Journal of medical microbiology最新文献

{"title":"Evaluation of the Allplex™ <i>H. pylori</i> & ClariR assay for the detection of clarithromycin-resistant <i>Helicobacter pylori</i> in gastric biopsies.","authors":"Callum J Portman Ross, Katherine Lock, Amaal Ibrahim, Dawn Hedges, Shukri Mohamed, Molly Hales, Takudzwa Edwards, Claire Jenkins, Israel Olonade, Craig Swift","doi":"10.1099/jmm.0.002195","DOIUrl":"10.1099/jmm.0.002195","url":null,"abstract":"<p><p><b>Introduction.</b> <i>Helicobacter pylori</i> colonize the gastrointestinal tract of large proportions of the global population and is associated with the development of gastric ulcers and cancer. Antimicrobial resistance (AMR) to clarithromycin is recognized as a major contributing factor in treatment failure.<b>Hypothesis/Gap Statement.</b> Real-time PCR may be used to detect 23S rRNA gene mutations associated with AMR to clarithromycin in <i>H. pylori</i> and has advantages over classical culture and phenotypic susceptibility testing, including no strict requirement for the transport of gastric biopsies.<b>Aim.</b> In this study, we compare the use of the Allplex™ <i>H. pylori</i> & ClariR assay (Seegene Inc) for detection of clarithromycin-resistant <i>H. pylori</i> with current culture and phenotypic susceptibility testing in 1149 gastric biopsy specimens within our laboratory at the Gastrointestinal Bacteria Reference Unit, UK Health Security Agency.<b>Methodology.</b> PCR was performed using the Allplex™ <i>H. pylori</i> & ClariR assay (Seegene Inc) on genomic DNA recovered from gastric biopsy specimens using the MagNA Pure 96 DNA and Viral NA Small Volume Kit and the Pathogen Universal 200 protocol on an MP96 robotic workstation (Roche). Phenotypic susceptibility to clarithromycin was determined by Etest (bioMérieux).<b>Results.</b> We found 94.6% concordance for the presence of either clarithromycin-resistant or -susceptible strains of <i>H. pylori</i>.<b>Conclusion.</b> We recommend this assay be included in the UK Health Security Agency (UKHSA) <i>H. pylori</i> testing algorithm to improve patient management.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"75 8","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13502949/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148815329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rapid bacterial community profiling of equine faecal, skin, milk and saliva samples using Oxford Nanopore long-read 16S rRNA amplicon sequencing.","authors":"J Leng, C Tait, B Alsubaie, A H M Van Vliet, P Sells, R M La Ragione, C Proudman","doi":"10.1099/jmm.0.002176","DOIUrl":"10.1099/jmm.0.002176","url":null,"abstract":"<p><p><b>Introduction.</b> The composition of the equine gut microbiome is associated with many aspects of gastrointestinal, respiratory and musculoskeletal health that have been reported in the horse. Scientific studies exploring the microbiome non-intestinal ecological niches in or on horses are lacking. The clinical use of bacterial community profiling in horses is currently limited by cost and by slow analytical workflows.<b>Hypothesis/Gap Statement.</b> Most equine microbiome studies have relied on 16S rRNA amplicon sequencing of bacterial DNA, using high-throughput short-read sequencing technologies. This is often provided by an external service due to the cost of Illumina and other sequencers. Analysis of such sequencing files relies upon the researcher to have prior experience of coding-based programs.<b>Aim.</b> To explore the utility of Oxford Nanopore long-read sequencing in the analysis of microbiomes from several anatomical sites of the horse as a quicker and cheaper alternative to short-read sequencing.<b>Methodology.</b> Bacterial DNA was extracted from horse (udder) skin swabs, saliva swabs, faecal samples and milk samples. Samples were prepared for Oxford Nanopore long-read sequencing and sequenced using a flow cell on the MinION Mk1D. Sequencing data were analysed using EPI2ME, along with extra analyses on exported taxa abundance data in R.<b>Results.</b> Diversity measures and taxonomic relative abundance from phylum to family level were comparable to previously published equine studies that used Illumina sequencing. Sequencing data were acquired within 3 days costing around £30 per sample. Long-read sequencing gave accurate taxa assignment for two positive controls included at phylum, class, order and family levels of taxonomic classification.<b>Conclusion.</b> This work demonstrates that long-read technologies such as Oxford Nanopore MinION sequencing can provide a reliable, quick and cost-effective alternative to short-read Illumina sequencing when characterizing microbial communities from a range of anatomical locations on/in the horse.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"75 7","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13336655/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148400346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Erratum: Evaluation of the Hologic Aptima Vaginitis assays for microbiological diagnosis of vaginitis in women with abnormal vaginal discharge attending primary care.","authors":"Barry Vipond, Nicola Childs, Rich Hopes, David Hirst, Kshitij Soni, Paul North, Peter Muir","doi":"10.1099/jmm.0.002185","DOIUrl":"10.1099/jmm.0.002185","url":null,"abstract":"","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"75 7","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13345434/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148407771","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Role of zinc in growth, stress response and virulence gene expression of pathogenic Mucorale <i>Rhizopus arrhizus</i>.","authors":"Rachna Singh, Anjna Kumari, Pavneet Kaur, Jasdeep Kaur","doi":"10.1099/jmm.0.002184","DOIUrl":"10.1099/jmm.0.002184","url":null,"abstract":"&lt;p&gt;&lt;p&gt;&lt;b&gt;Introduction.&lt;/b&gt; During the coronavirus disease 2019 (COVID-19) pandemic, the cases of mucormycosis increased substantially, with rhino-orbito-cerebral form linked to uncontrolled diabetes being the predominant manifestation. Several risk factors were implicated in the emergence of COVID-19-associated mucormycosis (CAM), including inappropriate corticosteroid usage and COVID-19-associated glycaemic imbalance.&lt;b&gt;Gap statement.&lt;/b&gt; Some clinical and epidemiological studies associated the usage of zinc supplements with the occurrence of CAM, but experimental evidence remains limited.&lt;b&gt;Aim.&lt;/b&gt; This study aimed to elucidate the impact of zinc enrichment on &lt;i&gt;Rhizopus arrhizus,&lt;/i&gt; the predominant causative agent of mucormycosis.&lt;b&gt;Methodology.&lt;/b&gt; The effect of zinc supplementation (5 to 150 µM) on fungal growth, metabolic activity, antifungal susceptibility and biofilm formation, along with cell-wall (Congo red), oxidative (hydrogen peroxide) and osmotic (sodium chloride) stress was evaluated in Roswell Park Memorial Institute -1640 medium. Morphological changes were visualized by scanning electron microscopy. Gene expression and intracellular zinc levels were determined by RNA sequencing and inductively coupled plasma mass spectrometry, respectively. The cytotoxic potential of &lt;i&gt;R. arrhizus&lt;/i&gt; pre-cultured with and without zinc supplementation was assessed in the human embryonic kidney 293 cell line.&lt;b&gt;Results.&lt;/b&gt; Zinc supplementation promoted &lt;i&gt;R. arrhizus&lt;/i&gt; growth in a concentration-dependent manner, with the effect being particularly pronounced under less-favourable conditions, such as alkaline conditions resembling the nasal pH of diabetics. The results further suggested a zinc-specific effect: supplementation with another trace element (copper) suppressed &lt;i&gt;R. arrhizus&lt;/i&gt; growth, and the zinc chelator (1,10-phenanthroline) dose-dependently abrogated the zinc-induced growth enhancement. Exposure to zinc increased the metabolic activity, and partly alleviated cell-wall and oxidative stress. Susceptibility to amphotericin B and posaconazole was unchanged. Zinc-supplemented cultures over-expressed multiple genes, notably those associated with respiratory electron transport chain, ergosterol biosynthesis, chitosan production, oxidative stress response, mucoricin, high-affinity iron permease, iron transport multi-copper oxidase and ferric-reductase-like protein. &lt;i&gt;R. arrhizus&lt;/i&gt; cytotoxicity was also significantly enhanced upon pre-culturing with zinc supplementation. Additionally, zinc augmented the growth/metabolism of several other Mucorales but not &lt;i&gt;Aspergillus fumigatus&lt;/i&gt; and &lt;i&gt;Candida albicans&lt;/i&gt;.&lt;b&gt;Conclusion.&lt;/b&gt; Zinc supplementation promotes mucoralean growth, increases cytotoxic potential and enhances the expression of key virulence factors, including mucoricin and iron transporters. The findings contribute experimental evidence supporting the proposed association of zinc over-availability with the emergence of ","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"75 7","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148440334","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of machine learning pipeline for blood culture outcome prediction on prospectively collected emergency department data.","authors":"Benjamin R McFadden, Mark Reynolds, Antonio Celenza, Timothy J J Inglis","doi":"10.1099/jmm.0.002191","DOIUrl":"10.1099/jmm.0.002191","url":null,"abstract":"<p><p><b>Introduction.</b> Bloodstream infections (BSIs) are particularly problematic in the emergency department (ED) of hospitals, where patients often present with undiagnosed illness, one cause of which may be undetected BSI. Identifying whether a patient needs a blood culture (BC) performed is one component of this challenge with implications for diagnostic efficiency and avoidance of unnecessary resource expenditure.<b>Gap statement.</b> In Western Australia, there has been no previous study investigating methods to predict BC outcome in an ED patient cohort.<b>Aim.</b> This article assesses the feasibility of previously developed machine learning (ML) models for BC outcome prediction using a prospectively collected ED patient dataset.<b>Methodology.</b> An ML pipeline containing models previously trained using complete blood count (CBC), white blood cell differential (DIFF) and cell population data (CPD) generated by Sysmex XN-2000 haematology analysers was further evaluated using prospectively collected data containing patient sample results from the ED at Sir Charles Gairdner Hospital (SCGH), Perth, Western Australia. Blood samples used to produce CBC, DIFF and CPD were obtained at the same time as BC samples.<b>Results.</b> There were 59 samples from 58 unique patients. Forty-nine of those samples were associated with negative BC results and 10 with positive BC results. We evaluated previously developed XGBoost (XG) and random forest (RF) ML models for positive BC outcome prediction. The RF and XG models obtained mean area under the receiver operating characteristic curve scores of 0.865 (95% CI, 0.763-0.947) and 0.833 (95% CI, 0.683-0.953) with the ED dataset.<b>Conclusion.</b> The results presented in this study provide a foundation for further validation and shadow deployment of BC outcome prediction models in clinical settings and support future planning of clinical trials.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"75 7","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13419127/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148623373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Contributions of plasmid p1AB5075-encoded antibiotic resistance genes to multidrug resistance of <i>Acinetobacter baumannii</i> AB5075.","authors":"Orlaith Plunkett, Anna S Ershova, Kristina Schauer, Carsten Kröger","doi":"10.1099/jmm.0.002189","DOIUrl":"10.1099/jmm.0.002189","url":null,"abstract":"<p><p>Infections caused by multidrug-resistant <i>Acinetobacter baumannii</i> are considered a threat to human and animal health. The widely studied <i>A. baumannii</i> strain AB5075 displays a high degree of antibiotic resistance. In this study, we experimentally validated that antibiotic resistance is largely mediated by resistance genes located on plasmid p1AB5075. We used a p1AB5075-deficient AB5075 strain to assess individual contributions of p1AB5075-encoded antibiotic resistance genes by ectopically (over-)expressing each gene in the Δp1AB5075 background. By determining individual contributions of seven p1AB5075-encoded antibiotic resistance genes, we show individual and overlapping roles of genes for aminoglycoside resistance and uncover the importance of extended-spectrum <i>β</i>-lactamase <i>blaGES-11</i> for monobactam and cephalosporin resistance in <i>A. baumannii</i> AB5075. We discovered that aminoglycoside <i>N</i>-acetyltransferase <i>aaC(6')-Ib3</i> (<i>aacA4</i>), which was previously shown to confer resistance to tobramycin, provides broad resistance to gentamicin, kanamycin, amikacin, streptomycin and tobramycin when overexpressed in <i>A. baumannii</i> AB5075. Because p1AB5075 is transferable to a wide range of environmental and clinical <i>A. baumannii</i> strains and non-<i>baumannii Acinetobacter</i> species, the relevance of our findings extends beyond <i>A. baumannii</i> AB5075.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"75 7","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13405486/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148581818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The metabolic trap: <i>Candida parapsilosis</i> inhibits <i>Staphylococcus aureus</i> biofilm maturation by disrupting pH homeostasis and inducing premature exodus.","authors":"Ciara Furlong, Salini Mohapatra, Denise Harold, Emma Finlay, Linda Holland","doi":"10.1099/jmm.0.002186","DOIUrl":"10.1099/jmm.0.002186","url":null,"abstract":"<p><p><b>Introduction.</b> Hospital-acquired infections (HAIs) frequently manifest as device-related biofilms that exhibit enhanced tolerance to conventional therapies contributing to antimicrobial resistance. Polymicrobial biofilms involving <i>Candida</i> and <i>Staphylococcus</i> species are a major cause of persistent nosocomial infections. However, while the synergism between <i>Candida albicans</i> and <i>Staphylococcus aureus</i> is well-characterized, the interactions involving non-albicans <i>Candida</i> remain poorly understood.<b>Hypothesis/Gap Statement.</b> The specific interactions between <i>Candida parapsilosis</i> and <i>S. aureus</i> were entirely unknown, although it was broadly assumed they would be synergistic in nature, mirroring known <i>Candida-Staphylococcus</i> models.<b>Aim.</b> This study investigated the interspecies dynamics between <i>C. parapsilosis</i> and <i>S. aureus</i> within a mixed biofilm context.<b>Methodology.</b> <i>C. parapsilosis</i> secretome fractions were isolated and screened against methicillin-sensitive (MSSA) and methicillin-resistant (MRSA) <i>S. aureus</i> strains. Their effects on biofilm formation, primary attachment, planktonic growth and eradication were evaluated under varying glucose concentrations, followed by transcriptomic analysis of treated staphylococcal cells.<b>Results.</b> We report the discovery of a small (<10 kDa), heat-stable fungal-secreted factor that significantly inhibits the maturation of MSSA biofilms and disperses preformed biomass without affecting primary attachment or planktonic growth, although MRSA strains remained recalcitrant. This antagonism is strictly glucose-dependent; the inhibitory effect is potent in 0.2% glucose but is abolished in both 0.5 and 1.0% glucose. Transcriptome analysis revealed that the fungal secretome triggers a pleiotropic 'Metabolic Trap' in <i>S. aureus</i>, characterized by the downregulation of the glycolytic pathway (e.g. <i>tpiA</i>, <i>gapA</i>) and a failure to induce critical-acid-tolerance systems, including the arginine deiminase and urease operons. This metabolic reprogramming maintains a near-neutral local pH (5.8-6), which in turn provides an optimal environment for the observed upregulation of staphylococcal nuclease (<i>nuc</i>) ultimately degrading the extracellular matrix and preventing the development of a mature biofilm architecture.<b>Conclusion.</b> We propose that the <i>C. parapsilosis</i> secretome effectively tricks <i>S. aureus</i> into a premature exodus phase, where nuclease-mediated matrix degradation prevents the establishment of a stable biofilm architecture. These findings underscore the highly species-specific nature of fungal-bacterial interactions and identify a specific metabolic vulnerability in <i>S. aureus</i> that may be exploited to develop novel anti-biofilm strategies against polymicrobial communities.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"75 7","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13421106/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148611582","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrated clinical and genomic characterization of <i>Acinetobacter baumannii</i> causing bloodstream infections in a Chinese tertiary hospital.","authors":"Jingyun Ye, Kun Ye, Yuqing Lu, Rui Qiu, Liyan Ye, Jiyong Yang, Lifeng Wang","doi":"10.1099/jmm.0.002177","DOIUrl":"10.1099/jmm.0.002177","url":null,"abstract":"<p><p><b>Introduction.</b> <i>Acinetobacter baumannii</i> is an opportunistic pathogen responsible for severe hospital-acquired infections, including bloodstream infections (BSIs). Although major epidemic clones and resistance mechanisms have been described, integrated analyses combining clinical features, patient outcomes and genomic characteristics of BSI isolates remain limited, particularly in China.<b>Gap Statement.</b> Comprehensive analyses integrating clinical outcomes, high-resolution genotyping, capsule locus diversity and their associations with mortality are still lacking.<b>Aim.</b> This study aimed to characterize the clinical characteristics and outcomes of patients with <i>A. baumannii</i> BSIs, as well as the phenotypic and genomic characteristics of the causative isolates. Specifically, we sought to identify high-risk clones and their association with 30-day mortality to improve diagnostic and therapeutic strategies.<b>Methodology.</b> A retrospective cohort study was conducted on 151 cases of <i>A. baumannii</i> BSIs in a tertiary hospital in China. Isolates were analysed using whole-genome sequencing to determine sequence types (STs), capsule loci and resistance and virulence gene profiles.<b>Results.</b> The 151 isolates were classified into 11 different STs using the Pasteur MLST scheme, with ST2_Pasteur predominating (88.1%). One isolate represented a novel Pasteur ST (ST2831_Pasteur). Using the Oxford MLST scheme, 22 STs were identified, with ST195_Oxford, ST208_Oxford and ST540_Oxford being the most common. Four novel Oxford STs (ST2457_Oxford, ST2458_Oxford, ST2459_Oxford and ST2460_Oxford) were identified. Twenty-three capsule locus (KL) types were detected, with KL3 being the most prevalent. Phylogenetic analysis showed clear clustering according to STs and KL types. The ST2_Pasteur lineage was characterized by the presence of the <i>OXA-23</i> gene and carbapenem resistance, as well as an expanded virulence gene repertoire, suggesting enhanced pathogenic potential. The overall 30-day mortality rate was 35.1%. Patients in the death group had shorter hospital stays, fewer surgical interventions and higher rates of complications, invasive procedures and intensive care unit admission. Certain clone combinations, including ST369_Oxford-KL9, ST938_Oxford-KL210 and ST195_Oxford-KL3, were associated with higher mortality rates.<b>Conclusion.</b> ST369_Oxford-KL9, ST938_Oxford-KL210 and ST195_Oxford-KL3 represent high-risk clones associated with <i>A. baumannii</i> BSIs. Early identification of ST and capsule type, alongside clinical risk stratification, may improve diagnosis and guide treatment strategies.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"75 7","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13340785/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148400399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Suggestive associations between genetically predicted gut microbiota and endometriosis: a two-sample Mendelian randomization study.","authors":"Liyun Liao, Zhixiang Zhou, Xiaoyang Ye, Yi Lin, Panpan Hu, Qiaoyun Zhang, Zhifen Wang, Dandan Yang, Huan Lu, Minna Wang, Jianshuo Lu","doi":"10.1099/jmm.0.002174","DOIUrl":"10.1099/jmm.0.002174","url":null,"abstract":"<p><p><b>Introduction.</b> Endometriosis affects 10-20% of reproductive-age women. Emerging evidence links the gut microbiota to endometriosis pathogenesis, but observational studies are limited by confounding, reverse causation and uncertainty about whether reported microbial signals represent reproducible aetiological associations.<b>Hypothesis/Gap Statement.</b> Whether genetically predicted gut microbial genera are associated with endometriosis risk remains unclear, and available observational evidence does not establish robust causal effects after accounting for multiple testing.<b>Aim.</b> This study aimed to explore potential Mendelian randomization (MR)-based associations between genetically predicted gut microbiota composition and endometriosis using a two-sample MR framework.<b>Methodology.</b> Genome-wide association study (GWAS) summary statistics for 119 bacterial genera (MiBioGen consortium: <i>n</i>=18,340) and endometriosis (FinnGen: 8,288 cases, 68,969 controls) were used. Single nucleotide polymorphisms (SNPs) associated with each genus (<i>P</i><5×10⁻⁵) were selected as instrumental variables after linkage disequilibrium clumping and weak instrument exclusion. The primary method was inverse-variance weighting (IVW), supplemented by four complementary methods. Benjamini-Hochberg false discovery rate (FDR) correction was applied across all 119 genera.<b>Results.</b> Seven genera showed nominally significant IVW associations with endometriosis (<i>P</i><0.05): <i>Lactococcus</i>, <i>Olsenella</i>, <i>Senegalimassilia</i>, Ruminococcaceae UCG-002, <i>Holdemania</i>, <i>Eubacterium ruminantium</i> group and <i>Anaerotruncus</i>. <i>Olsenella</i>, Ruminococcaceae UCG-002 and <i>Anaerotruncus</i> were directionally associated with increased risk, whereas the remaining four were directionally associated with reduced risk. However, none survived FDR correction (all FDR-adjusted <i>P</i>=0.731). No significant heterogeneity or horizontal pleiotropy was detected.<b>Conclusion.</b> These findings provide exploratory and suggestive MR evidence for potential associations between specific gut microbial genera and endometriosis, rather than definitive causal evidence. As no associations survived multiple testing correction, these results should be interpreted as hypothesis-generating and require replication in larger, ancestry-matched cohorts.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"75 7","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13322561/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148371588","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characteristics of gut microbiota structure and composition in diabetic patients from the Chaoshan region of China.","authors":"Kun Lin, Baolong Chen, Xinyi Zhang, Ming Fan, Panpan Wang, Yike Wang, Xianhui Cheng, Zeming Ma, Xiaojing Chen, Xingying Xue, Wenting Jia, Songjian Yuan, Bangzhou Zhang, Xiaoman Du, Wenxin Hong, Zhenqiang Hong, Chuanxing Xiao","doi":"10.1099/jmm.0.002156","DOIUrl":"10.1099/jmm.0.002156","url":null,"abstract":"<p><p><b>Introduction.</b> Diabetes mellitus, a condition characterized by chronic hyperglycaemia, is categorized into type 1 diabetes mellitus (T1DM) and type 2 diabetes mellitus (T2DM). Recent research has identified a significant association between diabetes and modifications in the gut microbiota.<b>Gap Statement.</b> Although numerous analyses have been conducted on the gut microbiota of patients with diabetes, regional variations due to factors such as lifestyle and dietary habits remain poorly understood.<b>Aim.</b> This study aimed to compare the gut microbiota structures of adult patients with T1DM, T2DM and healthy controls (HCs) in the Chaoshan region of China, providing theoretical support for gut microbiota-based targeted therapies for diabetes in the Chaoshan region.<b>Methodology.</b> This study enrolled 33 patients with T1DM, 35 patients with T2DM and 30 HCs in the Chaoshan region of China. Faecal samples were collected and subjected to 16S rDNA sequencing and bioinformatics analysis.<b>Results.</b> Our data demonstrated significant variations in gut microbiota diversity among individuals with T1DM, T2DM and HC, accompanied by changes in microbial composition across multiple taxonomic levels. Furthermore, linear discriminant analysis effect size analysis identified distinct dominant species within each group: 27 bacterial genera, including <i>Megasphaera</i>, were significantly enriched in T2DM patients; 27 bacterial genera, including <i>Bacteroides</i>, were significantly enriched in T1DM patients; and 18 bacterial genera, including <i>Alloprevotella</i>, were significantly enriched in the HC group. Metabolic pathway analyses using Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Genes (COG) databases demonstrated a significant enrichment of pathways and enzymes associated with starch and sucrose metabolism in both T1DM and T2DM cohorts, compared to HC. Additionally, a diagnostic model based on gut microbiota data at the class level yielded an area under the curve value of 0.861, indicating its high diagnostic efficacy in distinguishing between T1DM and T2DM. Furthermore, an analysis of the abundance of various bacterial phenotypes and probiotic species revealed notable differences among the three groups.<b>Conclusion.</b> This study demonstrates distinct gut microbiota composition, structure and functional profiles in Chaoshan T1DM, T2DM and HC populations, supporting microbiota modulation as a promising therapeutic strategy for diabetes.</p>","PeriodicalId":94093,"journal":{"name":"Journal of medical microbiology","volume":"75 7","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13367372/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148440371","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}