Microbiology Research

31 pages, 5083 KB

Open AccessArticle

Inhibition of Staphylococcus epidermidis Biofilm Formation by a Synthetic Breitfussin Analogue

by 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 and Jeanette Hammer Andersen

Microbiol. Res. 2026, 17(6), 105; https://doi.org/10.3390/microbiolres17060105 - 28 May 2026

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Section Antimicrobials and Antimicrobial Resistance)

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12 pages, 1052 KB

Open AccessArticle

Evaluation of an SNP-Based Diagnostic Assay for Enteric Fever Detection in Resource-Limited Settings

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

Microbiol. Res. 2026, 17(6), 104; https://doi.org/10.3390/microbiolres17060104 - 28 May 2026

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Section Medical and Veterinary Microbiology)

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19 pages, 1241 KB

Open AccessArticle

Potential Association Between Glucosamine Supplementation and Gut Microbiota Composition in Middle-Aged Japanese Adults: A Cross-Sectional Analysis Using 16S rRNA Sequencing

by Tomoya Shintani

Microbiol. Res. 2026, 17(6), 103; https://doi.org/10.3390/microbiolres17060103 - 27 May 2026

Abstract

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, [...] Read more.

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. Full article

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17 pages, 848 KB

Open AccessArticle

Halogen-Substituted Cinnamide Derivatives with Activity Against Toxoplasma gondii Parasites

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

Microbiol. Res. 2026, 17(6), 102; https://doi.org/10.3390/microbiolres17060102 - 23 May 2026

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Section Medical and Veterinary Microbiology)

11 pages, 2537 KB

Open AccessArticle

Prevalence of Norovirus (NoV), Hepatitis A Virus (HAV), and Hepatitis E Virus (HEV) in Mussels (Mytilus galloprovincialis) from Bulgarian Black Sea Coast

by Gergana Krumova-Valcheva, Eva Gyurova, Gergana Mateva, Mihail Milanov, Magdalena Baymakova and Ilia Tsachev

Microbiol. Res. 2026, 17(6), 101; https://doi.org/10.3390/microbiolres17060101 - 23 May 2026

Abstract

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) [...] Read more.

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. Full article

(This article belongs to the Section Food and Agricultural Microbiology)

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11 pages, 427 KB

Open AccessArticle

Multidrug-Resistant Bacterial Strains in Northern Mexico: Clinical Impact and Vitek 2-Based Characterization

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

Microbiol. Res. 2026, 17(5), 100; https://doi.org/10.3390/microbiolres17050100 - 21 May 2026

Abstract

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 [...] Read more.

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. Full article

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13 pages, 261 KB

Open AccessArticle

Prevalence and Genotyping of Human Papillomavirus in Oral Squamous Cell Carcinoma, Oral Potentially Malignant Disorders, and Healthy Oral Mucosa: A Cross-Sectional Study

by Teodora Bolyarova, Pavel Stanimirov, Ivo Sirakov, Emilia Naseva, Bilyana Sirakova, Konstantin Stamatov and Samuil Dzhenkov

Microbiol. Res. 2026, 17(5), 99; https://doi.org/10.3390/microbiolres17050099 - 21 May 2026

Cited by 1

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Section Medical and Veterinary Microbiology)

15 pages, 1051 KB

Open AccessArticle

Association of HHV-6 Reactivation with NLRP3 Inflammasome Activation in Chemotherapy-Treated Iraqi Cancer Patients: A Cross-Sectional Study

by Nadia Habeeb Sarhan, Maroua Gdoura-Ben Amor, Saif Jabbar Yasir and Radhouane Gdoura

Microbiol. Res. 2026, 17(5), 98; https://doi.org/10.3390/microbiolres17050098 - 19 May 2026

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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17 pages, 842 KB

Open AccessArticle

Bioactivity of Pod and Seed Extracts from Leucaena leucocephala, Prosopis laevigata, and Pithecellobium dulce Collected in Oaxaca, Mexico

by Jesús Andres Morales-López, Teodulfo Aquino-Bolaños, Angélica Bautista-Cruz, Tamara Aquino-Aguilar, Edgar García-Sánchez, Tlacaelel Aquino-López and Keyla Cruz-García

Microbiol. Res. 2026, 17(5), 97; https://doi.org/10.3390/microbiolres17050097 - 19 May 2026

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Advances in Plant–Pathogen Interactions)

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13 pages, 6093 KB

Open AccessArticle

Real-Time Fluorescence Imaging Platform for Screening Arbuscular Mycorrhizal Fungi by Hyphal Transport Kinetics

by Guangle Zhang, Lixue Yuan, Yongxin Zhang, Xiaohang Wang, Li Zhang, Xinyuan Zhang, Ruxue Chen, Zhuangzhuang Wang, Bo Yu and Yonghua Wang

Microbiol. Res. 2026, 17(5), 96; https://doi.org/10.3390/microbiolres17050096 - 19 May 2026

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Topic New Challenges on Plant–Microbe Interactions)

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19 pages, 1244 KB

Open AccessArticle

Optimization of IAA Production by Halotolerant Vreelandella titanicae J113 Through Fermentation Process Engineering with Response Surface Methodology

by Dilbar Tursun, Zulhumar Yakup, Huifang Bao, Faqiang Zhan, Yingwu Shi, Hongmei Yang, Jiusheng Sun, Shijie Fang and Ning Wang

Microbiol. Res. 2026, 17(5), 95; https://doi.org/10.3390/microbiolres17050095 - 12 May 2026

Abstract

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 [...] Read more.

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. Full article

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18 pages, 6291 KB

Open AccessReview

Engineering Escherichia coli for Aromatic Compound Biosynthesis: Integrating Metabolic Engineering and Synthetic Biology

by Silvana M. Tapia-Cabrera, Adelfo Escalante and Francisco Bolívar

Microbiol. Res. 2026, 17(5), 94; https://doi.org/10.3390/microbiolres17050094 - 9 May 2026

Abstract

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 [...] Read more.

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. Full article

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13 pages, 518 KB

Open AccessArticle

Molecular Epidemiology of Drug-Resistant Mycobacterium tuberculosis: Mutation Profiles and Resistance Associations

by Mandlenkosi Manika, Lindiwe Modest Faye, Ntandazo Dlatu and Mojisola Clara Hosu

Microbiol. Res. 2026, 17(5), 93; https://doi.org/10.3390/microbiolres17050093 - 8 May 2026

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Topic Multidrug Resistance Across Pathogens: Fungi, Bacteria, Parasites, and Viruses)

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22 pages, 1290 KB

Open AccessSystematic Review

Molecular and Proteomic Determinants of Trypanosoma cruzi Adaptation Within Triatomine Vectors: Insights from Current Experimental Models

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

Microbiol. Res. 2026, 17(5), 92; https://doi.org/10.3390/microbiolres17050092 - 8 May 2026

Abstract

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. [...] Read more.

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. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

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17 pages, 1612 KB

Open AccessArticle

Impact of Pre-Existing Uterine Microbiome on Pregnancy Success After Embryo Transfer in Cattle

by 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 and Rainer M. Lopez Lapa

Microbiol. Res. 2026, 17(5), 91; https://doi.org/10.3390/microbiolres17050091 - 8 May 2026

Abstract

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 [...] Read more.

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. Full article

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13 pages, 5857 KB

Open AccessArticle

Detection and Host Range Investigation of Phytopythium helicoides and Phytopythium palingenes

by Petya Koeva Christova

Microbiol. Res. 2026, 17(5), 90; https://doi.org/10.3390/microbiolres17050090 - 30 Apr 2026

Abstract

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, [...] Read more.

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. Full article

(This article belongs to the Special Issue Advances in Plant–Pathogen Interactions)

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12 pages, 732 KB

Open AccessArticle

Enterococcus durans Secretome Modulates Interleukins Gene Expressions in Intestinal Epithelial Cells Challenged by Staphylococcus aureus Secretome: In Vitro Study on the HT-29 Cell Line

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

Microbiol. Res. 2026, 17(5), 89; https://doi.org/10.3390/microbiolres17050089 - 30 Apr 2026

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Cell Culture Advances in Food Microbiology: Innovative In Vitro Models for Safety, Quality, and Functionality)

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8 pages, 199 KB

Open AccessCommunication

Serological Investigation of Infectious Bovine Rhinotracheitis in Dromedary Camels and Dairy Herds in Tunisia: Preliminary Results

by 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 and Giovanni Pezzotti

Microbiol. Res. 2026, 17(5), 88; https://doi.org/10.3390/microbiolres17050088 - 29 Apr 2026

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Emerging and Re-Emerging Viruses in Animal Health: Pathogenesis, Diagnosis, and One Health Strategies)

28 pages, 510 KB

Open AccessReview

Rapid Antimicrobial Susceptibility Testing (AST): Overview of New Commercially Available Automated Phenotypic Tools for Minimum Inhibitory Concentration (MIC) Determination

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

Microbiol. Res. 2026, 17(5), 87; https://doi.org/10.3390/microbiolres17050087 - 29 Apr 2026

Abstract

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. [...] Read more.

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. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: New Diagnostic Strategies)

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