RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids
RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids
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DOI：
10.1128/msystems.00349-18
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发表时间：
2019-01-01
期刊：
影响因子：
6.4
通讯作者：
Shade, Ashley
中科院分区：
文献类型：
--
作者：
Dunivin, Taylor K.;Choi, Jinlyung;Shade, Ashley
质粒含有可转移的基因，有助于微生物群落的功能库，但它们对宏基因组的贡献往往被忽视。环境质粒有可能将抗生素耐药性传播到临床微生物菌株。在土壤中，微生物组的高度多样性和质粒特征的高度变异性对研究质粒提出了挑战。为了提高对土壤质粒的理解，我们提出了RefSoil+，一个包含来自922种土壤微生物的质粒序列的数据库。土壤质粒大于其他描述的质粒，这是一个与质粒移动性相关的性状。染色体大小与质粒大小之间的相关性较弱，而与质粒数量之间的相关性不明显，说明这些基因组性状在土壤中是独立的。我们使用RefSoil+来了解土壤微生物与非土壤微生物之间抗生素抗性基因的分布。土壤相关质粒，而不是染色体，比其他微生物具有更少的抗生素抗性基因。这些数据表明，土壤可能提供有限的机会，质粒介导的转移所描述的抗生素耐药基因。RefSoil+可以作为土壤中质粒携带的功能基因的多样性，组成和宿主关联的参考，随着数据库的扩展，这种实用性将得到增强。我们的研究提高了对土壤质粒的理解，并为评估它们携带的基因的动态提供了资源，特别是赋予抗生素抗性的基因。重要意义土壤相关质粒有可能将抗生素抗性基因从环境转移到临床微生物菌株，这是一个公共卫生问题。需要一个特定的资源来聚合土壤质粒特性的知识，以便可以评估抗生素耐药基因的内容，宿主协会和动态，然后在环境和临床之间进行跟踪。在这里，我们提出了RefSoil+，一个土壤相关质粒的数据库。RefSoil+提供了土壤中抗生素抗性基因的当代快照，可以作为发现新质粒和转移抗生素抗性的参考。我们的研究拓宽了我们对土壤中质粒的理解，并提供了重要质粒相关基因的社区资源，包括抗生素抗性基因。
Plasmids harbor transferable genes that contribute to the functional repertoire of microbial communities, yet their contributions to metagenomes are often overlooked. Environmental plasmids have the potential to spread antibiotic resistance to clinical microbial strains. In soils, high microbiome diversity and high variability in plasmid characteristics present a challenge for studying plasmids. To improve the understanding of soil plasmids, we present RefSoil+, a database containing plasmid sequences from 922 soil microorganisms. Soil plasmids were larger than other described plasmids, which is a trait associated with plasmid mobility. There was a weak relationship between chromosome size and plasmid size and no relationship between chromosome size and plasmid number, suggesting that these genomic traits are independent in soil. We used RefSoil+ to inform the distributions of antibiotic resistance genes among soil microorganisms compared to those among nonsoil microorganisms. Soil-associated plasmids, but not chromosomes, had fewer antibiotic resistance genes than other microorganisms. These data suggest that soils may offer limited opportunity for plasmid-mediated transfer of described antibiotic resistance genes. RefSoil+ can serve as a reference for the diversity, composition, and host associations of plasmid-borne functional genes in soil, a utility that will be enhanced as the database expands. Our study improves the understanding of soil plasmids and provides a resource for assessing the dynamics of the genes that they carry, especially genes conferring antibiotic resistances.IMPORTANCE Soil-associated plasmids have the potential to transfer antibiotic resistance genes from environmental to clinical microbial strains, which is a public health concern. A specific resource is needed to aggregate the knowledge of soil plasmid characteristics so that the content, host associations, and dynamics of antibiotic resistance genes can be assessed and then tracked between the environment and the clinic. Here, we present RefSoil+, a database of soil-associated plasmids. RefSoil+ presents a contemporary snapshot of antibiotic resistance genes in soil that can serve as a reference as novel plasmids and transferred antibiotic resistances are discovered. Our study broadens our understanding of plasmids in soil and provides a community resource of important plasmid-associated genes, including antibiotic resistance genes.