Microbiome research reports最新文献

{"title":"Faecal microbiota transplant revisited - potential metabolic outcomes of regional microbiome mismatches.","authors":"Elisabeth A A O'Flaherty, Douwe van Sinderen","doi":"10.20517/mrr.2026.29","DOIUrl":"https://doi.org/10.20517/mrr.2026.29","url":null,"abstract":"","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"5 3","pages":"24"},"PeriodicalIF":5.2,"publicationDate":"2026-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13678541/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149229723","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 microbiome bone axis in osteomyelitis: integrating evidence from bone oral and gut microbiota.","authors":"Chanon Kunasol, Chaloemwut Piyaphattachai, Jirawat Saengsin, Nipon Chattipakorn, Siriporn C Chattipakorn","doi":"10.20517/mrr.2026.63","DOIUrl":"https://doi.org/10.20517/mrr.2026.63","url":null,"abstract":"<p><p>Osteomyelitis is an inflammatory bone disorder that includes both infectious and noninfectious forms and remains a major cause of bone destruction, impaired skeletal repair, and long-term disability. Although bacterial infection is the predominant cause, disease progression is influenced by interactions among microorganisms, host immunity, inflammation, and bone remodeling. This review critically evaluates current evidence from genome-wide association and Mendelian randomization studies, clinical investigations, and experimental animal models. Clinical studies demonstrate that osteomyelitic bone contains polymicrobial communities enriched with anaerobic and biofilm-forming bacteria, whereas oral microbial dysbiosis differs between chronic bacterial and chronic nonbacterial osteomyelitis. Experimental studies indicate that gut microbial dysbiosis is associated with impaired intestinal barrier function, altered microbial metabolites, systemic inflammation, and delayed bone repair. Current evidence therefore suggests that microbial communities detected at local sites are associated with infection, biofilm formation, and local inflammatory responses, whereas the gut microbiome may influence systemic immunity, inflammatory tone, and bone remodeling. Although microbiome-targeted interventions have shown beneficial effects in experimental models, current evidence remains largely associative, and mechanistic and longitudinal studies are limited. A better understanding of microbiome-host interactions may facilitate the development of microbiome-based strategies for the prevention and treatment of osteomyelitis.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"5 3","pages":"23"},"PeriodicalIF":5.2,"publicationDate":"2026-09-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13678545/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149229729","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":"Recombination-mediated gene-specific sweeps in motion across the human gut microbiome.","authors":"Matthew Foley, Rodolphe Barrangou","doi":"10.20517/mrr.2026.32","DOIUrl":"https://doi.org/10.20517/mrr.2026.32","url":null,"abstract":"","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"5 3","pages":"22"},"PeriodicalIF":5.2,"publicationDate":"2026-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13678539/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149225768","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":"Intratumoral microbiota and their emerging role in the tumor microenvironment.","authors":"Xianfeng Hui, Shihuan Ding, Ge Gao, Shuoxiang Gao, Jiaqi Tian, Shuochen Xu, Bingqi Yan, Rujing Zhang, Tiesuo Zhao, Hui Wang","doi":"10.20517/mrr.2026.18","DOIUrl":"https://doi.org/10.20517/mrr.2026.18","url":null,"abstract":"<p><p>Intratumoral microbiota, as an important component of the tumor microenvironment, have attracted increasing attention in recent years for their roles in tumor initiation, progression, and therapeutic regulation. Accumulating evidence indicates that low-abundance yet relatively stable microbial communities are present in a variety of solid tumors, exhibiting marked tumor-type specificity and spatial heterogeneity. Current studies suggest that intratumoral microorganisms contribute to tumor progression through multiple mechanisms, including activation of oncogenic signaling pathways, modulation of chronic inflammatory responses, remodeling of the immunosuppressive microenvironment, and regulation of metabolic reprogramming and drug responsiveness. Meanwhile, their bidirectional effects on chemotherapy, radiotherapy, targeted therapy, and immunotherapy highlight their potential roles in determining therapeutic sensitivity and the development of resistance. Despite existing challenges such as low microbial biomass, contamination control, and difficulties in functional validation, advances in spatial multi-omics and single-cell technologies are continuously enhancing the potential clinical value of intratumoral microbiota in tumor diagnosis, prognostic assessment, and precision therapy. This review summarizes the sources, colonization mechanisms, biological functions, roles in therapeutic modulation, and clinical applications of intratumoral microbiota, aiming to provide a theoretical basis for future research and clinical translation.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"5 3","pages":"21"},"PeriodicalIF":5.2,"publicationDate":"2026-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13678546/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149225741","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":"Long-term <i>in vitro</i> evolution of human-associated bifidobacteria provides insights into genome-based strain delineation.","authors":"Gabriele Andrea Lugli, Chiara Argentini, Giulia Longhi, Leonardo Mancabelli, Christian Milani, Francesca Turroni, Douwe van Sinderen, Marco Ventura","doi":"10.20517/mrr.2026.37","DOIUrl":"https://doi.org/10.20517/mrr.2026.37","url":null,"abstract":"","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"1 3","pages":"20"},"PeriodicalIF":5.2,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13678542/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149229715","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":"Gut microbiota profiles as potential indicators of irradiation-induced quality loss in mass-reared <i>Aedes albopictus</i> males.","authors":"Paerhande Dilinuer, Jehangir Khan, Ming Li, Yu Wu, Xiaoying Zheng, Zhongdao Wu, Datao Lin, Hanano Yamada, Jeremy Bouyer, Kostas Bourtzis, Dongjing Zhang","doi":"10.20517/mrr.2026.25","DOIUrl":"https://doi.org/10.20517/mrr.2026.25","url":null,"abstract":"<p><p><b>Aim:</b> The Sterile Insect Technique is a promising method for <i>Aedes albopictus</i> control, but its effectiveness hinges on male quality, which may be compromised during mass-rearing and irradiation. Reliable biological indicators capable of reflecting irradiation-induced quality loss remain limited. Gut microbiota regulates mosquito development, immunity, and metabolism and may therefore provide potential indicators of sterile male quality. This study explored whether gut microbiota composition can reflect irradiation-induced quality impairment in males of a long-term (over 3 years) mass-reared <i>Ae. albopictus</i> GT strain. <b>Methods:</b> Male pupae were exposed to X-ray irradiation without filtration at an estimated absorbed dose of 78 Gy. Emergence rate, flight ability, longevity, metabolic capacity, and gut microbiota (via 16S <i>rRNA</i> gene sequencing, culture-based methods, and qPCR) were compared between irradiated and non-irradiated males. <b>Results:</b> Irradiation significantly reduced emergence rate, flight ability, and longevity. It did not alter gut microbiota diversity, but reshaped its composition, including the emergence of <i>Sphingobacterium</i>, increased abundance of <i>Stenotrophomonas</i> and <i>Comamonas</i>, and decreased levels of <i>Delftia</i> and <i>Achromobacter</i>. Similarity was observed in the culturable gut bacterial community, confirmed by qPCR with eight selected key taxa. Metabolic changes included reduced glutamine synthetase activity and elevated glucose levels in irradiated males. <b>Conclusion:</b> These results show that irradiation-induced quality loss is accompanied by reproducible shifts in gut microbiota composition and metabolic status. These findings suggest that gut microbiota profiles may serve as potential indicators of irradiation-associated quality changes in sterile males and provide preliminary evidence for microbiota-informed quality assessment approaches in <i>Ae. albopictus</i> SIT programs.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"5 3","pages":"19"},"PeriodicalIF":5.2,"publicationDate":"2026-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13678544/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149229736","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":"Genome-scale insights into the metabolic landscape and evolutionary development of <i>Bifidobacterium bifidum</i>.","authors":"Emanuele Selleri, Giulia Longhi, Chiara Tarracchini, Erica de Carolis, Silvia Petraro, Leonardo Mancabelli, Christian Milani, Francesca Turroni, Marco Ventura, Gabriele Andrea Lugli","doi":"10.20517/mrr.2026.19","DOIUrl":"https://doi.org/10.20517/mrr.2026.19","url":null,"abstract":"<p><p><b>Background:</b> <i>Bifidobacterium bifidum</i> (<i>B. bifidum</i>) is an infant gut symbiont specialized in degrading host-derived glycans. Despite its relevance in early life, the species' genomic diversity has not yet been comprehensively surveyed, and current reference collections capture only a fraction of the global <i>B. bifidum</i> pangenome. <b>Methods:</b> In this study, we reconstructed the first comprehensive pangenome of <i>B. bifidum</i> using 1,351 high-quality genomes, including metagenome-assembled genomes. This dataset was used for <i>in silico</i> comparative genomics analyses to identify species-specific genetic and functional features. <i>In vitro</i> transcriptomics analyses were further performed to validate and functionally characterize selected species-specific traits. <b>Results:</b> Comparative genomic analysis with other human-associated bifidobacteria species identified 667 <i>B. bifidum</i>-specific clusters of orthologous genes mostly involved in carbohydrate utilization, osmotic regulation, and host interaction. Notably, <i>B. bifidum</i> displays the most extensive enzymatic repertoire for host-glycan degradation, dedicating 43% of its conserved glycoside hydrolases to these substrates. We identified significant gain-of-function events, including two unique phosphotransferase systems (PTS) for disaccharide uptake. Transcriptomic profiling corroborated the functional relevance of these PTS clusters, which were significantly up-regulated during growth on human milk oligosaccharides, mucin, and N-acetylglucosamine. While the species exhibits high genomic stability, a localized divergence (average nucleotide identitiy, ANI < 98.5%) was identified in rural, non-Westernized populations, reflecting niche-specific adaptations. <b>Conclusion:</b> The identified genomic framework highlighted a distinct evolutionary path of <i>B. bifidum</i>, placing this taxon as a metabolic cornerstone in the neonatal gut via extensive metabolic specialization toward glycan hosts.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"5 3","pages":"18"},"PeriodicalIF":5.2,"publicationDate":"2026-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13678547/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149229707","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":"Gut microbiome metabolism of plant phenolic glycosides and its relationship with human health.","authors":"Clara G de Los Reyes-Gavilán, Nuria Salazar","doi":"10.20517/mrr.2026.17","DOIUrl":"10.20517/mrr.2026.17","url":null,"abstract":"","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"5 3","pages":"17"},"PeriodicalIF":5.2,"publicationDate":"2026-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13459116/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148715128","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":"We need to talk about the virome.","authors":"Colin Hill","doi":"10.20517/mrr.2026.13","DOIUrl":"10.20517/mrr.2026.13","url":null,"abstract":"","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"5 2","pages":"16"},"PeriodicalIF":5.2,"publicationDate":"2026-06-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13459111/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148715138","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":"Early-life microbiome trajectories as biomarkers to predict health outcomes.","authors":"Raphaela Joos, Aonghus Lavelle, Eugene Dempsey, Catherine Stanton, R Paul Ross","doi":"10.20517/mrr.2026.03","DOIUrl":"10.20517/mrr.2026.03","url":null,"abstract":"<p><p>The early-life gut microbiome is tightly linked to different aspects of infant development. Microbial colonisation patterns have been repeatedly shown to play a role in a variety of paediatric outcomes, ranging from metabolism and immune function to neurodevelopment. Concomitantly, the identification of early-life biomarkers is crucial, especially considering that for various conditions, reliable diagnostic tools only emerge in early childhood. As such, microbiome data collected in the first two years of life may offer valuable prospects for early detection, prevention, quantification or even correction of adverse health trajectories. With the increasing availability of high-resolution microbiome data, researchers are leveraging both traditional statistical approaches and machine learning (ML) methods to analyse the evolution of these complex microbial communities. While statistical models are well-suited for identifying associations between microbiome features and health states, ML methods allow for predicting health outcomes from those features. This review explores the role of the early-life gut microbiome in infant health and development, with a focus on how data acquisition and analytical methods can shape current knowledge. We contrast statistical approaches with ML methods, summarising key findings on microbial succession and factors influencing it. By addressing current challenges and identifying areas for methodological refinement, we aim to discuss the potential of the microbiome in the assessment of current and future health states of an individual and aid in the development of more robust, clinically-relevant models for paediatric care.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"5 2","pages":"15"},"PeriodicalIF":5.2,"publicationDate":"2026-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13459118/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148715118","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}