Winston E Anthony, Steven D Allison, Caitlin M Broderick, Luciana Chavez Rodriguez, Alicia Clum, Hugh Cross, Emiley Eloe-Fadrosh, Sarah Evans, Dawson Fairbanks, Rachel Gallery, Júlia Brandão Gontijo, Jennifer Jones, Jason McDermott, Jennifer Pett-Ridge, Sydne Record, Jorge Luiz Mazza Rodrigues, William Rodriguez-Reillo, Katherine L Shek, Tina Takacs-Vesbach, Jeffrey L Blanchard
{"title":"从土壤到序列:填补基因组解析元基因组学的关键空白对土壤微生物生态学的未来至关重要。","authors":"Winston E Anthony, Steven D Allison, Caitlin M Broderick, Luciana Chavez Rodriguez, Alicia Clum, Hugh Cross, Emiley Eloe-Fadrosh, Sarah Evans, Dawson Fairbanks, Rachel Gallery, Júlia Brandão Gontijo, Jennifer Jones, Jason McDermott, Jennifer Pett-Ridge, Sydne Record, Jorge Luiz Mazza Rodrigues, William Rodriguez-Reillo, Katherine L Shek, Tina Takacs-Vesbach, Jeffrey L Blanchard","doi":"10.1186/s40793-024-00599-w","DOIUrl":null,"url":null,"abstract":"<p><p>Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":6.2000,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11295382/pdf/","citationCount":"0","resultStr":"{\"title\":\"From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology.\",\"authors\":\"Winston E Anthony, Steven D Allison, Caitlin M Broderick, Luciana Chavez Rodriguez, Alicia Clum, Hugh Cross, Emiley Eloe-Fadrosh, Sarah Evans, Dawson Fairbanks, Rachel Gallery, Júlia Brandão Gontijo, Jennifer Jones, Jason McDermott, Jennifer Pett-Ridge, Sydne Record, Jorge Luiz Mazza Rodrigues, William Rodriguez-Reillo, Katherine L Shek, Tina Takacs-Vesbach, Jeffrey L Blanchard\",\"doi\":\"10.1186/s40793-024-00599-w\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.</p>\",\"PeriodicalId\":48553,\"journal\":{\"name\":\"Environmental Microbiome\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":6.2000,\"publicationDate\":\"2024-08-02\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11295382/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Environmental Microbiome\",\"FirstCategoryId\":\"93\",\"ListUrlMain\":\"https://doi.org/10.1186/s40793-024-00599-w\",\"RegionNum\":2,\"RegionCategory\":\"环境科学与生态学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Environmental Microbiome","FirstCategoryId":"93","ListUrlMain":"https://doi.org/10.1186/s40793-024-00599-w","RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology.
Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.
期刊介绍:
Microorganisms, omnipresent across Earth's diverse environments, play a crucial role in adapting to external changes, influencing Earth's systems and cycles, and contributing significantly to agricultural practices. Through applied microbiology, they offer solutions to various everyday needs. Environmental Microbiome recognizes the universal presence and significance of microorganisms, inviting submissions that explore the diverse facets of environmental and applied microbiological research.