candidatus_Koribacter, thereby reshaping a distinct rhizosphere-specific community structure. Metabolomic analyses further revealed that 129 metabolites were significantly enriched in the rhizosphere, including four major classes of compounds associated with plant stress resistance: lipids and lipid-like molecules, organoheterocyclic compounds, organic acids and derivatives, and phenylpropanoids and polyketides. The enrichment of these metabolites likely contributes substantially to stress tolerance in C. hystrix. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis identified six defense-related metabolic pathways, including pyrimidine metabolism, steroid biosynthesis, nucleotide metabolism, plant hormone signal transduction, ATP-binding cassette transporter (ABC transporters), and the biosynthesis of various plant secondary metabolites. Further correlation analysis and co-occurrence network analysis suggested that C. hystrix may potentially influence the enrichment of beneficial microorganisms through rhizosphere metabolites selectively, which could reduce the reliance on external nutrient acquisition and enhance the stress resilience of C. hystrix. Our study provides a comprehensive perspective for elucidating rhizosphere interaction networks and their ecological functions in C. hystrix, thereby enhancing our understanding of the environmental adaptability of dominant tree species in subtropical forests.

Microbiology Research doi: 10.3390/microbiolres17040072

Authors: Sookyung Oh Bradd J. Haley Jitendra Patel

Whole-genome sequencing followed by comprehensive genomic analyses was used to characterize 16 Salmonella isolates from water-overlying sediments in Conococheague Creek (PA), an agricultural irrigation water source. Our goal was to characterize the genomic profiles and diversity of these Salmonella isolates. We identified eight distinct serotypes, including Newport, the most prevalent (43.8%), providing environmental context relevant to agricultural water systems. Genomic surveys showed various Salmonella Pathogenicity Island (SPI) profiles. Although widespread antimicrobial resistance (AMR) genes were not detected, the consistent presence of the aac(6’)-Iaa gene across all isolates and a parC (T57S) mutation in 14 isolates were identified as inherent genotypic markers. Six distinct plasmid replicon types were observed in over 60% of isolates. Replicons for IncF and IncI2 plasmids, frequently associated with β-lactamase genes, were found, documenting the presence of mobile genetic elements despite a lack of acquired AMR genes. Restriction-Modification (RM) systems and CRISPR/Cas loci were also detected, suggesting Salmonella genomic plasticity. Our study showed that sediment-associated Salmonella, notably serotype Newport, harbored diverse virulence-associated genomic features. These findings contributed to the genomic baseline for irrigation water quality and food safety.

Microbiology Research doi: 10.3390/microbiolres17040071

Authors: Xuanxuan Feng Zhenghua Xie Jianmin Wang Xinzhou Yang

While the gut microbiota of pollen-carrying bees (e.g., honeybees and bumblebees) has been well studied, the gut microbiota of vespine wasps remains poorly understood. Unlike pollen-carrying bees, which primarily consume pollen and nectar, vespine wasp larvae mainly feed on insects, suggesting that their gut bacterial communities may be different. Therefore, this study aimed to reveal the differences in larval gut bacterial communities between pollen-carrying bees and vespine wasps. Using datasets obtained from our own samplings and public resources released by other researchers, we compared the diversity and composition of larval gut bacterial communities between vespine wasps and pollen-carrying bees. Alpha diversity and beta diversity of bacterial communities were measured. Results showed that vespine wasp larvae harbored distinct gut bacterial communities from those of pollen-carrying bees, dominated by Leuconostoc, Hafnia-Obesumbacterium and Lactobacillus. Significant differences in bacterial composition were observed at both the community level and the dominant taxa level between pollen-carrying bee larvae and vespine wasp larvae. Moreover, significant differences were also found among larval gut bacteria of vespine wasps. These findings provide insights into the bacterial composition of aculeate wasps with different dietary habits.

Microbiology Research doi: 10.3390/microbiolres17040070

Authors: Anna-Marie Ilic Jan Werner Böhm Michael Kube

Increasing genomic data are driving changes in the selection of phylogenetic markers and analysis strategies. Databases enable the extraction of established markers, such as single and multilocus sequence typing (MLST), but are often limited by the number of informative sites or availability with respect to incomplete source data sets or reductive evolution in bacteria such as the Mollicutes. Genome-wide analyses like average nucleotide identity (ANI) often overcome these problems but also depend on the alignment percentage. Complementary analyses help validate results and address limitations of primary approaches. However, how genome-wide compositional signals and reduced core gene sets affect phylogenomic resolution across a large and taxonomically diverse dataset of complete Mollicutes genomes remains unclear. Therefore, we applied an advanced MLST approach based on single-copy orthologs (SCOs), alongside codon usage analysis. The reliability and impact of these approaches were first analyzed using Acholeplasmatales as the foundation, with 16S rRNA gene, ANI, SCOs, and codon usage. Codon usage analysis revealed lineage-associated compositional signatures across the 52 strains that were broadly consistent with current genus and subgroup assignments, whereas ANI and 16S rRNA gene identified species with ≥96.5% and ≥97%, respectively. Among these, SCOs showed the most matches to the current taxonomy, supporting the approach being extended to Mollicutes. Applied to 807 Mollicutes strains, the analysis revealed 16 shared SCOs. Concatenation of this core set significantly enhanced phylogenomic resolution, providing a robust framework for reconstructing evolutionary relationships within Mollicutes.

Microbiology Research doi: 10.3390/microbiolres17040069

Authors: Olga Jakovljević Željka Milovanović Miloš Stupar Željko Savković Marija Pećić Dragana Jerinkić Slađana Popović

Cave microbiota comprise metabolically diverse organisms, including microalgae, among which Bacillariophyta (diatoms) represent one of the most prominent groups, inhabiting a wide range of substrates within cave ecosystems. In contrast to aerophytic cave habitats, aquatic cave environments remain poorly studied. Therefore, the main aims of this study were to determine the diversity, spatial distribution, and seasonal dynamics of diatom assemblages in the Ponorac Stream flowing through Ravništarka Cave, and to assess the influence of environmental variables on diatom diversity and distribution. Samples were collected from six sites along the Ponorac stream in May and November 2023. Physical and chemical water parameters showed only minor variation among sampling sites. In total, 148 diatom taxa belonging to 54 genera were recorded, including several rare diatom taxa. Diatom assemblages in the Ponorac stream were characterized by high taxonomic richness, high α-diversity, and pronounced community heterogeneity. Many taxa occurred in both seasons and across multiple sites, whereas several were restricted to a single season or exhibited clear site specificity. Most diatom index values indicated generally high ecological status. This study highlights the importance of aquatic cave habitats as reservoirs of diatom diversity and their value in studying temporal and spatial variation of their communities.

Microbiology Research doi: 10.3390/microbiolres17040068

Authors: Sabīna Ribačuka Viktorija Bankoviča Ingus Skadiņš

The global rise in antimicrobial resistance has spurred increased interest in alternative antimicrobial agents, particularly essential oils (EOs). These oils are complex mixtures of volatile compounds that exhibit documented biological activity. This study evaluated antimicrobial and antibiofilm effects of selected EOs against clinically relevant bacterial and fungal pathogens. Antimicrobial activity against planktonic cells was assessed using disc diffusion assays with DMSO-diluted EO solutions against Escherichia coli (E.coli), Staphylococcus aureus (S.aureus), Pseudomonas aeruginosa, Klebsiella pneumoniae, and Candida albicans. Antibiofilm activity of E. coli and S. aureus was examined using ethanol-based EO formulations, with biofilm viability quantified by colony forming unit (CFU) enumeration. Cinnamon (Cinnamomum verum) oil showed the strongest and most consistent activity, inhibiting planktonic and biofilm models. Tea tree (Melaleuca alternifolia), lemongrass (Cymbopogon citratus), rosemary (Rosmarinus officinalis), rose (Rosa damascena), and jasmine (Jasminum officinale) oils showed significant planktonic antimicrobial effects, while jasmine oil (Jasminum officinale) demonstrated pronounced antibiofilm activity against S. aureus, including strong biofilm eradication in several replicates. In contrast, chamomile (Matricaria chamomilla) and sandalwood (Santalum austocaledonicum) oils showed limited or no activity. These findings highlight differences between planktonic and biofilm responses, emphasizing the importance of incorporating biofilm models into antimicrobial evaluation. Overall, Cinnamomum verum and Jasminum officinale oils may serve as complementary antimicrobial agents, warranting further investigation.

Microbiology Research doi: 10.3390/microbiolres17040067

Authors: Gagandeep Brar Ramandeep Kaur Mandeep Kaur Gill Navjot Singh Rupinderjeet Kaur

Climate change is intensifying winters in temperate regions, posing a serious threat to Apis mellifera health. The gut microbiome, a distinct community of core bacterial species, is central to overwintering success by supporting immune function, nutrient assimilation, and pathogen resistance, but is highly sensitive to environmental stressors such as cold temperatures and dietary shifts. Stress-induced perturbations can reshape the composition and relative abundance of the gut microbiome in honey bees, leading to adverse effects on host health, physiological functions, and overwinter survival. Cold temperatures and additional stressors further destabilize the microbiome, compounding these effects. This review is the first to synthesize current knowledge on how extrinsic factors, such as diet, antibiotics, and pathogens, and intrinsic factors, including age and strain, influence the composition and function of the honey bee gut microbiota during the overwintering period. Given the increasing severity of winter conditions under climate change, a deeper understanding of microbiome–host–environment interactions is essential for improving honey bee resilience. By integrating evidence on the microbiome’s roles in nutrient utilization, immune modulation, and pathogen defense, this review outlines a framework to guide future research aimed at sustaining pollinator health and nutrition in a changing global climate.

Microbiology Research doi: 10.3390/microbiolres17040066

Authors: Yaodong He Zhengwei Peng Fenglin Wang Peitao Liu Shirui Mu Yaqiong Wang Xiumei Zhang

Eukaryotic microorganisms, including microalgae, protists, fungi, and micro-metazoans, act as drivers of energy flow and nutrient cycling, collectively forming the microbial food loop, and also serve as important indicators of environmental health. To investigate the seasonal variation in eukaryotic microorganisms in a mussel farming area, a total of 96 seawater samples were collected from surface and bottom layers of water across different seasons. High-throughput sequencing of the 18S rRNA gene was employed to characterize shifts in microbial community structure and identify key influencing factors. Our results indicated significant seasonal differences in eukaryotic microbial communities between surface and bottom waters. Redundancy Analysis (RDA) revealed that seasonal variations in community structure were primarily driven by environmental factors such as temperature, dissolved oxygen (DO), and salinity. Co-occurrence network analysis indicated that surface water networks exhibited higher numbers of nodes and edges, as well as greater modularity, suggesting more distinct niche differentiation and higher natural connectivity within the community. These findings provide fundamental data for understanding the response mechanisms of eukaryotic microbial communities to seasonal changes in the mussel cultivation area of Gouqi Island.

Microbiology Research doi: 10.3390/microbiolres17040065

Authors: Mayur J. Nath Shubham R. Choudhury Priyanka Sourav Khan Manabendra Mandal Sanjay K. S. Patel

This study investigated the antibiofilm and anti-quorum-sensing (QS) potential of endophyte extracts isolated from medicinal plants and their validation against Pseudomonas aeruginosa. Endophytes were isolated from the plants using the serial dilution method, and the extracts produced by these endophytes were screened for antimicrobial and biofilm-inhibition activity using assays. The efficient extract was biochemically characterized, followed by validation of its secondary metabolite content. Furthermore, QS-regulatory gene expression levels and microscopy were used to confirm inhibition of biofilm formation. A total of 12 cultures, including 8 bacterial and 4 fungal, were isolated and screened, demonstrating efficient antimicrobial activity (zone of inhibition of 18.8 mm) and 64.3% antibiofilm activity. The efficient endophyte isolated from Paederia foetida was identified as Bacillus xiamenensis MM07 by 16S rRNA gene sequencing. MM07 extract analyses by biochemical and Fourier transform infrared methods revealed the presence of diverse biomolecules. A dose-dependent inhibition was observed, achieving up to 83.5, 60.3, 73.2, 82.7, 83.2, and 15.1 in biofilm formation and exopolysaccharide, violacein, pyocyanin, protease, and alginate production, along with 63.2% swimming ability at 30 µg/mL, respectively. Gas chromatography-mass spectrometry analyses validated the presence of major secondary metabolites, including 3,3-dimethyl-4-methylamino-butan-2-one, 6-amino-2-methyl-, 1-iodo-2-methylundecane, and hexadecanoic acid, with the potential to inhibit biofilm and QS activity. Quantitative real-time polymerase chain reaction of QS regulatory genes (lasI, lasR, rhlI, and rhlR) and microscopy analysis confirmed the anti-QS properties, evidenced by a 40.3% decline in gene expression and biofilm inhibition by MM07 extract. These findings highlight the potential of novel B. xiamenensis MM07 endophyte from P. foetida as a sustainable source of biomolecules for combating biofilm-associated infections.

Microbiology Research doi: 10.3390/microbiolres17030064

Authors: Shaun Cawthraw Andrew Wales Tom Huby Rob Davies

Introduction: Salmonella may contaminate livestock feed at several stages of production, transport and storage. Formaldehyde is an effective anti-Salmonella feed treatment, but it is now banned for this use in Europe. Organic acid-based additives are an alternative. Gap Statement: The efficacy of organic acid feed additives against natural Salmonella feed contamination is uncertain due to a paucity of reported work investigating low levels of infection that may be relevant for real-world situations. Aim: To compare the anti-Salmonella effects of feed additives based on formaldehyde versus those based on organic acids. Methodology: Experimental contamination of poultry feed with one of three Salmonella serovars at moderate (between 10 and 200 CFU/g) or low (around 1 CFU/g) levels was preceded (‘prevention’ mode) or followed (‘decontamination’ mode) by application of commercial antimicrobial additives. Storage at room temperature for 24 h was followed by pre-enrichment then culture. Results: Organic acid-based products at recommended application rates only eliminated detectable Salmonella from samples with the lowest degree of contamination. The effect was partial, with a proportion of samples still yielding Salmonella in most experiments, and only one such product showed efficacy above 50% of samples for the decontamination mode. The two formaldehyde-based products showed partial efficacy against moderate contamination, and one was entirely effective against low-level contamination even at its lower inclusion rate. Conclusions: Organic acid-based feed additives have a lesser anti-Salmonella effect than formaldehyde-based products at their respective recommended inclusion rates. However, some non-formaldehyde products may be substantially effective against a low, natural degree of contamination. Impact Statement: Chemical suppression of Salmonella in animal feed is an important element of measures to safeguard livestock health and, consequentially, public health too. The European ban on using formaldehyde for this purpose has necessitated the use of alternative products. The present work includes very low levels of Salmonella in feed, possibly mimicking natural contamination, to show that under these circumstances some such alternatives may be as efficacious as formaldehyde products.

Microbiology Research doi: 10.3390/microbiolres17030063

Authors: Khin Zar Linn Su Zar Chi Lwin Aye Thida Maung Marwa Nabil Sayed Abdelaziz Catherine Damaso Hofilena Yuzhi Lin Haomin Ye Yoshimitsu Masuda Takahisa Miyamoto Ken-ichi Honjoh

Nontyphoidal Salmonella (NTS) is a zoonotic pathogen that threatens public health worldwide. This study investigated the prevalence, serotype, virulence, and antimicrobial resistance of NTS isolated from chicken meat in Fukuoka, Japan. Of 50 samples, 64% were positive for Salmonella spp., and 32 NTS strains were isolated from positive samples. Serotyping identified three serotypes: S. enterica ser. Schwarzengrund (78.1%), S. enterica ser. Thompson (15.6%), and S. enterica ser. Oranienburg (6.3%). Multilocus sequence typing revealed three sequence types (STs), and MALDI-TOF MS analysis revealed six distinct clusters, reflecting heterogeneity in protein expression among isolates with the same STs. All isolates harbored the virulence genes hilA, spiC, and ssrB, but not spvC. Microplate assays showed that all S. enterica ser. Schwarzengrund and S. enterica ser. Thompson strains formed biofilms with varying strengths. Antimicrobial susceptibility tests demonstrated that S. enterica ser. Thompson and S. enterica ser. Oranienburg strains were sensitive to all the antimicrobials tested. However, S. enterica ser. Schwarzengrund strains showed resistance to multiple antibiotic classes, and 36% of the isolates were multidrug resistant. These findings suggest a potential public health concern, particularly from S. enterica ser. Schwarzengrund, and underscore the importance of continuous surveillance that integrates both genotypic and phenotypic methods.

Microbiology Research doi: 10.3390/microbiolres17030062

Authors: Zizipho Z. A. Mbulawa Laston Gonah Lindiwe M. Faye Charles B. Businge

Anal human papillomavirus (HPV) and cancer prevalence are increasing. Therefore, this study investigated the prevalence of anal HPV and associated risk factors, as well as HPV genotype-specific concordance at cervical and anal sites and associated risk factors among women of Eastern Cape Province, South Africa. A total of 326 women aged 18–60 were recruited from an Eastern Cape community health facility. HPV DNA was detected in cervical and anal specimens using the Seegene Anyplex™ and Allplex™ II HPV28 assay (Seegene Inc., Seoul, Republic of Korea), respectively. Anal HPV was detected in 68.1% (95% CI: 62.9–72.9) and independent predictors were cervical HPV positivity (AOR: 2.40, 95% CI: 1.39–4.14, p = 0.002), abnormal cytology (AOR: 3.12, 95% CI: 1.29–7.55, p = 0.012), single marital status (AOR: 3.55, 95% CI: 1.24–10.17, p = 0.018), and having more than three lifetime sexual partners (AOR: 1.75, 95% CI: 1.03–2.98, p = 0.039). Anal high risk (HR)-HPV types were detected in 50.9%, with HPV-58 (13.2%), HPV-68 (11.0%) and HPV-52 (9.2%) being the most dominant types. HPV genotype-specific cervical and anal concordance was observed in 33.5% of cases, with HPV-58 (7.1%), HPV-68 (4.9%), and HPV-35 (4.6%) being the most dominant. Women who were positive for cervical HPV infection (AOR: 3.24, 95% CI: 2.36–4.45, p < 0.001), anal HPV infection (AOR: 2.70, 95% CI: 2.01–3.63, p < 0.001) and abnormal cervical cytology (AOR: 2.01, 95% CI: 1.36–2.96, p < 0.001) had substantially higher odds of anal–cervical HPV concordance compared to those who were negative. High anal HPV prevalence and HPV genotype-specific anal and cervical concordance were observed among Eastern Cape women. Understanding anal HPV, HPV genotype-specific anal–cervical concordance, and associated factors can contribute to strategies towards anal HPV and associated disease prevention. These findings warrant further longitudinal investigation in future studies.

Microbiology Research doi: 10.3390/microbiolres17030061

Authors: Vincenzo Verdura Pasquale Bisceglia Luigi Annacontini Luigi Cagiano Francesca Sanguedolce Martina Miracapillo Fabrizia Fusco Sergio Lo Caputo Francesco Drago Gaetano Serviddio Aurelio Portincasa Giulia Ciccarese

Dermatofibrosarcoma protuberans (DFSP) is a rare tumor presenting as a slow-growing, plaque-like or multinodular, brownish lesion on the trunk in adult patients. Diagnosis is established by histological examination and surgical excision is the primary treatment. Typically, DFSP has an indolent course and local spread. In the present work, we describe the clinical–histologic features, surgical treatment and follow-up of a case of DFSP in a patient living with HIV infection (PLWH). A 40-year-old man was referred to us with confluent lesions on the left shoulder, present for about 3 years. His medical history was positive for HIV-1 infection, for which he was taking antiretroviral therapy. Microscopic examination showed dermal and hypodermic proliferation of spindle cells in a storiform pattern, confirming the clinical diagnosis of DFSP. A wide excision was performed with 3 cm clinically healthy tissue margins, and the defect was repaired using an artificial bilaminar dermal matrix. The histological examination revealed tumor-free margins, and a split-thickness skin graft was harvested from the same arm. After 10 months, the patient was free from the disease. As observed with other skin cancers, DFSP may have a higher incidence and greater aggressiveness in immunosuppressed than in immunocompetent patients. DFSP has been reported only twice in PLWH. Our case constitutes a third report, adding to the evidence that there may be an over-representation of this cancer in immunosuppressed individuals.

Microbiology Research doi: 10.3390/microbiolres17030060

Authors: Jianmin Liu Mingliang Geng Yi Chen Zhenhui Wang

Catalpol, one of the primary bioactive components in Rehmannia glutinosa, is an iridoid glycoside with significant pharmacological activities. To expand the microbial sources of catalpol, endophytic bacteria were isolated from R. glutinosa (cultivated in Jiaozuo, China) using the dilution plating method combined with vanillin–sulfuric acid colorimetric assay. High-performance liquid chromatography (HPLC) and liquid chromatography–mass spectrometry (LC-MS) were employed for screening and identification. The isolated strain was identified through morphological characterization and 16S rDNA gene sequence analysis, while single-factor experiments coupled with response surface methodology were utilized to optimize its fermentation conditions. Results indicated that the strain DH14 formed circular, cream-white, opaque colonies and was Gram-negative. It was identified as Brevundimonas olei. The optimal fermentation conditions were determined to be 190 rpm, pH 7.6, 31 °C, and 0% NaCl. Meanwhile, the results revealed a positive correlation between the pH of the fermentation broth and catalpol production. Under the optimized conditions, the maximum catalpol yield reached 0.142 mg/mL after 3 days of cultivation. This study provides a promising microbial resource and optimized fermentation parameters for the microbial production of catalpol.

Microbiology Research doi: 10.3390/microbiolres17030059

Authors: Kaloyan D. Georgiev Deyan Dzhenkov Marieta Georgieva Antoaneta Tsvetkova

Probiotics are live microorganisms that, when administered in adequate amounts, confer health benefits to the host. The present study aimed to evaluate the protective effects of a probiotic against experimentally induced gastric ulcers in rats. Male Wistar rats were allocated into five groups (n = 6 per group): Control, Model (indomethacin-induced ulcers, IND), Positive control (IND + famotidine), IND + Laktera Nature (LN) probiotic (800 mg/kg), and IND + LN probiotic (1600 mg/kg). The study duration was 14 days. On day 15, rats in groups 2–5 received 1 mL of indomethacin (40 mg/kg) orally. All rats were euthanized four hours later via cervical dislocation under diethyl ether anesthesia. LN probiotics have demonstrated dose-dependent protection against indomethacin-induced gastric ulcers, as assessed by both macroscopic and microscopic evaluation. Therefore, LN probiotics may represent a valuable adjunctive strategy in the management of gastric ulcers.

Microbiology Research doi: 10.3390/microbiolres17030058

Authors: Christopher T. Piatnichouk Joshua V. Ruppel Nicole L. Snyder

Tuberculosis, caused by Mycobacterium tuberculosis, remains a global health challenge, particularly due to multidrug-resistant strains. Photodynamic therapy using porphyrin-based photosensitizers offers a promising alternative by targeting the trehalose-rich cell wall of the bacillus. Motivated by prior experimental observations that shorter linkers improve efficacy, this study probes the molecular basis of linker-length-dependent activity in trehalose–porphyrin glycoconjugates. Here, we show that shorter linker lengths are consistent with improved activity in vitro and, in an Ag85B docking model, constrain conformational flexibility, reduce solvent exposure, and promote tighter packing consistent with stronger predicted interactions. Using computational docking, we analyzed binding scores, RMSD variability, steric clashes, and protein–ligand interactions for conjugates docked into Ag85B, a key enzyme in cell wall synthesis. Shorter linkers (0–2 carbons) were found to exhibit superior binding scores, lower RMSD variability, and stronger interactions with residues such as ARG 43, including unique π–cation interactions. In contrast, longer linkers displayed increased flexibility, reduced binding specificity, and greater solvent exposure. These findings, which support our experimental observations, suggest a molecular basis for linker-dependent efficacy and provide a framework for designing next-generation porphyrin-based therapeutics for tuberculosis treatment.

Microbiology Research doi: 10.3390/microbiolres17030057

Authors: Valery M. Dembitsky Alexander O. Terent’ev Sergey V. Baranin

Siderophores are classically understood as microbial iron-acquisition metabolites: low-molecular-weight ligands secreted by bacteria to solubilize and transport Fe(III) under iron-limited conditions. In this review, we expand that paradigm by highlighting an emerging and underappreciated chemical axis—boron coordination by siderophores—that links terrestrial (soil/rhizosphere) and marine microbiomes. Across diverse bacterial taxa, siderophore production is widespread and central to competitive fitness because Fe(III) is poorly soluble and frequently sequestered in environmental or host matrices. Yet in boron-rich settings (seawater and borate-enriched soils), the same oxygen-donor architectures that support Fe(III) chelation can also engage boron chemistry. We synthesize evidence that carboxylate/α-hydroxyacid (dicitrate-type) and catecholate siderophores can form tetrahedral borate/boronate complexes, whereas hydroxamate siderophores generally lack the vicinal dianionic O,O motif required for stable boron binding. Structurally characterized examples—including vibrioferrin, rhizoferrin, and petrobactin—demonstrate that boron complexation is experimentally observable by ESI-MS and multinuclear NMR and can be modulated by pH and microenvironment. Integrating these findings with datasets on boron-tolerant bacteria, we propose that when iron is scarce and boron is available, boron–siderophore complexation becomes chemically feasible and may influence microbial physiology by altering ligand conformation, metal selectivity, and potentially extracellular signaling behavior—especially in marine systems where borate is abundant at oceanic pH. Overall, this review frames boron-binding siderophores as a cross-ecosystem phenomenon and a promising conceptual bridge between environmental boron geochemistry, microbial metal economy, and metalloid-mediated signaling.

Microbiology Research doi: 10.3390/microbiolres17030056

Authors: Gonçalo Melo Raquel Abreu Gonçalo Pereira Eva Cunha Lélia Chambel Luís Tavares Manuela Oliveira

Semi-aquatic turtles are popular companion animals and represent an important One Health interface in Portugal due to their potential to harbour zoonotic pathogens. This study aimed to characterize the virulence and antimicrobial resistance (AMR) profiles of Aeromonas spp. isolated from captive semi-aquatic turtles in Portugal. Cloacal swabs (n = 31) were collected from turtles under human care, and Aeromonas spp. were isolated using selective media and identified by multiplex PCR. Antimicrobial susceptibility was assessed by disk diffusion using eleven antibiotics, while the phenotypic virulence profile was evaluated by determining isolates’ ability to express five hydrolytic enzymes and to form biofilm. A total of 86 Aeromonas isolates were recovered, with A. hydrophila being the most prevalent (77.9%). Most isolates displayed high pathogenic potential: over 87% produced DNase, haemolysin, and lecithinase, while nearly all produced protease and gelatinase. Also, 44.2% of the isolates were resistant to at least one antibiotic, and 12 (14.0%) were multidrug resistant. Higher Multiple Antibiotic Resistance (MAR) indices were significantly associated with turtles housed in indoor aquariums (p < 0.05). These findings indicate that captive semi-aquatic turtles may act as reservoirs of virulent and antimicrobial-resistant Aeromonas spp., highlighting potential zoonotic risks and supporting the need for a One Health approach in their management.