ISME communications最新文献_第6页

Chlamydiae in corals: shared functional potential despite broad taxonomic diversity. 珊瑚中的衣原体：尽管分类广泛多样，但仍具有共同的功能潜力。

ISME communications Pub Date : 2024-04-15 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae054

Justin Maire, Astrid Collingro, Matthias Horn, Madeleine J H van Oppen

{"title":"Chlamydiae in corals: shared functional potential despite broad taxonomic diversity.","authors":"Justin Maire, Astrid Collingro, Matthias Horn, Madeleine J H van Oppen","doi":"10.1093/ismeco/ycae054","DOIUrl":"https://doi.org/10.1093/ismeco/ycae054","url":null,"abstract":"Cnidarians, such as corals and sea anemones, associate with a wide range of bacteria that have essential functions, including nutrient cycling and the production of antimicrobial compounds. Within cnidarians, bacteria can colonize all microhabitats including the tissues. Among them are obligate intracellular bacteria of the phylum Chlamydiota (chlamydiae) whose impact on cnidarian hosts and holobionts, especially corals, remain unknown. Here, we conducted a meta-analysis of previously published 16S rRNA gene metabarcoding data from cnidarians (e.g. coral, jellyfish, and anemones), eight metagenome-assembled genomes (MAGs) of coral-associated chlamydiae, and one MAG of jellyfish-associated chlamydiae to decipher their diversity and functional potential. While the metabarcoding dataset showed an enormous diversity of cnidarian-associated chlamydiae, six out of nine MAGs were affiliated with the Simkaniaceae family. The other three MAGs were assigned to the Parasimkaniaceae, Rhabdochlamydiaceae, and Anoxychlamydiaceae, respectively. All MAGs lacked the genes necessary for an independent existence, lacking any nucleotide or vitamin and most amino acid biosynthesis pathways. Hallmark chlamydial genes, such as a type III secretion system, nucleotide transporters, and genes for host interaction, were encoded in all MAGs. Together these observations suggest an obligate intracellular lifestyle of coral-associated chlamydiae. No unique genes were found in coral-associated chlamydiae, suggesting a lack of host specificity. Additional studies are needed to understand how chlamydiae interact with their coral host, and other microbes in coral holobionts. This first study of the diversity and functional potential of coral-associated chlamydiae improves our understanding of both the coral microbiome and the chlamydial lifestyle and host range.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae054"},"PeriodicalIF":0.0,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11070183/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140853788","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

When simplicity triumphs: niche specialization of gut bacteria exists even for simple fiber structures. 当简单取胜时：即使是简单的纤维结构，也存在肠道细菌的生态位特化。

ISME communications Pub Date : 2024-04-11 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae037

Haidi Xu, Nicholas A Pudlo, Thaisa M Cantu-Jungles, Yunus E Tuncil, Xin Nie, Amandeep Kaur, Bradley L Reuhs, Eric C Martens, Bruce R Hamaker

{"title":"When simplicity triumphs: niche specialization of gut bacteria exists even for simple fiber structures.","authors":"Haidi Xu, Nicholas A Pudlo, Thaisa M Cantu-Jungles, Yunus E Tuncil, Xin Nie, Amandeep Kaur, Bradley L Reuhs, Eric C Martens, Bruce R Hamaker","doi":"10.1093/ismeco/ycae037","DOIUrl":"https://doi.org/10.1093/ismeco/ycae037","url":null,"abstract":"Structurally complex corn bran arabinoxylan (CAX) was used as a model glycan to investigate gut bacteria growth and competition on different AX-based fine structures. Nine hydrolyzate segments of the CAX polymer varying in chemical structure (sugars and linkages), CAX, five less complex non-corn arabinoxylans, and xylose and glucose were ranked from structurally complex to simple. The substrate panel promoted different overall growth and rates of growth of eight Bacteroides xylan-degrading strains. For example, Bacteroides cellulosilyticus DSM 14838 (Bacteroides cellulosilyticus) grew well on an array of complex and simple structures, while Bacteroides ovatus 3-1-23 grew well only on the simple structures. In a competition experiment, B. cellulosilyticus growth was favored over B. ovatus on the complex AX-based structure. On the other hand, on the simple structure, B. ovatus strongly outcompeted B. cellulosilyticus, which was eliminated from the competitive environment by Day 11. This adaptation to fine structure and resulting competition dynamics indicate that dietary fiber chemical structures, whether complex or simple, favor certain gut bacteria. Overall, this work supports a concept that fiber degraders diversify their competitive abilities to access substrates across the spectrum of heterogeneity of fine structural features of dietary fibers.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae037"},"PeriodicalIF":0.0,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11032216/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140874311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Varied microbial community assembly and specialization patterns driven by early life microbiome perturbation and modulation in young ruminants. 幼年反刍动物生命早期微生物组扰动和调节驱动的各种微生物群落组合和特化模式。

ISME communications Pub Date : 2024-04-09 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae044

Zhe Pan, Tao Ma, Michael Steele, Le Luo Guan

{"title":"Varied microbial community assembly and specialization patterns driven by early life microbiome perturbation and modulation in young ruminants.","authors":"Zhe Pan, Tao Ma, Michael Steele, Le Luo Guan","doi":"10.1093/ismeco/ycae044","DOIUrl":"https://doi.org/10.1093/ismeco/ycae044","url":null,"abstract":"Perturbations and modulations during early life are vital to affect gut microbiome assembly and establishment. In this study, we assessed how microbial communities shifted during calf diarrhea and with probiotic yeast supplementation (Saccharomyces cerevisiae var. boulardii, SCB) and determined the key bacterial taxa contributing to the microbial assembly shifts using a total of 393 fecal samples collected from 84 preweaned calves during an 8-week trial. Our results revealed that the microbial assembly patterns differed between healthy and diarrheic calves at 6- and 8-week of the trial, with healthy calves being stochastic-driven and diarrheic calves being deterministic-driven. The two-state Markov model revealed that SCB supplementation had a higher possibility to shift microbial assembly from deterministic- to stochastic-driven in diarrheic calves. Furthermore, a total of 23 and 21 genera were specific ecotypes to assembly patterns in SCB-responsive (SCB-fed calves did not exhibit diarrhea) and nonresponsive (SCB-fed calves occurred diarrhea) calves, respectively. Among these ecotypes, the area under a receiver operating characteristic curve revealed that Blautia and Ruminococcaceae UCG 014, two unidentified genera from the Ruminococcaceae family, had the highest predictiveness for microbial assembly patterns in SCB-responsive calves, while Prevotellaceae, Blautia, and Escherichia-Shigella were the most predictive bacterial taxa for microbial assembly patterns in SCB-nonresponsive calves. Our study suggests that microbiome perturbations and probiotic yeast supplementation serving as deterministic factors influenced assembly patterns during early life with critical genera being predictive for assembly patterns, which sheds light on mechanisms of microbial community establishment in the gut of neonatal calves during early life.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae044"},"PeriodicalIF":0.0,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11033733/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140869765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Co-occurring microflora and mucin drive Pseudomonas aeruginosa diversification and pathoadaptation. 共生微生物菌群和粘蛋白驱动铜绿假单胞菌的多样化和病理适应。

ISME communications Pub Date : 2024-03-28 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae043

Michael J Bottery, Helle Krogh Johansen, Jon W Pitchford, Ville-Petri Friman

{"title":"Co-occurring microflora and mucin drive Pseudomonas aeruginosa diversification and pathoadaptation.","authors":"Michael J Bottery, Helle Krogh Johansen, Jon W Pitchford, Ville-Petri Friman","doi":"10.1093/ismeco/ycae043","DOIUrl":"https://doi.org/10.1093/ismeco/ycae043","url":null,"abstract":"While several environmental factors contribute to the evolutionary diversification of the pathogenic bacterium Pseudomonas aeruginosa during cystic fibrosis lung infections, relatively little is known about the impact of the surrounding microbiota. By using in vitro experimental evolution, we show that the presence of Stenotrophomonas maltophilia, Staphylococcus aureus, or them both, prevent the evolution of loss of virulence, which repeatedly occurs in the absence of these species due to mutations in regulators of the Pseudomonas Quinolone Signal quorum sensing system, vqsM and pqsR. Moreover, the strength of the effect of co-occurring species is attenuated through changes in the physical environment by the addition of mucin, resulting in selection for phenotypes resembling those evolved in the absence of the co-occurring species. Together, our findings show that variation in mucosal environment and the surrounding polymicrobial environment can determine the evolutionary trajectory of P. aeruginosa, partly explaining its diversification and pathoadaptation from acute to chronic phenotype during cystic fibrosis lung infections.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae043"},"PeriodicalIF":0.0,"publicationDate":"2024-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11067959/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140873732","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Predicting bacterial interaction outcomes from monoculture growth and supernatant assays. 通过单培养基生长和上清液检测预测细菌相互作用结果

IF 5.1

ISME communications Pub Date : 2024-03-27 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae045

Désirée A Schmitz, Tobias Wechsler, Ingrid Mignot, Rolf Kümmerli

{"title":"Predicting bacterial interaction outcomes from monoculture growth and supernatant assays.","authors":"Désirée A Schmitz, Tobias Wechsler, Ingrid Mignot, Rolf Kümmerli","doi":"10.1093/ismeco/ycae045","DOIUrl":"10.1093/ismeco/ycae045","url":null,"abstract":"How to derive principles of community dynamics and stability is a central question in microbial ecology. Bottom-up experiments, in which a small number of bacterial species are mixed, have become popular to address it. However, experimental setups are typically limited because co-culture experiments are labor-intensive and species are difficult to distinguish. Here, we use a four-species bacterial community to show that information from monoculture growth and inhibitory effects induced by secreted compounds can be combined to predict the competitive rank order in the community. Specifically, integrative monoculture growth parameters allow building a preliminary competitive rank order, which is then adjusted using inhibitory effects from supernatant assays. While our procedure worked for two different media, we observed differences in species rank orders between media. We then parameterized computer simulations with our empirical data to show that higher order species interactions largely follow the dynamics predicted from pairwise interactions with one important exception. The impact of inhibitory compounds was reduced in higher order communities because their negative effects were spread across multiple target species. Altogether, we formulated three simple rules of how monoculture growth and supernatant assay data can be combined to establish a competitive species rank order in an experimental four-species community.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae045"},"PeriodicalIF":5.1,"publicationDate":"2024-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11287475/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141857255","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Quantifying microbial guilds. 量化微生物行会。

ISME communications Pub Date : 2024-03-27 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae042

Juan Rivas-Santisteban, Pablo Yubero, Semidán Robaina-Estévez, José M González, Javier Tamames, Carlos Pedrós-Alió

{"title":"Quantifying microbial guilds.","authors":"Juan Rivas-Santisteban, Pablo Yubero, Semidán Robaina-Estévez, José M González, Javier Tamames, Carlos Pedrós-Alió","doi":"10.1093/ismeco/ycae042","DOIUrl":"https://doi.org/10.1093/ismeco/ycae042","url":null,"abstract":"The ecological role of microorganisms is of utmost importance due to their multiple interactions with the environment. However, assessing the contribution of individual taxonomic groups has proven difficult despite the availability of high throughput data, hindering our understanding of such complex systems. Here, we propose a quantitative definition of guild that is readily applicable to metagenomic data. Our framework focuses on the functional character of protein sequences, as well as their diversifying nature. First, we discriminate functional sequences from the whole sequence space corresponding to a gene annotation to then quantify their contribution to the guild composition across environments. In addition, we identify and distinguish functional implementations, which are sequence spaces that have different ways of carrying out the function. In contrast, we found that orthology delineation did not consistently align with ecologically (or functionally) distinct implementations of the function. We demonstrate the value of our approach with two case studies: the ammonia oxidation and polyamine uptake guilds from the Malaspina circumnavigation cruise, revealing novel ecological dynamics of the latter in marine ecosystems. Thus, the quantification of guilds helps us to assess the functional role of different taxonomic groups with profound implications on the study of microbial communities.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae042"},"PeriodicalIF":0.0,"publicationDate":"2024-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11069341/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140856076","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Galactosamine and mannosamine are integral parts of bacterial and fungal extracellular polymeric substances. 半乳糖胺和甘露胺是细菌和真菌胞外聚合物物质的组成部分。

ISME communications Pub Date : 2024-03-22 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae038

Rebeca Leme Oliva, Carla Vogt, Tábata Aline Bublitz, Tessa Camenzind, Jens Dyckmans, Rainer Georg Joergensen

{"title":"Galactosamine and mannosamine are integral parts of bacterial and fungal extracellular polymeric substances.","authors":"Rebeca Leme Oliva, Carla Vogt, Tábata Aline Bublitz, Tessa Camenzind, Jens Dyckmans, Rainer Georg Joergensen","doi":"10.1093/ismeco/ycae038","DOIUrl":"https://doi.org/10.1093/ismeco/ycae038","url":null,"abstract":"Extracellular polymeric substances (EPS) are produced by microorganisms and interact to form a complex matrix called biofilm. In soils, EPS are important contributors to the microbial necromass and, thus, to soil organic carbon (SOC). Amino sugars (AS) are used as indicators for microbial necromass in soil, although the origin of galactosamine and mannosamine is largely unknown. However, indications exist that they are part of EPS. In this study, two bacteria and two fungi were grown in starch medium either with or without a quartz matrix to induce EPS production. Each culture was separated in two fractions: one that directly underwent AS extraction (containing AS from both biomass and EPS), and another that first had EPS extracted, followed then by AS determination (exclusively containing AS from EPS). We did not observe a general effect of the quartz matrix neither of microbial type on AS production. The quantified amounts of galactosamine and mannosamine in the EPS fraction represented on average 100% of the total amounts of these two AS quantified in cell cultures, revealing they are integral parts of the biofilm. In contrast, muramic acid and glucosamine were also quantified in the EPS, but with much lower contribution rates to total AS production, of 18% and 33%, respectively, indicating they are not necessarily part of EPS. Our results allow a meaningful ecological interpretation of mannosamine and galactosamine data in the future as indicators of microbial EPS, and also attract interest of future studies to investigate the role of EPS to SOC and its dynamics.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae038"},"PeriodicalIF":0.0,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11014887/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140874117","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Phage-driven coevolution reveals trade-off between antibiotic and phage resistance in Salmonella anatum. 噬菌体驱动的共同进化揭示了锐毒沙门氏菌抗生素和噬菌体抗药性之间的权衡。

ISME communications Pub Date : 2024-03-22 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae039

Yuanyang Zhao, Mei Shu, Ling Zhang, Chan Zhong, Ningbo Liao, Guoping Wu

{"title":"Phage-driven coevolution reveals trade-off between antibiotic and phage resistance in Salmonella anatum.","authors":"Yuanyang Zhao, Mei Shu, Ling Zhang, Chan Zhong, Ningbo Liao, Guoping Wu","doi":"10.1093/ismeco/ycae039","DOIUrl":"https://doi.org/10.1093/ismeco/ycae039","url":null,"abstract":"Phage therapy faces challenges against multidrug-resistant (MDR) Salmonella due to rapid phage-resistant mutant emergence. Understanding the intricate interplay between antibiotics and phages is essential for shaping Salmonella evolution and advancing phage therapy. In this study, MDR Salmonella anatum (S. anatum) 2089b coevolved with phage JNwz02 for 30 passages (60 days), then the effect of coevolution on the trade-off between phage and antibiotic resistance in bacteria was investigated. Our results demonstrated antagonistic coevolution between bacteria and phages, transitioning from arms race dynamics (ARD) to fluctuating selection dynamics (FSD). The fitness cost of phage resistance, manifested as reduced competitiveness, was observed. Bacteria evolved phage resistance while simultaneously regaining sensitivity to amoxicillin, ampicillin, and gentamicin, influenced by phage selection pressure and bacterial competitiveness. Moreover, the impact of phage selection pressure on the trade-off between antibiotic and phage resistance was more pronounced in the ARD stage than in the FSD stage. Whole genome analysis revealed mutations in the btuB gene in evolved S. anatum strains, with a notably higher mutation frequency in the ARD stage compared to the FSD stage. Subsequent knockout experiments confirmed BtuB as a receptor for phage JNwz02, and the deletion of btuB resulted in reduced bacterial competitiveness. Additionally, the mutations identified in the phage-resistant strains were linked to multiple single nucleotide polymorphisms (SNPs) associated with membrane components. This correlation implies a potential role of these SNPs in reinstating antibiotic susceptibility. These findings significantly advance our understanding of phage-host interactions and the impact of bacterial adaptations on antibiotic resistance.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae039"},"PeriodicalIF":0.0,"publicationDate":"2024-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11014889/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140861023","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","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 flexible high-throughput cultivation protocol to assess the response of individuals' gut microbiota to diet-, drug-, and host-related factors. 灵活的高通量培养方案，用于评估个体肠道微生物群对饮食、药物和宿主相关因素的反应。

IF 5.1

ISME communications Pub Date : 2024-03-12 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae035

Janina N Zünd, Serafina Plüss, Denisa Mujezinovic, Carmen Menzi, Philipp R von Bieberstein, Tomas de Wouters, Christophe Lacroix, Gabriel E Leventhal, Benoit Pugin

{"title":"A flexible high-throughput cultivation protocol to assess the response of individuals' gut microbiota to diet-, drug-, and host-related factors.","authors":"Janina N Zünd, Serafina Plüss, Denisa Mujezinovic, Carmen Menzi, Philipp R von Bieberstein, Tomas de Wouters, Christophe Lacroix, Gabriel E Leventhal, Benoit Pugin","doi":"10.1093/ismeco/ycae035","DOIUrl":"10.1093/ismeco/ycae035","url":null,"abstract":"The anaerobic cultivation of fecal microbiota is a promising approach to investigating how gut microbial communities respond to specific intestinal conditions and perturbations. Here, we describe a flexible protocol using 96-deepwell plates to cultivate stool-derived gut microbiota. Our protocol aims to address gaps in high-throughput culturing in an anaerobic chamber. We characterized the influence of the gas phase on the medium chemistry and microbial physiology and introduced a modular medium preparation process to enable the testing of several conditions simultaneously. Furthermore, we identified a medium formulation that maximized the compositional similarity of ex vivo cultures and donor microbiota while limiting the bloom of Enterobacteriaceae. Lastly, we validated the protocol by demonstrating that cultivated fecal microbiota responded similarly to dietary fibers (resistant dextrin, soluble starch) and drugs (ciprofloxacin, 5-fluorouracil) as reported in vivo. This high-throughput cultivation protocol has the potential to facilitate culture-dependent studies, accelerate the discovery of gut microbiota-diet-drug-host interactions, and pave the way to personalized microbiota-centered interventions.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae035"},"PeriodicalIF":5.1,"publicationDate":"2024-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10982853/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140337899","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Taxonomic resolution of different 16S rRNA variable regions varies strongly across plant-associated bacteria. 植物相关细菌不同 16S rRNA 可变区的分类分辨率差异很大。

ISME communications Pub Date : 2024-03-08 eCollection Date: 2024-01-01 DOI: 10.1093/ismeco/ycae034

Katarina Hrovat, Bas E Dutilh, Marnix H Medema, Chrats Melkonian

{"title":"Taxonomic resolution of different 16S rRNA variable regions varies strongly across plant-associated bacteria.","authors":"Katarina Hrovat, Bas E Dutilh, Marnix H Medema, Chrats Melkonian","doi":"10.1093/ismeco/ycae034","DOIUrl":"10.1093/ismeco/ycae034","url":null,"abstract":"Plant-microbiome research plays a pivotal role in understanding the relationships between plants and their associated microbial communities, with implications for agriculture and ecosystem dynamics. Metabarcoding analysis on variable regions of the 16S ribosomal RNA (rRNA) gene remains the dominant technology to study microbiome diversity in this field. However, the choice of the targeted variable region might affect the outcome of the microbiome studies. In our in silico analysis, we have evaluated whether the targeted variable region has an impact on taxonomic resolution in 16 plant-related microbial genera. Through a comparison of 16S rRNA gene variable regions with whole-genome data, our findings suggest that the V1-V3 region is generally a more suitable option than the widely used V3-V4 region for targeting microbiome analysis in plant-related genera. However, sole reliance on one region could introduce detection biases for specific genera. Thus, we are suggesting that while transitioning to full-length 16S rRNA gene and whole-genome sequencing for plant-microbiome analysis, the usage of genus-specific variable regions can achieve more precise taxonomic assignments. More broadly, our approach provides a blueprint to identify the most discriminating variable regions of the 16S rRNA gene for genera of interest.","PeriodicalId":73516,"journal":{"name":"ISME communications","volume":"4 1","pages":"ycae034"},"PeriodicalIF":0.0,"publicationDate":"2024-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10980831/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140337901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0