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Adapting macroecology to microbiology: using occupancy modelling to assess functional profiles across metagenomes

Angus S. Hilts, Manjot S. Hunjan, View ORCID ProfileLaura A. Hug
doi: https://doi.org/10.1101/2021.06.21.449349
Angus S. Hilts
aDepartment of Biology, University of Waterloo, Waterloo, Ontario, Canada
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Manjot S. Hunjan
aDepartment of Biology, University of Waterloo, Waterloo, Ontario, Canada
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Laura A. Hug
aDepartment of Biology, University of Waterloo, Waterloo, Ontario, Canada
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  • ORCID record for Laura A. Hug
  • For correspondence: laura.hug@uwaterloo.ca
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Abstract

Metagenomic sequencing provides information on the metabolic capacities and taxonomic affiliations for members of a microbial community. When assessing metabolic functions in a community, missing genes in pathways can occur in two ways: the genes may legitimately be missing from the community whose DNA was sequenced, or the genes were missed during shotgun sequencing or failed to assemble, and thus the metabolic capacity of interest is wrongly absent from the sequence data. Here, we borrow and adapt occupancy modelling from macroecology to provide mathematical context to metabolic predictions from metagenomes. We review the five assumptions underlying occupancy modelling through the lens of microbial community sequence data. Using the methane cycle, we apply occupancy modelling to examine the presence and absence of methanogenesis and methanotrophy genes from nearly 10,000 metagenomes spanning global environments. We determine that methanogenesis and methanotrophy are positively correlated across environments, and note that the lack of available standardized metadata for most metagenomes is a significant hindrance to large-scale statistical analyses. We present this adaptation of macroecology’s occupancy modelling to metagenomics as a tool for assessing presence/absence of traits in environmental microbiological surveys. We further initiate a call for stronger metadata standards to accompany metagenome deposition, to enable robust statistical approaches in the future.

  • Abbreviations

    IMG/M
    Integrated Microbial Genomes and Microbiomes
    JGI
    Joint Genome Institute
    KEGG
    Kyoto Encyclopedia of Genes and Genomes
    KO
    KEGG Orthology
    mcr
    Methyl-coenzyme M reductase (referring to the gene)
    MCR
    Methyl coenzyme M reductase (referring to the enzyme)
    pmo
    Particulate methane monooxygenase (referring to the gene)
    pMMO
    Particulate methane monooxygenase (referring to the enzyme)
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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    Posted June 22, 2021.
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    Adapting macroecology to microbiology: using occupancy modelling to assess functional profiles across metagenomes
    Angus S. Hilts, Manjot S. Hunjan, Laura A. Hug
    bioRxiv 2021.06.21.449349; doi: https://doi.org/10.1101/2021.06.21.449349
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    Adapting macroecology to microbiology: using occupancy modelling to assess functional profiles across metagenomes
    Angus S. Hilts, Manjot S. Hunjan, Laura A. Hug
    bioRxiv 2021.06.21.449349; doi: https://doi.org/10.1101/2021.06.21.449349

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