npj Biofilms and Microbiomes最新文献_第4页

A functionally augmented carbohydrate utilization locus from herbivore gut microbiota fueled by dietary β-glucans. 来自食草动物肠道微生物群的功能增强型碳水化合物利用位点，由食物中的β-葡聚糖提供燃料。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-10-14 DOI: 10.1038/s41522-024-00578-6

Fernanda Mandelli, Marcele Pandeló Martins, Mariana Chinaglia, Evandro Antonio de Lima, Mariana Abrahão Bueno Morais, Tatiani Brenelli Lima, Lucélia Cabral, Renan Augusto Siqueira Pirolla, Felipe Jun Fuzita, Douglas Antônio Alvaredo Paixão, Maxuel de Oliveira Andrade, Lucia Daniela Wolf, Plinio Salmazo Vieira, Gabriela Felix Persinoti, Mario Tyago Murakami

{"title":"A functionally augmented carbohydrate utilization locus from herbivore gut microbiota fueled by dietary β-glucans.","authors":"Fernanda Mandelli, Marcele Pandeló Martins, Mariana Chinaglia, Evandro Antonio de Lima, Mariana Abrahão Bueno Morais, Tatiani Brenelli Lima, Lucélia Cabral, Renan Augusto Siqueira Pirolla, Felipe Jun Fuzita, Douglas Antônio Alvaredo Paixão, Maxuel de Oliveira Andrade, Lucia Daniela Wolf, Plinio Salmazo Vieira, Gabriela Felix Persinoti, Mario Tyago Murakami","doi":"10.1038/s41522-024-00578-6","DOIUrl":"https://doi.org/10.1038/s41522-024-00578-6","url":null,"abstract":"Gut microbiota members from the Bacteroidota phylum play a pivotal role in mammalian health and metabolism. They thrive in this diverse ecosystem due to their notable ability to cope with distinct recalcitrant dietary glycans via polysaccharide utilization loci (PULs). Our study reveals that a PUL from an herbivore gut bacterium belonging to the Bacteroidota phylum, with a gene composition similar to that in the human gut, exhibits extended functionality. While the human gut PUL targets mixed-linkage β-glucans specifically, the herbivore gut PUL also efficiently processes linear and substituted β-1,3-glucans. This gain of function emerges from molecular adaptations in recognition proteins and carbohydrate-active enzymes, including a β-glucosidase specialized for β(1,6)-glucosyl linkages, a typical substitution in β(1,3)-glucans. These findings broaden the existing model for non-cellulosic β-glucans utilization by gut bacteria, revealing an additional layer of functional and evolutionary complexity within the gut microbiota, beyond conventional gene insertions/deletions to intricate biochemical interactions.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"105"},"PeriodicalIF":7.8,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11471779/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142471036","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

Gut and oral microbiota in gynecological cancers: interaction, mechanism, and therapeutic value. 妇科癌症中的肠道和口腔微生物群：相互作用、机制和治疗价值。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-10-10 DOI: 10.1038/s41522-024-00577-7

Jian Wu, Jiarui Li, Meina Yan, Ze Xiang

引用次数: 0

Secreted nucleases reclaim extracellular DNA during biofilm development. 分泌的核酸酶在生物膜发育过程中回收细胞外 DNA。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-10-07 DOI: 10.1038/s41522-024-00575-9

Stephen M Lander, Garth Fisher, Blake A Everett, Peter Tran, Arthur Prindle

引用次数: 0

Dynamics of drinking water biofilm formation associated with Legionella spp. colonization. 与军团菌定植相关的饮用水生物膜形成动态。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-10-06 DOI: 10.1038/s41522-024-00573-x

Céline Margot, William Rhoads, Marco Gabrielli, Margot Olive, Frederik Hammes

{"title":"Dynamics of drinking water biofilm formation associated with Legionella spp. colonization.","authors":"Céline Margot, William Rhoads, Marco Gabrielli, Margot Olive, Frederik Hammes","doi":"10.1038/s41522-024-00573-x","DOIUrl":"10.1038/s41522-024-00573-x","url":null,"abstract":"Understanding how Legionella spp. proliferate in multispecies biofilms is essential to develop strategies to control their presence in building plumbing. Here, we analyzed biofilm formation and Legionella spp. colonization on new plumbing material during 8 weeks. Biofilm formation was characterized by an initial increase in intact cell concentrations up to 9.5 × 105 cells/cm2, followed by a steady decrease. We identified Comamonas, Caulobacter, Schlegella, Blastomonas and Methyloversatilis as pioneer genera in the biofilm formation process. Importantly, L. pneumophila was the dominant Legionella spp. and rapidly colonized the biofilms, with culturable cell concentrations peaking at 3.1 × 104 MPN/cm2 after 4 weeks already. Moreover, several Legionella species co-occurred and had distinct dynamics of biofilm colonization. Vermamoeba vermiformis (V. vermiformis) was the dominant protist identified with 18S rRNA gene amplicon sequencing. Together our results highlight that biofilm formation upon introduction of new building plumbing material is a dynamic process where pathogenic Legionella species can be part of the earliest colonizers.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"101"},"PeriodicalIF":7.8,"publicationDate":"2024-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11455961/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142378144","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

Staphylococcus aureus SaeRS impairs macrophage immune functions through bacterial clumps formation in the early stage of infection. 金黄色葡萄球菌 SaeRS 在感染早期通过细菌团块的形成损害巨噬细胞的免疫功能。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-10-06 DOI: 10.1038/s41522-024-00576-8

Mingzhang Li, Boyong Wang, Jiani Chen, Luhui Jiang, Yawen Zhou, Geyong Guo, Feng Jiang, Yujie Hu, Changming Wang, Yi Yang, Jin Tang, Pei Han, Jinlong Yu, Hao Shen

{"title":"Staphylococcus aureus SaeRS impairs macrophage immune functions through bacterial clumps formation in the early stage of infection.","authors":"Mingzhang Li, Boyong Wang, Jiani Chen, Luhui Jiang, Yawen Zhou, Geyong Guo, Feng Jiang, Yujie Hu, Changming Wang, Yi Yang, Jin Tang, Pei Han, Jinlong Yu, Hao Shen","doi":"10.1038/s41522-024-00576-8","DOIUrl":"10.1038/s41522-024-00576-8","url":null,"abstract":"The Staphylococcus aureus (S. aureus) SaeRS two-component system (TCS) regulates over 20 virulence factors. While its impact on chronic infection has been thoroughly discussed, its role in the early stage of infection remains elusive. Since macrophages serve as the primary immune defenders at the onset of infection, this study investigates the influence of SaeRS on macrophage functions and elucidates the underlying mechanisms. Macrophage expression of inflammatory and chemotactic factors, phagocytosis, and bactericidal activity against S. aureus were assessed, along with the evaluation of cellular oxidative stress. SaeRS was found to impair macrophage function. Mechanistically, SaeRS inhibited NF-κB pathway activation via toll-like receptor 2 (TLR2). Its immune-modulating effect could partially be explained by the strengthened biofilm formation. More importantly, we found SaeRS compromised macrophage immune functions at early infection stages even prior to biofilm formation. These early immune evasion effects were dependent on bacterial clumping as cytokine secretion, phagocytosis, and bactericidal activity were repaired when clumping was inhibited. We speculate that the bacterial clumping-mediated antigen mask is responsible for SaeRS-mediated immune evasion at the early infection stage. In vivo, ΔsaeRS infection was cleared earlier, accompanied by early pro-inflammatory cytokines production, and increased tissue oxidative stress. Subsequently, macrophages transitioned to an anti-inflammatory state, thereby promoting tissue repair. In summary, our findings underscore the critical role of the SaeRS TCS in S. aureus pathogenicity, particularly during early infection, which is likely initiated by SaeRS-mediated bacterial clumping.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"102"},"PeriodicalIF":7.8,"publicationDate":"2024-10-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11456606/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142381355","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

Adaptation of a methanogen to Fe⁰ corrosion via direct contact. 甲烷发生器通过直接接触适应 Fe0 腐蚀。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-10-04 DOI: 10.1038/s41522-024-00574-w

Satoshi Kawaichi, Rhitu Kotoky, Jacek Fiutowski, Amelia-Elena Rotaru

引用次数: 0

Bacillus subtilis EpsA-O: A novel exopolysaccharide structure acting as an efficient adhesive in biofilms. 枯草杆菌 EpsA-O：一种新型外多糖结构可作为生物膜中的高效粘合剂。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-10-02 DOI: 10.1038/s41522-024-00555-z

Iztok Dogsa, Barbara Bellich, Mojca Blaznik, Cristina Lagatolla, Neil Ravenscroft, Roberto Rizzo, David Stopar, Paola Cescutti

{"title":"Bacillus subtilis EpsA-O: A novel exopolysaccharide structure acting as an efficient adhesive in biofilms.","authors":"Iztok Dogsa, Barbara Bellich, Mojca Blaznik, Cristina Lagatolla, Neil Ravenscroft, Roberto Rizzo, David Stopar, Paola Cescutti","doi":"10.1038/s41522-024-00555-z","DOIUrl":"10.1038/s41522-024-00555-z","url":null,"abstract":"Extracellular polysaccharides are crucial components for biofilm development. Although Bacillus subtilis is one of the most characterized Gram-positive biofilm model system, the structure-function of its exopolysaccharide, EpsA-O, remains to be elucidated. By combining chemical analysis, NMR spectroscopy, rheology, and molecular modeling, high-resolution data of EpsA-O structure from atom to supramolecular scale was obtained. The repeating unit is composed of the trisaccharide backbone [→3)-β-D-QuipNAc4NAc-(1→3)-β-D-GalpNAc-(1→3)-α-D-GlcpNAc-(1]n, and the side chain β-D-Galp(3,4-S-Pyr)-(1→6)-β-D-Galp(3,4-S-Pyr)-(1→6)-α-D-Galp-(1→ linked to C4 of GalNAc. Close agreement between the primary structure and rheological behavior allowed us to model EpsA-O macromolecular and supramolecular solution structure, which can span the intercellular space forming a gel that leads to a complex 3D biofilm network as corroborated by a mutant strain with impaired ability to produce EpsA-O. This is a comprehensive structure-function investigation of the essential biofilm adhesive exopolysaccharide that will serve as a useful guide for future studies in biofilm architecture formation.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"98"},"PeriodicalIF":7.8,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11447030/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142365959","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

Colon or semicolon: gut sampling microdevices for omics insights. 结肠还是分号：肠道取样微型设备，用于omics洞察。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-10-02 DOI: 10.1038/s41522-024-00536-2

Sunil Nagpal, Sarvesh Kumar Srivastava

引用次数: 0

Metabolic interactions shape emergent biofilm structures in a conceptual model of gut mucosal bacterial communities. 在肠道粘膜细菌群落的概念模型中，代谢相互作用形成了新出现的生物膜结构。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-10-02 DOI: 10.1038/s41522-024-00572-y

Amin Valiei, Andrew Dickson, Javad Aminian-Dehkordi, Mohammad R K Mofrad

{"title":"Metabolic interactions shape emergent biofilm structures in a conceptual model of gut mucosal bacterial communities.","authors":"Amin Valiei, Andrew Dickson, Javad Aminian-Dehkordi, Mohammad R K Mofrad","doi":"10.1038/s41522-024-00572-y","DOIUrl":"10.1038/s41522-024-00572-y","url":null,"abstract":"The gut microbiome plays a major role in human health; however, little is known about the structural arrangement of microbes and factors governing their distribution. In this work, we present an in silico agent-based model (ABM) to conceptually simulate the dynamics of gut mucosal bacterial communities. We explored how various types of metabolic interactions, including competition, neutralism, commensalism, and mutualism, affect community structure, through nutrient consumption and metabolite exchange. Results showed that, across scenarios with different initial species abundances, cross-feeding promotes species coexistence. Morphologically, competition and neutralism resulted in segregation, while mutualism and commensalism fostered high intermixing. In addition, cooperative relations resulted in community properties with little sensitivity to the selective uptake of metabolites produced by the host. Moreover, metabolic interactions strongly influenced colonization success following the invasion of newcomer species. These results provide important insights into the utility of ABM in deciphering complex microbiome patterns.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"99"},"PeriodicalIF":7.8,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11447261/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142365961","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

A population-scale analysis of 36 gut microbiome studies reveals universal species signatures for common diseases. 对 36 项肠道微生物组研究进行的群体规模分析揭示了常见疾病的普遍物种特征。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-10-01 DOI: 10.1038/s41522-024-00567-9

Wen Sun, Yue Zhang, Ruochun Guo, Shanshan Sha, Changming Chen, Hayan Ullah, Yan Zhang, Jie Ma, Wei You, Jinxin Meng, Qingbo Lv, Lin Cheng, Shao Fan, Rui Li, Xiaohong Mu, Shenghui Li, Qiulong Yan

{"title":"A population-scale analysis of 36 gut microbiome studies reveals universal species signatures for common diseases.","authors":"Wen Sun, Yue Zhang, Ruochun Guo, Shanshan Sha, Changming Chen, Hayan Ullah, Yan Zhang, Jie Ma, Wei You, Jinxin Meng, Qingbo Lv, Lin Cheng, Shao Fan, Rui Li, Xiaohong Mu, Shenghui Li, Qiulong Yan","doi":"10.1038/s41522-024-00567-9","DOIUrl":"10.1038/s41522-024-00567-9","url":null,"abstract":"The gut microbiome has been implicated in various human diseases, though findings across studies have shown considerable variability. In this study, we reanalyzed 6314 publicly available fecal metagenomes from 36 case-control studies on different diseases to investigate microbial diversity and disease-shared signatures. Using a unified analysis pipeline, we observed reduced microbial diversity in many diseases, while some exhibited increased diversity. Significant alterations in microbial communities were detected across most diseases. A meta-analysis identified 277 disease-associated gut species, including numerous opportunistic pathogens enriched in patients and a depletion of beneficial microbes. A random forest classifier based on these signatures achieved high accuracy in distinguishing diseased individuals from controls (AUC = 0.776) and high-risk patients from controls (AUC = 0.825), and it also performed well in external cohorts. These results offer insights into the gut microbiome's role in common diseases in the Chinese population and will guide personalized disease management strategies.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":"10 1","pages":"96"},"PeriodicalIF":7.8,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11442664/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142351060","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