npj Biofilms and Microbiomes最新文献

Life stage shifts in salivary microbiota determinants: a cross-sectional study in twins. 唾液微生物群决定因素的生命阶段转变：对双胞胎的横断面研究。

IF 11.4 1区生物学

npj Biofilms and Microbiomes Pub Date : 2026-09-16 DOI: 10.1038/s41522-026-01134-0

Simon Haworth, Eftychia Bellou, Ralf Kuja-Halkola, Wai-Lok Yau, Ingegerd Johansson, Anders Esberg

{"title":"Life stage shifts in salivary microbiota determinants: a cross-sectional study in twins.","authors":"Simon Haworth, Eftychia Bellou, Ralf Kuja-Halkola, Wai-Lok Yau, Ingegerd Johansson, Anders Esberg","doi":"10.1038/s41522-026-01134-0","DOIUrl":"10.1038/s41522-026-01134-0","url":null,"abstract":"Both host genetics and environmental exposures shape the salivary microbiota; however, the relative contributions of these factors from early life to adulthood remain unclear. To address this, we profiled the salivary microbiota of 3387 twin pairs: 939 infant pairs (9-12 months) and 2,448 adult pairs (23-52 years) using full-length 16S rRNA gene sequencing. In infants, the shared environment dominated: richness, diversity, and overall community composition were driven primarily by shared environmental effects, accounting for >50% of variance across key metrics. Host genetics had no detectable effect on community composition or species presence and only modest effects on species abundances and predicted functions. By contrast, in adults, the pattern reversed: shared environment contributed little, while host genetics exerted a broader, stronger influence, explaining 19-45% of variance in core diversity metrics and significantly affecting both species' presence, abundance, and predicted functions. Several clinically relevant oral taxa showed substantial heritability in adults, with roughly one-third of their variance attributable to genetic factors. These results reveal a life-stage shift in determinants of the salivary microbiota and their predicted functions: infancy is largely shaped by environmental exposures, whereas adult communities increasingly reflect host genetic architecture. These findings suggest that interventions to promote healthy oral microbiota may need to be tailored to life-stage.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"12 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13582848/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148983334","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}

引用次数: 0

Ageing processes in the bonobo gut microbiome mirror human patterns. 倭黑猩猩肠道微生物群的衰老过程反映了人类的模式。

IF 11.4 1区生物学

npj Biofilms and Microbiomes Pub Date : 2026-09-03 DOI: 10.1038/s41522-026-01032-5

Jonas R R Torfs, Mélodie Kreyer, Stijn Wittouck, Sarah Ahannach, Sarah Lebeer, Marcel Eens, Barbara Fruth, Nicky Staes

{"title":"Ageing processes in the bonobo gut microbiome mirror human patterns.","authors":"Jonas R R Torfs, Mélodie Kreyer, Stijn Wittouck, Sarah Ahannach, Sarah Lebeer, Marcel Eens, Barbara Fruth, Nicky Staes","doi":"10.1038/s41522-026-01032-5","DOIUrl":"10.1038/s41522-026-01032-5","url":null,"abstract":"Ageing is associated with changes in the human gut bacterial microbiome: with age, it becomes more diverse, intra- and interindividual variability increases and it shows a decline in core bacterial genera and an expansion of rarer genera. While recent evidence in model organisms suggests these patterns may arise through stochastic processes rather than host-driven selection, the role of life-time exposures, or the exposome, remains poorly understood. Here, we characterise age-related gut microbiome dynamics in 165 bonobos (Pan paniscus) from wild and zoo-housed populations, aged 2 to 71 years, providing a comparative framework to disentangle conserved from context-dependent ageing trajectories in the gut microbiome in hominids. Across both environments, ageing was associated with increased microbial diversity and reduced core microbiome abundance, paralleled by a rise in low-abundance taxa, recapitulating patterns seen in humans. Notably, instability and uniqueness increased with age in zoo-housed, but not wild bonobos, mirroring patterns restricted to industrialised human populations. Moreover, cumulative exposure to distinct environments over an individual's lifetime substantially contributes to microbiome uniqueness. Our findings suggest that while gut microbiome ageing is broadly conserved across hominids, its expression is modulated by environmental context, offering insight into the evolutionary and ecological drivers of microbial ageing in humans.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"12 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13642333/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149112204","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}

引用次数: 0

Eradication of catheter-associated MDR Acinetobacter baumannii biofilms mediated by novel phage encoded depolymerase activity. 新型噬菌体编码解聚合酶活性介导的导管相关性耐多药鲍曼不动杆菌生物膜的根除。

IF 11.4 1区生物学

npj Biofilms and Microbiomes Pub Date : 2026-09-01 DOI: 10.1038/s41522-026-01137-x

Medhavi Vashisth, Pawan Kumar, Prexha Kapoor, Indu Rani, Priya Sharma, Karan Bhutani, Dheeraj Bansal, Nitin Virmani, Bidhan Chand Bera, Rajesh Kumar Vaid, Meenakshi Sharma, Taruna Anand

{"title":"Eradication of catheter-associated MDR Acinetobacter baumannii biofilms mediated by novel phage encoded depolymerase activity.","authors":"Medhavi Vashisth, Pawan Kumar, Prexha Kapoor, Indu Rani, Priya Sharma, Karan Bhutani, Dheeraj Bansal, Nitin Virmani, Bidhan Chand Bera, Rajesh Kumar Vaid, Meenakshi Sharma, Taruna Anand","doi":"10.1038/s41522-026-01137-x","DOIUrl":"10.1038/s41522-026-01137-x","url":null,"abstract":"Bacteriophage-derived depolymerases provide promising scaffolds for the rational design of next-generation anti-biofilm peptides. We report two novel lytic Caudoviricetes phages φAB440 and φAB441, targeting multidrug-resistant hypermucoviscous Acinetobacter baumannii, encoding tail-associated depolymerases with pectate lyase domains and endolysins featuring glycoside hydrolase motifs. Depolymerases and endolysins demonstrated high binding affinity towards capsular polysaccharide K15 (-9.2 kcal/mol) and NAG-NAM tetramers (-7.86 kcal/mol). Synteny analysis revealed significant genome rearrangement and divergence in both phages, more strongly in φAB441. Phage φAB441's rare codon bias enables efficient depolymerase expression with altered tRNA availability in biofilms. Phages φAB440 and φAB441 suppressed bacterial growth over 24 h at low MOIs (10⁻¹ and 10⁻³), without evidence of resistance development. Four-day-old biofilms formed on urinary catheters were completely eradicated at 10⁹-108 PFU/ml, with ~7.2-7.4 log₁₀ CFU reductions. Phage φAB441, when tested against A. baumannii infection in Caenorhabditis elegans, increased survival of nematodes to 75.97%, 73.97%, and 73.7% at MOIs 1000, 100, and 10, respectively. Our findings highlight the importance of structural validation and in silico analysis towards determining the therapeutic potential of phage lytic proteins.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"12 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13658222/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149170333","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}

引用次数: 0

Megamonas hypermegale with indole-3-lactic acid-producing capacity ameliorates hepatic fibrosis. 具有吲哚-3-乳酸生成能力的超大单胞菌可改善肝纤维化。

IF 11.4 1区生物学

npj Biofilms and Microbiomes Pub Date : 2026-08-22 DOI: 10.1038/s41522-026-01141-1

Lu Zhang, Jing Chen, Wei Huang, Yu-Yan Chen, Yang Yan, Zhao-Xiu Liu, Cui-Hua Lu

{"title":"Megamonas hypermegale with indole-3-lactic acid-producing capacity ameliorates hepatic fibrosis.","authors":"Lu Zhang, Jing Chen, Wei Huang, Yu-Yan Chen, Yang Yan, Zhao-Xiu Liu, Cui-Hua Lu","doi":"10.1038/s41522-026-01141-1","DOIUrl":"10.1038/s41522-026-01141-1","url":null,"abstract":"Hepatic fibrosis lacks effective direct antifibrotic therapy. Human V3-V4 16S rRNA profiling identified a sequence feature provisionally assigned to M. hypermegale that was depleted in hepatic fibrosis; subsequent functional experiments used a cultured M. hypermegale strain. Administered from the onset of fibrosis induction, oral M. hypermegale attenuated CCl₄- and DDC-induced fibrosis in preventive/early-intervention models, reduced liver injury and collagen accumulation, and partially preserved intestinal epithelial integrity. M. hypermegale-conditioned medium suppressed transforming growth factor-β-induced hepatic stellate cell (HSC) activation, with activity retained after heat treatment, proteinase K digestion, and <3-kDa fractionation. Targeted metabolomics and germ-free mono-colonization identified indole-3-lactic acid (ILA) as a prominent M. hypermegale-associated metabolite. Purified ILA reproduced the antifibrotic phenotype and inhibited HSC contractility through aryl hydrocarbon receptor (AHR)-dependent suppression of RhoA/ROCK/p-MLC2 signaling. HSC-selective Ahr knockdown in mice and CRISPR/Cas9-mediated AHR disruption in HSCs weakened these effects. Arabinoxylan increased M. hypermegale abundance and portal ILA availability in association with reduced fibrosis. Circulating ILA was decreased in patients and inversely associated with indices of liver injury and fibrosis. These findings identify an M. hypermegale-ILA-AHR pathway that restrains HSC activation and supports microbiota-metabolite-directed strategies for experimental hepatic fibrosis.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"12 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13646272/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149128312","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}

引用次数: 0

Global analysis of infant gut microbiota revealed distinctive maturation dynamics across lifestyles. 婴儿肠道微生物群的全球分析揭示了不同生活方式的不同成熟动态。

IF 11.4 1区生物学

npj Biofilms and Microbiomes Pub Date : 2026-08-19 DOI: 10.1038/s41522-026-01130-4

Robert Bücking, Greta Pasquali, Ulrike Löber, Claudia Buss, Dorothee Viemann, Víctor Hugo Jarquín-Díaz, Sofia Kirke Forslund-Startceva

{"title":"Global analysis of infant gut microbiota revealed distinctive maturation dynamics across lifestyles.","authors":"Robert Bücking, Greta Pasquali, Ulrike Löber, Claudia Buss, Dorothee Viemann, Víctor Hugo Jarquín-Díaz, Sofia Kirke Forslund-Startceva","doi":"10.1038/s41522-026-01130-4","DOIUrl":"https://doi.org/10.1038/s41522-026-01130-4","url":null,"abstract":"The infant gut microbiome develops during the first years of life and influences long-term health through its interaction with immune system development. However, our understanding of early-life microbiome assembly is biased by the predominance of infants with industrialized lifestyles from North America and Europe. Here, we address this bias by assembling a globally representative dataset of 14,979 infant gut microbiomes from 2746 individuals to train a microbiome maturation model that can characterize lifestyle-specific patterns of microbial maturation as a function of age. Models trained exclusively on industrialized infants perform poorly when applied to non-industrialized datasets. In contrast, more diverse models, including individuals from both lifestyles, achieve increased correlation between microbial and chronological age (ΔR2 = 0.123). We identified differences in relevant taxa associated with the maturation in the different lifestyles. Additionally, our modeling approach detects a delay in the microbial maturation of independent cohorts of severely malnourished and preterm infants compared to healthy ones. Our results underscore the relevance of global diversity in microbiome research and provide deeper insights into context-dependent maturation dynamics of the infant gut microbiome.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"12 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13490558/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148796106","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}

引用次数: 0

Bifidobacterium animalis subsp. lactis BD1 restores neurotransmitter homeostasis in chronic restraint stress mice via tryptophan metabolic reprogramming 动物双歧杆菌亚种。乳酸BD1通过色氨酸代谢重编程恢复慢性约束应激小鼠的神经递质稳态

1区生物学

npj Biofilms and Microbiomes Pub Date : 2026-08-05 DOI: 10.1038/s41522-026-01049-w

Meng Tian, Yue Li, Jialin Wang, Ji Wang, Bin Jiang, Yue Leng, Dayong Ren, Binghua Wang

引用次数: 0

Role of cervicovaginal microbiome and metabolome in ALA-PDT-mediated HPV clearance in patients with cervical HSIL. 宫颈HSIL患者宫颈阴道微生物组和代谢组在ala - pdt介导的HPV清除中的作用。

IF 11.4 1区生物学

npj Biofilms and Microbiomes Pub Date : 2026-07-31 DOI: 10.1038/s41522-026-01120-6

Ting Zhang, Chunyan Zhang, Shuyu Yuan, Yimeng Wang, Mengzhuo Zhang, Kaili Dai, Yiduo Yu, Lijuan Zhang, Lili Cao, Mengzhen Zhang, Yuehui Su

{"title":"Role of cervicovaginal microbiome and metabolome in ALA-PDT-mediated HPV clearance in patients with cervical HSIL.","authors":"Ting Zhang, Chunyan Zhang, Shuyu Yuan, Yimeng Wang, Mengzhuo Zhang, Kaili Dai, Yiduo Yu, Lijuan Zhang, Lili Cao, Mengzhen Zhang, Yuehui Su","doi":"10.1038/s41522-026-01120-6","DOIUrl":"https://doi.org/10.1038/s41522-026-01120-6","url":null,"abstract":"The cervicovaginal microbiome and its associated metabolites play a pivotal role in the persistence of human papillomavirus (HPV) infection. Here, we investigated the contribution of the cervicovaginal microbiome and metabolome to 5-aminolevulinic acid photodynamic therapy (ALA-PDT)-mediated HPV clearance in patients with cervical high-grade squamous intraepithelial lesions (HSIL). 16S ribosomal RNA sequencing analysis identified significant differences in cervicovaginal microbiota before ALA-PDT between the HPV clearance and non-clearance groups. The HPV non-clearance group exhibited higher abundances of Anaerococcus and Gemella. ALA-PDT exerted a more substantial impact on cervicovaginal microbiota diversity in the HPV clearance group, characterized by increased abundances of Finegoldia, Corynebacterium, Lancefieldella, and Winkia, and a decreased abundance of Anaeroglobus following treatment. Global untargeted metabolomics analysis further revealed distinct cervicovaginal metabolic profiles before ALA-PDT between the two groups. The pathways of mineral absorption and valine, leucine, and isoleucine biosynthesis were significantly enriched in the HPV clearance group. Alterations in cervicovaginal metabolic profiles following ALA-PDT were also observed. Moreover, several key differential metabolites were observed to be significantly correlated with Anaeroglobus. Our findings underscore the critical involvement of the cervicovaginal microbiome and metabolome in ALA-PDT-mediated HPV clearance, providing valuable clues for predicting and improving the effect of HPV clearance following ALA-PDT.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"12 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149224552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Modulation of gut microbiota by nardosinone augments the efficacy of levodopa in rotenone-induced Parkinson's disease rats 纳多西酮调节肠道微生物群增强左旋多巴对鱼藤酮诱导的帕金森病大鼠的疗效

IF 11.4 1区生物学

npj Biofilms and Microbiomes Pub Date : 2026-07-30 DOI: 10.1038/s41522-026-01110-8

Mengmeng Liu, Jingwen Xue, Yuxin Cao, Zhuangzhuang Hao, Yuqing Wang, Jiayuan Li, Tingyue Jiang, Ge Zhang, Jinli Shi

引用次数: 0

OAPGC: a high-quality oral and airway prokaryotic genome catalog for enhanced ecological resolution and disease inference. OAPGC：用于增强生态分辨率和疾病推断的高质量口腔和气道原核基因组目录。

IF 11.4 1区生物学

npj Biofilms and Microbiomes Pub Date : 2026-07-27 DOI: 10.1038/s41522-026-01042-3

Xiaohui Zou, Yawen Ni, Qing Zhang, Shenghui Li, Yue Zhang, Chun Wang, Xiaoxuan Yao, Kang Chang, Binghuai Lu, Ruochun Guo, Guorui Xing, Hailong Yu, Jiabao Yin, Ning Gan, Zhong Wang, Qiulong Yan, Bin Cao

{"title":"OAPGC: a high-quality oral and airway prokaryotic genome catalog for enhanced ecological resolution and disease inference.","authors":"Xiaohui Zou, Yawen Ni, Qing Zhang, Shenghui Li, Yue Zhang, Chun Wang, Xiaoxuan Yao, Kang Chang, Binghuai Lu, Ruochun Guo, Guorui Xing, Hailong Yu, Jiabao Yin, Ning Gan, Zhong Wang, Qiulong Yan, Bin Cao","doi":"10.1038/s41522-026-01042-3","DOIUrl":"10.1038/s41522-026-01042-3","url":null,"abstract":"The human oral cavity and airway harbor diverse microbiomes that are implicated in oral and respiratory diseases, yet comprehensive genomic catalogs remain scarce. Here, we present the Oral and Airway Prokaryotic Genome Catalog (OAPGC), comprising 99,215 high-quality, non-redundant genomes reconstructed from public and newly sequenced metagenomes and isolates. OAPGC was clustered into 2474 species using refined, phylum-specific nucleotide identity thresholds, and 29.5% of them are uncultured. Habitat-driven divergence was evident across 15 oral and 8 airway sites, with airway microbiomes showing greater inter-individual variability and enriched antibiotic resistance genes. Across 25 case-control comparisons covering 12 diseases, disease status explained significant community shifts in 19 datasets, with classifiers achieving an AUC > 0.70 in 20 datasets. Shared microbial signatures were identified for diseases such as periodontitis and pneumonia, including uncultured taxa. We also detected 12.3% of OAPGC species in the gut, whose enrichment was linked to multiple diseases and improved cross-cohort classification performance. OAPGC establishes a foundational, disease-relevant genomic framework for oral and airway microbiome studies.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"12 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2026-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13612585/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149039901","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}

引用次数: 0

Kocuria rosea LAT6 enhances wheat salt tolerance via modulation of rhizosphere microbial function and nitrogen cycling. 红曲蕊LAT6通过调控根际微生物功能和氮循环增强小麦耐盐性。

IF 11.4 1区生物学

npj Biofilms and Microbiomes Pub Date : 2026-07-21 DOI: 10.1038/s41522-026-01103-7

Weifeng Song, Zhen Wang, Ying Liu, Qian Wang, Mingcong Li, Wenchong Shi, Zheng Gao, Yuan Chen

引用次数: 0