BMC Microbiology最新文献

{"title":"Statistical optimization of melanin-like pigment biosynthesis by marine Streptomyces isolate MOE3 and evaluation of its cytotoxic activity against A-431 cells.","authors":"Moaz M Hamed, Sahar W M Hassan, Eman H Zaghloul","doi":"10.1186/s12866-026-05590-8","DOIUrl":"10.1186/s12866-026-05590-8","url":null,"abstract":"<p><p>Marine actinomycetes represent a promising source of biologically active natural pigments. In the present study, isolate MOE3, recovered from mangrove sediment along the Egyptian Red Sea coast, was provisionally assigned to Streptomyces lateritius based on partial 16 S rRNA gene sequencing and phylogenetic analysis, showing approximately 99% sequence similarity to closely related Streptomyces taxa. The extracted pigment exhibited UV-Visible and FTIR characteristics consistent with a melanin-like pigment, including an absorption maximum at 255 nm. Plackett-Burman screening produced a maximum observed response approximately 1.65-fold relative to the basal response, while the highest experimentally observed response within the Box-Behnken design represented an approximately 2.3-fold increase relative to the basal response. The pigment also exhibited concentration-dependent in vitro cytotoxicity against A-431 human epidermoid carcinoma cells, with an IC₅₀ of 45.11 µg/mL after 24 h. These findings identify MOE3 as a promising microbial source of a melanin-like pigment and provide a basis for further structural, biological, and process-development studies.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13675996/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149214961","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The biliary microbiome in symptomatic cholelithiasis: a prospective comparison across distinct bacterial niches.","authors":"Ulrich Wirth, Ramiro Vilchez-Vargas, Franziska Fuchs, Josefine Schardey, Nadine Koch, Florian Kühn, Bernhard W Renz, Jens Werner, Christian Schulz, Joachim Andrassy","doi":"10.1186/s12866-026-05756-4","DOIUrl":"10.1186/s12866-026-05756-4","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Cholelithiasis is highly prevalent in the Western world and frequently requires surgical or endoscopic intervention. However, the composition and role of the biliary microbiome remain poorly understood. This study aimed to characterize and compare bacterial communities of the biliary niche with saliva and faeces in patients with cholelithiasis.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;In this prospective observational study, patients with symptomatic cholecystolithiasis, chronic or acute cholecystitis, and choledocholithiasis were included. Bacterial community composition was characterized across bile, gallstone, saliva, and faecal samples using 16 S rRNA-based sequencing. Community-level and genus-level differences were assessed according to anatomical niche and clinical diagnosis, complemented by compositional sensitivity analyses and predicted functional profiling.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;A total of 227 samples from 81 patients were analyzed. Bacterial community composition was strongly determined by anatomical niche (PERMANOVA, R² = 0.273, P &lt; 0.001), with bile and gallstone communities being most closely related but remaining significantly distinct (R² = 0.146, q &lt; 0.001). Diagnosis-associated differences were predominantly confined to the biliary compartments and remained significant after adjustment for age, explaining 7.9% of variation in bile and 14.1% in gallstones, whereas no significant associations were observed in saliva or faeces. Compositionally aware analysis with continuous age adjustment identified robust diagnosis-associated signals in bile, including Escherichia/Shigella, Leptotrichia, Serratia, and Pseudomonas. Biliary communities were characterized by taxa including Enterococcus, Escherichia/Shigella, Serratia, and Pseudomonas. In bile, Escherichia/Shigella increased with inflammatory disease, while Pseudomonas decreased; compositionally aware analysis confirmed diagnosis-associated differences for Escherichia/Shigella, Leptotrichia, and Serratia. Predicted bacterial functions showed even stronger anatomical compartmentalization (R² = 0.507, P = 0.001), whereas diagnosis-associated functional differences were limited to two MetaCyc pathways in gallstones. Sensitivity analyses provided no evidence that prolonged antibiotic exposure significantly affected biliary bacterial diversity or community composition.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusion: &lt;/strong&gt;This comprehensive multi-niche analysis demonstrates pronounced taxonomic and predicted functional compartmentalization of bacterial communities across saliva, bile, gallstones, and faeces in patients with cholelithiasis. Diagnosis-associated alterations were predominantly observed within biliary niches, with Escherichia/Shigella emerging as a consistent taxon associated with inflammatory biliary disease. These findings identify anatomical niche as a major determinant of bacterial community structure and support disease-associated alterations within the bil","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13640319/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149104497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prophylactic administration of probiotic strains Weizmannia coagulans and Saccharomyces boulardii attenuates early dysplastic changes in an AOM/DSS-induced mouse model.","authors":"Marwa Matboli, Sanaa Eissa, Reham Hussein Mohamed, Nada Kotb, Ghada Galal Hamam, Mai Tarek, Nagwa M Abo El Magd, Abdullah M Abdo, Aisha Mohamed Hussein, Naydeen Mostafa, Marwa Mostafa Kamel","doi":"10.1186/s12866-026-05634-z","DOIUrl":"10.1186/s12866-026-05634-z","url":null,"abstract":"<p><strong>Background: </strong>Colorectal dysplasia represents an early stage of colorectal carcinogenesis and is closely associated with chronic inflammation and altered microRNA (miRNA) expression. Probiotic strains such as Weizmannia coagulans (formerly Bacillus coagulans) and Saccharomyces boulardii possess anti-inflammatory properties and may influence host miRNA expression, suggesting their potential as prophylactic agents against inflammation-associated colorectal dysplasia.</p><p><strong>Methods: </strong>Mice received prophylactic oral administration of Weizmannia coagulans or Saccharomyces boulardii beginning one week before azoxymethane/dextran sulfate sodium (AOM/DSS) induction and continuing throughout the experimental period. Histopathological examination, TNF-α immunohistochemistry, serum pro-inflammatory cytokine measurements, and miRNA expression profiling using reverse transcription quantitative polymerase chain reaction (RT-qPCR) were performed to evaluate the prophylactic effects of both probiotic strains.</p><p><strong>Results: </strong>Prophylactic administration of both probiotic strains significantly attenuated early dysplastic alterations and inflammatory cell infiltration compared with the AOM/DSS group (p < 0.05). These histopathological improvements were accompanied by significantly lower serum levels of the pro-inflammatory cytokines IL-6 and IL-1β, together with reduced TNF-α immunoreactivity (p < 0.05). In addition, probiotic pretreatment attenuated the altered miRNA expression profile induced by AOM/DSS. Compared with the model group, expression of miR-122-5p, miR-29b-5p, and miR-15b-5p was significantly reduced, whereas miR-98-5p, miR-202-5p, miR-21-5p, and let-7i-5p showed increased expression and were associated with miRNA expression patterns that more closely resembled those of the control group (p < 0.01).</p><p><strong>Conclusion: </strong>Prophylactic administration of Weizmannia coagulans and Saccharomyces boulardii reduced inflammation-associated early dysplastic changes while preserving normal miRNA expression patterns in an AOM/DSS-induced murine model. These findings support the potential of probiotic prophylaxis as an early preventive strategy against colorectal dysplasia and provide a foundation for future studies investigating its clinical applicability.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13675988/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149206520","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenomic analysis of rhizosphere soil microbiota in wild and cultivated Notopterygium incisum, an umbelliferae medicinal herb.","authors":"Tianqing Feng, Jun Shang, Yonggui Ma, Juan Li, Yanrong Qin, Jitao Zhang, Shiyan Cheng, Gaosen Zhang, Huichun Xie","doi":"10.1186/s12866-026-05269-0","DOIUrl":"https://doi.org/10.1186/s12866-026-05269-0","url":null,"abstract":"<p><p>Notopterygium incisum is not only a traditional Chinese medicine but also an endemic herb. Artificial domestication and large-scale cultivation are crucial for resolving the crisis of wild resources and the supply-demand imbalance of N. incisum, yet current techniques have failed to stably provide the herb medicine in good quality. Metagenomic analyses revealed significant differences in the rhizomicrobiota between wild and cultivated N. incisum, particularly in microbial composition, gene functions, and community assembly. The rhizomicrobiota of the wild N. incisum from 3 different sites with an altitude drop over 1400 m had a similar composition when being compared with the cultivated samples. The wild N. incisum had higher abundances of beneficial microbes, particularly Hyphomicrobiales (Rhizobiales) (21.27% on average). In contrast, the rhizosphere microbial communities of the cultivated N. incisum showed a high prevalence of functional genes involved in the pathways of DNA repair and recombination proteins, replication and repair, peptidases and inhibitors, DNA replication proteins, and transfer RNA biogenesis. The co-occurrence networks analysis indicated that the stability of the wild samples' network remained significantly more robust when nodes were proportionally removed, as the wild samples' network had approximately the same positive and negative links while the cultivated samples' network had nearly all positive links and many fewer connectors. This is related to the conclusion that wild N. incisum exhibits superior efficacy, as reported in previous studies. Additionally, it can be observed from the sampling images that the root surface of wild N. incisum has more pronounced tiny protrusions, which may be associated with rhizobial attachment, thereby enhancing the nitrogen fixation process. Importantly, the observed shifts in rhizosphere microbial communities, particularly the enrichment of beneficial rhizobia in wild plants, are closely linked to enhanced accumulation of bioactive secondary metabolites such as coumarins and volatile oils. These microbiome-driven differences are likely associated with the superior medicinal quality of wild N. incisum compared to cultivated counterparts, highlighting the pivotal role of rhizosphere microbes in shaping therapeutic efficacy.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13637344/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149104465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Potential mechanisms of endophytic Bacillus velezensis JR4 as a biocontrol agent against Sclerotinia sclerotiorum causing postharvest rot in carrot.","authors":"Mohammed A E Selim, Abdelrahman M Elattaapy, Sabrien A Omar, Xingfeng Shao, Elsherbiny A Elsherbiny","doi":"10.1186/s12866-026-05623-2","DOIUrl":"10.1186/s12866-026-05623-2","url":null,"abstract":"<p><p>Carrot production regions worldwide incur enormous annual economic losses due to postharvest white mold caused by Sclerotinia sclerotiorum. Biological control is a promising approach for controlling postharvest pathogens. This study investigated the biocontrol efficacy of using Bacillus velezensis JR4 against Sclerotinia rot and its potential mechanisms of action. The results showed that the JR4 strain achieved 91.1% inhibition of S. sclerotiorum in a dual-culture assay. B. velezensis JR4 was able to produce extracellular enzymes such as protease, cellulase, and chitinase. Applying JR4 bacterial suspension at 1 × 10⁸ CFU mL^- 1 on postharvest carrots infected with the pathogen reduced rot incidence by 65.4% and lesion length by 80.6% on day 5. The same concentration increased the levels of total phenolics and total flavonoids, as well as the activity of defense-related enzymes, including peroxidase (POD), polyphenol oxidase (PPO), and phenylalanine ammonia-lyase (PAL). It also increased the expression of three defense-related genes in postharvest carrots over four days. Compared to untreated carrots, it exhibited lower levels of cell membrane permeability, malondialdehyde (MDA), superoxide anion (O₂^-), and hydrogen peroxide (H₂O₂). Furthermore, the cell-free culture filtrate of JR4 showed minimal to no toxicity on WI-38 and Vero cells across all concentrations. The results suggest that B. velezensis JR4 could be an effective and sustainable biocontrol agent for controlling white mold in postharvest carrots. However, further safety assessments are needed for its successful application.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13617733/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149069128","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Beyond lethal doses: sub-MIC levels of multi-class antibiotics induce species- and isolate-dependent biofilm inhibition in gram-negative pathogens.","authors":"Raghda Elawady, Aliaa G Aboulela, Ahmed N Amer, Abeer A Ghazal, Ahmed Gaballah","doi":"10.1186/s12866-026-05620-5","DOIUrl":"10.1186/s12866-026-05620-5","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Biofilm-associated infections remain a major clinical challenge due to their intrinsic tolerance to antimicrobial therapy. Sub-minimum inhibitory concentrations (sub-MICs) of antibiotics are frequently encountered in vivo, particularly at sites of infection and on indwelling medical devices. However, their influence on biofilm formation is controversial, with evidence of both stimulatory and inhibitory effects. Clarifying these responses may reveal novel therapeutic opportunities for managing nosocomial biofilm-related infections. This study aims to investigate the effects of three sub-MIC concentrations (25%, 50%, and 75% of MIC) of five antibiotic classes on biofilm formation in Pseudomonas aeruginosa, Escherichia coli, and Klebsiella pneumoniae using two distinct biofilm quantification methods.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Materials and methods: &lt;/strong&gt;In this study, the effects of 5 different antimicrobial agents, namely, azithromycin, gentamicin, ciprofloxacin, doxycycline, and imipenem, at different sub-MIC concentrations (12.5%, 25%, and 50% of MIC) were tested on 5 different clinical isolates of P. aeruginosa, E. coli, and K. pneumoniae. Clinical isolates were exposed to sub-MIC levels of antibiotics in a standardized biofilm assay, with statistical comparisons conducted to determine significant biofilm modulation using crystal violet (CV) staining to measure total biomass accumulation and quantitative PCR (qPCR) to assess qPCR-derived genome-equivalent DNA abundance within biofilms. qPCR detects DNA originating from viable, dead, damaged, or lysed cells, as well as extracellular DNA (eDNA).&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Across the 75 tested conditions (5 antibiotics × 3 sub-MIC concentrations × 5 clinical isolates per species), sub-inhibitory antibiotic exposure produced pronounced, species- and target-dependent biofilm responsiveness varied by species: P. aeruginosa demonstrated the highest biomass modulation (62% CV significance), E. coli exhibited the greatest molecular responsiveness (55% qPCR significance), and K. pneumoniae showed lower overall modulation (47% CV, 32% qPCR significance). Imipenem exerted the highest biomass suppression in P. aeruginosa (80% CV vs. 13% qPCR inhibition), whereas doxycycline predominantly reduced genome equivalents in P. aeruginosa (73% qPCR vs. 7% CV inhibition). In E. coli, azithromycin produced peak biomass inhibition (73% CV vs. 7% qPCR inhibition), while gentamicin led to molecular suppression (60% qPCR vs. 27% CV inhibition). In K. pneumoniae, azithromycin and ciprofloxacin directed to biomass inhibition (both 40% CV), while azithromycin produced the highest qPCR reduction (33% qPCR). Bidirectional modulation was widespread across drug classes. Azithromycin acted as a primary inducer in P. aeruginosa (80% CV, 67% qPCR induction), while imipenem shifted from a biomass inhibitor in P. aeruginosa (80% CV inhibition) to a primary inducer in K. pneumoniae (47% CV, 60% qPCR induct","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13615587/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149058504","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Detection of cefotaxime- and enrofloxacin-resistant and mcr-1-positive Escherichia coli at farm level in younger and older calf groups across different production systems in Germany.","authors":"Caroline Robé, Jorinde Baer, Roswitha Merle, Lisa Gorisek, Uwe Roesler, Anika Friese","doi":"10.1186/s12866-026-05693-2","DOIUrl":"10.1186/s12866-026-05693-2","url":null,"abstract":"<p><strong>Objective: </strong>Studies on antibiotic resistance in calves rarely differentiate between production systems or younger and older calf groups within farms and commonly rely on non-selective laboratory methods. We investigated the qualitative farm-level detection and genetic diversity of antimicrobial-resistant E. coli from calves in different production systems in Germany using selective culture. Production systems included closed dairy farms (A), farms purchasing veal calves < 10 weeks (B), farms purchasing veal calves aged ≥ 10 weeks (C), suckler cow herds (D), and traders/collection points (E).</p><p><strong>Methods: </strong>Eighty-one farms were sampled. Two pooled fecal samples representing younger and older calf groups, without recording exact ages, were collected from production systems A-C, and one sample each from D and E. Samples were cultured on MacConkey agar supplemented with cefotaxime (CTX), enrofloxacin (ENR) or colistin (COL) for qualitative detection of E. coli subpopulations. Recovered isolates were characterized by PCR for mobile ESBL-/pAmpC-associated genes, plasmid-mediated colistin resistance genes, quinolone resistance-determining region substitutions, and plasmid-mediated quinolone resistance genes. Phylogenetic relatedness of selected isolates was assessed by cgMLST-based hierarchical clustering.</p><p><strong>Results: </strong>In systems A-C and among traders CTX- and ENR-resistant E. coli were widespread at farm level (> 70%), whereas suckler cow herds had substantially lower detection rates (< 25%). In systems A-C, resistant E. coli were detected more frequently at farm level in younger than older calf groups. Dominant ESBL genes were bla_{CTX-M-1, -15} and _- 14. Common amino acid substitutions associated with quinolone resistance included S83L and D87N/Y/H in GyrA and S80I in ParC, in addition to the detection of the qnrS and aac(6')-Ib-cr genes. Mcr-1-positive E. coli recovered from COL-supplemented agar were detected less frequently (< 20%) in all production systems examined. Analysis of two samples from production systems A-C identified highly related isolates (HC10) within individual farms but not between farms.</p><p><strong>Conclusion: </strong>Differences in the qualitative farm-level detection and genetic diversity of CTX- and ENR-resistant and mcr-1-positive E. coli subpopulations were observed between production systems and between younger and older calf groups within farms. These findings suggest that production system and sampled calf group should be considered in the surveillance of antibiotic-resistant E. coli in calves.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13595704/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149023955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Taxonomic insights and preliminary enzyme assays of Rhytidhysteron species (Hysteriales, Hysteriaceae) from litter layer in the Yuan Jiang savanna, China.","authors":"Hai-Xia Wu, Jin-Chen Li, Kai-Yang Niu, Wei-Feng Ding, Nalin N Wijayawardene, Handong Wen","doi":"10.1186/s12866-026-05631-2","DOIUrl":"10.1186/s12866-026-05631-2","url":null,"abstract":"<p><p>Six terrestrial hysteriaceous fungi were collected from litter in dry-hot valleys, China, all exhibiting the typical morphological characteristics of the genus Rhytidhysteron. Detailed morphological examimation combined with RAxML phylogenetic analysis of combined LSU, SSU, ITS, and tef-1α loci revealed that the specimens represent one new species Rhytidhysteron savanniense sp. nov. and two new geographical records R. hongheense and R. tectonae. Comprehensive descriptions, illustrations, and a phylogenetic tree are provided to clarify the taxonomic placement of these taxa. As a preliminary observation, lignocellulose-related enzymes screening was conducted to explore potential ecological roles of Rhytidhysteron. The results indicated variation in cellulase production capacity among species, with Rhytidhysteron savanniense exhibiting the highest cellulase activity under laboratory conditions. These findings highlight the taxonomic diversity of Rhytidhysteron in dry-hot valley ecosystems and suggest possible functional capapcites that warrant further ecological investigation.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13647791/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149135187","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dietary fiber source-dependent modulation of pregnant sow fecal microbiota, gas profiles, and short-chain fatty acids in vitro.","authors":"Weikang Huangfu, Yujie Zheng, Boshuai Liu, Yalei Cui, Zhichang Wang, Yinghua Shi","doi":"10.1186/s12866-026-05568-6","DOIUrl":"10.1186/s12866-026-05568-6","url":null,"abstract":"<p><strong>Background: </strong>Growing evidence indicates that dietary fiber (DF) modulates gut microbiota and microbial fermentation metabolites, but the dynamic fermentation outcomes of different DF sources remain difficult to monitor directly under physiological conditions. This study used an in vitro batch fermentation model inoculated with pregnant sow fecal microbiota to compare the effects of a fiber-free control (CON), commercial concentrated fiber (CCF), beet pulp (BP), and alfalfa meal (AM) on microbial composition, gas concentration profiles, and short-chain fatty acid (SCFA) concentrations at 8, 12, 24, and 36 h.</p><p><strong>Results: </strong>Different fiber substrates generated distinct fermentation profiles. CO₂ was the predominant gas throughout fermentation, whereas H₂ showed clearer substrate-dependent differences. AM generally resulted in higher total measured gas concentration, H₂ concentration, and total SCFA concentration than the other treatments. 16 S rRNA sequencing showed that different fiber substrates shaped the overall fecal microbial community structure, with selected genus-level taxa, including Lactobacillus, norank_f__Muribaculaceae, Prevotellaceae_NK3B31_group, Holdemanella, and Fusobacterium, exhibiting substrate-associated variation patterns. Correlation analysis further linked H₂ with SCFAs and selected fermentation-associated taxa. PICRUSt2 prediction suggested that AM fermentation was associated with differences in predicted microbial functional potential.</p><p><strong>Conclusions: </strong>These findings indicate that different DF sources generate substrate-specific fecal microbial fermentation patterns in vitro. Among the tested substrates, AM produced a stronger SCFA- and H₂-associated fermentation response and was linked with selected microbial response patterns. Integrated correlation analysis suggested microbiota-associated co-variation between H₂ and SCFAs during DF fermentation, which requires further validation.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-09-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13573441/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148966455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Inferred functional microbiome features are associated with clinical trajectories of low-grade cervical lesions.","authors":"Milan Stosic, Mariano A Molina, Dhananjay Mukhedkar, Sadaf Sakina Hassan, Anna Sahlin, Cristina Ruiz Ballester, Jiangrong Wang, Laila Sara Arroyo Mühr","doi":"10.1186/s12866-026-05648-7","DOIUrl":"10.1186/s12866-026-05648-7","url":null,"abstract":"<p><strong>Background: </strong>The cervicovaginal microbiome has been associated with human papillomavirus (HPV)-related cervical disease, but its role in determining the clinical trajectory of low-grade squamous intraepithelial lesions (LSIL) remains unclear. We investigated whether microbial taxonomic, ecological, and inferred functional features could distinguish LSIL regression from progression and improve risk stratification.</p><p><strong>Results: </strong>The cervicovaginal microbiome of 90 women with LSIL and known clinical outcomes was profiled using 16S rRNA gene sequencing. Overall microbiome diversity and composition did not differ significantly between regression and progression groups. Instead, microbial profiles clustered primarily by community state type (CST), with CST I-B nominally more frequent among regression cases. Within Lactobacillus-dominated communities, CST I-B exhibited distinct inferred functional profiles characterized by enrichment of carbohydrate metabolism and fermentation pathways and relative depletion of nucleotide biosynthesis pathways compared with CST I-A. Exploratory logistic regression models based on age, or microbiome taxa alone, showed limited discriminatory performance, whereas an integrated model incorporating age, microbiome, and inferred functional pathway features improved apparent discrimination between regression and progression in this cohort (AUC = 0.76, 95% CI 0.66-0.86).</p><p><strong>Conclusions: </strong>Differences in microbial community organization and inferred functional profiles were observed to be associated with LSIL clinical trajectories, whereas taxonomic composition alone showed limited discriminatory value. Integrating microbial taxonomic, ecological, and functional features modestly improved the apparent discrimination of LSIL outcomes, suggesting that inferred functional features may provide complementary information that warrants future research.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13570522/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148954821","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}