npj Biofilms and Microbiomes最新文献

{"title":"(p)ppGpp imposes graded transcriptional changes to impair motility and promote antibiotic tolerance in biofilms.","authors":"Florian Engelhardt, Kathryn Turnbull, Melisa Gür, Mathias Müsken, Matthias Preusse, Susanne Häussler, Mohammad Roghanian","doi":"10.1038/s41522-025-00795-7","DOIUrl":"10.1038/s41522-025-00795-7","url":null,"abstract":"<p><p>(p)ppGpp is the master regulator of bacterial stress responses, orchestrating cellular physiology via the stringent response to promote survival and adaptation. In response to nutritional challenges and stress, (p)ppGpp extensively rewires the transcriptome. Here, we demonstrate that (p)ppGpp production in Pseudomonas aeruginosa is gradual and relative to stress severity, rather than binary (on/off). Transcriptomic analysis reveals that (p)ppGpp ensures proportionate cellular responses to stress by imposing a layer-by-layer regulation of gene expression. These effects intensify as (p)ppGpp levels rise, with up to a quarter of the genome differentially regulated at maximal levels. Initial increases in (p)ppGpp reduce growth and metabolism while suppressing motility and pyocyanin production. At higher levels, biofilm-related genes are upregulated at the expense of virulence genes, promoting the formation of condensed biofilms. Finally, (p)ppGpp-driven reprogramming induces antimicrobial tolerance, particularly under biofilm conditions, independently of its effects on growth.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"148"},"PeriodicalIF":9.2,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12316884/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144765118","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 combination of potential psychobiotics alleviates anxiety and depression behaviors induced by chronic unpredictable mild stress.","authors":"Chen Meng, Siyuan Feng, Zikai Hao, Hong Liu","doi":"10.1038/s41522-025-00779-7","DOIUrl":"10.1038/s41522-025-00779-7","url":null,"abstract":"<p><p>Strains of Roseburia inulinivorans, Bacteroides uniformis, and Eubacterium rectale have exhibited multi-pathway therapeutic efficacy against anxiety and depression-like behaviors in chronic unpredictable mild stress (CUMS) rats. However, the combined therapeutic effects of these strains remain to be elucidated. Behavioral tests showed that a mixture of these strains reduced anxiety and depression-like behaviors. 16S rRNA sequencing revealed that the mixtures decrease the relative abundance of potentially pathogenic bacteria within the gut microbiota. Furthermore, the mixture increased the levels of butyric, isobutyric, and isovaleric acids in the gut and decreased pro-inflammatory factors in serum. It also lowered diamine oxidase, histamine in brain tissue, increased DL-kynurenine, and reduced cortisol secretion by the hypothalamic pituitary adrenal axis. In summary, the mixture significantly alleviated anxiety and depression-like behaviors.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"147"},"PeriodicalIF":9.2,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12310955/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144753908","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 microbiota and SCFAs improve the treatment efficacy of chemotherapy and immunotherapy in NSCLC.","authors":"Yanping Yang, Maosong Ye, Yijun Song, Wenyu Xing, Xing Zhao, Yufan Li, Jiacheng Shen, Jian Zhou, Kinji Arikawa, Shengdi Wu, Yuanlin Song, Nuo Xu","doi":"10.1038/s41522-025-00785-9","DOIUrl":"10.1038/s41522-025-00785-9","url":null,"abstract":"<p><p>The role of gut dysbiosis in shaping immunotherapy responses is well-recognized, yet its effect on the therapeutic efficacy of chemotherapy and immunotherapy combinations remains poorly understood. We analyzed gut microbiota in non-small cell lung cancer (NSCLC) patients treated with chemo-immunotherapy, comparing responders and non-responders using 16S rRNA sequencing. Responders showed higher microbial richness and abundance of specific genera like Faecalibacterium and Subdoligranulum, and the phylum Firmicutes. Support vector machine (SVM), a machine learning model based on microbial composition, predicted treatment efficacy with the area under the curve (AUC) values of 0.763 for genera and 0.855 for species. Metagenomic analysis revealed significant differences in metabolic pathways, with responders exhibiting higher short-chain fatty acids (SCFAs) production. Fecal microbiota transplantation (FMT) and SCFAs supplementation in mouse models enhanced treatment efficacy by promoting effector T cell activity in tumors. Our study suggests that gut microbiota, through SCFAs production, regulates chemo-immunotherapy efficacy, offering new strategies to improve NSCLC treatment outcomes.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"146"},"PeriodicalIF":9.2,"publicationDate":"2025-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12304354/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144732458","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":"Integrating metagenomics and cultivation unveils oral phage diversity and potential impact on hosts.","authors":"Zhuye Jie, Hewei Liang, Yanzheng Meng, Jiahao Zhang, Tao Zhang, Wenxi Li, Xiaoqian Lin, Tongyuan Hu, Mo Han, Weiting Liang, Yanmei Ju, Xin Tong, Xin Jin, Xun Xu, Wenwei Zhang, Jian Wang, Huanming Yang, Karsten Kristiansen, Liang Xiao, Yuanqiang Zou","doi":"10.1038/s41522-025-00773-z","DOIUrl":"10.1038/s41522-025-00773-z","url":null,"abstract":"<p><p>Bacteriophages play important roles in the regulation of bacterial communities and may thus impact human health. However, the scarcity of genomic data of oral microorganism has limited information on oral phages. We collected data on 5427 metagenomic samples and 2178 cultivated bacterial genomes across different geographical areas and populations, generating the Oral Phage Database (OPD), comprising 189,859 representative phage genome sequences, including 3416 huge phages (genome size > 200 kbp). OPD reveals that most oral viruses are unknown and encode an enormous variety of dark proteins. Numerous oral phages infecting a broad range of hosts carry anti-defense genes, auxiliary metabolic genes, and virulence factors that may affect bacterial metabolism and influence human health. The composition of oral phages varies among different populations, and several phages have the potential to act as biomarkers for disease. OPD expands our knowledge of phage-bacteria interactions, huge phages diversity, and potential impacts on human health.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"145"},"PeriodicalIF":9.2,"publicationDate":"2025-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12297358/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144718187","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 microbiota shapes cancer immunotherapy responses.","authors":"Wanting Lei, Kexun Zhou, Ye Lei, Qiu Li, Hong Zhu","doi":"10.1038/s41522-025-00786-8","DOIUrl":"10.1038/s41522-025-00786-8","url":null,"abstract":"<p><p>The gut microbiota significantly influences cancer immunotherapy efficacy by modulating immune responses, remodeling the tumor microenvironment (TME), and producing key metabolites. Strategies such as FMT, probiotics, and dietary interventions show promise in enhancing responses to ICIs and ACTs while reducing immune-related adverse events (irAEs). This review summarizes clinical and preclinical findings and discusses microbiota-based interventions and future directions for precision immunotherapy.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"143"},"PeriodicalIF":9.2,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12297587/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144718185","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":"Immune dysfunction during S. aureus biofilm-associated implant infections: opportunities for novel therapeutic strategies.","authors":"Nichole D Brandquist, Tammy Kielian","doi":"10.1038/s41522-025-00782-y","DOIUrl":"10.1038/s41522-025-00782-y","url":null,"abstract":"<p><p>Staphylococcus aureus is a common cause of biofilm infections, particularly on implanted medical devices. Biofilms are heterogeneous bacterial communities contained in a self-produced matrix that are poorly cleared by the immune system. This review discusses mechanisms employed by the biofilm, such as alterations in bacterial metabolism and toxin production, to induce immune dysfunction by highlighting recent bacterial single-cell sequencing studies. Additionally, the role of immune recognition and metabolism in biofilm containment is examined with an emphasis on the role of granulocytic myeloid-derived suppressor cells and how responses are tailored to distinct tissue niches. We also address emerging evidence revealing the importance of the infection microenvironment, host genetic variability, and bacterial heterogeneity in shaping immune responses during S. aureus biofilm infections.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"144"},"PeriodicalIF":9.2,"publicationDate":"2025-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12297603/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144718186","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":"Human gut microbiome gene co-expression network reveals a loss in taxonomic and functional diversity in Parkinson's disease.","authors":"Rémy Villette, Polina V Novikova, Cédric C Laczny, Brit Mollenhauer, Patrick May, Paul Wilmes","doi":"10.1038/s41522-025-00780-0","DOIUrl":"10.1038/s41522-025-00780-0","url":null,"abstract":"<p><p>Gut microbiome alterations are linked to various diseases, including neurodegeneration, but their ecological and functional impacts remain unclear. Using integrated multi-omics (metagenomics and metatranscriptomics), we analyse microbiome gene co-expression networks in Parkinson's disease (PD) and healthy controls (HC). We observe a significant depletion of hub genes in PD, including genes involved in secondary bile acid biosynthesis, bacterial microcompartments (BMCs), polysaccharides transport and flagellar assembly (FA). Blautia, Roseburia, Faecalibacterium and Anaerobutyricum genera are the main contributors to these functions, showing significantly lower expression in PD. Additionally, we identify a strong correlation between BMC and FA expression, and an apparent dysregulation in cross-feeding between commensals in PD. Finally, PD also exhibits reduced gene expression diversity compared to HC, whereby higher gene expression correlates with greater diversity. We identify disruptions in gut metabolic functions, at both taxonomic and functional level, and microbiome-wide ecological features, highlighting targets for future gut microbiome restoration efforts.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"142"},"PeriodicalIF":9.2,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12289924/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144708347","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 essential role of gut microbiota in dsRNA-mediated pest control of the phytophagous ladybird beetle, Henosepilachna vigintioctopunctata.","authors":"Yujie Huang, Jinman Huang, Dae Sung Kim, Jiang Zhang","doi":"10.1038/s41522-025-00767-x","DOIUrl":"10.1038/s41522-025-00767-x","url":null,"abstract":"<p><p>RNA interference (RNAi) has proven to be an effective measure in combating insect pests. RNA-based pesticides have already made their way to the market for pest control. We previously have demonstrated the pivotal role of gut microbiota in influencing the efficacy of RNAi against the leaf beetle Plagiodera versicolora (Coleoptera), a species highly susceptible to RNAi. However, the role of the gut microbiota in different insect species remains ambiguous. We delved into the intricate interplay between gut bacterial communities and RNAi in the phytophagous ladybird beetle, Henosepilachna vigintioctopunctata (HV), a significant agricultural pest targeting solanaceous plants. By administering double-stranded RNA targeting HV β-Actin gene (dsACT) or utilizing transplastomic (plastid genome transformed) potato plants expressing dsACT on HV axenic larvae, a substantial decrease in lethality was observed compared to non-axenic controls. This underscores the critical role of microbiota in enhancing the effectiveness of RNAi. The disruption of microbial diversity and functionality due to dysbiosis induced by dsRNA feeding amplified physiological stress and mortality rates in HV. Notably, the optimal bacterial densities were crucial for maximizing mortality rates, as elevated concentrations of gut bacteria could disrupt the native microbial equilibrium. These findings underscore the importance of microbiota-aware strategies in RNAi applications, particularly in the context of sustainable pest management within solanaceous crop systems.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"141"},"PeriodicalIF":7.8,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12280057/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144682836","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":"Probiotic-mediated modulation of gut microbiome in students exposed to academic stress: a randomized controlled trial.","authors":"Jorge Francisco Vázquez-Castellanos, Lucas Ferreira Maciel, Lucas Wauters, Ann Gregory, Lukas Van Oudenhove, Karlien Geboers, Kristin Verbeke, Tamara Smokvina, Jan Tack, Tim Vanuytsel, Muriel Derrien, Jeroen Raes","doi":"10.1038/s41522-025-00776-w","DOIUrl":"10.1038/s41522-025-00776-w","url":null,"abstract":"<p><p>Probiotics have been widely tested for their effect on mental well-being, albeit with heterogeneous outcomes. Direct and indirect effects through the gut microbiome might lie at the basis of these observations. Here, in a post-hoc analysis, we assessed the effect of 4-week consumption of a probiotic candidate strain on the gut microbiome in students exposed to academic stress. Healthy students were randomized to consume a fermented milk product with Lacticaseibacillus rhamnosus CNCM I-3690 (N = 39) or an acidified non-fermented milk product (N = 40) twice daily for 4 weeks before academic exams. The gut microbiome was analysed by Quantitative Microbiome Profiling based on 16S rRNA gene amplicon and shotgun metagenomic sequencing. Stress and anxiety were assessed using both objective and self-reported markers. Changes of alpha-diversity markers and community shifts from baseline (beta diversity) were lower in L. rhamnosus treated individuals over controls, suggesting lower overall changes of gut microbiota during psychological stress in the Probiotic group. The intake of L. rhamnosus CNCM I-3690 induced differential abundance of some species, such as the maintenance of the quantitative abundance of Ruminococcus bicirculans, and co-varied with species, which differed according to visits (i.e., stress level), suggesting a potential beneficial effect of the strain before the highest increase of stress level. The higher quantitative abundance of F. prausnitzii induced by the probiotic intake was associated with lowered self-reported anxiety levels before the exam. Functional analysis revealed minor changes upon intake of the probiotic strain. Taken together, using a quantitative framework, we found that L. rhamnosus CNCM I-3690 has a potential effect on gut microbiome response to stress, although further studies are needed to better understand the precise interaction.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"140"},"PeriodicalIF":7.8,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12280152/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144682835","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":"Parabacteroides as a promising target for disease intervention: current stage and pending issues.","authors":"Jing Liu, Hui Qiu, Jiamin Zhao, Nan Shao, Chao Chen, Zhixu He, Xu Zhao, Juanjuan Zhao, Ya Zhou, Lin Xu","doi":"10.1038/s41522-025-00772-0","DOIUrl":"10.1038/s41522-025-00772-0","url":null,"abstract":"<p><p>Parabacteroides, a promising candidate for the next generation of probiotics, plays a significant role in various diseases. In this review, we provide a comprehensive examination of the biological properties of Parabacteroides, summarize its effects on host health and potential associations with diseases, and discuss unresolved scientific questions regarding this genus. Our aim is to offer novel insights for the development of targeted gut microbiota interventions and their translational applications.</p>","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"137"},"PeriodicalIF":7.8,"publicationDate":"2025-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12274597/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668115","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}