npj Biofilms and Microbiomes最新文献

{"title":"Comparative study of gut microbiota reveals the adaptive strategies of gibbons living in suboptimal habitats.","authors":"Li-Ying Lan, Tai-Cong Liu, Shao-Ming Gao, Qi Li, Li Yang, Han-Lan Fei, Xu-Kai Zhong, Yu-Xin Wang, Chang-Yue Zhu, Christoph Abel, Peter M Kappeler, Li-Nan Huang, Peng-Fei Fan","doi":"10.1038/s41522-025-00653-6","DOIUrl":"10.1038/s41522-025-00653-6","url":null,"abstract":"<p><p>Wild animals face numerous challenges in less ideal habitats, including the lack of food as well as changes in diet. Understanding how the gut microbiomes of wild animals adapt to changes in food resources within suboptimal habitats is critical for their survival. Therefore, we conducted a longitudinal sampling of three gibbon species living in high-quality (Nomascus hainanus) and suboptimal (Nomascus concolor and Hoolock tianxing) habitats to address the dynamics of gut microbiome assembly over one year. The three gibbon species exhibited significantly different gut microbial diversity and composition. N. hainanus showed the lowest alpha diversity and highest nestedness, suggesting a more specialized and potentially stable microbial community in terms of composition, while H. tianxing displayed high species turnover and low nestedness, reflecting a more dynamic microbial ecosystem, which may indicate greater sensitivity to environmental changes or a flexible response to habitat variability. The gut microbial community of N. concolor was influenced by homogeneous selection in the deterministic process, primarily driven by Prevotellaceae. In contrast, the gut microbial communities of H. tianxing and N. hainanus were influenced by dispersal limitation in the stochastic process, driven by Acholeplasmataceae and Fibrobacterota, respectively. Further, the microbial response patterns to leaf feeding in N. hainanus differed from those of the other two gibbon species. In conclusion, this first cross-species comparative study provides initial insights into the different ecological adaptive strategies of gut microbiomes from a point of community assembly, which could contribute to the long-term conservation of wild primates. In this study, we conducted longitudinal sampling of three gibbon species living in high-quality (Nomascus hainanus) and suboptimal (Nomascus concolor and Hoolock tianxing) habitats to address the dynamics of gut microbiome (composition, alpha diversity, beta diversity and assembly process) over one year.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"29"},"PeriodicalIF":7.8,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11828964/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143425874","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":"Assembly, network and functional compensation of specialists and generalists in poplar rhizosphere under salt stress.","authors":"Yao Du, Lei Zhang, Yan Yang, Kexin Cheng, Kaihang Li, Yingwen Zhou, Lu Li, Yi Jin, Xiaoqing He","doi":"10.1038/s41522-025-00662-5","DOIUrl":"10.1038/s41522-025-00662-5","url":null,"abstract":"<p><p>Salinity is a major challenge for plant growth, but Populus euphratica, a species native to desert regions, has a remarkable ability to tolerate salt stress. This study aimed to explore how salinity affects the rhizosphere microbiome of P. euphratica, focusing on diversity patterns, assembly mechanisms, network characterization, and the functional roles of specialists and generalists under salt stress conditions. The findings revealed that increased salinity enhances the complexity of the rhizosphere microbial network and the diversity of bacterial specialists. Specialists demonstrated a wider range of environmental adaptation and played a pivotal role in species interactions within the microbial network. Notably, salinity stress altered the structure and assembly of plant rhizosphere specialists, facilitating functional compensation and potentially augmenting the health of P. euphratica. This research offers critical insights into the microbiome dynamics of P. euphratica under salinity stress, advancing the understanding of specialists and generalists in the rhizosphere.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"28"},"PeriodicalIF":7.8,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11825717/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143414851","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":"Bifidobacterium longum NSP001-derived extracellular vesicles ameliorate ulcerative colitis by modulating T cell responses in gut microbiota-(in)dependent manners.","authors":"Xinke Nie, Qiqiong Li, Haihua Ji, Shanshan Zhang, Yuchen Wang, Junhua Xie, Shaoping Nie","doi":"10.1038/s41522-025-00663-4","DOIUrl":"10.1038/s41522-025-00663-4","url":null,"abstract":"<p><p>Recent studies have shown that intestinal commensal bacteria-derived vesicles may have potential effects in alleviating ulcerative colitis (UC). Although Bifidobacterium longum is widely used to prevent colitis, the potential role of B. longum-derived extracellular vesicles has yet to be explored. Here, we extracted B. longum NSP001-derived extracellular vesicles (NEVs) and investigated the regulatory roles of NEVs in colitis. Our results demonstrated that NEVs alleviate UC by improving intestinal barrier, modulating immune cell differentiation, and promoting the production of SCFAs. NEVs' improvement of inflammation in pseudo-germ-free mice implies that the anti-inflammatory effect of NEVs does not exclusively depend on the regulation of gut microbiota. In conclusion, we suggest that B. longum NSP001 improves UC through the secretion of NEVs. In addition, the study emphasizes the critical role of NEVs in maintaining host immune homeostasis via suppressing STAT3 pathway, thereby highlighting their potential as a novel postbiotic to alleviate UC.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"27"},"PeriodicalIF":7.8,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11811157/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143391371","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 anti-inflammatory properties of mannose oligosaccharides in the treatment of inflammatory bowel disease via LGALS3 modulation.","authors":"Yaqi Du, Yan Fan, Xin Li, Fenqin Chen","doi":"10.1038/s41522-025-00648-3","DOIUrl":"10.1038/s41522-025-00648-3","url":null,"abstract":"<p><p>This study investigates the role of Gum Arabic Mannose Oligosaccharides (GA-MOS) in modulating gut microbiota and alleviating symptoms of Inflammatory Bowel Disease (IBD). Employing both in vitro and in vivo models, we explored how GA-MOS influences microbial communities, particularly focusing on their capacity to enhance health-associated bacteria and reduce pathogenic species within the gut environment. Our findings reveal that GA-MOS treatment significantly altered the gut microbiota composition, increasing the abundance of anti-inflammatory bacteria while decreasing pro-inflammatory species, thus contributing to a reduction in gut inflammation and an improvement in intestinal barrier function. Detailed molecular analyses further demonstrated that these changes in microbiota were associated with modifications in the host's immune response, particularly through the suppression of key inflammatory pathways and cytokines involved in IBD progression. These results underscore the potential of dietary polysaccharides like GA-MOS as therapeutic agents in managing dysbiosis and inflammatory conditions in the gut, offering a promising approach for enhancing microbial health and overall disease management in IBD. This study provides novel insights into the bioactive properties of MOS and their interactions with gut microbiota, suggesting broader implications for their use in microbiome-centered therapies.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"26"},"PeriodicalIF":7.8,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11806110/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143370812","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":"Personalized prediction of glycemic responses to food in women with diet-treated gestational diabetes: the role of the gut microbiota.","authors":"Polina V Popova, Artem O Isakov, Anastasiia N Rusanova, Stanislav I Sitkin, Anna D Anopova, Elena A Vasukova, Alexandra S Tkachuk, Irina S Nemikina, Elizaveta A Stepanova, Angelina I Eriskovskaya, Ekaterina A Stepanova, Evgenii A Pustozerov, Maria A Kokina, Elena Y Vasilieva, Lyudmila B Vasilyeva, Soha Zgairy, Elad Rubin, Carmel Even, Sondra Turjeman, Tatiana M Pervunina, Elena N Grineva, Omry Koren, Evgeny V Shlyakhto","doi":"10.1038/s41522-025-00650-9","DOIUrl":"10.1038/s41522-025-00650-9","url":null,"abstract":"<p><p>We developed a prediction model for postprandial glycemic response (PPGR) in pregnant women, including those with diet-treated gestational diabetes mellitus (GDM) and healthy women, and explored the role of gut microbiota in improving prediction accuracy. The study involved 105 pregnant women (77 with GDM, 28 healthy), who underwent continuous glucose monitoring (CGM) for 7 days, provided food diaries, and gave stool samples for microbiome analysis. Machine learning models were created using CGM data, meal content, lifestyle factors, biochemical parameters, and microbiota data (16S rRNA gene sequence analysis). Adding microbiome data increased the explained variance in peak glycemic levels (GLUmax) from 34 to 42% and in incremental area under the glycemic curve (iAUC120) from 50 to 52%. The final model showed better correlation with measured PPGRs than one based only on carbohydrate count (r = 0.72 vs. r = 0.51 for iAUC120). Although microbiome features were important, their contribution to model performance was modest.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"25"},"PeriodicalIF":7.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11806021/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143370813","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":"Population-level gut microbiome and its associations with environmental factors and metabolic disorders in Southwest China.","authors":"Qianyu Qu, Qingyu Dou, Zhejun Xiang, Bin Yu, Lili Chen, Zhenxin Fan, Xing Zhao, Shujuan Yang, Peibin Zeng","doi":"10.1038/s41522-025-00661-6","DOIUrl":"10.1038/s41522-025-00661-6","url":null,"abstract":"<p><p>Gut microbiota affects host health and disease. Large-scale cohorts have explored the interactions between the microbiota, host, and environment to reveal the disease-associated microbiota variation. A population-level gut metagenomic cohort is still rare in China. Here, we performed metagenomic sequencing on fecal samples from the CMEC Microbiome Project in Southwest China. In this study, we identified host socioeconomics, diet, lifestyle, and medical measurements that were significantly associated with microbiome function and composition. We revealed extensive novel associations between the host microbiome and common metabolic disorders. Our results provide new insight into associations of gut microbiota with metabolic disorders so as to support the translation of gut microbiome findings into potential clinical practice.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"24"},"PeriodicalIF":7.8,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11794850/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143190086","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":"Soft X-ray tomography reveals variations in B. subtilis biofilm structure upon tasA deletion.","authors":"Anthoula Chatzimpinou, Anne Diehl, A Tobias Harhoff, Kristina Driller, Bieke Vanslembrouck, Jian-Hua Chen, Kristaps Kairišs, Valentina Loconte, Mark A Le Gros, Carolyn Larabell, Kürşad Turgay, Hartmut Oschkinat, Venera Weinhardt","doi":"10.1038/s41522-025-00659-0","DOIUrl":"10.1038/s41522-025-00659-0","url":null,"abstract":"<p><p>Bacterial biofilms are complex cell communities within a self-produced extracellular matrix, crucial in various fields but challenging to analyze in 3D. We developed a \"biofilm-in-capillary\" growth method compatible with full-rotation soft X-ray tomography, enabling high-resolution 3D imaging of bacterial cells and their matrix during biofilm formation. This approach offers 50 nm isotropic spatial resolution, rapid imaging, and quantitative native analysis of biofilm structure. Using Bacillus subtilis biofilms, we detected coherent alignment and chaining of wild-type cells towards the oxygen-rich capillary tip. In contrast, the ΔtasA genetic knock-out showed a loss of cellular orientation and changes in the extracellular matrix. Adding TasA protein to the ΔtasA strain restored matrix density and led to cell assembly compaction, but without the chaining observed in wild-type biofilms. This scalable and transferable approach opens new avenues for examining biofilm structure and function across various species, including mixed biofilms, and response to genetic and environmental factors.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"23"},"PeriodicalIF":7.8,"publicationDate":"2025-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11788442/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143080839","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":"Author Correction: 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/s41522-025-00656-3","DOIUrl":"10.1038/s41522-025-00656-3","url":null,"abstract":"","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"22"},"PeriodicalIF":7.8,"publicationDate":"2025-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11782515/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143067015","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":"Time-resolved compositional and dynamics analysis of biofilm maturation and dispersal via solid-state NMR spectroscopy.","authors":"Yi Xue, Xue Kang","doi":"10.1038/s41522-025-00655-4","DOIUrl":"10.1038/s41522-025-00655-4","url":null,"abstract":"<p><p>Dispersal plays a crucial role in the development and ecology of biofilms. While extensive studies focused on elucidating the molecular mechanisms governing this process, few have characterized the associated temporal changes in composition and structure. Here, we employed solid-state nuclear magnetic resonance (NMR) techniques to achieve time-resolved characterization of Bacillus subtilis biofilms over a 5-day period. The mature biofilm, established within 48 h, undergoes significant degradation in following 72 h. The steepest decline of proteins precedes that of exopolysaccharides, likely reflecting their distinct spatial distribution. Exopolysaccharide sugar units display clustered temporal patterns, suggesting the presence of distinct polysaccharide types. A sharp rise in aliphatic carbon signals on day 4 probably corresponds to a surge in biosurfactant production. Different dynamic regimes respond differently to dispersal: the mobile domain exhibits increased rigidity, while the rigid domain remains stable. These findings provide novel insights and perspectives on the complex process of biofilm dispersal.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"21"},"PeriodicalIF":7.8,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11779841/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143067027","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":"Pharmacodynamics of interspecies interactions in polymicrobial infections.","authors":"C Herzberg, J G C van Hasselt","doi":"10.1038/s41522-024-00621-6","DOIUrl":"10.1038/s41522-024-00621-6","url":null,"abstract":"<p><p>The pharmacodynamic response of bacterial pathogens to antibiotics can be influenced by interactions with other bacterial species in polymicrobial infections (PMIs). Understanding the complex eco-evolutionary dynamics of PMIs and their impact on antimicrobial treatment response represents a step towards developing improved treatment strategies for PMIs. Here, we investigated how interspecies interactions in a multi-species bacterial community affect the pharmacodynamic response to antimicrobial treatment. To this end, we developed an in silico model which combined agent-based modeling with ordinary differential equations. Our analyses suggest that both interspecies interactions, modifying either drug sensitivity or bacterial growth rate, and drug-specific pharmacological properties drive the bacterial pharmacodynamic response. Furthermore, lifestyle of the bacterial population and the range of interactions can influence the impact of species interactions. In conclusion, this study provides a foundation for the design of antimicrobial treatment strategies for PMIs which leverage the effects of interspecies interactions.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"20"},"PeriodicalIF":7.8,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11751299/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143009045","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}