Advancing Genome-Resolved Metagenomics beyond the Shotgun

ABSTRACT Exploration of environmental microbiomes has shed light on the ecological and evolutionary principles at play in natural ecosystems and has been further accelerated through the reconstruction of population genomes to provide genome-centric context. Yet technical challenges with traditional...

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Autores principales:	Rex R. Malmstrom, Emiley A. Eloe-Fadrosh
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	DNA-SIP genome-resolved metagenomics microbiome Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/d2bdbc671f6447a78c67d5cd0ef1533c
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spelling	oai:doaj.org-article:d2bdbc671f6447a78c67d5cd0ef1533c2021-12-02T18:44:38ZAdvancing Genome-Resolved Metagenomics beyond the Shotgun10.1128/mSystems.00118-192379-5077https://doaj.org/article/d2bdbc671f6447a78c67d5cd0ef1533c2019-06-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00118-19https://doaj.org/toc/2379-5077ABSTRACT Exploration of environmental microbiomes has shed light on the ecological and evolutionary principles at play in natural ecosystems and has been further accelerated through the reconstruction of population genomes to provide genome-centric context. Yet technical challenges with traditional shotgun metagenomics remain for computationally intense short-read assembly, strain heterogeneity within communities, and depth of coverage required for low-abundance microbes. In this Perspective, we highlight three main avenues for promising future developments, including coupling stable isotope probing and genome-resolved metagenomics, applying fluorescence-activated cell sorting approaches to target mini-metagenomes within a larger community, and utilizing single-molecule long-read and synthetic long-read technology to link mobile elements to host microbial cells. These developments on the horizon will undoubtedly advance genome-resolved metagenomic approaches and enable a better understanding of uncultivated microbes in their natural environments.Rex R. MalmstromEmiley A. Eloe-FadroshAmerican Society for MicrobiologyarticleDNA-SIPgenome-resolved metagenomicsmicrobiomeMicrobiologyQR1-502ENmSystems, Vol 4, Iss 3 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	DNA-SIP genome-resolved metagenomics microbiome Microbiology QR1-502
spellingShingle	DNA-SIP genome-resolved metagenomics microbiome Microbiology QR1-502 Rex R. Malmstrom Emiley A. Eloe-Fadrosh Advancing Genome-Resolved Metagenomics beyond the Shotgun
description	ABSTRACT Exploration of environmental microbiomes has shed light on the ecological and evolutionary principles at play in natural ecosystems and has been further accelerated through the reconstruction of population genomes to provide genome-centric context. Yet technical challenges with traditional shotgun metagenomics remain for computationally intense short-read assembly, strain heterogeneity within communities, and depth of coverage required for low-abundance microbes. In this Perspective, we highlight three main avenues for promising future developments, including coupling stable isotope probing and genome-resolved metagenomics, applying fluorescence-activated cell sorting approaches to target mini-metagenomes within a larger community, and utilizing single-molecule long-read and synthetic long-read technology to link mobile elements to host microbial cells. These developments on the horizon will undoubtedly advance genome-resolved metagenomic approaches and enable a better understanding of uncultivated microbes in their natural environments.
format	article
author	Rex R. Malmstrom Emiley A. Eloe-Fadrosh
author_facet	Rex R. Malmstrom Emiley A. Eloe-Fadrosh
author_sort	Rex R. Malmstrom
title	Advancing Genome-Resolved Metagenomics beyond the Shotgun
title_short	Advancing Genome-Resolved Metagenomics beyond the Shotgun
title_full	Advancing Genome-Resolved Metagenomics beyond the Shotgun
title_fullStr	Advancing Genome-Resolved Metagenomics beyond the Shotgun
title_full_unstemmed	Advancing Genome-Resolved Metagenomics beyond the Shotgun
title_sort	advancing genome-resolved metagenomics beyond the shotgun
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/d2bdbc671f6447a78c67d5cd0ef1533c
work_keys_str_mv	AT rexrmalmstrom advancinggenomeresolvedmetagenomicsbeyondtheshotgun AT emileyaeloefadrosh advancinggenomeresolvedmetagenomicsbeyondtheshotgun
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Advancing Genome-Resolved Metagenomics beyond the Shotgun

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