npj Biofilms and Microbiomes最新文献

{"title":"Multi-omics approach identifies gut microbiota variations associated with depression.","authors":"Adrián Hernández-Cacho, Jesús F García-Gavilán, Alessandro Atzeni, Prokopis Konstanti, Clara Belzer, Jesús Vioque, Dolores Corella, Montserrat Fitó, Josep Vidal, Virginia Mela, Liming Liang, Laura Torres-Collado, Oscar Coltell, Nancy Babio, Clary Clish, Javier Hernando-Redondo, Miguel Á Martínez-González, Fenglei Wang, Isabel Moreno-Indias, Jiaqi Ni, Courtney Dennis, Miguel Ruiz-Canela, Francisco J Tinahones, Frank B Hu, Jordi Salas-Salvadó","doi":"10.1038/s41522-025-00707-9","DOIUrl":"https://doi.org/10.1038/s41522-025-00707-9","url":null,"abstract":"<p><p>The gut microbiota plays a potential role in the pathophysiology of depression through the gut-brain axis. This cross-sectional study in 400 participants from the PREDIMED-Plus study investigates the interplay between gut microbiota and depression using a multi-omics approach. Depression was defined as antidepressant use or high Beck Depression Inventory-II scores. Gut microbiota was characterized by 16S rRNA sequencing, and faecal metabolites were analysed via liquid chromatography-tandem mass spectrometry. Participants with depression exhibited significant differences in gut microbial composition and metabolic profiles. Differentially abundant taxa included Acidaminococcus, Christensenellaceae R-7 group, and Megasphaera, among others. Metabolomic analysis revealed 15 significantly altered metabolites, primarily lipids, organic acids, and benzenoids, some of which correlated with gut microbial features. This study highlights the interplay between the gut microbiota and depression, paving the way for future research to determine whether gut microbiota influences depression pathophysiology or reflects changes associated with depression.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"68"},"PeriodicalIF":7.8,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12038053/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143983687","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}

{"title":"Effect of initiation of antiretroviral drugs for HIV prevention or treatment on the vaginal microbiome of pregnant women in Malawi.","authors":"Friday Saidi, Lauren A Graybill, Jennifer H Tang, Twambilile Phanga, Beteniko Milala, Gabriel Banda, Manley Kamija, Margaret Kasaro, Wilbroad Mutale, Joan Price, Lameck Chinula, Jeffrey Stringer, Mina C Hosseinipour, Benjamin H Chi, Jacques Ravel, Johanna B Holm","doi":"10.1038/s41522-025-00697-8","DOIUrl":"https://doi.org/10.1038/s41522-025-00697-8","url":null,"abstract":"<p><p>Lack of Lactobacillus and/or dysbiosis is linked to spontaneous preterm birth (sPTB). The impact of antiretrovirals (ARVs) for HIV treatment or prevention on the vaginal microbiome during pregnancy remains unclear. We examined vaginal microbiome changes in pregnant women in Lilongwe, Malawi. Women living with HIV (WLHIV) initiated antiretroviral therapy (ART), while HIV-negative women began oral pre-exposure prophylaxis (PrEP). Of 255 participants (191 HIV-negative, 64 WLHIV) who provided baseline vaginal swabs, 181 provided follow-up swabs one month after ARV initiation. At enrollment, WLHIV had higher Shannon diversity and were more likely to have CST IV-B than CST I or III. After ARV initiation, α-diversity decreased in WLHIV but increased in HIV-negative women. Women initiating PrEP had a lower risk of sPTB compared to WLHIV initiating ART, but transitioning to CST IV during pregnancy increased the odds of sPTB. Larger studies are needed to explore ARV impact on pregnancy outcomes.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"67"},"PeriodicalIF":7.8,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12033299/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143983685","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}

{"title":"Toxic cultures: e-cigarettes and the oral microbial exposome.","authors":"Michelle Lee-Scott Beverly, Prem Prashant Chaudhary, Shareef Majid Dabdoub, Shinae Kim, Emmanouli Chatzakis, Kathryn Williamson, Sukirth Murthy Ganesan, Manoj Yadav, Grace Ratley, Brandon N D'Souza, Ian A Myles, Purnima S Kumar","doi":"10.1038/s41522-025-00709-7","DOIUrl":"https://doi.org/10.1038/s41522-025-00709-7","url":null,"abstract":"<p><p>We tested the hypothesis that e-cigarette aerosol is metabolized by the indigenous oral microbiome, leading to structural and functional alterations. We combined untargeted metabolomics of in vitro commensal-rich and pathogen-rich biofilms with metatranscriptomics and fluorescent microscopy and verified the results in human samples. Spectral deconvolution of 4215 peaks identified 969 exposomal and endogenous metabolites that mapped to 23 metabolic pathways. The metabolites clustered by both aerosol characteristics and biofilm composition; and several were verified in human saliva of vapers. E-cigarette exposure upregulated xenobiotic degradation, capsule, peptidoglycan biosynthesis, organic carbon-compound metabolism, antimicrobial resistance, and secretion systems. E-cigarette exposure also altered biofilm architecture characterized by low surface-area to biovolume ratio, high biomass, and diffusion distance. In conclusion, our data suggest that bacterial metabolism of e-cigarette aerosol triggers a quorum-sensing-regulated stress response which mediates the formation of dense, exopolysaccharide-rich biofilms in health-compatible communities and antibiotic resistance and virulence amplification in disease-associated communities.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"66"},"PeriodicalIF":7.8,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12032151/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144005134","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}

{"title":"Novel two-stage expansion of Streptococcus mutans biofilm supports EPS-targeted prevention strategies for early childhood caries.","authors":"Jeongmi Moon, Kyoungjin Seo, Jae-Sung Kwon","doi":"10.1038/s41522-025-00699-6","DOIUrl":"https://doi.org/10.1038/s41522-025-00699-6","url":null,"abstract":"<p><p>Early childhood caries (ECC) affects nearly half of preschool children worldwide and characterized by rapid progression across multiple teeth. While Streptococcus mutans (S. mutans) is a keystone species in dental caries, its process for rapid biofilm expansion remains unclear. Using an air-solid interface model simulating the oral environment, we uncovered a novel expansion for S. mutans biofilms. Our findings reveal that S. mutans employs a distinct two-step expansion strategy. Through osmotic pressure, extracellular polymeric substances (EPS) spread and transport bacterial clusters to new sites. Subsequently, the hydroxyapatite surface enables new colony formation. Hydroxyapatite's acid-neutralization properties appear critical for bacterial growth and colonization. Despite successful EPS spreading, environments without hydroxyapatite failed to support new colony formation. These results reveal the unique pattern of rapid ECC progression in sugar-rich environments and establish EPS as a promising therapeutic target, advancing understanding of cariogenic biofilm behavior and preventative strategies for ECC prevention.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"65"},"PeriodicalIF":7.8,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12022157/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144015275","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}

{"title":"The dynamics of microbiome and virome in migratory birds of southwest China.","authors":"Qingqing Luo, Hongyan Gao, Yujia Xiang, Jian Li, Lin Dong, Xingran Wang, Fangqing Liu, Yuhong Guo, Chao Shen, Qiang Ding, Chengfeng Qin, Guanxiang Liang, Longying Wen","doi":"10.1038/s41522-025-00703-z","DOIUrl":"https://doi.org/10.1038/s41522-025-00703-z","url":null,"abstract":"<p><p>Migratory birds carry pathogens, posing a significant threat to environmental and human health. We documented the metatranscriptome and RNA virome of 896 stool samples from migratory birds and environmental samples over four consecutive years in southwest China. Our analysis identified Catellicoccus marimammalium as the predominant bacterium in the gut of black-headed gulls, with an average relative abundance of 79.3%. Strain-level analysis of C. marimammalium revealed a dominant population with some longitudinal diversity over the four years. Additionally, the gut of black-headed gulls was found to harbor numerous viruses, including a novel hepatovirus. Lysates of cells of C. marimammalium but not other bacteria derived from black-headed gulls could inhibit the replication of human hepatovirus, suggesting a potential regulatory role for gut commensal bacteria in modulating viral carriage. These findings enhance our understanding of the microbiome and RNA virome diversity in migratory birds and provide insights into the modulation of asymptomatic infections.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"64"},"PeriodicalIF":7.8,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12018928/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144020723","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}

{"title":"OSaMPle workflow for salivary metaproteomics analysis reveals dysbiosis in inflammatory bowel disease patients.","authors":"Jinhui Yuan, Boyan Sun, Murong Li, Congyi Yang, Lingqiang Zhang, Ning Chen, Feng Chen, Leyuan Li","doi":"10.1038/s41522-025-00692-z","DOIUrl":"https://doi.org/10.1038/s41522-025-00692-z","url":null,"abstract":"<p><p>The human oral microbiome has been associated with multiple inflammatory conditions including inflammatory bowel disease (IBD). Identifying functional changes in oral microbiome by metaproteomics helps understanding the factors driving dysbiosis related to intestinal diseases. However, enriching bacterial cells from oral samples (such as saliva and mouth rinse) rich in host proteins is challenging. Here, we present an Optimized Salivary MetaProteomic sample analysis workflow (OSaMPle) to enrich salivary bacteria and reduce host-derived interferences for in-depth analysis of the oral metaproteome. Compared to a conventional approach, OSaMPle improved the identification of bacterial peptides and proteins by 3.2 folds and 1.7 folds, respectively. Furthermore, applying OSaMPle to analyze mouth rinse samples from IBD patients revealed significant alterations in bacterial protein expressions under disease conditions. Specifically, proteins involved in the fatty acid elongation pathway in Peptostreptococcus were significantly less abundant in IBD patients, whereas proteins associated with the TCA cycle in Neisseria were significantly more abundant. The OSaMPle workflow is capable of processing small-volume oral samples and adaptable to high-throughput automation. It holds promise as a strategy for investigating the functional responses of oral microbiomes under disease conditions and identifying disease-associated microbes with their proteins, providing critical insights for detecting disease-related biomarkers within the oral microbiome.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"63"},"PeriodicalIF":7.8,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12018957/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144009382","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}

{"title":"Multi-omics profiling of dairy cattle oxidative stress identifies hindgut-derived Phascolarctobacterium succinatutens exhibiting antioxidant activity.","authors":"Duo Gao, Yimin Zhuang, Shuai Liu, Boyan Ma, Yiming Xu, Hongxing Zhang, Yiliyaer Nuermaimaiti, Tianyu Chen, Guobin Hou, Wenli Guo, Jingtao You, Zhiyu Huang, Jianxin Xiao, Wei Wang, Mengmeng Li, Shengli Li, Zhijun Cao","doi":"10.1038/s41522-025-00698-7","DOIUrl":"https://doi.org/10.1038/s41522-025-00698-7","url":null,"abstract":"<p><p>An imbalance between oxidative and antioxidant processes in the host can lead to excessive oxidation, a condition known as oxidative stress (OS). Although changes in the hindgut microbiota have been frequently linked to OS, the specific microbial and metabolic underpinnings of this association remain unclear. In this study, we enrolled 81 postpartum Holstein cows and stratified them into high oxidative stress (HOS, n = 9) and low oxidative stress (LOS, n = 9) groups based on the oxidative stress index (OSi). Using a multi-omics approach, we performed 16S rRNA gene sequencing to evaluate microbial diversity, conducted metagenomic analysis to identify functional bacteria, and utilized untargeted metabolomics to profile serum metabolites. Our analyses revealed elevated levels of kynurenine, formyl-5-hydroxykynurenamine, and 5-hydroxyindole-3-acetic acid in LOS dairy cows. Additionally, the LOS cows had a higher abundance of short-chain fatty acids (SCFAs)-producing bacteria, including Bacteroidetes bacterium, Paludibacter propionicigenes, and Phascolarctobacterium succinatutens (P. succinatutens), which were negatively correlated with OSi. To explore the potential role of these bacteria in mitigating OS, we administered P. succinatutens (10⁸ cfu/day for 14 days) to C57BL/6 J mice (n = 10). Oral administration of P. succinatutens significantly increased serum total antioxidant capacity, decreased total oxidants, and reduced OSi in mice. Moreover, this treatment promoted activation of the Nrf2-Keap1 antioxidant pathway, significantly enhancing the enzymatic activities of GSH-Px and SOD, as well as the concentrations of acetate and propionate in the colon. In conclusion, our findings suggest that systemic tryptophan metabolism and disordered SCFAs production are concurrent factors influenced by hindgut microbiota and associated with OS development. Modulating the hindgut microbiota, particularly by introducing specific SCFAs-producing bacteria, could be a promising strategy for combating OS.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"61"},"PeriodicalIF":7.8,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12015594/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143974826","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}

{"title":"Unraveling the pathogenesis and prevention strategies of acute high-altitude illness through gut microecology.","authors":"Ping Qi, Xiansen Jiang, Xiaojuan Wang, Liang Sheng, Jiawen Liang, Lei Zhang","doi":"10.1038/s41522-025-00701-1","DOIUrl":"https://doi.org/10.1038/s41522-025-00701-1","url":null,"abstract":"<p><p>High-altitude environments, characterized by hypobaric and hypoxic conditions, induce acute hypoxia, resulting in decreased blood oxygen saturation. This hypoxic stress perturbs gut microecological homeostasis, significantly contributing to the pathogenesis of acute mountain sickness. Consequently, elucidating the mechanisms by which high altitude affects gut homeostasis is crucial for developing effective interventions.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"62"},"PeriodicalIF":7.8,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12015534/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143995826","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}

{"title":"Multiple stressors affect function rather than taxonomic structure of freshwater microbial communities.","authors":"Rose Fuggle, Miguel G Matias, Mariana Mayer-Pinto, Ezequiel M Marzinelli","doi":"10.1038/s41522-025-00700-2","DOIUrl":"https://doi.org/10.1038/s41522-025-00700-2","url":null,"abstract":"<p><p>Microbial community responses to environmental stressors are often characterised by assessing changes in taxonomic structure, but such changes, or lack thereof, may not reflect functional changes that are critical to ecosystem processes. We investigated the individual and combined effects of nutrient enrichment ( + 10 mg/L N, + 1 mg/L P) and salinisation ( + 15 g/L NaCl)-key stressors in freshwater systems-on the taxonomic structure and metabolic function of benthic microbial communities using 1000 L open freshwater ponds established >10 years ago in the field. Combined stressors drove strong decreases in maximum and mean total carbon metabolic rates and shifted carbon metabolic profiles compared to either stressor individually and compared to ambient conditions. These metabolic functional changes did not recover through time and occurred without significant alterations in bacterial community taxonomic structure. These results imply that critical functions, including organic carbon release, are likely to be impaired under multiple stressors, even when taxonomic structure remains stable.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"60"},"PeriodicalIF":7.8,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12008304/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144030350","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}

{"title":"Statin therapy associated Lactobacillus intestinalis attenuates pancreatic fibrosis through remodeling intestinal homeostasis.","authors":"Yuhang Sui, Tao Zhang, Suwen Ou, Guanqun Li, Liwei Liu, Tianqi Lu, Can Zhang, Yukai Cao, Rui Bai, Haoxin Zhou, Xinbo Zhao, Yue Yuan, Gang Wang, Hua Chen, Rui Kong, Bei Sun, Le Li","doi":"10.1038/s41522-025-00695-w","DOIUrl":"https://doi.org/10.1038/s41522-025-00695-w","url":null,"abstract":"<p><p>Chronic pancreatitis (CP) is characterized by irreversible fibrotic destruction and impaired pancreatic function. CP disrupts lipid metabolism and causes the imbalance of gut microbiota which in turn exacerbates pancreatic fibrosis. Statins alter gut microbiota and exert anti-inflammatory effects, but its role in CP has not been fully elucidated. Here, we found that statins-associated higher abundance of Lactobacillus intestinalis (L.intestinalis) maintained gut homeostasis that restrained bacteria translocation from gut to the pancreas, which eventually aggravated pancreatic fibrosis through inhibiting CD8⁺T cells-dependent immunity. Fecal microbiota transplantation (FMT) or L.intestinalis administration inhibited the infiltration of CD8⁺T cells and macrophages that delayed CP progression. L.intestinalis restrained the recruitment of M1 macrophages and limited the release of Ccl2/7 in the colon, which prevented epithelial damage and epithelial barrier dysfunction through blocking Ccl2/7-Ccr1 signaling. Our findings elucidate that the utilization of statin therapy or supplementation of L.intestinalis can be potential approach for the therapies of CP.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"59"},"PeriodicalIF":7.8,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12000565/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144009384","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}