npj Biofilms and Microbiomes最新文献_第9页

The impact of antioxidant-ciprofloxacin combinations on the evolution of antibiotic resistance in Pseudomonas aeruginosa biofilms. 抗氧化剂-环丙沙星组合对铜绿假单胞菌生物膜中抗生素耐药性演变的影响

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-12-30 DOI: 10.1038/s41522-024-00640-3

Doaa Higazy, Marwa N Ahmed, Oana Ciofu

{"title":"The impact of antioxidant-ciprofloxacin combinations on the evolution of antibiotic resistance in Pseudomonas aeruginosa biofilms.","authors":"Doaa Higazy, Marwa N Ahmed, Oana Ciofu","doi":"10.1038/s41522-024-00640-3","DOIUrl":"10.1038/s41522-024-00640-3","url":null,"abstract":"The evolution of antimicrobial resistance (AMR) in biofilms, driven by mechanisms like oxidative stress, is a major challenge. This study investigates whether antioxidants (AOs) such as N-acetyl-cysteine (NAC) and Edaravone (ED) can reduce AMR in Pseudomonas aeruginosa biofilms exposed to sub-inhibitory concentrations of ciprofloxacin (CIP). In vitro experimental evolution studies were conducted using flow cells and glass beads biofilm models. Results showed that combining CIP with antioxidants (CIP-AOs) effectively reduced the development of CIP resistance. Isolates from biofilms treated with CIP-AO had significantly lower minimum inhibitory concentrations (MICs) of CIP compared to those treated with CIP alone. Whole-genome sequencing (WGS) revealed mutations in the negative regulators of efflux pumps, nfxB, and nalC, in CIP-only treated biofilm populations. The occurrence of nfxB mutations was significantly lower in flow cell biofilms treated with CIP-AO compared to CIP alone. These findings suggest that antioxidants could play a role in mitigating AMR development in biofilms.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"156"},"PeriodicalIF":7.8,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11685532/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142907362","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

Structure and composition of early biofilms formed on dental implants are complex, diverse, subject-specific and dynamic. 牙种植体上形成的早期生物膜结构和组成复杂多样，具有主体特异性和动态性。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-12-24 DOI: 10.1038/s41522-024-00624-3

Sophie Dieckow, Szymon P Szafrański, Jasmin Grischke, Taoran Qu, Katharina Doll-Nikutta, Matthias Steglich, Ines Yang, Susanne Häussler, Meike Stiesch

{"title":"Structure and composition of early biofilms formed on dental implants are complex, diverse, subject-specific and dynamic.","authors":"Sophie Dieckow, Szymon P Szafrański, Jasmin Grischke, Taoran Qu, Katharina Doll-Nikutta, Matthias Steglich, Ines Yang, Susanne Häussler, Meike Stiesch","doi":"10.1038/s41522-024-00624-3","DOIUrl":"10.1038/s41522-024-00624-3","url":null,"abstract":"Biofilm-associated peri-implant infections pose a major problem in modern medicine. The understanding of biofilm development is hampered by biofilm complexity and the lack of robust clinical models. This study comprehensively characterized the dynamics of early biofilm formation in the transmucosal passage of implant abutments in 12 patients. Biofilm structures and compositions were complex, diverse, subject-specific and dynamic. A total of 371 different bacterial species were detected. 100 phylogenetically diverse unnamed species and 35 taxonomically diverse disease-associated species comprised an average 4.3% and 3.1% of the community, respectively, but reached up to 12.7% and 21.7% in some samples. Oral taxa formed numerous positive associations and clusters and were characterized by a high potential for metabolic interactions. The subspecies diversity was highly patient-specific and species-dependent, with 1427 ASVs identified in total. The unprecedented depth of early biofilm characterization in this study will support the development of individualized preventive and early diagnostic strategies.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"155"},"PeriodicalIF":7.8,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11668855/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142886100","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

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