BMC Microbiology最新文献

{"title":"Talaromyces marinus (Eurotiales, Trichocomaceae): a new marine fungus from the Red Sea, Egypt, with distinguished enzymatic capabilities.","authors":"Ahmed Elbadry Abdel-Aziz, Enas Mahmoud Amer, Mahmoud Saadeldin Bakhit","doi":"10.1186/s12866-026-05566-8","DOIUrl":"10.1186/s12866-026-05566-8","url":null,"abstract":"<p><strong>Background: </strong>Talaromyces C. R. Benj., is a large and taxonomically important genus within Ascomycota, established to accommodate the teleomorphs of certain Penicillium Link, species and is now recognized as a monophyletic lineage distinct from Penicillium. Multigene phylogenetic analyses demonstrated that species formerly placed in Penicillium subgenus Biverticillium belong within Talaromyces, leading to their reclassification under the single-name nomenclature system. Currently, the genus comprises 237 species arranged into nine sections supported by multi-locus phylogeny. Species of Talaromyces are cosmopolitan, occurring in diverse habitats and substrates. It is notable for their medical, industrial, and ecological significance. In Egypt, several species of Talaromyces have been reported from a variety of substrates, highlighting the regional diversity and ecological relevance of the genus. Through the ongoing work a new Talaromyces species was isolated and identified.</p><p><strong>Methodology: </strong>Morphological characterization combined with multi-locus phylogenetic analyses based on ITS (internal transcribed spacers of rDNA), LSU (nuclear large subunit rDNA), BenA (β-tubulin), and RPB2 (RNA polymerase II second largest subunit) loci were employed to accurately determine the systematic placement of the new species. In addition, the enzymatic potential of the proposed new taxon was evaluated using standard screening assays.</p><p><strong>Results: </strong>A new marine taxon, Talaromyces marinus is reported from decaying woody samples of Avicennia marina (Forssk.) Vierh., collected from Wadi El-Jimal area, Red Sea Governorate, Egypt. Multi-locus analyses of the combined ITS, LSU, BenA, and RPB2 sequences dataset placed the new species within Talaromyces section Trachyspermi series Diversi but distinct from previously described species. The new taxon is characterized by restricted growth on different media, long stipes, biverticillate penicilli, the shortest acerose phialides in series Diversi, globose to subglobose or ellipsoidal, smooth-walled conidia, acid production, and soluble pigments.</p><p><strong>Conclusion: </strong>Talaromyces marinus sp. nov. is described, illustrated, phylogenetically analyzed, and its enzymatic potential is evaluated, it also compared with other species in the section Trachyspermi series Diversi.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13548588/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148905081","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":"Multi-approach integrating water quality variables, remote sensing, eDNA and histopathology for assessing the impact of microbial pollution on Nile Tilapia from Kitchener Drain, Northern Egypt.","authors":"Muhammad A El-Alfy, Ahmad M Alzeny, Ahmed E Abouelwafa, Engy T Megahed, Marwa M AbouHadied, Mohamed M Toubar, Hazem T Abd El-Hamid, Mohamed A H El-Kady, Hala A Mansour","doi":"10.1186/s12866-026-05559-7","DOIUrl":"10.1186/s12866-026-05559-7","url":null,"abstract":"<p><p>This study integrated environmental DNA (eDNA) metabarcoding, conventional bacteriology, histopathology, water quality variables, and remote sensing indices to investigate how environmental gradients are associated with pathogen-associated taxa communities and influence Nile tilapia (Oreochromis niloticus) health in Kitchener Drain, Northern Egypt. Physicochemical analyses revealed elevated nutrient concentrations, chlorophyll-a (59.21-226.35 µg L⁻¹), with localized hypoxia (dissolved oxygen as low as 2.14 mg L⁻¹ in site 2). High-throughput 16S rRNA metabarcoding revealed microbial communities dominated by Actinobacteriota (27.35%) and Proteobacteria (26.73%), with beta-diversity patterns driven primarily by species turnover, indicating strong environmental filtering along the pollution gradient. eDNA metabarcoding detected pathogen-associated taxa, including Mycobacterium, Legionella, Burkholderiaceae, Erysipelothrix, Leptospira, and Flavobacterium, many of which were not recovered by culture-based methods. Cross-database integration of SILVA (v138) and GTDB (r214) references identified 256 ASVs assigned to pathogen-associated taxa across 32 genera, with the dual-database strategy detecting 20-52% additional pathogen-associated ASVs relative to either database alone. Spearman correlation was examined for the 27 taxa with physicochemical parameters; phosphate, chlorophyll-a, dissolved oxygen, and BOD came up most often. Spearman correlation analysis revealed two perfect taxon-environment associations: a positive correlation between G_Pseudomonas and nitrate (ρ = + 1.00) and a negative correlation between G_Acinetobacter and chlorophyll-a (ρ = - 1.00). Both associations were nominally significant before multiple-testing correction (uncorrected p = 0.017); however, neither remained statistically significant after correction for multiple comparisons. These findings were therefore interpreted as exploratory associations rather than evidence of environmental drivers or causal relationships. Integration of remote sensing indices (NDWI, NDTI, NDCI, CDOM, NDVI) and water variables aids in identification of the surrounding environment associated with the presence of species. Culture-dependent analyses identified Aeromonas spp. as the dominant intestinal isolate and the only genus consistently observed by both approaches, suggesting selective host filtering between environmental and gut-associated communities. Histopathological examination revealed epithelial necrosis, villous atrophy, and goblet cell hyperplasia, with the most severe lesions at sites of highest organic loading. This approach can aid as a database for further future work, and for establishing more advanced models of pathogen-associated eDNA distributions and targeted fish-health surveillance, and for maintaining biodiversity.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13555907/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148918736","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 carbapenem resistance mechanisms in difficult-to-treat Pseudomonas aeruginosa clinical isolates from a tertiary care hospital in Egypt.","authors":"Dalia Salem, Manar Zaiton, Ahmed El-Shenawy, Heba Dahroug, Samah El-Dein, Doaa Gamal, Azza Ali Althoqapy, Amr Aw Mohamed, Mohamed A Shemis, Manal Diab, Soheir S Maklad","doi":"10.1186/s12866-026-05550-2","DOIUrl":"10.1186/s12866-026-05550-2","url":null,"abstract":"<p><strong>Background: </strong>The increasing incidence of carbapenem-resistant Pseudomonas aeruginosa (CRPA) poses a significant global health concern, particularly with the emergence of difficult-to-treat resistance (DTR), which seriously restricts therapeutic options. Therefore, we aimed to characterize DTR-PA isolates among the studied CRPA; regarding their resistance mechanisms to carbapenems and their antimicrobial susceptibility profiles.</p><p><strong>Methods: </strong>Fifty-two non-duplicate CRPA isolates were collected from clinical specimens. Antimicrobial susceptibility testing was performed using disc diffusion and VITEK2 compact system. Isolates were classified as multidrug-resistant P. aeruginosa (MDR-PA), extensively drug-resistant P. aeruginosa (XDR-PA), and DTR-PA. Conventional PCR was used to detect carbapenemase genes (bla_NDM, bla_VIM, bla_IMP, bla_KPC, and bla_OXA-48). Quantitative real-time PCR (qRT-PCR) identified the over expression of efflux pump genes (mexB, mexY) and the down regulation of outer membrane porin (oprD) gene.</p><p><strong>Results: </strong>Fifty-two (52) CRPA isolates were categorized according to resistance phenotype into three main groups where 46% were identified as DTR-PA, 38% as XDR-PA, 8% as MDR-PA and 8% remained uncategorized. In DTR-PA, carbapenemase genes were detected in 92% of isolates with bla_NDM being the most prevalent (75%), followed by bla_VIM (54%) and bla_OXA-48 (38%). Co-existence of multiple carbapenemase genes was common. Efflux pump mechanism was the most common mechanism of resistance as overexpression of MexB and MexY was observed in 98% and 71% of isolates, respectively, whereas downregulation of oprD was detected in 92%. The DTR-PA phenotype demonstrated the least sensitive profiles and most of the isolates (92%) were positive to all the studied resistant mechanisms (carbapenemase production, overexpression of efflux pump, and porin loss) with a statistically significant association (P = 0.001).</p><p><strong>Conclusions: </strong>Difficult to treat Pseudomonas aeruginosa is highly prevalent among CRPA isolates in our setting and is caused by multiple resistance mechanisms, particularly bla_NDM carriage, efflux pump overexpression, and oprD downregulation. These findings underscore the urgent need for enhanced molecular surveillance and antimicrobial stewardship to limit further dissemination of highly resistant Pseudomonas aeruginosa (P. aeruginosa) iaolates. Future studies utilizing the DTR-PA definition are needed, as this category highlights the most resistant CRPA isolates with maximum resistance profiles that most likely to pose clinical challenges.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13543481/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148886285","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":"Bio-functional Levilactobacillus brevis strains of feline origin: the potential probiotic food adjunct for companion animals.","authors":"Aneela Munir, Saman Javed, Ghulam Ayesha Javed, Maria Mushtaq, Babar Shahzad, Mammona Hameed, Sania Asif, Anam Saif, Najma Arshad","doi":"10.1186/s12866-026-05309-9","DOIUrl":"10.1186/s12866-026-05309-9","url":null,"abstract":"<p><p>Although autochthonous probiotic application is considered standard for the host-specific environment, the allochthonous probiotics also deliver valuable physiological or therapeutic benefits during their transit period before being eliminated naturally. This study evaluated the probiotic and bio-functional attributes of seven zoo feline-derived Levilactobacillus brevis strains for their potential application in companion animals or functional food industry. In vitro methods were employed to assess their survival under simulated gastrointestinal tract (GIT) conditions, safety profiles (hemolytic activity, DNase activity, and antibiotic susceptibility), and bio-functional potential (antimicrobial, antioxidant, and hypocholesterolemic activities). All strains exhibited high survival in the presence of lysozyme (69.0-96.7%), gastric juice (60.7-91.3%), and bile concentrations (up to 78.4-92.2% at 1.8% bile). The isolates displayed strong hydrophobicity (41.7-85.5%) and auto-aggregation properties (29.8-75.2%), and no signs of toxicity (non-hemolytic and DNase negative). Significant variations were noticed among strains with reference to their probiotic and bio-functional properties (p < 0.05). Furthermore, the strains secreted antioxidant metabolites capable of scavenging 2, 2-diphenyl-1-picrylhydrazyl (62-72%), hydroxyl (54-65%), and superoxide (57-69%) radicals. Among selected isolates, strain Lb I (L. brevis MZ400640) demonstrated the strongest antagonistic activity against both Gram-positive and Gram-negative pathogens. The bile salt hydrolase (BSH) gene was conserved across all seven isolates, confirming their ability to deconjugate major mammalian bile salts, sodium glycoholate and taurocholate. Out of the 14 parameters evaluated, strain Lb VII (L. brevis MW450245) exhibited most robust overall performance highlighting the potential of Lb VII as a functional probiotic feed additive to promote health and manage hypercholesterolemia in companion animals.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13540957/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148886331","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":"Integrated transcriptomic and proteomic profiling reveals alteration of oxidative phosphorylation in omega-3 polyunsaturated fatty acid-mediated inhibition of Candida albicans biofilm formation.","authors":"Shuai Wang, Peng Wang, Yan Liu, Qingchuan Yu, Yong Zhang, Xiao Ma, Ming Wei","doi":"10.1186/s12866-026-05595-3","DOIUrl":"10.1186/s12866-026-05595-3","url":null,"abstract":"<p><strong>Background: </strong>Candida albicans biofilms are highly tolerant to conventional antifungals, posing a major clinical challenge. Omega-3 polyunsaturated fatty acids (PUFAs), particularly docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), exhibit antibiofilm activity, but their mechanisms remain incompletely understood.</p><p><strong>Methods: </strong>Integrated transcriptomic and proteomic approaches were used to investigate the antibiofilm activity of DHA and EPA against C. albicans ATCC 90028. Biofilm inhibition was assessed by crystal violet staining and XTT reduction assays. Biofilm cells treated with 1 mM DHA or EPA (sub-MIC, both MICs > 1 mM) were subjected to RNA‑seq and DIA proteomics. Differentially expressed genes (DEGs) and proteins (DEPs) were identified, and integrated KEGG pathway analysis was conducted.</p><p><strong>Results: </strong>Both DHA and EPA inhibited biofilm formation at 1 mM without affecting planktonic growth. DHA altered 1787 transcripts (750 up, 1037 down) and 554 proteins (170 up, 384 down). EPA altered 905 transcripts (446 up, 459 down) and 259 proteins (104 up, 155 down). DHA suppressed ribosome biogenesis and oxidative phosphorylation at both mRNA and protein levels. In contrast, EPA transcriptionally down-regulated DNA replication genes while affecting oxidative phosphorylation predominantly via post-transcriptional mechanisms. Integrated analysis identified oxidative phosphorylation and central carbon metabolism as core convergent targets, with DHA showing more extensive metabolic disruption than EPA.</p><p><strong>Conclusion: </strong>DHA and EPA suppress C. albicans biofilms through distinct regulatory modes that converge on pathways linked to mitochondrial energy metabolism. These findings provide a molecular framework for omega-3 PUFA-based antibiofilm strategies and underscore the value of multi-omics integration in generating insights into complex drug mechanisms.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13560230/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148929025","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":"Occurrence and relevance of Gardnerella vaginalis in urine cultures of kidney transplant recipients- a retrospective cohort analysis.","authors":"Sabrina Klein, Silke Deininger, Iris Schröter, Dennis Nurjadi, Claudia Sommerer","doi":"10.1186/s12866-026-05522-6","DOIUrl":"10.1186/s12866-026-05522-6","url":null,"abstract":"<p><strong>Background: </strong>Gardnerella vaginalis is known to be associated with the development of bacterial vaginosis. In contrast, its cultivation from urine specimen in significant number is not generally regarded as causative for urinary tract infections. In a previous study, we detected G. vaginalis predominantly in urine cultures of renal transplant recipients and questioned whether this is of relevance. To address this, we conducted a retrospective cohort study over a period of two years on renal transplant recipients who presented at the outpatient clinic of the Department of Nephrology of Heidelberg University Hospital. Patient characteristics and laboratory parameters of renal transplant recipients with G. vaginalis in urine cultures were compared to those of renal transplant recipients presenting in the same outpatient clinic with urine specimen culturing other bacteria than G. vaginalis, using a multivariable logistic regression analysis.</p><p><strong>Results: </strong>During the study period, G. vaginalis was detected in 70 urine samples of 38 patients. The majority of patients was female (86.8%, n = 33/38), and the age was significantly lower than in the control group (median 41 years and 51 years; OR 0.94, 95% CI 0.92-0.98, p = 0.001). a significant number of culture-forming units (CFU, ≥ 10⁵ /ml) were detected in half of the samples containing G. vaginalis; a second microorganism was cultured in 64.3% (n = 45/70), while more than two species grew in 53.9% (n = 82/152) of the control group samples. Besides age, bacterial load of ≥ 10⁵ CFU/ml was significantly associated the presence of G. vaginalis in urine cultures (OR 2.71, 95% CI 1.12-6.56, p = 0.003). The medical record was lacking information on clinical signs and symptoms of urinary tract infections.</p><p><strong>Conclusion: </strong>As clinical symptoms were not documented, the occurrence of G. vaginalis in urine samples of kidney transplant recipients cannot be finally assessed. Further studies are needed to clarify its significance, particularly in immunocompromised hosts.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13531783/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148873164","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":"Conserved protein folds underpin the diversification of secreted proteins in a fungal pathogen.","authors":"Thaís C S Dal'Sasso, Eva H Stukenbrock","doi":"10.1186/s12866-026-05518-2","DOIUrl":"10.1186/s12866-026-05518-2","url":null,"abstract":"<p><strong>Background: </strong>During host colonization, fungal plant pathogens secrete effector-like proteins that alter host cell physiology and target plant-associated microbes. However, rapid evolution and low sequence conservation hinder the study and characterization of these proteins. The fungus Zymoseptoria passerinii infects Hordeum spp. and includes lineages adapted to wild and domesticated barley. To date, the evolution of effector-like proteins in this species has not been addressed.</p><p><strong>Results: </strong>We combined multiple structure-based and network analyses to unravel the secretome of Z. passerinii. We first compared AlphaFold2 and ESMFold predictions to establish the baseline for structural analyses. We identified 72 structural clusters in the secretome, revealing fold-level relationships across divergent sequences. We showed that effector-like proteins with predicted host immune-interfering functions evolved from a limited group of protein folds, whereas proteins with predicted antimicrobial properties were distributed across fold groups. Physicochemical comparisons indicate that putative antimicrobial effectors predominantly emerged through amino acid replacements on common effector-enriched scaffolds in Z. passerinii, reconfiguring surface charge and electrostatics. We analyzed intra- and interspecific variation in selected effector-enriched families by comparing Z. passerinii proteins and homologs across the genus Zymoseptoria. We describe constrained core folds, with local variation in loop and surface-exposed regions, consistent with fold stability while still enabling protein diversification. We further report that putative antimicrobial effector homologs are broadly distributed across the genus despite sequence divergence.</p><p><strong>Conclusions: </strong>The secretome of Z. passerinii is organized around common structural folds that support diverse biological roles, including host manipulation and host-associated microbial interactions. Conserved scaffolds combined with surface and physicochemical variation likely contribute to rapid adaptive evolution of effector-like proteins in Z. passerinii.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13525658/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148856918","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":"Age-related shifts of dissolved hydrogen and its impact on rumen fermentation dynamics and microbial communities in goats (Capra hircus).","authors":"Weiwei Wang, You Tian, Wei Guo, Yuntao Dong, Jiandui Mi, Anum Ali Ahmad, Xiaoping Jing, Ruijun Long, Xuezhao Sun, Qing Deng, Lizhuang Hao, Xiaoyang Lv, Wei Sun, Xiang Chen","doi":"10.1186/s12866-026-05563-x","DOIUrl":"10.1186/s12866-026-05563-x","url":null,"abstract":"<p><p>The rumen is a complex anaerobic fermentation ecosystem in which microbial communities undergo dynamic changes during host development, influencing fermentation efficiency, hydrogen utilization, and methane (CH₄) production. However, how rumen maturation reshapes hydrogen redistribution and the associated microbial interactions remains poorly understood. This study compared rumen fermentation characteristics, microbial communities (bacteria, archaea, fungi, and protozoa), and Gibbs free energy profiles between 0.5-year-old and 2-year-old goats to elucidate age-related changes in hydrogen metabolism. Adult goats exhibited significantly higher concentrations of dissolved methane (dCH₄), dissolved hydrogen (dH₂), and total short-chain fatty acids (SCFAs), including acetate, propionate, and butyrate, than young goats (P < 0.05). Thermodynamic analyses indicated that glucose fermentation and methanogenesis were energetically feasible under rumen conditions (ΔG < 0), while age-related differences in Gibbs free energy (ΔG) suggested altered hydrogen partitioning during rumen maturation. The mature rumen was characterized by enrichment of carbohydrate-fermenting microorganisms, particularly Segatella, Anaeroplasma, and the anaerobic fungus Cyllamyces, which were positively associated with glucose conversion pathways, metabolic hydrogen, and SCFA production. In contrast, younger goats showed enrichment of amino acid metabolism pathways together with microbial taxa associated with early rumen development, including Christensenellaceae_R-7_group and Caecomyces. The archaeal community also shifted with age, with significantly higher abundances of Methanosphaera and Methanosarcina in adult goats, consistent with enhanced hydrogen utilization through methanogenic pathways. Functional predictions further revealed enrichment of carbohydrate and energy metabolism in adult goats, whereas amino acid metabolism predominated in young goats. These findings demonstrate that rumen maturation is accompanied by coordinated changes in microbial community structure, metabolic hydrogen redistribution, and thermodynamic characteristics, resulting in a transition from amino acid-oriented metabolism in young goats to a more specialized carbohydrate-fermenting ecosystem in adults. This integrated analysis identifies key microbial groups involved in hydrogen turnover and may provide new insights into the microbial mechanisms underlying rumen maturation, offering potential targets for improving feed efficiency and mitigating methane emissions in ruminants.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13540943/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148886333","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":"Comprehensive in silico genomics analysis of global trends and host-specific emergence of aminoglycoside resistance in Staphylococcus aureus: a One-Health perspective.","authors":"Amr Ali Mohamed Abdelgawwad El-Sehrawy, Saade Abdalkareem Jasim, Haneen Fadhil Jasim, Ozodbek Nematov, Mirza R Baig, Aseel Smerat, Muhammad Shahid Iqbal, Tina Saeed Basunduwah, Masoumeh Beig","doi":"10.1186/s12866-026-05542-2","DOIUrl":"10.1186/s12866-026-05542-2","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;Aminoglycosides remain clinically valuable against Staphylococcus aureus. Aminoglycoside resistance in S. aureus represents a critical One Health concern and is primarily driven by aminoglycoside-modifying enzymes (AMEs), which are frequently plasmid-encoded. Although regional studies have provided valuable insights, the global epidemiology of aminoglycoside resistance determinants remains poorly characterized because comprehensive data integrating human, animal, and environmental reservoirs are still lacking. This study addresses this gap by analyzing over 110,000 S. aureus genomes (2000-2025) to map the global resistome, quantify temporal and host-specific trends, and assess the association between genetic determinants and phenotypic resistance.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Methods: &lt;/strong&gt;We performed a retrospective One Health meta-analysis of 110,309 S. aureus genomes collected between 2000 and 2025 from 128 countries. Genomes were quality-filtered and aminoglycoside resistance determinants were identified using NCBI AMRFinderPlus (v4.0.23). Multilocus sequence typing and host-source harmonization (Human, Animal, Environment, Unknown) enabled clonal and reservoir stratification. Temporal trends in gene prevalence and resistance burden were modeled with robust regression. Geographic and host-associated structuring of key genes was assessed via χ&lt;sup&gt;2&lt;/sup&gt; and enrichment tests. Machine-learning models (elastic-net, random forests, XGBoost) were benchmarked for minimum inhibitory concentration (MIC) prediction via nested cross-validation, with performance evaluated by mean absolute error, RMSE, and SHAP-based feature importance. All analyses were conducted in R and Python using publicly available, de-identified genomic data.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Aminoglycoside resistance-associated genes were dominated by modifying enzyme determinants, with ant(6)-Ia, ant(9)-Ia, aph(3')-IIIa, sat4, aadD1, and aac(6')-Ie/aph(2'')-Ia occurring in 14-22% of isolates worldwide. Temporal analysis revealed significant declines in several major determinants, most notably ant(9)-Ia (-2.22 percentage points per year, p &lt; 0.001), whereas apmA exhibited a non-significant decreasing trend in animal isolates. Host structuring was marked: human clinical isolates concentrated common determinants, while animal and environmental isolates harbored rare alleles (apmA, spw, str, spd). Geographic mapping confirmed near-universal distribution of common genes but focal restriction of rare ones. Publicly available phenotypic data indicated strong activity of amikacin, whereas gentamicin showed a distinct resistant subpopulation that closely corresponded with AME gene carriage. Genotype-phenotype analyses demonstrated strong concordance, with gene-rich complements predicting resistant MIC strata and absence of determinants predicting susceptibility. Analysis across different gene classes revealed frequent co-occurrence of aminoglycoside resistance genes ","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13520274/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148839279","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":"Acinetobacter guillouiae, a lipolytic strain isolated from sludge capable of partially depolymerising polyethylene terephthalate: genomic, proteomic, and biochemical insights.","authors":"Naheed Akhtar, Afef Najjari, Anna Magnone, Esma Ceylan Yerebakan, Katja Bernfur, Cecilia Tullberg, Muhammad Siddique Awan, Zahid Majeed, Carl Grey, Baozhong Zhang, Javier A Linares-Pastén","doi":"10.1186/s12866-026-05567-7","DOIUrl":"10.1186/s12866-026-05567-7","url":null,"abstract":"<p><p>Acinetobacter guillouiae I-MWF was isolated by incubating amorphous polyethylene terephthalate (PET) film in sludge samples. The strain partially depolymerised PET powder with 11.3% crystallinity, as confirmed by FT-IR, HPLC-UV, and LC-MS analyses. Extracellular enzymes released terephthalic acid (TPA), mono(2-hydroxyethyl) terephthalate (MHET), and bis(2-hydroxyethyl) terephthalate (BHET). Genomic analysis identified 18 putative extracellular hydrolases, including lipases and esterases, each with a conserved catalytic triad. Proteomic profiling revealed expression of two triacylglycerol lipases and two additional lipase-family proteins when the strain was cultivated with PET or a PET-Tween 80 mixture. These enzymes were cloned in Escherichia coli, but most formed insoluble, inactive inclusion bodies, and one was not expressed. Molecular modelling highlighted structural features likely to influence their catalytic interaction with PET. Although the strain partially depolymerised PET powder, it was unable to grow on PET, TPA, or ethylene glycol, indicating that PET depolymerisation occurs as a side activity rather than supporting growth. Instead, A. guillouiae displayed strong lipolytic activity and a clear preference for lipid-based substrates, achieving its highest growth with Tween 80. A lipid transporter was also expressed under these conditions, suggesting adaptation to hydrocarbon-rich environments. These findings indicate that A. guillouiae I-MWF can mediate partial PET depolymerisation without assimilating the resulting monomers, while preferentially growing on lipid-like substrates.</p>","PeriodicalId":9233,"journal":{"name":"BMC Microbiology","volume":"26 1","pages":""},"PeriodicalIF":5.4,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13520237/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148824982","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}