RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids

ABSTRACT 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 micr...

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Autores principales:	Taylor K. Dunivin, Jinlyung Choi, Adina Howe, Ashley Shade
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	antibiotic resistance genes database isolates metagenomics microbial ecology microbiome dynamics Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/d9b09673dc60467398282af12b2f6f0c
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spelling	oai:doaj.org-article:d9b09673dc60467398282af12b2f6f0c2021-12-02T18:15:45ZRefSoil+: a Reference Database for Genes and Traits of Soil Plasmids10.1128/mSystems.00349-182379-5077https://doaj.org/article/d9b09673dc60467398282af12b2f6f0c2019-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00349-18https://doaj.org/toc/2379-5077ABSTRACT 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.Taylor K. DunivinJinlyung ChoiAdina HoweAshley ShadeAmerican Society for Microbiologyarticleantibiotic resistance genesdatabaseisolatesmetagenomicsmicrobial ecologymicrobiome dynamicsMicrobiologyQR1-502ENmSystems, Vol 4, Iss 1 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	antibiotic resistance genes database isolates metagenomics microbial ecology microbiome dynamics Microbiology QR1-502
spellingShingle	antibiotic resistance genes database isolates metagenomics microbial ecology microbiome dynamics Microbiology QR1-502 Taylor K. Dunivin Jinlyung Choi Adina Howe Ashley Shade RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids
description	ABSTRACT 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.
format	article
author	Taylor K. Dunivin Jinlyung Choi Adina Howe Ashley Shade
author_facet	Taylor K. Dunivin Jinlyung Choi Adina Howe Ashley Shade
author_sort	Taylor K. Dunivin
title	RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids
title_short	RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids
title_full	RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids
title_fullStr	RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids
title_full_unstemmed	RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids
title_sort	refsoil+: a reference database for genes and traits of soil plasmids
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/d9b09673dc60467398282af12b2f6f0c
work_keys_str_mv	AT taylorkdunivin refsoilareferencedatabaseforgenesandtraitsofsoilplasmids AT jinlyungchoi refsoilareferencedatabaseforgenesandtraitsofsoilplasmids AT adinahowe refsoilareferencedatabaseforgenesandtraitsofsoilplasmids AT ashleyshade refsoilareferencedatabaseforgenesandtraitsofsoilplasmids
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RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids

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