npj Biofilms and Microbiomes最新文献

{"title":"The engineering of TBBPA-degrading synthetic microbiomes with integrated strategies.","authors":"Tong Wu, Sheng-Zhi Guo, Yi Zhang, Xi-Ze Zhao, Cong-Guo Ran, Feng-Lan Liu, Run-Hua Wang, De-Feng Li, Hai-Zhen Zhu, Cheng-Ying Jiang, Xi-Hui Shen, Shuang-Jiang Liu","doi":"10.1038/s41522-025-00777-9","DOIUrl":"10.1038/s41522-025-00777-9","url":null,"abstract":"<p><p>The capability to understand and construct synthetic microbiomes is crucial in biotechnological innovation and application. Tetrabromobisphenol A (TBBPA) is an emerging pollutant, and the understanding of its biodegradation is very limited. Here, a top-down approach was applied for the enrichment of TBBPA-degrading microbiomes from natural microbiomes. Ten keystone taxa correlated to TBBPA degradation and their co-occurrence interactions were identified by the dissection of the degrading microbiomes. Those keystone taxa were targeted and cultivated, and the genomic information was obtained by genome sequencing of strains and metagenomic binning. The keystone bacterial strains showed efficient degradation of TBBPA, and L-amino acids were important co-metabolic substrates to promote the degradation. Guided by this knowledge, a bottom-up approach was applied to design and construct a simplified synthetic consortium SynCon2, that consisted of four strains. The SynCon2 demonstrated efficient TBBPA degradation activity and soil bioremediation. Our study demonstrates the importance of the application of multiple tools in understanding the functions of microbiomes and provides an integrated top-down and bottom-up strategy for the construction of synthetic microbiomes with various applications.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"139"},"PeriodicalIF":7.8,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12276246/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668116","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":"Interplay between antipredator behavior, parasitism, and gut microbiome in wild stickleback populations.","authors":"Javier Edo Varg, Jaelle C Brealey, David Benhaïm, Rafael Losada-Germain, Janette W Boughman","doi":"10.1038/s41522-025-00758-y","DOIUrl":"10.1038/s41522-025-00758-y","url":null,"abstract":"<p><p>The impact of microbial composition on stress-related behavior in aquatic organisms is poorly understood. This study explored the link between antipredator behavior, parasitism, and the gut microbiome in wild stickleback from two lakes: clear, spring-fed Galtaból and turbid, glacial-fed Þristikla. Behavioral analysis revealed differences between populations, with each exhibiting unique baseline behaviors. Microbiome analysis showed that a small proportion of its variation was explained by population, likely reflecting differences in lake environments. Only the marine genus Pseudoalteromonas abundance differed between populations. Our findings suggest that behavior and microbiome correlations may primarily reflect environmental adaptations and parasite status rather than direct gut-brain interactions. However, some tentative evidence suggests a potential innate connection between some antipredator behavior and microbiome composition. The study highlights the complexity of the gut-brain axis in wild populations and suggests future research directions, including experimental manipulations to uncover causal relationships between microbiome composition and behavior.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"138"},"PeriodicalIF":7.8,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12276351/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668114","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":"Chinese soy-based microbiome and associated microbial risks: a metagenomic investigation.","authors":"Xuesong Xiang, Yingying Li, Junbin Ye, Baolong Li, Guozhong He, Mingyu Zhu, Jiawen Zhang, Bike Zhang, Ming Miao, Yuexin Yang","doi":"10.1038/s41522-025-00768-w","DOIUrl":"10.1038/s41522-025-00768-w","url":null,"abstract":"<p><p>Fermented foods are a longstanding part of the Chinese diet and have been recognized for promoting gut microbial diversity. However, their microbial composition remains poorly defined, raising concerns about potential exposure to pathogens and antibiotic resistance genes (ARGs). Using shotgun metagenomics, we examined microbiota of 93 representative samples spanning three major categories of traditional Chinese fermented soybean products. We identified distinct microbial and functional profiles across food types, with antagonism between beneficial taxa (Bacillales and Lactobacillales) and harmful Enterobacterales. Comparative analysis with public Chinese gut microbiomes revealed species- and strain-sharing between fermented foods and human gut microbiota, identifying certain products as sources of clinically relevant pathogens, including Klebsiella pneumoniae and Klebsiella quasipneumoniae. Horizontal gene transfer analysis highlighted potential transfer of ARGs (e.g., efflux pump genes) from food microbes to gut microbiota. Our findings underscore the need to integrate microbial surveillance into traditional fermentation to balance health benefits with food safety.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"136"},"PeriodicalIF":7.8,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12274573/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668113","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":"Gut microbes and their metabolites in relation to the classic tumor suppressor gene P53: a novel narrative.","authors":"Jia-Xuan Li, Chen-Guang Liu, Jun Chen","doi":"10.1038/s41522-025-00775-x","DOIUrl":"10.1038/s41522-025-00775-x","url":null,"abstract":"<p><p>Gut microbes are considered to be key factors regulating host health and are closely related to tumorigenesis. Although the exact mechanism has not been clearly explained, many studies have shown that specific bacteria can affect cancer-related bioactive molecules, such as p53, Wnt, MAPK, and EGFR. Among them, p53 is the most commonly mutated gene in all tumor types. In this review, we systematically examine the gut microbes and metabolites that affect the tumor process by regulating p53, as well as the role of p53 in shaping the gut microbiota, and discuss their potential in the diagnosis and prognosis of tumors and the application value of clinical anti-tumor therapy. This study provides an important theoretical basis for the in-depth understanding and development of relevant treatment strategies.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"135"},"PeriodicalIF":7.8,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12271359/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144659734","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":"Environmental factors drive bacterial degradation of gastrointestinal mucus.","authors":"Sandra L Arias, Ellen W van Wijngaarden, Diana Balint, Joshua Jones, Carl C Crawford, Parul J Shukla, Meredith Silberstein, Ilana L Brito","doi":"10.1038/s41522-025-00741-7","DOIUrl":"10.1038/s41522-025-00741-7","url":null,"abstract":"<p><p>The mucus layer lining the gastrointestinal tract is essential for gut health, providing a protective barrier while maintaining host-microbiome symbiosis. Its disruption is a hallmark of diseases like ulcerative colitis, yet how bacterial activity impacts mucus structure remains unclear. We developed a method to collect human-cell-derived mucus that mimics human colonic mucus and used it to investigate mucus degradation by commensal bacteria. Glycan foraging by species such as Bacteroides thetaiotaomicron and Bacteroides fragilis did not alter mucus rheology. Instead, secreted proteases were the primary drivers of degradation. Protease activity by B. fragilis and Bifidobacterium longum subsp. infantis was nutrient-dependent, while Enterococcus faecalis was further influenced by oxygen. Under oxidative stress, E. faecalis upregulated carbohydrate metabolism and virulence genes. These results reveal that bacterial mucus degradation is context-dependent and shaped by environmental factors. Our findings underscore the value of human cell-derived mucus models for understanding bacteria-mucus interactions in health and disease.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"133"},"PeriodicalIF":7.8,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12267731/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144649946","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":"Geocaulosphere soil bacterial community drives potato common scab outcomes beyond pathogen abundance.","authors":"Wenchong Shi, Minghao Lv, Ruiqi Wang, Muhammad Saleem, Lujun Wang, Mingcong Li, Bing Wang, Rongshan Lin, Bingjie Xu, Chunyu Yang, Tangyuan Ning, Bo Zhou, Zheng Gao","doi":"10.1038/s41522-025-00774-y","DOIUrl":"10.1038/s41522-025-00774-y","url":null,"abstract":"<p><p>The assembly mechanisms of soil microbiome during plant disease progression remain incomplete. This study linked potato common scab (PCS) severity to destabilized soil microbiome dynamics in potato geocausphere soil (GS) through integrated metagenomic analysis and culture-based experiments. Across four Shandong fields, PCS-infected GS exhibited an 11.66% reduction in bacterial α-diversity (Shannon index) and elevated stochastic community assembly. Bacterial community structure explained 39.28% (GS) and 15.96% (bulk soil) of PCS variance, outperforming pathogen abundance contributions (14.39% GS, 7.33% BS). Two microbial interaction patterns emerged in GS: 1) synchronized shifts between pathogens and beneficial taxa as PCS intensified; 2) stochastic assembly governing entire communities but deterministic processes dominating specialized subgroups. These results propose a microbial stability framework connecting soil microbiome structural rules to plant disease progression, emphasizing community-level dynamics over pathogen-centric explanations.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"134"},"PeriodicalIF":7.8,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12267564/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144649947","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":"Gut bacteria and the host synergies promote resveratrol metabolism and induce tolerance in ALD mice.","authors":"Song-Xia Zhang, Fang-Fang Hu, Huan Chen, Jing Guo, Zhong-Wen Xiang, Xin Ding, Meng-Ling Ye, Wen-Li Ye, Jun-Hong Chen, Xin Wang, Wen-Jing Han, Hong-Hao Zhou, Wei Zhang, Yun Huang, Lie-Lin Wu, Guang-Hui Lian, Yao Chen","doi":"10.1038/s41522-025-00766-y","DOIUrl":"10.1038/s41522-025-00766-y","url":null,"abstract":"<p><p>Drug tolerance is clinically common but its mechanism is unclear. Previous studies found RSV tolerance in ALD treatment. This study explores mechanisms involving gut bacteria and host factors. Male C57BL/6J mice were induced into ALD with the Lieber-DeCarli alcohol diet, then ALD-RSV group mice were gavaged RSV (150 mg/kg/day) for 5 weeks. Throughout the experiment, ALD and ALD-RSV mice were on the Lieber-DeCarli alcohol diet, while the Vehicle group received a control diet. By week 5, tolerance to RSV efficacy emerged, with markedly reduced RSV exposure at the final dose. ALD-RSV group exhibited increased levels of Eggerthella lenta (E.lent), which metabolizes RSV into dihydroresveratrol (DHR). Chronic RSV treatment upregulated UGT1A1, the enzyme converting RSV into its primary metabolite, trans-resveratrol-3-O-β-D-glucuronide (R3G). The synergy between gut bacteria and host factors enhances RSV metabolism in ALD mice, driving tolerance and offering insights into other clinical drugs tolerance mechanisms.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"132"},"PeriodicalIF":7.8,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12259939/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144637678","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":"A contributory citizen science project reveals the impact of dietary keys to microbiome health in Spain.","authors":"Zaida Soler, Gerard Serrano-Gómez, Marc Pons-Tarín, Sara Vega-Abellaneda, Zixuan Xie, Isaac Manjón, Chloe Cognard, Encarna Varela, Francisca Yañez, Arnau Noguera-Segura, Melina Roca-Bosch, Chaysavanh Manichanh","doi":"10.1038/s41522-025-00769-9","DOIUrl":"10.1038/s41522-025-00769-9","url":null,"abstract":"<p><p>Low consumption of whole grains, fruits, and vegetables has been identified as dietary risks for non-communicable diseases such as inflammatory bowel diseases (IBDs). We explore how individual and lifestyle factors influence these risks by shaping gut microbiome composition. 1001 healthy participants from all Spanish regions provided personal and dietary data at baseline, six, and twelve months, yielding 2475 responses. Gut microbiome data were analyzed for 500 healthy participants and 321 IBD patients. Our findings reveal that adherence to national dietary guidelines-characterized by diets rich in nuts, seeds, fruits, and vegetables-was associated with greater microbial diversity and reduced IBD-related dysbiosis. Finally, we observed variations in dietary patterns and microbiome diversity and composition across age groups, genders, regions, seasons, and transit time. This study is among the first to uncover dietary intake associated with IBD-related dysbiosis and to propose an interactive website for participants ( https://manichanh.vhir.org/POP/en ).</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"131"},"PeriodicalIF":7.8,"publicationDate":"2025-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12254420/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144619455","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":"Benefits and challenges of host depletion methods in profiling the upper and lower respiratory microbiome.","authors":"Chun Wang, Li Zhang, Chuanwen Kan, Junyan He, Weijie Liang, Ruiyan Xia, Linyu Zhu, Jing Yang, Xuan Jiang, Wentai Ma, Zhihang Liang, Zhiqing Xiao, Juanjuan Zhang, Jiaxin Zhong, Xiao Sun, De Chang, Zhang Wang, Guoliang Zhang, Mingkun Li","doi":"10.1038/s41522-025-00762-2","DOIUrl":"10.1038/s41522-025-00762-2","url":null,"abstract":"<p><p>Metagenomic sequencing for respiratory pathogen detection faces two challenges: efficient host DNA depletion and the representativeness of upper respiratory samples for lower tract infections. In this study, we benchmarked seven host depletion methods, including a new method (F_ase), using bronchoalveolar lavage fluid (BALF), oropharyngeal swab (OP), and mock samples. All methods significantly increased microbial reads, species richness, genes richness, and genome coverage while reduced bacterial biomass, introduced contamination, and altered microbial abundance. Some commensals and pathogens, including Prevotella spp. and Mycoplasma pneumoniae, were significantly diminished. F_ase demonstrated the most balanced performance. High-resolution microbiomes profiling revealed distinct microbial niche preferences and microbiome disparities between the upper and lower respiratory tract. In pneumonia patients, 16.7% of high-abundance species (>1%) in BALF were underrepresented (<0.1%) in OP, highlighting OP's limitations as lower respiratory proxies. This study underscores both the potential and challenges of metagenomic sequencing in advancing microbial ecology and clinical research.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"130"},"PeriodicalIF":7.8,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12234985/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144584442","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-kingdom microbiota analysis reveals bacteria-viral interplay in IBS with depression and anxiety.","authors":"Qin Liu, Wenyu Fang, Ping Zheng, Shicai Xie, Xuanting Jiang, Wen Luo, Lijuan Han, Ling Zhao, Lin Lu, Lixiang Zhai, Danny J Yu, Wei Yang, Chengyuan Lin, Xiaodong Fang, Zhaoxiang Bian","doi":"10.1038/s41522-025-00760-4","DOIUrl":"10.1038/s41522-025-00760-4","url":null,"abstract":"<p><p>Irritable Bowel Syndrome (IBS) is a common gastrointestinal disorder frequently accompanied by psychological symptoms. Bacterial microbiota plays a critical role in mediating local and systemic immunity, and alterations in these microbial communities have been linked to IBS. Emerging data indicate that other intestinal organisms, including bacteriophages, are closely interlinked with the bacterial microbiota and their host, yet their collective role remains to be elucidated. Here, we analyze the gut multi-kingdom microbiota of 360 IBS patients from a prospective cohort study in Hong Kong, with participants phenotyped through psychological assessment. Our findings reveal significantly lower intra-community correlations in IBS patients compared to healthy controls and highlight unique taxa patterns associated with IBS and mental disorders. Utilizing multi-omic data alongside machine learning techniques, we successfully predicted psychiatric comorbidities in IBS, achieving an average AUC of 0.78. Notably, gut viruses emerged as significant contributors to our predictive model, indicating a vital role for bacteriophages in the gut microbiome of IBS patients. We found that lysogenic phages in IBS displayed a broader host range, with Bilophia containing the most abundant prophages. Our analysis further indicates that IBS patients with depression exhibited a higher prevalence of viral-encoded auxiliary metabolic genes, specifically those involved in the sulfur metabolic pathway related to ubiquinone biosynthesis. The gut virome is increasingly reported to play an important role in the pathogenesis of many diseases. The study provides a systematic characterization of the drivers of the gut viral community and further expands our knowledge of the distinct interaction of gut viruses with their prokaryotic hosts, which is critical for understanding the viral-bacterial environment in IBS.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"129"},"PeriodicalIF":7.8,"publicationDate":"2025-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12228763/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144567703","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}