npj Biofilms and Microbiomes最新文献_第7页

Roles of gut microbiome-associated metabolites in pulmonary fibrosis by integrated analysis. 综合分析肠道微生物相关代谢物在肺纤维化中的作用

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-12-19 DOI: 10.1038/s41522-024-00631-4

Jie Li, Wenqing Wu, Xinyi Kong, Xia Yang, Kui Li, Zicheng Jiang, Chunlan Zhang, Jun Zou, Ying Liang

{"title":"Roles of gut microbiome-associated metabolites in pulmonary fibrosis by integrated analysis.","authors":"Jie Li, Wenqing Wu, Xinyi Kong, Xia Yang, Kui Li, Zicheng Jiang, Chunlan Zhang, Jun Zou, Ying Liang","doi":"10.1038/s41522-024-00631-4","DOIUrl":"10.1038/s41522-024-00631-4","url":null,"abstract":"Lung diseases often coincide with imbalances in gut microbiota, but the role of gut microbiota in pulmonary fibrosis (PF) remains unclear. This study investigates the impact of gut microbiota and their metabolites on PF. Serum and lung tissues of normal, bleomycin (BLM)- and silica-induced mice showed significant differences in gut microbiota. L-Tryptophan was upregulated within pulmonary tissue and serum metabolites both in the BLM and Silica groups. The dominant gut microbiota associated with L-tryptophan metabolism included Lachnospiraceae_NK4A136_Group, Allobaculum, Alistipes, and Candidatus_Saccharimonas. L-Tryptophan promoted BLM- and silica-induced pathological damage in PF mice. L-Tryptophan promoted TGF-β1-induced EMT and fibroblast activation in vitro via activating the mTOR/S6 pathway. In conclusion, PF mice exhibited alterations in gut microbiota and serum and lung tissue metabolites. L-Tryptophan level was associated with changes in gut microbiota, and L-tryptophan promoted PF progression in both in vivo and in vitro models, potentially through activation of the mTOR/S6 pathway.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"154"},"PeriodicalIF":7.8,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11659409/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864943","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

Revealing an unprecedented diversity of episymbiotic Saccharibacteria in a high-quality genome collection. 在高质量的基因组收集中揭示了前所未有的表观共生糖菌多样性。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-12-19 DOI: 10.1038/s41522-024-00617-2

Wenxin He, Hewei Liang, Wenxi Li, Xiaowei Gao, Tongyuan Hu, Xiaoqian Lin, Zhinan Wu, Jingxi Sun, Xiaofang Li, Mengmeng Wang, Xiaoxue Hou, Zhuye Jie, Xin Tong, Xin Jin, Liang Xiao, Yuanqiang Zou

{"title":"Revealing an unprecedented diversity of episymbiotic Saccharibacteria in a high-quality genome collection.","authors":"Wenxin He, Hewei Liang, Wenxi Li, Xiaowei Gao, Tongyuan Hu, Xiaoqian Lin, Zhinan Wu, Jingxi Sun, Xiaofang Li, Mengmeng Wang, Xiaoxue Hou, Zhuye Jie, Xin Tong, Xin Jin, Liang Xiao, Yuanqiang Zou","doi":"10.1038/s41522-024-00617-2","DOIUrl":"10.1038/s41522-024-00617-2","url":null,"abstract":"The episymbiotic Candidatus Saccharibacteria is the most studied lineage of candidate phyla radiation. Living an epiparasitic lifestyle, Saccharibacteria might be associated with human mucosal diseases by modulating the structure of the oral microbiome through interactions with host bacteria. However, the knowledge of Saccharibacterial genomic diversity and the potential underlying their adaptation to a wide range of habitats remains limited. Here, we construct a high-quality genome collection of Saccharibacteria from multiple sources, providing 2041 high-quality genomes and previously unidentified taxa. The comparative genomic analysis shows the widespread metabolic defects of Saccharibacteria. Specific metabolic modules are commonly found in Saccharibacteria of different habitats, suggesting Saccharibacteria might have undergone habitat adaptation during the transition from different environments. We additionally show that Saccharibacteria account for ~1% of the Chinese oral microbiome. A preliminary analysis of rheumatoid arthritis individuals and healthy controls implies that Saccharibacteria might be associated with human systemic disease.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"153"},"PeriodicalIF":7.8,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11659515/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864937","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

Diverse polysaccharide production and biofilm formation abilities of clinical Klebsiella pneumoniae. 临床肺炎克雷伯氏菌的多种多糖生产和生物膜形成能力。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-12-19 DOI: 10.1038/s41522-024-00629-y

Robert L Beckman, Elenora Cella, Taj Azarian, Olaya Rendueles, Renee M Fleeman

{"title":"Diverse polysaccharide production and biofilm formation abilities of clinical Klebsiella pneumoniae.","authors":"Robert L Beckman, Elenora Cella, Taj Azarian, Olaya Rendueles, Renee M Fleeman","doi":"10.1038/s41522-024-00629-y","DOIUrl":"10.1038/s41522-024-00629-y","url":null,"abstract":"Klebsiella pneumoniae infections have become a growing threat for human health. The lack of understanding of the relationship between antibiotic resistance, mucoviscosity, and biofilm formation impedes our abilities to effectively predict K. pneumoniae infection outcomes. The Multidrug-Resistant Organism Repository and Surveillance Network offers a unique opportunity into the genetic and phenotypic variabilities in the K. pneumoniae isolates. To this end, we compared the genetic profiles of these isolates with the phenotypic biofilm formation, percent mucoviscosity, and growth rates. There was a significant phenotype-genotype correlation with decreased biofilm formation and an insertion sequence in the transcriptional activator of the type III fimbrial system. Interestingly, the most mucoid strains in the populations were lacking the genetic element regulating the mucoid phenotype and three of these isolates were able to form robust biofilms. The combination of phenotypic, genomic, and image analyses revealed an intricate relation between growth, mucoviscosity and specific virulence-associated genetic determinants.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"151"},"PeriodicalIF":7.8,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11659406/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864932","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

Machine learning analysis of sex and menopausal differences in the gut microbiome in the HELIUS study. 对 HELIUS 研究中肠道微生物组的性别和更年期差异的机器学习分析。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-12-19 DOI: 10.1038/s41522-024-00628-z

Esther M C Vriend, Henrike Galenkamp, Hilde Herrema, Max Nieuwdorp, Bert-Jan H van den Born, Barbara J H Verhaar

{"title":"Machine learning analysis of sex and menopausal differences in the gut microbiome in the HELIUS study.","authors":"Esther M C Vriend, Henrike Galenkamp, Hilde Herrema, Max Nieuwdorp, Bert-Jan H van den Born, Barbara J H Verhaar","doi":"10.1038/s41522-024-00628-z","DOIUrl":"10.1038/s41522-024-00628-z","url":null,"abstract":"Sex differences in the gut microbiome have been examined previously, but results are inconsistent, often due to small sample sizes. We investigated sex and menopausal differences in the gut microbiome in a large multi-ethnic population cohort study, including 5166 participants. Using machine learning models, we revealed modest associations between sex and menopausal status, and gut microbiota composition (AUC 0.61-0.63). After adjustments for age, cardiovascular risk factors, and diet, a part of the associations of the highest-ranked gut microbes with sex were attenuated, but most associations remained significant. In contrast, most associations with menopausal status were driven by age and lost significance after adjustment. Using pathway analyses on metagenomic data, we identified sex differences in vitamin B6 synthesis and stachyose degradation pathways. Since some of sex differences in gut microbiome composition and function could not be explained by covariates, we recommend sex stratification in future microbiome studies.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"152"},"PeriodicalIF":7.8,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11659428/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864934","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

Root carbon inputs outweigh litter in shaping grassland soil microbiomes and ecosystem multifunctionality. 在塑造草地土壤微生物群和生态系统多功能性方面，根系碳输入超过了枯落物。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-12-19 DOI: 10.1038/s41522-024-00616-3

Jiayin Feng, Linlin Wang, Changchun Zhai, Lin Jiang, Yunfeng Yang, Xiaowei Huang, Jingyi Ru, Jian Song, Limei Zhang, Shiqiang Wan

{"title":"Root carbon inputs outweigh litter in shaping grassland soil microbiomes and ecosystem multifunctionality.","authors":"Jiayin Feng, Linlin Wang, Changchun Zhai, Lin Jiang, Yunfeng Yang, Xiaowei Huang, Jingyi Ru, Jian Song, Limei Zhang, Shiqiang Wan","doi":"10.1038/s41522-024-00616-3","DOIUrl":"10.1038/s41522-024-00616-3","url":null,"abstract":"Global change has the potential to alter soil carbon (C) inputs from above- and below-ground sources, with subsequent influences on soil microbial communities and ecological functions. Using data from a 13-year field experiment in a semi-arid grassland, we investigated the effects of litter manipulations and plant removal on soil microbiomes and ecosystem multifunctionality (EMF). Litter addition did not affect soil microbial α-diversity whereas litter removal reduced bacterial and fungal α-diversity due to decreased C substrate supply and soil moisture. By contrast, plant removal led to larger declines in bacterial and fungal α-diversity, lower microbial network stability and complexity. EMF was enhanced by litter addition but largely reduced by plant removal, primarily attributed to the loss of fungal diversity. Our findings underscore the importance of C inputs in shaping soil microbiomes and highlight the dominant role of plant root-derived C inputs in maintaining ecological functions under global change scenarios.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"150"},"PeriodicalIF":7.8,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11659613/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142864949","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

Saliva microbiome profiling by full-gene 16S rRNA Oxford Nanopore Technology versus Illumina MiSeq sequencing. 全基因16S rRNA牛津纳米孔技术与Illumina MiSeq测序的唾液微生物组分析。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-12-18 DOI: 10.1038/s41522-024-00634-1

Anders Esberg, Niklas Fries, Simon Haworth, Ingegerd Johansson

引用次数: 0

Probiotics as an adjunctive therapy in periodontitis treatment-reality or illusion-a clinical perspective. 益生菌作为牙周炎治疗的辅助疗法-现实或幻想-临床观点。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-12-16 DOI: 10.1038/s41522-024-00614-5

Lamyae Baddouri, Matthias Hannig

引用次数: 0

Author Correction: Rumen microbiome and fat deposition in sheep: insights from a bidirectional mendelian randomization study. 作者更正：绵羊瘤胃微生物组与脂肪沉积：双向泯灭随机研究的启示

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-12-14 DOI: 10.1038/s41522-024-00620-7

Yukun Zhang, Xiaoxue Zhang, Chong Li, Huibin Tian, Xiuxiu Weng, Changchun Lin, Deyin Zhang, Yuan Zhao, Xiaolong Li, Jiangbo Cheng, Liming Zhao, Dan Xu, Xiaobin Yang, Zhihua Jiang, Fadi Li, Weimin Wang

引用次数: 0

Long-chain 4-aminoquinolines inhibit filamentation and increase efficacy of nystatin against Candida albicans infections in vivo. 长链 4-氨基喹啉类抑制丝状化并提高奈司他丁对体内白色念珠菌感染的疗效。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-12-13 DOI: 10.1038/s41522-024-00608-3

Aleksandar Pavic, Natasa Radakovic, Ivana Moric, Nada Stankovic, Dejan Opsenica, Lidija Senerovic

{"title":"Long-chain 4-aminoquinolines inhibit filamentation and increase efficacy of nystatin against Candida albicans infections in vivo.","authors":"Aleksandar Pavic, Natasa Radakovic, Ivana Moric, Nada Stankovic, Dejan Opsenica, Lidija Senerovic","doi":"10.1038/s41522-024-00608-3","DOIUrl":"10.1038/s41522-024-00608-3","url":null,"abstract":"In exploring a growing demand for innovative approaches to tackle emerging and life threatening fungal diseases, we identified long-chain 4-aminoquinoline (4-AQ) derivatives as a new class of anti-virulence agents. For the first time, we demonstrated that 4-AQs effectively prevent filamentation of Candida albicans, a key virulence trait, under multiple triggering conditions. Selected 4-AQ derivatives inhibited filament formation in a zebrafish model of disseminated candidiasis at 1.56 µM, with no toxicity up to 50 µM. Combining nystatin with 4-AQs resulted in a 100% survival rate of infected embryos and complete eradication of C. albicans, compared to 65-75% survival with nystatin alone. The most potent 4-AQ derivatives also showed significant activity against C. albicans biofilms, with derivative 11 suppressing mixed C. albicans-Pseudomonas aeruginosa biofilms. This dual capability highlights the potential of 4-AQs as novel anti-virulence agents to enhance conventional antifungal therapies, marking a significant advance in treating complex fungal infections.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"146"},"PeriodicalIF":7.8,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11645407/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142822377","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

Pyoluteorin-deficient Pseudomonas protegens improves cooperation with Bacillus velezensis, biofilm formation, co-colonizing, and reshapes rhizosphere microbiome. pyoluteorindeficient假单胞菌蛋白改善与velezensis芽孢杆菌的合作，生物膜形成，共定植，并重塑根际微生物群。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-12-11 DOI: 10.1038/s41522-024-00627-0

Qian Zhao, Ruoyi Wang, Yan Song, Juan Lu, Bingjie Zhou, Fang Song, Lijuan Zhang, Qianqian Huang, Jing Gong, Jingjing Lei, Suomeng Dong, Qin Gu, Rainer Borriss, Xuewen Gao, Huijun Wu

{"title":"Pyoluteorin-deficient Pseudomonas protegens improves cooperation with Bacillus velezensis, biofilm formation, co-colonizing, and reshapes rhizosphere microbiome.","authors":"Qian Zhao, Ruoyi Wang, Yan Song, Juan Lu, Bingjie Zhou, Fang Song, Lijuan Zhang, Qianqian Huang, Jing Gong, Jingjing Lei, Suomeng Dong, Qin Gu, Rainer Borriss, Xuewen Gao, Huijun Wu","doi":"10.1038/s41522-024-00627-0","DOIUrl":"10.1038/s41522-024-00627-0","url":null,"abstract":"Plant-beneficial Pseudomonas and Bacillus have been extensively studied and applied in biocontrol of plant diseases. However, there is less known about their interaction within two-strain synthetic communities (SynCom). Our study revealed that Pseudomonas protegens Pf-5 inhibits the growth of several Bacillus species, including Bacillus velezensis. We established a two-strain combination of Pf-5 and DMW1 to elucidate the interaction. In this combination, pyoluteorin conferred the competitive advantage of Pf-5. Noteworthy, pyoluteorin-deficient Pf-5 cooperated with DMW1 in biofilm formation, production of metabolites, root colonization, tomato bacterial wilt disease control, as well as in cooperation with beneficial bacteria in tomato rhizosphere, such as Bacillus spp. RNA-seq analysis and RT-qPCR also proved the pyoluteorin-deficient Pf-5 mutant improved cell motility and metabolite production. This study suggests that the cooperative effect of Bacillus-Pseudomonas consortia depends on the balance of pyoluteorin. Our finding needs to be considered in developing efficient SynCom in sustainable agriculture.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"145"},"PeriodicalIF":7.8,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11634903/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142813843","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