Microbiome research reports最新文献

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Quantification of the absolute abundance of the jejunal mucosa-associated microbiota of pigs using spike-in control. 猪空肠黏膜相关微生物群绝对丰度的定量研究
IF 5.2
Microbiome research reports Pub Date : 2026-03-18 eCollection Date: 2026-01-01 DOI: 10.20517/mrr.2025.100
Jung Yeol Sung, Hyunjun Choi, Alexa R Gormley, Sung Woo Kim
{"title":"Quantification of the absolute abundance of the jejunal mucosa-associated microbiota of pigs using spike-in control.","authors":"Jung Yeol Sung, Hyunjun Choi, Alexa R Gormley, Sung Woo Kim","doi":"10.20517/mrr.2025.100","DOIUrl":"10.20517/mrr.2025.100","url":null,"abstract":"<p><p>The objective was to quantify the absolute abundance of the jejunal mucosa-associated microbiota in pigs and develop a standardized spike-in control protocol. The spike-in control, containing bacteria that are Gram-negative (<i>Imtechella halotolerans</i>) and Gram-positive (<i>Allobacillus halotolerans</i>), was diluted 100 times and 10 μL (100,000 bacterial cells of each species) was added to 100 mg of porcine jejunal mucosa samples. The relative abundance of the jejunal mucosa-associated microbiota differed between the diet groups, whereas no difference was observed in their absolute abundance. In conclusion, the spike-in control containing 100,000 cells of <i>Imtechella halotolerans</i> and <i>Allobacillus halotolerans</i> can be used to quantify the absolute abundance of microbiota in 100 mg of pig jejunal mucosa.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"5 1","pages":"5"},"PeriodicalIF":5.2,"publicationDate":"2026-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13091085/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147725384","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}
引用次数: 0
An overview of the role of the gut microbiota in rheumatoid arthritis. 肠道菌群在类风湿关节炎中的作用综述。
IF 5.2
Microbiome research reports Pub Date : 2026-03-09 eCollection Date: 2026-01-01 DOI: 10.20517/mrr.2025.69
Anastasia V Poznyak, Aleksey A Vatlin, Vsevolod V Pavshintsev, Nikita A Mitkin, Olga N Maltseva, Aleksandra S Utkina, Alexander N Orekhov
{"title":"An overview of the role of the gut microbiota in rheumatoid arthritis.","authors":"Anastasia V Poznyak, Aleksey A Vatlin, Vsevolod V Pavshintsev, Nikita A Mitkin, Olga N Maltseva, Aleksandra S Utkina, Alexander N Orekhov","doi":"10.20517/mrr.2025.69","DOIUrl":"10.20517/mrr.2025.69","url":null,"abstract":"<p><p>Rheumatoid arthritis (RA) is a chronic autoimmune disease preceded by a prolonged preclinical phase marked by the emergence of autoantibodies and mucosal immune dysregulation. Evidence from human studies and animal models consistently demonstrates that gut microbiota dysbiosis contributes to this transition, particularly through impaired intestinal barrier function, activation of pro-inflammatory pathways, and molecular mimicry. Specific taxa - including <i>Prevotella copri</i>, <i>Collinsella aerofaciens</i>, and reductions in butyrate-producing bacteria - have been linked to heightened systemic inflammation, increased T helper 17 responses, and the generation of RA-associated autoantibodies. Current research also indicates that anti-rheumatic medications such as methotrexate, sulfasalazine, and minocycline produce measurable shifts in gut microbial composition, suggesting that microbiota-drug interactions may influence treatment response. Therapeutic approaches aimed at modifying gut ecology - including dietary interventions, prebiotics, probiotics, and fecal microbiota transplantation - show early potential in restoring microbial balance, improving intestinal barrier integrity, and reducing inflammatory markers, although evidence in the preclinical RA stage remains limited. Additionally, emerging data highlight the importance of intestinal autophagy and microRNA networks in regulating epithelial integrity and systemic immune activation. Taken together, the literature supports a mechanistic link between gut dysbiosis and the onset of RA. It points to microbiota-targeted strategies as promising avenues for delaying or preventing disease progression. Future studies should prioritize longitudinal analyses and interventional trials focusing specifically on individuals at risk for RA.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"5 1","pages":"3"},"PeriodicalIF":5.2,"publicationDate":"2026-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13091088/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147725456","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}
引用次数: 0
A responder-informed gut microbial consortium enhances anti-PD-1 efficacy in a mouse cancer model. 在小鼠癌症模型中,应答告知肠道微生物联盟增强了抗pd -1的功效。
IF 5.2
Microbiome research reports Pub Date : 2026-02-09 eCollection Date: 2026-01-01 DOI: 10.20517/mrr.2025.117
Uk Jin Jeong, Mohammed Ali, Yun Jee Park, Jin Sun You, Sang Sun Yoon
{"title":"A responder-informed gut microbial consortium enhances anti-PD-1 efficacy in a mouse cancer model.","authors":"Uk Jin Jeong, Mohammed Ali, Yun Jee Park, Jin Sun You, Sang Sun Yoon","doi":"10.20517/mrr.2025.117","DOIUrl":"10.20517/mrr.2025.117","url":null,"abstract":"<p><p><b>Aim:</b> Immune checkpoint inhibitors (ICIs), particularly anti-programmed cell death protein 1 (PD-1) therapy, have improved cancer treatment outcomes, yet durable benefit is achieved in only a subset of patients. Growing evidence implicates the gut microbiome as a modulator of ICI responsiveness, but defined and experimentally validated microbial strategies remain limited. This study aimed to identify responder-associated gut microbes and to evaluate a defined bacterial consortium for enhancing PD-1 blockade efficacy. <b>Methods:</b> Publicly available shotgun metagenomic datasets from anti-PD-1-treated cancer patients were re-analyzed to compare gut microbiome profiles between responders and non-responders. Bacterial taxa reproducibly enriched in responders were selected based on consistency across analytical criteria and cultivability and assembled into a four-strain consortium (UJ-04). The immune-adjuvant potential of UJ-04, alone or combined with anti-PD-1 therapy, was evaluated in a B16-F10 melanoma mouse model, with tumor growth and immune responses assessed by flow cytometry. <b>Results:</b> Metagenomic re-analysis identified four commensal bacterial taxa consistently enriched in responder patients, forming the defined UJ-04 consortium. While UJ-04 alone showed minimal antitumor activity, combination treatment with anti-PD-1 significantly enhanced tumor growth inhibition compared with anti-PD-1 monotherapy. This effect was accompanied by increased intratumoral CD8<sup>+</sup> T cells and natural killer cells, with concordant immune trends in peripheral compartments. <b>Conclusion:</b> A responder-informed, defined microbial consortium functionally translates clinical microbiome associations into <i>in vivo</i> validation and enhances PD-1 blockade efficacy by modulating host antitumor immunity. These findings support defined bacterial consortia as microbiome-based immunomodulatory adjuncts for immunotherapy.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"5 1","pages":"2"},"PeriodicalIF":5.2,"publicationDate":"2026-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13091084/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147725374","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}
引用次数: 0
MUC2 shifts the metabolic profiles of commensal bacteria in defined microbial communities. MUC2改变了特定微生物群落中共生菌的代谢谱。
IF 5.2
Microbiome research reports Pub Date : 2026-01-21 eCollection Date: 2026-01-01 DOI: 10.20517/mrr.2025.91
Erin Chard, Adelaide E Horvath, Makenna Grozis, Renata Rocha do Nascimento, Paul R S Baker, Santosh Kapil Kumar Gorti, Robert Proos, Thomas D Horvath, Melinda A Engevik
{"title":"MUC2 shifts the metabolic profiles of commensal bacteria in defined microbial communities.","authors":"Erin Chard, Adelaide E Horvath, Makenna Grozis, Renata Rocha do Nascimento, Paul R S Baker, Santosh Kapil Kumar Gorti, Robert Proos, Thomas D Horvath, Melinda A Engevik","doi":"10.20517/mrr.2025.91","DOIUrl":"10.20517/mrr.2025.91","url":null,"abstract":"<p><p><b>Background:</b> The intestinal mucus layer is comprised of heavily glycosylated mucins, including mucin 2 (MUC2), that serve as a nutrient source for certain bacterial members of the gut microbiota. Only a subset of gut commensals encode the glycoside hydrolases required to degrade mucin glycans. However, mucin-degrading microbes can release glycans and generate compounds that can cross-fed non-mucin degrading microbes, creating complex microbial networks. While pairwise studies have shown that mucin degradation drives cross-feeding and metabolite exchange, the broader impact of mucins on community structure and metabolic output remains poorly understood. <b>Objective:</b> In this study, we sought to identify how a defined microbial consortium of human commensals with varied mucin-degrading capacities responds to MUC2 to shape community composition and metabolic output. <b>Methods:</b> A defined consortium of human gut commensals with varied mucin-degrading capacities was cultivated in anaerobic bioreactors in the presence or absence of porcine MUC2. Community composition was assessed, and extracellular metabolites were quantified using targeted and untargeted metabolomic profiling. <b>Results:</b> MUC2 supplementation significantly altered community structure, promoting the expansion of <i>Akkermansia muciniphila</i> while reducing <i>Prevotella</i>. MUC2 also reshaped microbial metabolism, decreasing acetate levels while increasing propionate, butyrate, and formate. In addition, MUC2 supplementation altered amino acid utilization and vitamin metabolism and reduced several neuroactive compounds, including glutamate, γ-aminobutyric acid (GABA), and anthranilic acid, while increasing tryptamine levels. <b>Conclusion:</b> These findings demonstrate that mucins exert broad effects on microbial community structure and metabolic output. Collectively, this work highlights the central role of bacterial cross-feeding in shaping gut ecosystem function.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"5 1","pages":"1"},"PeriodicalIF":5.2,"publicationDate":"2026-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13091087/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147725420","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}
引用次数: 0
Immunomodulatory properties of dietary polyphenols: a role for combating infections at mucosal surfaces? 膳食多酚的免疫调节特性:对抗粘膜表面感染的作用?
IF 3.8
Microbiome research reports Pub Date : 2025-12-10 eCollection Date: 2025-01-01 DOI: 10.20517/mrr.2025.81
Mona Sharma, Yves Desjardins, Andrew R Williams
{"title":"Immunomodulatory properties of dietary polyphenols: a role for combating infections at mucosal surfaces?","authors":"Mona Sharma, Yves Desjardins, Andrew R Williams","doi":"10.20517/mrr.2025.81","DOIUrl":"10.20517/mrr.2025.81","url":null,"abstract":"<p><p>Polyphenols are food components with antioxidant and anti-inflammatory properties, and their health benefits are increasingly recognized in the context of noncommunicable diseases such as type 2 diabetes. However, their role in regulating immunity to infection is not well understood. Here, we highlight the various mechanisms by which polyphenols may enhance mucosal immunity via both adaptive and innate immune responses. Polyphenols may directly interact with host receptors on mucosal epithelial and/or immune cells to regulate production of cytokines and antimicrobial peptides. They can also modify gut microbiota composition, yielding microbial-derived metabolites that play a key role in fine-tuning immune function at mucosal surfaces. We provide examples of how these immunological changes may alter the outcome of pathogen infection and propose that an increased understanding of polyphenol-microbiota-immune interaction will provide a framework for the application of new nutrition-based strategies in the management and prevention of infectious diseases.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"4 4","pages":"44"},"PeriodicalIF":3.8,"publicationDate":"2025-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12702655/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145770388","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}
引用次数: 0
Benchmarking and optimizing microbiome-based bioinformatics workflow for non-invasive detection of intestinal tumors. 对标和优化肠道肿瘤无创检测中基于微生物组的生物信息学工作流程。
IF 5.2
Microbiome research reports Pub Date : 2025-12-01 eCollection Date: 2025-01-01 DOI: 10.20517/mrr.2025.75
Yangyang Sun, Yongxiang Huang, Ruichen Li, Junhui Zhang, Xiaoqian Fan, Xiaoquan Su
{"title":"Benchmarking and optimizing microbiome-based bioinformatics workflow for non-invasive detection of intestinal tumors.","authors":"Yangyang Sun, Yongxiang Huang, Ruichen Li, Junhui Zhang, Xiaoqian Fan, Xiaoquan Su","doi":"10.20517/mrr.2025.75","DOIUrl":"10.20517/mrr.2025.75","url":null,"abstract":"<p><p><b>Background:</b> The human gut microbiome is closely linked to disease states, offering substantial potential for novel disease detection tools based on machine learning (ML). However, variations in feature types, data preprocessing strategies, feature selection strategies, and classification algorithms can all influence the model's predictive performance and robustness. <b>Methods:</b> To develop an optimized and systematically evaluated workflow, we conducted a comprehensive evaluation of ML methods for classifying colorectal cancer and adenoma using 4,217 fecal samples from diverse global regions. The area under the receiver operating characteristic curve was used to quantify model performance. We benchmarked 6,468 unique analytical pipelines, defined by distinct tools, parameters, and algorithms, utilizing a dual validation strategy that included both cross-validation and leave-one-dataset-out validation. <b>Results:</b> Our findings revealed that shotgun metagenomic (WGS) data generally outperformed 16S ribosomal RNA gene (16S) sequencing data, with features at the species-level genome bin, species, and genus levels demonstrating the greatest discriminatory power. For 16S data, Amplicon Sequence Variant-based features yielded the best disease classification performance. Furthermore, the application of specific feature selection tools, such as the Wilcoxon rank-sum test method, combined with appropriate data normalization, also optimized model performance. Finally, in the algorithm selection phase, we identified ensemble learning models (eXtreme Gradient Boosting and Random Forest) as the best-performing classifiers. <b>Conclusion:</b> Based on the comprehensive evaluation results, we developed an optimized Microbiome-based Detection Framework (MiDx) and validated its robust generalizability on an independent dataset, offering a systematic and practical framework for future 16S and WGS-based intestinal disease detection.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"4 4","pages":"43"},"PeriodicalIF":5.2,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12702651/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145770378","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}
引用次数: 0
Disclosing the effects of pea-derived proteins on the human gut microbiota. 揭示豌豆衍生蛋白对人类肠道微生物群的影响。
IF 3.8
Microbiome research reports Pub Date : 2025-11-25 eCollection Date: 2025-01-01 DOI: 10.20517/mrr.2025.77
Leonardo Mancabelli, Christian Milani, Giulia Longhi, Gabriele Andrea Lugli, Chiara Tarracchini, Francesca Turroni, Marco Ventura
{"title":"Disclosing the effects of pea-derived proteins on the human gut microbiota.","authors":"Leonardo Mancabelli, Christian Milani, Giulia Longhi, Gabriele Andrea Lugli, Chiara Tarracchini, Francesca Turroni, Marco Ventura","doi":"10.20517/mrr.2025.77","DOIUrl":"10.20517/mrr.2025.77","url":null,"abstract":"<p><p><b>Aim:</b> Plant-derived proteins have emerged as promising alternatives to animal-based proteins, offering not only environmental and nutritional benefits to the human host but also potential effects on the gut microbiota. Yellow pea (<i>Pisum sativum</i>) represents an attractive source due to its balanced amino acid composition and suitability for food applications. This preliminary study was designed to evaluate the effects of two commercial pea-derived protein preparations - a wet-extracted protein isolate (PPI) and a dry-fractionated protein concentrate (PPC) - on the human gut microbiota using a dual <i>in vitro</i> approach. <b>Methods:</b> We combined monoculture assays on selected representative intestinal bacterial strains with <i>in vitro</i> cultivation models of stabilized microbial communities derived from human fecal samples. <b>Results:</b> Monoculture experiments revealed selective growth responses in certain taxa, such as <i>Bacteroides thetaiotaomicron</i> and <i>Bifidobacterium</i> spp. Moreover, <i>in silico</i> genomic predictions of amino acid biosynthesis and proteolytic capabilities further supported these findings, highlighting functional differences among the tested strains. Furthermore, analysis based on stabilized microbial communities revealed moderate shifts in microbial richness and composition. Notably, PPC was associated with greater variation in taxonomic profiles across samples. Both protein ingredients exhibited similar directional effects on specific taxa, including increases in the load of <i>Bifidobacterium longum</i> and <i>Faecalibacterium duncaniae</i>, and decreases in members of <i>Bacteroides</i>, <i>Parabacteroides</i>, and <i>Phocaeicola</i>. <b>Conclusion:</b> These findings indicate that pea-derived proteins, especially when used as concentrates, exert selective pressure on gut microbial communities.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"4 4","pages":"42"},"PeriodicalIF":3.8,"publicationDate":"2025-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12702649/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145770403","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}
引用次数: 0
Taxonomic and mechanistic insights into gut microbiota bioaccumulation of entacapone using bioorthogonal drug labelling. 利用生物正交药物标记对恩他卡朋的肠道微生物群生物积累进行分类和机制研究。
IF 3.8
Microbiome research reports Pub Date : 2025-11-20 eCollection Date: 2025-01-01 DOI: 10.20517/mrr.2025.73
Linda M Guantai, Clementine E Bavinton, Juwairiyah B Shazzad, Sumeet Mahajan, Sam Thompson, Fatima C Pereira
{"title":"Taxonomic and mechanistic insights into gut microbiota bioaccumulation of entacapone using bioorthogonal drug labelling.","authors":"Linda M Guantai, Clementine E Bavinton, Juwairiyah B Shazzad, Sumeet Mahajan, Sam Thompson, Fatima C Pereira","doi":"10.20517/mrr.2025.73","DOIUrl":"10.20517/mrr.2025.73","url":null,"abstract":"<p><p><b>Aim:</b> The gut microbiota plays a key role in shaping individual responses to drugs, but current tools have limited potential to probe drug-microbe interactions within the complex, individualised gut environment. This study employed bioorthogonal labelling to track and identify gut microbial taxa and molecular mechanisms involved in the bioaccumulation of entacapone, a Parkinson's disease drug. <b>Methods:</b> We synthesised alkyne-tagged derivatives of entacapone and evaluated their suitability as molecular probes in <i>ex vivo</i> incubations with faecal communities or different <i>Escherichia coli</i> (<i>E. coli</i>) strains. Following incubation, tagged drugs were conjugated to a fluorescently labelled azide via click chemistry. Labelled cells were visualised, quantified, sorted via fluorescence-activated cell sorting (FACS), and identified via 16S ribosomal RNA (rRNA) gene amplicon sequencing. <b>Results:</b> Entacapone alkyne derivatives retained the biological activity and effects of the original drug on the microbiota, significantly reducing microbial loads and shifting community composition across the three donors tested. Conjugation of alkyne-entacapone with a labelled azide revealed that between 80% to 96% of all microbial cells in a donor's faecal sample accumulate entacapone. Nearly all taxa detected in incubations were recovered in labelled FACS fractions, confirming widespread uptake of the drug. Finally, we demonstrate that different <i>E. coli</i> strains exhibit varying levels of entacapone accumulation and identify a siderophore transporter that plays a role in this process. <b>Conclusion:</b> Our findings reveal that entacapone is widely bioaccumulated by the gut microbiota across three donors and identify a key molecular mediator of this accumulation. This study expands the toolkit for investigating drug-microbiome interactions and holds significant potential to advance our understanding of drug-microbiome dynamics and therapeutic outcomes.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"4 4","pages":"41"},"PeriodicalIF":3.8,"publicationDate":"2025-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12719382/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145822622","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}
引用次数: 0
Mechanistic roles and therapeutic potential of bacteriophages in inflammatory gastrointestinal diseases. 噬菌体在炎症性胃肠疾病中的机制作用和治疗潜力。
IF 3.8
Microbiome research reports Pub Date : 2025-11-12 eCollection Date: 2025-01-01 DOI: 10.20517/mrr.2025.62
Baiyun Ding, Mingze Fan, Yong-Peng Shi, Xingyao Chen, Yi Duan
{"title":"Mechanistic roles and therapeutic potential of bacteriophages in inflammatory gastrointestinal diseases.","authors":"Baiyun Ding, Mingze Fan, Yong-Peng Shi, Xingyao Chen, Yi Duan","doi":"10.20517/mrr.2025.62","DOIUrl":"10.20517/mrr.2025.62","url":null,"abstract":"<p><p>The gut virome, particularly its viral and phage components, is increasingly recognized as a key modulator of intestinal microbial dynamics in gastrointestinal inflammatory diseases. Beyond well-characterized bacterial dysbiosis, growing evidence suggests that virome alterations contribute to the development and progression of inflammatory bowel disease, metabolic dysfunction-associated steatohepatitis, alcoholic hepatitis, primary sclerosing cholangitis, primary biliary cholangitis, and pancreatitis. As the most abundant viruses in the gut, bacteriophages influence microbial ecosystem stability and host immune responses through lytic and lysogenic interactions with bacterial populations. Amid the growing burden of multidrug-resistant infections and heightened interest in microbiota-based interventions, phage therapy has re-emerged as a viable strategy in both preclinical and translational contexts. This review synthesizes recent insights into bacteriophage dynamics in the context of major gastrointestinal and hepatopancreatic inflammatory diseases, highlighting potential compositional shifts, proposed mechanisms of phage-microbe interactions, and supportive evidence from animal models and early clinical applications. We also discussed the critical challenges that had to be addressed to enable clinical translation, including host range restrictions, resistance and safety concerns, immunogenicity, and delivery limitations, while emphasizing emerging strategies such as phage engineering, encapsulation technologies, and standardized regulatory frameworks.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"4 4","pages":"40"},"PeriodicalIF":3.8,"publicationDate":"2025-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12702653/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145770430","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}
引用次数: 0
Gut bioengineered models to study host-microbiota-probiotics interactions. 研究宿主-微生物-益生菌相互作用的肠道生物工程模型。
IF 3.8
Microbiome research reports Pub Date : 2025-10-22 eCollection Date: 2025-01-01 DOI: 10.20517/mrr.2025.45
Elise Delannoy, Alexandre Grassart, Catherine Daniel
{"title":"Gut bioengineered models to study host-microbiota-probiotics interactions.","authors":"Elise Delannoy, Alexandre Grassart, Catherine Daniel","doi":"10.20517/mrr.2025.45","DOIUrl":"10.20517/mrr.2025.45","url":null,"abstract":"<p><p>The gastrointestinal tract is the major ecological niche in which gut microbes interact with epithelial and immune cells to maintain homeostasis in mammals. Moreover, probiotics modulate the gut microbiota and exert various health benefits after oral administration and persistence in the gut. Until now, animal models have been the gold standard for unravelling the mechanisms implicated in host-microbe interactions. However, their translational relevance to clinical trials and the associated ethical concerns underscore the need for alternative models. The emergence of microfluidic organ-on-chip technologies provides promising new alternative models to explore human host-microbe interactions while maintaining the tissue-level complexity and inter-individual variability. In this perspective, we discuss the potential of using mice, non-rodent models and gut-on-chip technologies to better characterize the interactions between the host, the gut microbiota, and orally administered probiotics, and to monitor microbial spatiotemporal dynamics at the tissue level.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"4 4","pages":"39"},"PeriodicalIF":3.8,"publicationDate":"2025-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12702652/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145770346","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}
引用次数: 0
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