CaltechAUTHORS
  A Caltech Library Service

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. and Orphan, Victoria J. (2018) 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. PeerJ, 2018 (6). Art. No. e5614. ISSN 2167-8359. PMCID PMC6147122. https://resolver.caltech.edu/CaltechAUTHORS:20180926-133207423

[img] PDF - Published Version
Creative Commons Attribution.

5Mb
[img] PDF - Submitted Version
Creative Commons Attribution.

5Mb
[img] PDF (Figure 1) - Supplemental Material
Creative Commons Attribution.

2037Kb
[img] PDF (Figure 2) - Supplemental Material
Creative Commons Attribution.

1850Kb
[img] PDF (Figure 3) - Supplemental Material
Creative Commons Attribution.

458Kb
[img] PDF (Figure 4) - Supplemental Material
Creative Commons Attribution.

1249Kb
[img] Plain Text (Supplemental File 1) - Supplemental Material
Creative Commons Attribution.

110Kb
[img] Plain Text (Supplemental File 2) - Supplemental Material
Creative Commons Attribution.

91Kb
[img] Plain Text (Supplemental File 3) - Supplemental Material
Creative Commons Attribution.

2326Kb
[img] Plain Text (Supplemental File 4) - Supplemental Material
Creative Commons Attribution.

923Kb
[img] Archive (GZIP) (Supplemental File 5) - Supplemental Material
Creative Commons Attribution.

4Mb

Use this Persistent URL to link to this item: https://resolver.caltech.edu/CaltechAUTHORS:20180926-133207423

Abstract

Over the past years, metagenomics has revolutionized our view of microbial diversity. Moreover, 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. We use our mcrA dataset to assess the environmental distribution of the Methanomassiliicoccales and reconstruct and analyze a draft genome belonging to the ‘Lake Pavin cluster’, an uncultivated environmental clade of the Methanomassiliicoccales. Analysis of the ‘Lake Pavin cluster’ draft genome suggests that this organism has a more restricted capacity for hydrogenotrophic methylotrophic methanogenesis than previously studied Methanomassiliicoccales, with only genes for growth on methanol present. However, the presence of the soluble subunits of methyltetrahydromethanopterin:CoM methyltransferase (mtrAH) provide hypothetical pathways for methanol fermentation, and aceticlastic methanogenesis that await experimental verification. Thus, we show that marker gene mining can enhance the discovery power of metagenomics, by identifying novel lineages and aiding selection of targets for in-depth analyses. Marker gene mining is less sensitive to strain heterogeneity and has a lower abundance threshold than genome-resolved metagenomics, as it only requires short contigs and there is no binning step. Additionally, it is computationally cheaper than genome resolved metagenomics, since only a small subset of reads needs to be assembled. It is therefore a suitable approach to extract knowledge from the many publicly available sequencing projects.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.7717/peerj.5614DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6147122PubMed CentralArticle
https://github.com/dspeth/bioinfo_scripts/tree/master/metagenome_screeningRelated ItemData availability
https://doi.org/10.7717/peerj.5614/supp-1DOIFigure 1
https://doi.org/10.7717/peerj.5614/supp-2DOIFigure 2
https://doi.org/10.7717/peerj.5614/supp-3DOIFigure 3
https://doi.org/10.7717/peerj.5614/supp-4DOIFigure 4
https://doi.org/10.7717/peerj.5614/supp-5DOISupplemental File 1
https://doi.org/10.7717/peerj.5614/supp-6DOISupplemental File 2
https://doi.org/10.7717/peerj.5614/supp-7DOISupplemental File 3
https://doi.org/10.7717/peerj.5614/supp-8DOISupplemental File 4
https://doi.org/10.7717/peerj.5614/supp-9DOISupplemental File 5
https://doi.org/10.1101/328906DOIDiscussion Paper
ORCID:
AuthorORCID
Speth, Daan R.0000-0002-2361-5935
Orphan, Victoria J.0000-0002-5374-6178
Alternate Title:Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds light on metabolic versatility of the Methanomassiliicoccales
Additional Information:© 2018 Speth and Orphan. Distributed under Creative Commons CC-BY 4.0. The authors declare there are no competing interests. Author Contributions: Daan R. Speth conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft. Victoria J. Orphan conceived and designed the experiments, authored or reviewed drafts of the paper, approved the final draft. Data Availability: The following information was supplied regarding data availability: https://github.com/dspeth/bioinfo_scripts/tree/master/metagenome_screening. This manuscript is based upon work supported by the US Department of Energy, Office of Science, Office of Biological and Environmental Research under award number DE-SC0016469 to Victoria J. Orphan. In addition, Daan R. Speth was supported by NWO Rubicon 019.153LW.039. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We thank Woody Fischer and Connor Skennerton for helpful discussion and Grayson Chadwick for critically reading the manuscript.
Funders:
Funding AgencyGrant Number
Department of Energy (DOE)DE-SC0016469
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)019.153LW.039
Issue or Number:6
PubMed Central ID:PMC6147122
Record Number:CaltechAUTHORS:20180926-133207423
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20180926-133207423
Official Citation:Speth DR, Orphan VJ. (2018) 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. PeerJ 6:e5614 https://doi.org/10.7717/peerj.5614
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:89965
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:26 Sep 2018 21:07
Last Modified:09 Mar 2020 13:19

Repository Staff Only: item control page