npj Biofilms and Microbiomes最新文献

Microbial diversity and secondary metabolism potential in relation to dark alterations in Paleolithic Lascaux Cave. 旧石器时代拉斯科洞穴中与黑暗变化有关的微生物多样性和次级代谢潜力。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-11-06 DOI: 10.1038/s41522-024-00589-3

Zélia Bontemps, Danis Abrouk, Sita Venier, Pierre Vergne, Serge Michalet, Gilles Comte, Yvan Moënne-Loccoz, Mylène Hugoni

{"title":"Microbial diversity and secondary metabolism potential in relation to dark alterations in Paleolithic Lascaux Cave.","authors":"Zélia Bontemps, Danis Abrouk, Sita Venier, Pierre Vergne, Serge Michalet, Gilles Comte, Yvan Moënne-Loccoz, Mylène Hugoni","doi":"10.1038/s41522-024-00589-3","DOIUrl":"10.1038/s41522-024-00589-3","url":null,"abstract":"Tourism in Paleolithic caves can cause an imbalance in cave microbiota and lead to cave wall alterations, such as dark zones. However, the mechanisms driving dark zone formation remain unclear. Using shotgun metagenomics in Lascaux Cave's Apse and Passage across two years, we tested metabarcoding-derived functional hypotheses regarding microbial diversity and metabolic potential in dark zones vs unmarked surfaces nearby. Taxonomic and functional metagenomic profiles were consistent across years but divergent between cave locations. Aromatic compound degradation genes were prevalent inside and outside dark zones, as expected from past biocide usage. Dark zones exhibited enhanced pigment biosynthesis potential (melanin and carotenoids) and melanin was evidenced chemically, while unmarked surfaces showed genes for antimicrobials production, suggesting that antibiosis might restrict the development of pigmented microorganisms and dark zone extension. Thus, this work revealed key functional microbial traits associated with dark zone formation, which helps understand cave alteration processes under severe anthropization.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":null,"pages":null},"PeriodicalIF":7.8,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11541736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142591321","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

Large-scale metagenomic assembly provide new insights into the genetic evolution of gut microbiomes in plateau ungulates. 大规模元基因组组装为了解高原蹄类动物肠道微生物群的遗传进化提供了新的视角。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-11-06 DOI: 10.1038/s41522-024-00597-3

Bo Xu, Pengfei Song, Feng Jiang, Zhenyuan Cai, Haifeng Gu, Hongmei Gao, Bin Li, Chengbo Liang, Wen Qin, Jingjie Zhang, Jingyan Yan, Daoxin Liu, Guo Sun, Tongzuo Zhang

{"title":"Large-scale metagenomic assembly provide new insights into the genetic evolution of gut microbiomes in plateau ungulates.","authors":"Bo Xu, Pengfei Song, Feng Jiang, Zhenyuan Cai, Haifeng Gu, Hongmei Gao, Bin Li, Chengbo Liang, Wen Qin, Jingjie Zhang, Jingyan Yan, Daoxin Liu, Guo Sun, Tongzuo Zhang","doi":"10.1038/s41522-024-00597-3","DOIUrl":"10.1038/s41522-024-00597-3","url":null,"abstract":"Trillions of microbes colonize the ungulate gastrointestinal tract, playing a pivotal role in enhancing host nutrient utilization by breaking down cellulose and hemicellulose present in plants. Here, through large-scale metagenomic assembly, we established a catalog of 131,416 metagenome-assembled genomes (MAGs) and 11,175 high-quality species-level genome bins (SGBs) from 17 species of ungulates in China. Our study revealed the convergent evolution of high relative abundances of carbohydrate-active enzymes (CAZymes) in the gut microbiomes of plateau-dwelling ungulates. Notably, two significant factors contribute to this phenotype: structural variations in their gut microbiome genomes, which contain more CAZymes, and the presence of novel gut microbiota species, particularly those in the genus Cryptobacteroides, which are undergoing independent rapid evolution and speciation and have higher gene densities of CAZymes. Furthermore, these enrichment CAZymes in the gut microbiomes are highly enrichment in known metabolic pathways for short-chain fatty acid (SCFA) production. Our findings not only provide a valuable genomic resource for understanding the gut microbiomes of ungulates but also offer fresh insights into the interaction between gut microbiomes and their hosts, as well as the co-adaptation of hosts and their gut microbiomes to their environments.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":null,"pages":null},"PeriodicalIF":7.8,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11541592/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142591319","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

Combating biofilm-associated Klebsiella pneumoniae infections using a bovine microbial enzyme. 利用牛微生物酶对抗生物膜相关的肺炎克雷伯菌感染。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-11-05 DOI: 10.1038/s41522-024-00593-7

Reshma Ramakrishnan, Abhilash V Nair, Kirti Parmar, Raju S Rajmani, Dipshikha Chakravortty, Debasis Das

{"title":"Combating biofilm-associated Klebsiella pneumoniae infections using a bovine microbial enzyme.","authors":"Reshma Ramakrishnan, Abhilash V Nair, Kirti Parmar, Raju S Rajmani, Dipshikha Chakravortty, Debasis Das","doi":"10.1038/s41522-024-00593-7","DOIUrl":"10.1038/s41522-024-00593-7","url":null,"abstract":"The emergence of multidrug-resistant Klebsiella pneumoniae poses significant clinical challenges with limited treatment options. Biofilm is an important virulence factor of K. pneumoniae, serving as a protective barrier against antibiotics and the immune system. Here, we present the remarkable ability of a bovine microbial enzyme to prevent biofilm formation (IC50 2.50 μM) and degrade pre-formed K. pneumoniae biofilms (EC50 1.94 μM) by degrading the matrix polysaccharides. The treatment was effective against four different clinical K. pneumoniae isolates tested. Moreover, the enzyme significantly improved the biofilm sensitivity of a poorly performing broad-spectrum antibiotic, meropenem, and immune cells, resulting in facile biofilm clearance from the mouse wound infection. Notably, well-known powerful enzymes of the same class, cellulase, and α-amylase, were nearly inactive against the K. pneumoniae biofilms. The enzyme exhibited antibiofilm activity without showing toxicity to the mammalian and microbial cells, highlighting the potential of the enzyme for in vivo applications.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":null,"pages":null},"PeriodicalIF":7.8,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11538315/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142583579","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

Kinetics of imidazole propionate from orally delivered histidine in mice and humans. 小鼠和人类口服组氨酸咪唑丙酸盐的动力学。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-11-04 DOI: 10.1038/s41522-024-00592-8

Moritz V Warmbrunn, Ilias Attaye, Anthony Horak, Rakhee Banerjee, William J Massey, Venkateshwari Varadharajan, Elena Rampanelli, Youling Hao, Sumita Dutta, Ina Nemet, Judith Aron-Wisnewsky, Karine Clément, Annefleur Koopen, Koen Wortelboer, Per-Olof Bergh, Mark Davids, Nadia Mohamed, E Marleen Kemper, Stanley Hazen, Albert K Groen, Daniel H van Raalte, Hilde Herrema, Fredrik Backhed, J Mark Brown, Max Nieuwdorp

{"title":"Kinetics of imidazole propionate from orally delivered histidine in mice and humans.","authors":"Moritz V Warmbrunn, Ilias Attaye, Anthony Horak, Rakhee Banerjee, William J Massey, Venkateshwari Varadharajan, Elena Rampanelli, Youling Hao, Sumita Dutta, Ina Nemet, Judith Aron-Wisnewsky, Karine Clément, Annefleur Koopen, Koen Wortelboer, Per-Olof Bergh, Mark Davids, Nadia Mohamed, E Marleen Kemper, Stanley Hazen, Albert K Groen, Daniel H van Raalte, Hilde Herrema, Fredrik Backhed, J Mark Brown, Max Nieuwdorp","doi":"10.1038/s41522-024-00592-8","DOIUrl":"10.1038/s41522-024-00592-8","url":null,"abstract":"Imidazole Propionate (ImP), a gut-derived metabolite from histidine, affects insulin signaling in mice and is elevated in type 2 diabetes (T2D). However, the source of histidine and the role of the gut microbiota remain unclear. We conducted an intervention study in mice and humans, comparing ImP kinetics in mice on a high-fat diet with varying histidine levels and antibiotics, and assessed ImP levels in healthy and T2D subjects with histidine supplementation. Results show that dietary histidine is metabolized to ImP, with antibiotic-induced gut microbiota suppression reducing ImP levels in mice. In contrast, oral histidine supplementation resulted in increases in circulating ImP levels in humans, whereas antibiotic treatment increased ImP levels, which was associated with a bloom of several bacterial genera that have been associated with ImP production, such as Lactobacilli. Our findings highlight the gut microbiota's crucial role in regulating ImP and the complexity of translating mouse models to humans.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":null,"pages":null},"PeriodicalIF":7.8,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11535228/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142576712","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

Autoinducer-2 relieves soil stress-induced dormancy of Bacillus velezensis by modulating sporulation signaling. 自诱导因子-2通过调节孢子信号转导缓解土壤胁迫诱导的韦氏芽孢杆菌休眠。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-11-03 DOI: 10.1038/s41522-024-00594-6

Qin Xiong, Huihui Zhang, Xia Shu, Xiting Sun, Haichao Feng, Zhihui Xu, Ákos T Kovács, Ruifu Zhang, Yunpeng Liu

{"title":"Autoinducer-2 relieves soil stress-induced dormancy of Bacillus velezensis by modulating sporulation signaling.","authors":"Qin Xiong, Huihui Zhang, Xia Shu, Xiting Sun, Haichao Feng, Zhihui Xu, Ákos T Kovács, Ruifu Zhang, Yunpeng Liu","doi":"10.1038/s41522-024-00594-6","DOIUrl":"10.1038/s41522-024-00594-6","url":null,"abstract":"The collective behavior of bacteria is regulated by quorum sensing (QS). Autoinducer-2 (AI-2) is a common QS signal that regulates the behavior of both Gram-positive and Gram-negative bacteria. Despite the plethora of processes described to be influenced by AI-2 in diverse Gram-negative bacteria, the AI-2-regulated processes in Bacilli are relatively unexplored. Here, we describe a novel function for AI-2 in Bacillus velezensis SQR9 related to the sporulation. AI-2 inhibited the initiation of sporulation through the phosphatase RapC and the DNA binding regulator ComA. Using biochemistry experiments, we demonstrated that AI-2 interacts with RapC to stimulate its binding to ComA, which leads to an inactive ComA and subsequently a sporulation inhibition. The AI-2 molecule could be shared across species for inhibiting Bacillus sporulation and it also plays the same role in different soil conditions. Our study revealed a novel function and regulatory mechanism of AI-2 in inhibiting sporulation in Bacilli.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":null,"pages":null},"PeriodicalIF":7.8,"publicationDate":"2024-11-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11532509/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142569111","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: Secreted nucleases reclaim extracellular DNA during biofilm development. 作者更正：分泌型核酸酶在生物膜发育过程中回收胞外 DNA

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-10-31 DOI: 10.1038/s41522-024-00595-5

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

引用次数: 0

A phosphate starvation induced small RNA promotes Bacillus biofilm formation. 磷酸盐饥饿诱导的小核糖核酸可促进芽孢杆菌生物膜的形成。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-10-29 DOI: 10.1038/s41522-024-00586-6

Yulong Li, Xianming Cao, Yunrong Chai, Ruofu Chen, Yinjuan Zhao, Rainer Borriss, Xiaolei Ding, Xiaoqin Wu, Jianren Ye, Dejun Hao, Jian He, Guibin Wang, Mingmin Cao, Chunliang Jiang, Zhengmin Han, Ben Fan

{"title":"A phosphate starvation induced small RNA promotes Bacillus biofilm formation.","authors":"Yulong Li, Xianming Cao, Yunrong Chai, Ruofu Chen, Yinjuan Zhao, Rainer Borriss, Xiaolei Ding, Xiaoqin Wu, Jianren Ye, Dejun Hao, Jian He, Guibin Wang, Mingmin Cao, Chunliang Jiang, Zhengmin Han, Ben Fan","doi":"10.1038/s41522-024-00586-6","DOIUrl":"10.1038/s41522-024-00586-6","url":null,"abstract":"Currently, almost all known regulators involved in bacterial phosphorus metabolism are proteins. In this study, we identified a conserved new small regulatory RNA (sRNA), named PhoS, encoded in the 3' untranslated region (UTR) of the phoPR genes in Bacillus velezensis and B. subtilis. Expression of phoS is strongly induced upon phosphorus scarcity and stimulated by the transcription factor PhoP. Conversely, PhoS positively regulates PhoP translation by binding to the ribosome binding site (RBS) of phoP mRNA. PhoS can promote Bacillus biofilm formation through, at least in part, enhancing the expression of the matrix-related genes, such as the eps genes and the tapA-sipW-tasA operon. The positive regulation of phoP expression by PhoS contributes to the promoting effect of PhoS on biofilm formation. sRNAs regulating biofilm formation have rarely been reported in gram-positive Bacillus species. Here we highlight the significance of sRNAs involved in two important biological processes: phosphate metabolism and biofilm formation.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":null,"pages":null},"PeriodicalIF":7.8,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11522486/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142546579","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 microbiota dysbiosis-mediated ceramides elevation contributes to corticosterone-induced depression by impairing mitochondrial function. 肠道微生物群失调介导的神经酰胺升高通过损害线粒体功能导致皮质酮诱发抑郁症。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-10-28 DOI: 10.1038/s41522-024-00582-w

Guanhao Wang, Lining Cao, Shuanqing Li, Meihui Zhang, Yingqi Li, Jinjin Duan, You Li, Zhangsen Hu, Jiaan Wu, Jianbo Ni, Danmei Lan, Tianming Li, Jianfeng Lu

{"title":"Gut microbiota dysbiosis-mediated ceramides elevation contributes to corticosterone-induced depression by impairing mitochondrial function.","authors":"Guanhao Wang, Lining Cao, Shuanqing Li, Meihui Zhang, Yingqi Li, Jinjin Duan, You Li, Zhangsen Hu, Jiaan Wu, Jianbo Ni, Danmei Lan, Tianming Li, Jianfeng Lu","doi":"10.1038/s41522-024-00582-w","DOIUrl":"10.1038/s41522-024-00582-w","url":null,"abstract":"The role of gut microbiota (GM) dysbiosis in the pathogenesis of depression has received widespread attention, but the mechanism remains elusive. Corticosterone (CORT)-treated mice showed depression-like behaviors, reduced hippocampal neurogenesis, and altered composition of the GM. Fecal microbial transplantation from CORT-treated mice transferred depression-like phenotypes and their dominant GM to the recipients. Fecal metabolic profiling exposed remarkable increase of gut ceramides in CORT-treated and recipient mice. Oral gavage with Bifidobacterium pseudolongum and Lactobacillus reuteri could induce elevations of gut ceramides in mice. Ceramides-treated mice showed depressive-like phenotypes, significant downregulation of oxidative phosphorylation-associated genes, and hippocampal mitochondrial dysfunction. Our study demonstrated a link between chronic exposure to CORT and its impact on GM composition, which induces ceramides accumulation, ultimately leading to hippocampal mitochondrial dysfunction. This cascade of events plays a critical role in reducing adult hippocampal neurogenesis and is strongly associated with the development of depression-like behaviors.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":null,"pages":null},"PeriodicalIF":7.8,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11519513/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142522458","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

Segatella clades adopt distinct roles within a single individual's gut. Segatella 支系在单个个体的肠道中扮演着不同的角色。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-10-27 DOI: 10.1038/s41522-024-00590-w

Xieyue Xiao, Adarsh Singh, Andrea Giometto, Ilana L Brito

引用次数: 0

DGCNN approach links metagenome-derived taxon and functional information providing insight into global soil organic carbon. DGCNN 方法将来源于元基因组的分类群和功能信息联系起来，有助于深入了解全球土壤有机碳。

IF 7.8 1区生物学

npj Biofilms and Microbiomes Pub Date : 2024-10-26 DOI: 10.1038/s41522-024-00583-9

Laura-Jayne Gardiner, Matthew Marshall, Katharina Reusch, Chris Dearden, Mark Birmingham, Anna Paola Carrieri, Edward O Pyzer-Knapp, Ritesh Krishna, Andrew L Neal

{"title":"DGCNN approach links metagenome-derived taxon and functional information providing insight into global soil organic carbon.","authors":"Laura-Jayne Gardiner, Matthew Marshall, Katharina Reusch, Chris Dearden, Mark Birmingham, Anna Paola Carrieri, Edward O Pyzer-Knapp, Ritesh Krishna, Andrew L Neal","doi":"10.1038/s41522-024-00583-9","DOIUrl":"10.1038/s41522-024-00583-9","url":null,"abstract":"Metagenomics can provide insight into the microbial taxa present in a sample and, through gene identification, the functional potential of the community. However, taxonomic and functional information are typically considered separately in downstream analyses. We develop interpretable machine learning (ML) approaches for modelling metagenomic data, combining the biological representation of species with their associated genetically encoded functions within models. We apply our methods to investigate soil organic carbon (SOC) stocks. First, we combine a diverse global set of soil microbiome samples with environmental data, improving the predictive performance of classic ML and providing new insights into the role of soil microbiomes in global carbon cycling. Our network analysis of predictive taxa identified by classical ML models provides context for their ecological significance, extending the focus beyond just the most predictive taxa to 'hidden' features within the model that might be considered less predictive using standard methods for explainability. We next develop unique graph representations for individual microbiomes, linking microbial taxa to their associated functions directly, enabling predictions of SOC via deep graph convolutional neural networks (DGCNNs). Interpretation of the DGCNNs distinguished between the importance of functions of key individual species, providing genome sequence differences, e.g., gene loss/acquisition, that associate with SOC. These approaches identify several members of the Verrucomicrobiaceae family and a range of genetically encoded functions, e.g., related to carbohydrate metabolism, as important for SOC stocks and effective global SOC predictors. These relatively understudied but widespread organisms could play an important role in SOC dynamics globally.","PeriodicalId":19370,"journal":{"name":"npj Biofilms and Microbiomes","volume":null,"pages":null},"PeriodicalIF":7.8,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11513995/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142504982","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