npj Biofilms and Microbiomes最新文献

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Bifidobacterium animalis Probio-M8 improves sarcopenia physical performance by mitigating creatine restrictions imposed by microbial metabolites. 动物双歧杆菌Probio-M8通过减轻微生物代谢物施加的肌酸限制来改善肌肉减少症的物理性能。
IF 7.8 1区 生物学
npj Biofilms and Microbiomes Pub Date : 2024-12-05 DOI: 10.1038/s41522-024-00618-1
Zeng Zhang, Yajing Fang, Yangli He, Mohamed A Farag, Min Zeng, Yukai Sun, Siqi Peng, Shuaiming Jiang, Xian Zhang, Kaining Chen, Meng Xu, Zhe Han, Jiachao Zhang
{"title":"Bifidobacterium animalis Probio-M8 improves sarcopenia physical performance by mitigating creatine restrictions imposed by microbial metabolites.","authors":"Zeng Zhang, Yajing Fang, Yangli He, Mohamed A Farag, Min Zeng, Yukai Sun, Siqi Peng, Shuaiming Jiang, Xian Zhang, Kaining Chen, Meng Xu, Zhe Han, Jiachao Zhang","doi":"10.1038/s41522-024-00618-1","DOIUrl":"10.1038/s41522-024-00618-1","url":null,"abstract":"<p><p>Sarcopenia is a major health challenge due to an aging population. Probiotics may improve muscle function through gut-muscle axis, but their efficacy and mechanisms in treating sarcopenia remain unclear. This study investigated the impact of Bifidobacterium animalis subsp. lactis Probio-M8 (Probio-M8) on old mice and sarcopenia patients. We analyzed 43 subjects, including gut microbiome, fecal metabolome, and serum metabolome, using a multi-omics approach to assess whether Probio-M8 can improve sarcopenia by modulating gut microbial metabolites. Probio-M8 significantly improved muscle function in aged mice and enhanced physical performance in sarcopenia patients. It reduced pathogenic gut species and increased beneficial metabolites such as indole-3-lactic acid, acetoacetic acid, and creatine. Mediating effect analyses revealed that Probio-M8 effectively reduced n-dodecanoyl-L-homoserine lactone level in gut concurrent with increased creatine circulation, to significantly enhance host physical properties. These findings provide new insights into probiotics as a potential treatment for sarcopenia by modulating gut microbiota metabolism.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"144"},"PeriodicalIF":7.8,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11618631/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142780724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Nutrient availability influences E. coli biofilm properties and the structure of purified curli amyloid fibers. 营养物质的有效性影响大肠杆菌生物膜的特性和纯化的卷曲淀粉样纤维的结构。
IF 7.8 1区 生物学
npj Biofilms and Microbiomes Pub Date : 2024-12-04 DOI: 10.1038/s41522-024-00619-0
Macarena Siri, Mónica Vázquez-Dávila, Carolina Sotelo Guzman, Cécile M Bidan
{"title":"Nutrient availability influences E. coli biofilm properties and the structure of purified curli amyloid fibers.","authors":"Macarena Siri, Mónica Vázquez-Dávila, Carolina Sotelo Guzman, Cécile M Bidan","doi":"10.1038/s41522-024-00619-0","DOIUrl":"10.1038/s41522-024-00619-0","url":null,"abstract":"<p><p>Bacterial biofilms are highly adaptable and resilient to challenges. Nutrient availability can induce changes in biofilm growth, architecture and mechanical properties. Their extracellular matrix plays an important role in achieving biofilm stability under different environmental conditions. Curli amyloid fibers are critical for the architecture and stiffness of E. coli biofilms, but how this major matrix component adapts to different environmental cues remains unclear. We investigated, for the first time, the effect of nutrient availability both on biofilm material properties and on the structure and properties of curli amyloid fibers extracted from similar biofilms. Our results show that biofilms grown on low nutrient substrates are stiffer, contain more curli fibers, and these fibers present higher β-sheet content and chemical stability. Our multiscale study sheds new light on the relationship between bacterial matrix molecular structure and biofilm macroscopic properties. This knowledge will benefit the development of both anti-biofilm strategies and biofilm-based materials.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"143"},"PeriodicalIF":7.8,"publicationDate":"2024-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11618413/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142780725","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Gingival spatial analysis reveals geographic immunological variation in a microbiota-dependent and -independent manner. 牙龈空间分析揭示了地理上的免疫变异是一种依赖微生物群和不依赖微生物群的方式。
IF 7.8 1区 生物学
npj Biofilms and Microbiomes Pub Date : 2024-12-03 DOI: 10.1038/s41522-024-00625-2
Yasmin Jaber, Avital Sarusi-Portuguez, Yasmin Netanely, Reem Naamneh, Shahd Yacoub, Or Saar, Nadeem Darawshi, Luba Eli-Berchoer, Hagit Shapiro, Eran Elinav, Asaf Wilensky, Avi-Hai Hovav
{"title":"Gingival spatial analysis reveals geographic immunological variation in a microbiota-dependent and -independent manner.","authors":"Yasmin Jaber, Avital Sarusi-Portuguez, Yasmin Netanely, Reem Naamneh, Shahd Yacoub, Or Saar, Nadeem Darawshi, Luba Eli-Berchoer, Hagit Shapiro, Eran Elinav, Asaf Wilensky, Avi-Hai Hovav","doi":"10.1038/s41522-024-00625-2","DOIUrl":"10.1038/s41522-024-00625-2","url":null,"abstract":"<p><p>In mucosal barriers, tissue cells and leukocytes collaborate to form specialized niches that support host-microbiome symbiosis. Understanding the spatial organization of these barriers is crucial for elucidating the mechanisms underlying health and disease. The gingiva, a unique mucosal barrier with significant health implications, exhibits intricate tissue architecture and likely contains specialized immunological regions. Through spatial transcriptomic analysis, this study reveals distinct immunological characteristics between the buccal and palate regions of the murine gingiva, impacting natural alveolar bone loss. The microbiota primarily affects gingival immunity in the buccal region. Additionally, a significant influence of the microbiota on the junctional epithelium facing the oral biofilm offers new insights into neutrophil recruitment. The microbiota also regulates the proliferation and barrier-sealing function of the gingival epithelium. This underscores the presence of immunological niches in the gingiva, with the microbiota differentially influencing them, highlighting the high complexity of this oral mucosal barrier.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"142"},"PeriodicalIF":7.8,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11615284/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142770807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Adaption mechanism and ecological role of CPR bacteria in brackish-saline groundwater. 微咸地下水中CPR细菌的适应机制及生态作用。
IF 7.8 1区 生物学
npj Biofilms and Microbiomes Pub Date : 2024-11-30 DOI: 10.1038/s41522-024-00615-4
Jiawen Wang, Haohui Zhong, Qian Chen, Jinren Ni
{"title":"Adaption mechanism and ecological role of CPR bacteria in brackish-saline groundwater.","authors":"Jiawen Wang, Haohui Zhong, Qian Chen, Jinren Ni","doi":"10.1038/s41522-024-00615-4","DOIUrl":"https://doi.org/10.1038/s41522-024-00615-4","url":null,"abstract":"<p><p>Candidate phyla radiation (CPR) constitutes a substantial fraction of bacterial diversity, yet their survival strategies and biogeochemical roles in brackish-saline groundwater remain unknown. By reconstructing 399 CPR metagenome-assembled genomes (MAGs) and 2007 non-CPR MAGs, we found that CPR, affiliated with 44 previously proposed phyla and 8 putative novel phyla, played crucial roles in maintaining the microbial stability and complexity in groundwater. Metabolic reconstructions revealed that CPR participated in diverse processes, including carbon, nitrogen, and sulfur cycles. Adaption of CPR to high-salinity conditions could be attributed to abundant genes associated with heat shock proteins, osmoprotectants, and sulfur reduction, as well as their cooperation with Co-CPR (non-CPR bacteria co-occurred with CPR) for metabolic support and resource exchange. Our study enhanced the understanding of CPR biodiversity in high-salinity groundwater, highlighting the collaborative roles of self-adaptive CPR bacteria and their reciprocal partners in coping with salinity stress, maintaining ecological stability, and mediating biogeochemical cycling.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"141"},"PeriodicalIF":7.8,"publicationDate":"2024-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11608272/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142770762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Microbial melatonin metabolism in the human intestine as a therapeutic target for dysbiosis and rhythm disorders. 将人体肠道中的微生物褪黑激素代谢作为菌群失调和节律紊乱的治疗靶点。
IF 7.8 1区 生物学
npj Biofilms and Microbiomes Pub Date : 2024-11-27 DOI: 10.1038/s41522-024-00605-6
Petra Zimmermann, Salome Kurth, Benoit Pugin, Nicholas A Bokulich
{"title":"Microbial melatonin metabolism in the human intestine as a therapeutic target for dysbiosis and rhythm disorders.","authors":"Petra Zimmermann, Salome Kurth, Benoit Pugin, Nicholas A Bokulich","doi":"10.1038/s41522-024-00605-6","DOIUrl":"10.1038/s41522-024-00605-6","url":null,"abstract":"<p><p>Melatonin (MT) (N-acetyl-5-methoxytryptamine) is an indoleamine recognized primarily for its crucial role in regulating sleep through circadian rhythm modulation in humans and animals. Beyond its association with the pineal gland, it is synthesized in various tissues, functioning as a hormone, tissue factor, autocoid, paracoid, and antioxidant, impacting multiple organ systems, including the gut-brain axis. However, the mechanisms of extra-pineal MT production and its role in microbiota-host interactions remain less understood. This review provides a comprehensive overview of MT, including its production, actions sites, metabolic pathways, and implications for human health. The gastrointestinal tract is highlighted as an additional source of MT, with an examination of its effects on the intestinal microbiota. This review explores whether the microbiota contributes to MT in the intestine, its relationship to food intake, and the implications for human health. Due to its impacts on the intestinal microbiota, MT may be a valuable therapeutic agent for various dysbiosis-associated conditions. Moreover, due to its influence on intestinal MT levels, the microbiota may be a possible therapeutic target for treating health disorders related to circadian rhythm dysregulation.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"139"},"PeriodicalIF":7.8,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11603051/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142740101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Mechanisms of S. agalactiae promoting G. vaginalis biofilm formation leading to recurrence of BV. S. agalactiae 促进 G. vaginalis 生物膜形成导致 BV 复发的机制。
IF 7.8 1区 生物学
npj Biofilms and Microbiomes Pub Date : 2024-11-27 DOI: 10.1038/s41522-024-00601-w
Meng Li, Zhen Zeng, Xiaoqian Wang, Ying Liu, Hongbo Wei, Jun Liu, Simin Zhu, Qingyun Jiang, Ke Zhang, Yifan Wu, Shuai Liu, Juhyun Kim, Qinping Liao, Lei Zhang
{"title":"Mechanisms of S. agalactiae promoting G. vaginalis biofilm formation leading to recurrence of BV.","authors":"Meng Li, Zhen Zeng, Xiaoqian Wang, Ying Liu, Hongbo Wei, Jun Liu, Simin Zhu, Qingyun Jiang, Ke Zhang, Yifan Wu, Shuai Liu, Juhyun Kim, Qinping Liao, Lei Zhang","doi":"10.1038/s41522-024-00601-w","DOIUrl":"10.1038/s41522-024-00601-w","url":null,"abstract":"<p><p>Previous research has established that the formation of Gardnerella vaginalis (GV) biofilm is one of the primary reasons for bacterial vaginosis (BV) recurrence. This study was the first to explore the impact of Streptococcus agalactiae (group B Streptococcus, GBS) on GV biofilm in a co-culture scenario. The results revealed that GBS could significantly increased the GV biomass in 48-hours dual-species biofilms. The luxS gene of GBS was significantly higher in dual-species biofilm, while knockdown of the luxS gene resulted in a significant decrease in mono- and dual-species biofilms. Meanwhile, in vitro addition of AI-2 (product of luxS gene) substantially increased biofilm biomass. Furthermore, we found that the expression of two genes related to biofilm formation was notably elevated in GV after receiving AI-2 signals. Collectively, these findings suggest that GBS enhances GV biofilm formation via luxS/AI-2 in an in vitro co-culture model, which in turn may promotes recurrence of BV.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"138"},"PeriodicalIF":7.8,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11603151/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142740100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","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 sex-dependent salivary bacterium influences oral mucositis severity after allogeneic hematopoietic cell transplantation. 唾液细菌的性别依赖性影响异体造血细胞移植后口腔黏膜炎的严重程度。
IF 7.8 1区 生物学
npj Biofilms and Microbiomes Pub Date : 2024-11-27 DOI: 10.1038/s41522-024-00611-8
Hakan Gem, Maryam Ebadi, Gale Sebastian, Rania Abasaeed, Michele Lloid, Samuel S Minot, David R Dean, Armin Rashidi
{"title":"A sex-dependent salivary bacterium influences oral mucositis severity after allogeneic hematopoietic cell transplantation.","authors":"Hakan Gem, Maryam Ebadi, Gale Sebastian, Rania Abasaeed, Michele Lloid, Samuel S Minot, David R Dean, Armin Rashidi","doi":"10.1038/s41522-024-00611-8","DOIUrl":"10.1038/s41522-024-00611-8","url":null,"abstract":"<p><p>The success of allogeneic hematopoietic cell transplantation (alloHCT) in curing hematologic disorders is limited by its short- and long-term toxicities. One such toxicity is oral mucositis (OM), causing pain, speech/swallowing difficulty, and prolonged hospitalization. Although conditioning chemoradiotherapy is the direct cause of OM, potential host-intrinsic mediators of mucosal injury remain elusive. We hypothesized that the oral microbiota may influence OM severity. We used a validated comprehensive scoring system based on specialized Oral Medicine examinations to longitudinally quantify OM severity in alloHCT recipients. High-throughput multi-site profiling of the oral microbiota was performed in parallel. We identify a sex-dependent commensal bacterium, Oribacterium asaccharolyticum, whose presence in saliva before transplantation is associated with more severe OM 14 days after transplantation. The sex predilection of this species correlated with higher uric acid levels in men. Our findings represent the first sex-dependent microbiota-mediated pathway in OM pathogenesis and introduce novel targets for preventative interventions.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"140"},"PeriodicalIF":7.8,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11603167/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142740099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Unlocking gut-liver-brain axis communication metabolites: energy metabolism, immunity and barriers. 解开肠肝脑轴沟通代谢物:能量代谢、免疫和障碍。
IF 7.8 1区 生物学
npj Biofilms and Microbiomes Pub Date : 2024-11-25 DOI: 10.1038/s41522-024-00610-9
Xiaoge Sun, Manish Shukla, Wei Wang, Shengli Li
{"title":"Unlocking gut-liver-brain axis communication metabolites: energy metabolism, immunity and barriers.","authors":"Xiaoge Sun, Manish Shukla, Wei Wang, Shengli Li","doi":"10.1038/s41522-024-00610-9","DOIUrl":"10.1038/s41522-024-00610-9","url":null,"abstract":"<p><p>The interaction between the gut-microbiota-derived metabolites and brain has long been recognized in both health and disease. The liver, as the primary metabolic organ for nutrients in animals or humans, plays an indispensable role in signal transduction. Therefore, in recent years, Researcher have proposed the Gut-Liver-Brain Axis (GLBA) as a supplement to the Gut-Brain Axis. The GLBA plays a crucial role in numerous physiological and pathological mechanisms through a complex interplay of signaling pathways. However, gaps remain in our knowledge regarding the developmental and functional influences of the GLBA communication pathway. The gut microbial metabolites serve as communication agents between these three distant organs, functioning prominently within the GLBA. In this review, we provide a comprehensive overview of the current understanding of the GLBA, focusing on signaling molecules role in animal and human health and disease. In this review paper elucidate its mechanisms of communication, explore its implications for immune, and energy metabolism in animal and human, and highlight future research directions. Understanding the intricate communication pathways of the GLBA holds promise for creating innovative treatment approaches for a wide range of immune and metabolic conditions.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"136"},"PeriodicalIF":7.8,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11589602/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142716456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Viruses in the female lower reproductive tract: a systematic descriptive review of metagenomic investigations. 女性下生殖道中的病毒:元基因组研究的系统描述性回顾。
IF 7.8 1区 生物学
npj Biofilms and Microbiomes Pub Date : 2024-11-25 DOI: 10.1038/s41522-024-00613-6
Layla Honorato, Heuder Gustavo Oliveira Paião, Antonio Charlys da Costa, Tânia Regina Tozetto-Mendoza, Maria Cássia Mendes-Correa, Steven S Witkin
{"title":"Viruses in the female lower reproductive tract: a systematic descriptive review of metagenomic investigations.","authors":"Layla Honorato, Heuder Gustavo Oliveira Paião, Antonio Charlys da Costa, Tânia Regina Tozetto-Mendoza, Maria Cássia Mendes-Correa, Steven S Witkin","doi":"10.1038/s41522-024-00613-6","DOIUrl":"10.1038/s41522-024-00613-6","url":null,"abstract":"<p><p>The lower female reproductive tract (FRT) hosts a complex microbial environment, including eukaryotic and prokaryotic viruses (the virome), whose roles in health and disease are not fully understood. This review consolidates findings on FRT virome composition, revealing the presence of various viral families and noting significant gaps in knowledge. Understanding interactions between the virome, microbiome, and immune system will provide novel insights for preventing and managing lower genital tract disorders.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"137"},"PeriodicalIF":7.8,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11589587/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142716462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
NMFGOT: a multi-view learning framework for the microbiome and metabolome integrative analysis with optimal transport plan. NMFGOT:用于微生物组和代谢组综合分析的多视角学习框架与最佳运输计划。
IF 7.8 1区 生物学
npj Biofilms and Microbiomes Pub Date : 2024-11-24 DOI: 10.1038/s41522-024-00612-7
Yuanyuan Ma, Lifang Liu
{"title":"NMFGOT: a multi-view learning framework for the microbiome and metabolome integrative analysis with optimal transport plan.","authors":"Yuanyuan Ma, Lifang Liu","doi":"10.1038/s41522-024-00612-7","DOIUrl":"10.1038/s41522-024-00612-7","url":null,"abstract":"<p><p>The rapid development of high-throughput sequencing techniques provides an unprecedented opportunity to generate biological insights into microbiome-related diseases. However, the relationships among microbes, metabolites and human microenvironment are extremely complex, making data analysis challenging. Here, we present NMFGOT, which is a versatile toolkit for the integrative analysis of microbiome and metabolome data from the same samples. NMFGOT is an unsupervised learning framework based on nonnegative matrix factorization with graph regularized optimal transport, where it utilizes the optimal transport plan to measure the probability distance between microbiome samples, which better dealt with the nonlinear high-order interactions among microbial taxa and metabolites. Moreover, it also includes a spatial regularization term to preserve the spatial consistency of samples in the embedding space across different data modalities. We implemented NMFGOT in several multi-omics microbiome datasets from multiple cohorts. The experimental results showed that NMFGOT consistently performed well compared with several recently published multi-omics integrating methods. Moreover, NMFGOT also facilitates downstream biological analysis, including pathway enrichment analysis and disease-specific metabolite-microbe association analysis. Using NMFGOT, we identified the significantly and stable metabolite-microbe associations in GC and ESRD diseases, which improves our understanding for the mechanisms of human complex diseases.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"135"},"PeriodicalIF":7.8,"publicationDate":"2024-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11586431/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142710807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","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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