Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales
Abstract
Over the past years, metagenomics has revolutionized our view of microbial diversity. Furthermore, extracting near-complete genomes from metagenomes has led to the discovery of known metabolic traits in unsuspected lineages. Genome-resolved metagenomics relies on assembly of the sequencing reads and subsequent binning of assembled contigs, which might be hampered by strain heterogeneity or low abundance of a target organism. Here we present a complementary approach, metagenome marker gene mining, and use it to assess the global diversity of archaeal methane metabolism through the mcrA gene. To this end, we have screened 18,465 metagenomes for the presence of reads matching a database representative of all known mcrA proteins and reconstructed gene sequences from the matching reads.
- Authors:
-
- California Inst. of Technology (CalTech), Pasadena, CA (United States)
- Publication Date:
- Research Org.:
- California Institute of Technology (CalTech), Pasadena, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1503317
- Grant/Contract Number:
- SC0016469
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PeerJ
- Additional Journal Information:
- Journal Volume: 6; Journal ID: ISSN 2167-8359
- Publisher:
- PeerJ Inc.
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Marker genes; mcrA; Data mining; Methanogens; Methanomassiliicoccales
Citation Formats
Speth, Daan R., and Orphan, Victoria J. Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales. United States: N. p., 2018.
Web. doi:10.7717/peerj.5614.
Speth, Daan R., & Orphan, Victoria J. Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales. United States. https://doi.org/10.7717/peerj.5614
Speth, Daan R., and Orphan, Victoria J. Mon .
"Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales". United States. https://doi.org/10.7717/peerj.5614. https://www.osti.gov/servlets/purl/1503317.
@article{osti_1503317,
title = {Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales},
author = {Speth, Daan R. and Orphan, Victoria J.},
abstractNote = {Over the past years, metagenomics has revolutionized our view of microbial diversity. Furthermore, extracting near-complete genomes from metagenomes has led to the discovery of known metabolic traits in unsuspected lineages. Genome-resolved metagenomics relies on assembly of the sequencing reads and subsequent binning of assembled contigs, which might be hampered by strain heterogeneity or low abundance of a target organism. Here we present a complementary approach, metagenome marker gene mining, and use it to assess the global diversity of archaeal methane metabolism through the mcrA gene. To this end, we have screened 18,465 metagenomes for the presence of reads matching a database representative of all known mcrA proteins and reconstructed gene sequences from the matching reads.},
doi = {10.7717/peerj.5614},
journal = {PeerJ},
number = ,
volume = 6,
place = {United States},
year = {Mon Sep 17 00:00:00 EDT 2018},
month = {Mon Sep 17 00:00:00 EDT 2018}
}
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