npj Biofilms and Microbiomes最新文献

{"title":"Microbiome modulation of implant-related infection by a novel miniaturized pulsed electromagnetic field device.","authors":"João Gabriel S Souza, Fabio Azevedo, Maria Helena Rossy Borges, Raphael Cavalcante Costa, Takahiko Shiba, Shlomo Barak, Yaniv Mayer, Luciene Cristina de Figueiredo, Magda Feres, Valentim A R Barão, Jamil A Shibli","doi":"10.1038/s41522-025-00667-0","DOIUrl":"10.1038/s41522-025-00667-0","url":null,"abstract":"<p><p>Dental implant-related infections, which lack effective therapeutic strategies, are considered the primary cause for treatment failure. Pulsed electromagnetic field (PEMF) technology has been introduced as a safe and effective modality for enhancing biological responses. However, the PEMF effect on modulating microbial diversity has not been explored. Thus, we tested a miniaturized PEMF biomedical device as a healing component for dental implants. PEMF activation did not alter the chemical composition, surface roughness, wettability, and electrochemical performance. PEMF effectively controlled chronic in vitro polymicrobial microbial accumulation. The in vivo study where devices were inserted in the patients' oral cavities and 16S RNA sequencing analysis evidenced a fivefold or more reduction in 23 bacterial species for PEMF group and the absence of some species for this group, including pathogens associated with implant-related infections. PEMF altered bacterial interactions and promoted specific bacterial pathways. PEMF has emerged as an effective strategy for controlling implant-related infections.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"36"},"PeriodicalIF":7.8,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11865433/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143516181","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":"Irrigation of the intramedullary channel improves outcome of DAIR in a sheep model.","authors":"Claudia Siverino, Lena Gens, Tim Buchholz, Caroline Constant, Manuela Ernst, Dominic Gehweiler, Mario Morgenstern, R Geoff Richards, Henning Richter, Niels Vanvelk, Maja Waschk, Markus Windolf, Stephan Zeiter, T Fintan Moriarty","doi":"10.1038/s41522-024-00643-0","DOIUrl":"10.1038/s41522-024-00643-0","url":null,"abstract":"<p><p>The management of fracture-related infection (FRI) with Debridement, Antibiotics, Irrigation, and Implant Retention (DAIR) is an appealing option, but its suitability is restricted to a relatively narrow proportion of patients. This study aimed to create a large animal model of DAIR after FRI and to evaluate outcomes after early (2 weeks) and delayed (5 weeks) DAIR. Additionally, intramedullary lavage (IML) of the intramedullary canal (IMC) is introduced as a novel technique to remove infected tissue. Our findings showed that DAIR failed to resolve infections in both early and delayed groups, whilst IML significantly reduced bacterial counts, leading to culture-negative results in the soft tissue and bone marrow. IML did not compromise long-term bone healing as revealed by an implant load sensor on the plate. In conclusion, DAIR was successfully achieved in a new large animal model with minimal losses. The IML method improves treatment efficacy, potentially broadening the range of patients suitable for DAIR.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"35"},"PeriodicalIF":7.8,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11850838/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143493139","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":"Hypertension inhibition by Dubosiella newyorkensis via reducing pentosidine synthesis.","authors":"Tian-Hao Liu, Ming-Hao Chen, Chen-Yang Zhang, Ting Xie, Sitong Zhang, Haining Hao, Zhen-Yu Bai, Yu-Zheng Xue, Jiong-Wei Wang, Ya Xiao, Hong Wei, Li-Guo Chen","doi":"10.1038/s41522-025-00645-6","DOIUrl":"10.1038/s41522-025-00645-6","url":null,"abstract":"<p><p>Gut dysbiosis has been associated with hypertension. Herein, we aimed to discover the potential association between gut microbiota and high-salt diet (HSD) induced endothelial dysfunction in conventional hypertensive mice. Dubosiella newyorkensis was found highly sensitive to salt in HSD-induced hypertension. The salt-sensitive nature of Dubosiella newyorkensis was confirmed by bacteria culture in vitro. Oral Dubosiella newyorkensis in HSD-induced hypertensive mice decreased blood pressure, inhibited activation of vascular endothelium, attenuated inflammation and alleviated intestinal vascular barrier injury. Similar effects of Dubosiella newyorkensis were observed in germ-free mice. Interestingly, serum pentosidine was found to function as a biomarker for Dubosiella newyorkensis in response to HSD in both metabolic modes. Supplement of pentosidine, deteriorated hypertension and vascular endothelial damage. Differential genes enriched in the glycerophospholipid metabolism were markedly altered in cultured bacteria. Our study has identified Dubosiella newyorkensis as a new salt-sensitive gut microbe that inhibits pentosidine production thereby alleviating hypertension.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"34"},"PeriodicalIF":7.8,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11846869/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476781","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":"Cardiometabolic disease risk in gorillas is associated with altered gut microbial metabolism.","authors":"Samuel Davison, Anna Mascellani Bergo, Zoe Ward, April Sackett, Anna Strykova, José Diógenes Jaimes, Dominic Travis, Jonathan B Clayton, Hayley W Murphy, Marietta D Danforth, B Katherine Smith, Ran Blekhman, Terence Fuh, Frédéric Stéphane Niatou Singa, Jaroslav Havlik, Klara Petrzelkova, Andres Gomez","doi":"10.1038/s41522-025-00664-3","DOIUrl":"10.1038/s41522-025-00664-3","url":null,"abstract":"<p><p>Cardiometabolic disease is the leading cause of death in zoo apes; yet its etiology remains unknown. Here, we investigated compositional and functional microbial markers in fecal samples from 57 gorillas across U.S. zoos, 20 of which are diagnosed with cardiovascular disease, in contrast with 17 individuals from European zoos and 19 wild gorillas from Central Africa. Results show that zoo-housed gorillas in the U.S. exhibit the most diverse gut microbiomes and markers of increased protein and carbohydrate fermentation, at the expense of microbial metabolic traits associated with plant cell-wall degradation. Machine learning models identified unique microbial traits in U.S. gorillas with cardiometabolic distress; including reduced metabolism of sulfur-containing amino acids and hexoses, increased abundance of potential enteric pathogens, and low fecal butyrate and propionate production. These findings show that cardiometabolic disease in gorillas is potentially associated with altered gut microbial function, influenced by zoo-specific diets and environments.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"33"},"PeriodicalIF":7.8,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11845621/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143472687","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":"Disentangling the feedback loops driving spatial patterning in microbial communities.","authors":"Alyssa Henderson, Alessia Del Panta, Olga T Schubert, Sara Mitri, Simon van Vliet","doi":"10.1038/s41522-025-00666-1","DOIUrl":"10.1038/s41522-025-00666-1","url":null,"abstract":"<p><p>The properties of multispecies biofilms are determined by how species are arranged in space. How these patterns emerge is a complex and largely unsolved problem. Here, we synthesize the known factors affecting pattern formation, identify the interdependencies and feedback loops coupling them, and discuss approaches to disentangle their effects. Finally, we propose an interdisciplinary research program that could create a predictive understanding of pattern formation in microbial communities.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"32"},"PeriodicalIF":7.8,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11842706/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143468619","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":"Bioenergetically constrained dynamical microbial interactions govern the performance and stability of methane-producing bioreactors.","authors":"Chao-Jui Chang, Chun-Wei Chang, Hsiao-Pei Lu, Chih-Hao Hsieh, Jer-Horng Wu","doi":"10.1038/s41522-025-00668-z","DOIUrl":"10.1038/s41522-025-00668-z","url":null,"abstract":"<p><p>Biogas generation from organic waste by anaerobic bioreactors as renewable energy largely depends on microbial community and species interplays involved. This microbial networking is complex and time-dependent, influencing community succession and reactor performance, but remains unexplored due to the challenges in quantifying dynamics. We employed empirical dynamic modeling to analyze daily networking from a newly established bioreactor converting sucrose to biogas. Over time, microbial interactions within the three trophic (fermentative, syntrophic, and methanogenic) groups varied substantially more than between groups. Notably, versatile syntrophic bacteria like Syntrophorhabdus exhibited stronger interaction strength (0.14 ± 0.22) to hydrogen-dependent methylotrophic Methanomassiliicoccus than strictly syntrophic bacteria associated with butyrate (0.01 ± 0.01 for Syntrophomonas) and propionate (0.00 ± 0.01 for Syntrophobacter). The time-varying interaction networks were closely linked to the system performance dynamics, particularly concerning hydrogen concentrations. As community succession progressed, the stability of interaction network increased through time, accompanied by increased complexity and higher interaction strength. Causal analyses revealed intricate feedback involving catabolic energetics, community structure, and microbial interactions. These feedback mechanisms played a crucial role in regulating anaerobic degradation processes, thereby offering strategies for manipulating microbial interactions to enhance bioreactor stability and efficiency.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"31"},"PeriodicalIF":7.8,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11840090/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143458747","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":"Newly identified species from the dog dental plaque microbiome highlight little overlap with humans.","authors":"Vitor Heidrich, Gloria Fackelmann, Milka Malesevic, Federica Armanini, Hrituraj Dey, Claudia Mengoni, Nemanja Stanisavljevic, Goran Vukotic, Nicola Segata","doi":"10.1038/s41522-025-00665-2","DOIUrl":"10.1038/s41522-025-00665-2","url":null,"abstract":"<p><p>Understudied pet-associated microbiomes represent a rich source for the discovery of microbial taxa important for pet and human health. From a cohort of 23 dogs, we sampled and metagenomically sequenced 64 dental plaque microbiomes, generating 1945 metagenome-assembled genomes spanning 347 microbial species, including 277 undercharacterized species without cultivated representatives. Integration with human microbiome data revealed the dog plaque microbiome is more diverse than - and shows little overlap (5.9% species in common) with - the human plaque microbiome, even though some shared periodontal pathobionts arise as a potential concern.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"30"},"PeriodicalIF":7.8,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11836392/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143449605","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":"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}