Microbiology Research

8 pages, 353 KB

Open AccessBrief Report

Dectin-3 Plays a Redundant Role in the Immune Response to Paracoccidioides brasiliensis

by 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 and Aldo Henrique Tavares

Microbiol. Res. 2026, 17(7), 128; https://doi.org/10.3390/microbiolres17070128 - 5 Jul 2026

Abstract

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 [...] Read more.

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. Full article

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

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19 pages, 1250 KB

Open AccessArticle

Characterization of the Fecal Microbiota of Urban Pigeons (Columba livia) in Northern Mexico: Taxonomic Composition and Predicted Functional Profiles

by 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 and Irene Pacheco-Torres

Microbiol. Res. 2026, 17(7), 127; https://doi.org/10.3390/microbiolres17070127 - 5 Jul 2026

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Section Microbial Ecology and Microbiomes)

15 pages, 811 KB

Open AccessArticle

Metabolic Stimulants as Functional Enhancers of Sustainable Microbial Omega-3 Fatty Acid Production

by Syed Ammar Hussain, Majher I. Sarker, Brajendra K. Sharma and Tony Z. Jin

Microbiol. Res. 2026, 17(7), 126; https://doi.org/10.3390/microbiolres17070126 - 3 Jul 2026

Abstract

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 [...] Read more.

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. Full article

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12 pages, 289 KB

Open AccessArticle

Invasive Bacterial Meningitis in Mali: Molecular Detection and Serotype Distribution of Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis

by 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 and Ahmed Aziz Bousfiha

Microbiol. Res. 2026, 17(7), 125; https://doi.org/10.3390/microbiolres17070125 - 30 Jun 2026

Abstract

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 [...] Read more.

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. Full article

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

29 pages, 5997 KB

Open AccessReview

Fungal and Bacterial Dysbiosis in Attention-Deficit/Hyperactivity Disorder: Implications for Candida, Diet, Probiotics, and Quality of Life—A Narrative Review

by Veroslava V. Stankovic, Dragana P. Jovic and Natasa K. Rancic

Microbiol. Res. 2026, 17(7), 124; https://doi.org/10.3390/microbiolres17070124 - 30 Jun 2026

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Candida Infections: Epidemiology and Impact on the Patient Health-Related Quality of Life)

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12 pages, 1244 KB

Open AccessReview

Postbiotics: Research Progress in Canines and Felines

by Jian Zhang, Weina Liu, Huaiyu Zhang, Jinquan Wang, Ruiyang Zhang, Xiumin Wang, Hui Tao, Zhenlong Wang, Yongli Zhang and Bing Han

Microbiol. Res. 2026, 17(7), 123; https://doi.org/10.3390/microbiolres17070123 - 30 Jun 2026

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue Probiotics, Prebiotics and Pet Health)

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11 pages, 516 KB

Open AccessArticle

Porcine Rotavirus A G3P[6] with a Putative Novel G3-XII Lineage and P[6]-Ig Sublineage Associated with Neonatal Diarrhea in Southern Brazil

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

Microbiol. Res. 2026, 17(7), 122; https://doi.org/10.3390/microbiolres17070122 - 28 Jun 2026

Abstract

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 [...] Read more.

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. Full article

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

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11 pages, 263 KB

Open AccessArticle

Effects of Synbiotic Supplementation on Fecal Characteristics and Microbiota in Dogs Submitted to an Abrupt Dietary Change

by 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 and Ananda Portella Felix

Microbiol. Res. 2026, 17(7), 121; https://doi.org/10.3390/microbiolres17070121 - 25 Jun 2026

Abstract

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 [...] Read more.

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. Full article

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

15 pages, 1230 KB

Open AccessArticle

A Cross-Sectional Study on the Association Between Hepatocellular Carcinoma and Gut Microbiota in Chronic Hepatitis B Virus Infection

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

Microbiol. Res. 2026, 17(7), 120; https://doi.org/10.3390/microbiolres17070120 - 23 Jun 2026

Abstract

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 [...] Read more.

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. Full article

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

25 pages, 2418 KB

Open AccessReview

Wesselsbron Virus as a Surveillance-Sensitive One Health Pathogen: Evidence Strength, Diagnostic Under-Detection, and Integrated Risk Assessment

by Koycho Koev and Gabriela Goujgoulova

Microbiol. Res. 2026, 17(7), 119; https://doi.org/10.3390/microbiolres17070119 - 23 Jun 2026

Abstract

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 [...] Read more.

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. Full article

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

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14 pages, 2045 KB

Open AccessArticle

Adaptive Laboratory Evolution of Ashbya gossypii in Sugarcane Molasses: Biomass-Driven Riboflavin Overproduction

by Xiang Zhang, Wenjuan Zhai and Shijuan Gao

Microbiol. Res. 2026, 17(6), 118; https://doi.org/10.3390/microbiolres17060118 - 22 Jun 2026

Abstract

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 [...] Read more.

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. Full article

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27 pages, 13773 KB

Open AccessArticle

Antimicrobial Activity and Antibiotic Synergy of Saponin-Enriched Bark Extracts from Argania spinosa: Influence of Ecogeographical Origin

by Fatma Benlekhal, Ouahiba Moumen, Widad Hadjab, Adam Grzywaczyk, Wojciech Smułek, Urszula Guzik and Omar Kharoubi

Microbiol. Res. 2026, 17(6), 117; https://doi.org/10.3390/microbiolres17060117 - 22 Jun 2026

Abstract

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 [...] Read more.

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. Full article

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

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16 pages, 6438 KB

Open AccessArticle

Ecological Characterization and Taxonomic Divergence of Microbial Communities Along the Oral–Upper Gastrointestinal Axis

by Yuri Song and Hee Sam Na

Microbiol. Res. 2026, 17(6), 116; https://doi.org/10.3390/microbiolres17060116 - 17 Jun 2026

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Section Microbial Ecology and Microbiomes)

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13 pages, 9253 KB

Open AccessArticle

Preliminary Assessment of Commercial Biofertilizers as Biocontrol Agents of Oak Wilt

by Samira Islas-Valdez, Robert Rubiano, Ryan L. Peterson and Nicole Wagner

Microbiol. Res. 2026, 17(6), 115; https://doi.org/10.3390/microbiolres17060115 - 10 Jun 2026

Abstract

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 [...] Read more.

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. Full article

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

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15 pages, 12802 KB

Open AccessArticle

Klebsiella variicola Alleviates Chromium-Induced Growth Inhibition in Chicory by Modulating the Rhizosphere Microecology

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

Microbiol. Res. 2026, 17(6), 114; https://doi.org/10.3390/microbiolres17060114 - 10 Jun 2026

Abstract

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, [...] Read more.

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. Full article

(This article belongs to the Special Issue Rhizosphere Processes and Plant–Microbiome Interactions)

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18 pages, 1509 KB

Open AccessReview

Schmallenberg Virus: Pathogenesis, Diagnostic Challenges, and Control Gap in Endemic Europe

by Silvia Preziuso, Anna-Rita Attili, Chiara Storoni, Lorenza Di Perna, Yubao Li and Vincenzo Cuteri

Microbiol. Res. 2026, 17(6), 113; https://doi.org/10.3390/microbiolres17060113 - 9 Jun 2026

Abstract

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 [...] Read more.

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. Full article

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

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17 pages, 9847 KB

Open AccessArticle

Characteristics and Biocontrol Activity of Soil Bacterial Isolates Against the Emerging Pathogen Fusarium solani in Thai Durian (Durio zibethinus)

by Parima Boontanom, Praphaphorn Prasertsit, Sukitta Kosol, Taweesak Srithong and Aiya Chantarasiri

Microbiol. Res. 2026, 17(6), 112; https://doi.org/10.3390/microbiolres17060112 - 8 Jun 2026

Abstract

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 [...] Read more.

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. Full article

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

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17 pages, 1677 KB

Open AccessReview

Oral Microbiome–Host Genomic Crosstalk in Oral Carcinogenesis—A Narrative Overview of the Literature

by Evgeniy Aleksiev, Zornitsa Mihaylova and Dimitar Kosturkov

Microbiol. Res. 2026, 17(6), 111; https://doi.org/10.3390/microbiolres17060111 - 5 Jun 2026

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Section Microbial Ecology and Microbiomes)

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14 pages, 2039 KB

Open AccessArticle

Isolation and Characterization of Yeast-like and Filamentous Fungi from Lutzomyia longipalpis (Lutz & Neiva, 1912)

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

Microbiol. Res. 2026, 17(6), 110; https://doi.org/10.3390/microbiolres17060110 - 5 Jun 2026

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Topic Microbiota Diversity and Its Broader Biological Implications Across Human and Animal Health)

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