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

Speth, Daan R.; Orphan, Victoria J.

doi:10.7717/peerj.5614

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

Journal Article · Mon Sep 17 00:00:00 EDT 2018 · PeerJ

DOI:https://doi.org/10.7717/peerj.5614· OSTI ID:1503317

Speth, Daan R. ^[1]; Orphan, Victoria J. ^[1]

California Inst. of Technology (CalTech), Pasadena, CA (United States)

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.

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Research Organization:: California Institute of Technology (CalTech), Pasadena, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0016469

OSTI ID:: 1503317

Journal Information:: PeerJ, Vol. 6; ISSN 2167-8359

Publisher:: PeerJ Inc.Copyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 15 works

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59 BASIC BIOLOGICAL SCIENCES
Marker genes
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Data mining
Methanogens
Methanomassiliicoccales

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

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