npj Biofilms and Microbiomes最新文献

Author Correction: Metaproteomic portrait of the healthy human gut microbiota.

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-01-03 DOI: 10.1038/s41522-024-00635-0

Alessandro Tanca, Antonio Palomba, Giovanni Fiorito, Marcello Abbondio, Daniela Pagnozzi, Sergio Uzzau

引用次数: 0

PreLect: Prevalence leveraged consistent feature selection decodes microbial signatures across cohorts.

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-01-03 DOI: 10.1038/s41522-024-00598-2

Yin-Cheng Chen, Yin-Yuan Su, Tzu-Yu Chu, Ming-Fong Wu, Chieh-Chun Huang, Chen-Ching Lin

{"title":"PreLect: Prevalence leveraged consistent feature selection decodes microbial signatures across cohorts.","authors":"Yin-Cheng Chen, Yin-Yuan Su, Tzu-Yu Chu, Ming-Fong Wu, Chieh-Chun Huang, Chen-Ching Lin","doi":"10.1038/s41522-024-00598-2","DOIUrl":"10.1038/s41522-024-00598-2","url":null,"abstract":"The intricate nature of microbiota sequencing data-high dimensionality and sparsity-presents a challenge in identifying informative and reproducible microbial features for both research and clinical applications. Addressing this, we introduce PreLect, an innovative feature selection framework that harnesses microbes' prevalence to facilitate consistent selection in sparse microbiota data. Upon rigorous benchmarking against established feature selection methodologies across 42 microbiome datasets, PreLect demonstrated superior classification capabilities compared to statistical methods and outperformed machine learning-based methods by selecting features with greater prevalence and abundance. A significant strength of PreLect lies in its ability to reliably identify reproducible microbial features across varied cohorts. Applied to colorectal cancer, PreLect identifies key microbes and highlights crucial pathways, such as lipopolysaccharide and glycerophospholipid biosynthesis, in cancer progression. This case study exemplifies PreLect's utility in discerning clinically relevant microbial signatures. In summary, PreLect's accuracy and robustness make it a significant advancement in the analysis of complex microbiota data.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"3"},"PeriodicalIF":7.8,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11698977/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142927560","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

The dynamic oral-gastric microbial axis connects oral and gastric health: current evidence and disputes.

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-01-02 DOI: 10.1038/s41522-024-00623-4

Mengying Xia, Lei Lei, Linyong Zhao, Wenqing Xu, Hongyu Zhang, Mingming Li, Jiankun Hu, Ran Cheng, Tao Hu

{"title":"The dynamic oral-gastric microbial axis connects oral and gastric health: current evidence and disputes.","authors":"Mengying Xia, Lei Lei, Linyong Zhao, Wenqing Xu, Hongyu Zhang, Mingming Li, Jiankun Hu, Ran Cheng, Tao Hu","doi":"10.1038/s41522-024-00623-4","DOIUrl":"10.1038/s41522-024-00623-4","url":null,"abstract":"Emerging evidence indicates that oral microbes are closely related to gastric microbes and gastric lesions, including gastric atrophy, intestinal metaplasia and gastric cancer (GC). Helicobacter pylori is a key pathogen involved in GC. However, the increasing prevalence of H. pylori-negative GC and gastric dysbiosis in GC patients emphasize the potential role of other microbial factors. In this review, we discussed the current evidence about the relationship between the oral-gastric microbial axis and oral and gastric health. Epidemiologic evidence indicates that poor oral hygiene is related to greater GC risk. Multiple oral-associated microbes are enriched in the stomach of GC patients. Once colonizing the stomach, oral-associated microbes Streptococcus anginosus and Prevotella melaninogenica, are involved in gastric inflammation or carcinogenesis. Microbial metabolites such as lactate, nitrite, and acetaldehyde promote malignant transformation. The stomach, as a checkpoint of microbial transmission in the digestive tract, is of great importance since the link between oral microbes and intestinal diseases has been emphasized. Still, new technologies and standardized metrics are necessary to identify potential pathogenetic microbes for GC and the core microbiota, interactions, richness, colonization, location and effect (CIRCLE). In the future, oral microbes could be candidates for noninvasive indicators to predict gastric diseases.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"1"},"PeriodicalIF":7.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11696714/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142922336","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

Air pollution modifies colonisation factors in beneficial symbiont Snodgrassella and disrupts the bumblebee gut microbiome.

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2025-01-02 DOI: 10.1038/s41522-024-00632-3

Hannah R Sampson, Natalie Allcock, Eamonn B Mallon, Julian M Ketley, Julie A Morrissey

{"title":"Air pollution modifies colonisation factors in beneficial symbiont Snodgrassella and disrupts the bumblebee gut microbiome.","authors":"Hannah R Sampson, Natalie Allcock, Eamonn B Mallon, Julian M Ketley, Julie A Morrissey","doi":"10.1038/s41522-024-00632-3","DOIUrl":"10.1038/s41522-024-00632-3","url":null,"abstract":"Particulate air pollutants, a major air pollution component, are detrimental to human health and a significant risk to wildlife and ecosystems globally. Here we report the effects of particulate pollutant black carbon on the beneficial gut microbiome of important global insect pollinator, the buff-tailed bumblebee (Bombus terrestris). Our data shows that exposure to black carbon particulates alters biofilm structure, gene expression and initial adhesion of beneficial bee gut coloniser, Snodgrassella alvi. Exposure of adult Bombus terrestris to non-toxic black carbon particulates significantly increased viable bacteria on MRS agar and 16S absolute abundance of beneficial bacteria Bombilactobacillus in Post-treated bumblebees compared to Pre-treated, demonstrating disruption of the bumblebee gut microbiome. These findings show that black carbon exposure has direct, measurable effects on bees' beneficial commensal bacteria and microbiome. Together these data highlight that black carbon, a single type of particulate pollution, is an underexplored risk to insect pollinator health.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"11 1","pages":"2"},"PeriodicalIF":7.8,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11699285/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142927557","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

Author Correction: Gingival spatial analysis reveals geographic immunological variation in a microbiota-dependent and -independent manner.

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-12-31 DOI: 10.1038/s41522-024-00636-z

Yasmin Jaber, Avital Sarusi-Portuguez, Yasmin Netanely, Reem Naamneh, Shahd Yacoub, Or Saar, Nadeem Darawshi, Luba Eli-Berchoer, Hagit Shapiro, Eran Elinav, Asaf Wilensky, Avi-Hai Hovav

引用次数: 0

Clostridium difficile-derived membrane vesicles promote fetal growth restriction via inhibiting trophoblast motility through PPARγ/RXRα/ANGPTL4 axis.

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-12-31 DOI: 10.1038/s41522-024-00630-5

Zhiqiang Zha, Chunhong Jia, Ruisi Zhou, Qinlan Yin, Yu Hu, Zhipeng Huang, Linyu Peng, Yichi Zhang, Xiaowei Qiu, Ying Chen, Yawen Zhong, Yu Wang, Menglan Pang, Shijing Lu, Chao Sheng, Liping Huang

{"title":"Clostridium difficile-derived membrane vesicles promote fetal growth restriction via inhibiting trophoblast motility through PPARγ/RXRα/ANGPTL4 axis.","authors":"Zhiqiang Zha, Chunhong Jia, Ruisi Zhou, Qinlan Yin, Yu Hu, Zhipeng Huang, Linyu Peng, Yichi Zhang, Xiaowei Qiu, Ying Chen, Yawen Zhong, Yu Wang, Menglan Pang, Shijing Lu, Chao Sheng, Liping Huang","doi":"10.1038/s41522-024-00630-5","DOIUrl":"10.1038/s41522-024-00630-5","url":null,"abstract":"Fetal growth restriction (FGR) is a common complication of pregnancy, which seriously endangers fetal health and still lacks effective therapeutic targets. Clostridium difficile (C. difficile) is associated with fetal birth weight, and its membrane vesicles (MVs) are pathogenic vectors. However, the role of C. difficile and its MVs in FGR remains unclear. Here we found that supplementation with C. difficile altered the characteristics of gut microbiota and reduced the birth weight in mice. Interestingly, C. difficile MVs entered placenta, inhibited trophoblast motility, and induced fetal weight loss in mice. Mechanistically, C. difficile MVs activated the PPAR pathway via enhancing the transcriptional activity of PPARγ promoter, consequently inhibiting trophoblast motility. Moreover, PPARγ expression was significantly elevated in FGR placenta, and negatively correlated with fetal birth weight. Together, our findings reveal the significance of C. difficile and its MVs in FGR, providing new insights into the mechanisms of FGR development.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"158"},"PeriodicalIF":7.8,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11688498/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142909898","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

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.

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.

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.

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