METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M.; Liu, Yang; Kieft, Kristopher; Cowley, Elise S.; Karaoz, Ulas; Anantharaman, Karthik

doi:10.1186/s40168-021-01213-8

Title: METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

Journal Article · 16 February 2022 · Microbiome

DOI: https://doi.org/10.1186/s40168-021-01213-8 · OSTI ID:1891286

Zhou, Zhichao ^[1]; Tran, Patricia Q. ^[1]; Breister, Adam M. ^[1]; Liu, Yang ^[2]; Kieft, Kristopher ^[1]; Cowley, Elise S. ^[1]; Karaoz, Ulas ^[3];

^[1]

Univ. of Wisconsin, Madison, WI (United States)
Shenzhen Univ. (China)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Background Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling. Results We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric “MW-score” (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~ 3 h with 40 CPU threads to process ~ 100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~ 45 min, while it takes ~ 5 h to complete hmmsearch for ~ 3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut. Conclusion METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3 at https://github.com/AnantharamanLab/METABOLIC.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: National Library of Medicine (NLM); National Science Foundation (NSF); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1891286

Journal Information:: Microbiome, Journal Name: Microbiome Journal Issue: 1 Vol. 10; ISSN 2049-2618

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
biogeochemistry
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microbiome

Additional file 10 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19185512 The current record is supplemented by this dataset	dataset	January 2022
Additional file 10 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19185512.v1 The current record is supplemented by this dataset	dataset	January 2022
Additional file 11 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19185515 The current record is supplemented by this dataset	dataset	January 2022
Additional file 11 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19185515.v1 The current record is supplemented by this dataset	dataset	January 2022
Additional file 12 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19185518 The current record is supplemented by this dataset	dataset	January 2022
Additional file 12 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19185518.v1 The current record is supplemented by this dataset	dataset	January 2022
Additional file 13 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19185521 The current record is supplemented by this dataset	dataset	January 2022
Additional file 13 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19185521.v1 The current record is supplemented by this dataset	dataset	January 2022
Additional file 14 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19185524 The current record is supplemented by this dataset	dataset	January 2022
Additional file 14 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19185524.v1 The current record is supplemented by this dataset	dataset	January 2022
Additional file 2 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19185527 The current record is supplemented by this text	text	January 2022
Additional file 2 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19185527.v1 The current record is supplemented by this text	text	January 2022
Additional file 3 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19185530.v1 The current record is supplemented by this text	text	January 2022
Additional file 4 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19185533 The current record is supplemented by this text	text	January 2022
Additional file 4 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19185533.v1 The current record is supplemented by this text	text	January 2022
Additional file 5 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19186282 The current record is supplemented by this text	text	January 2022
Additional file 5 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19186282.v1 The current record is supplemented by this text	text	January 2022
Additional file 6 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19186285 The current record is supplemented by this text	text	January 2022
Additional file 6 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19186285.v1 The current record is supplemented by this text	text	January 2022
Additional file 7 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19186288 The current record is supplemented by this text	text	January 2022
Additional file 7 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19186288.v1 The current record is supplemented by this text	text	January 2022
Additional file 8 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19186291.v1 The current record is supplemented by this text	text	January 2022
Additional file 9 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19186294 The current record is supplemented by this dataset	dataset	January 2022
Additional file 9 of METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks Zhou, Zhichao; Tran, Patricia Q.; Breister, Adam M. https://doi.org/10.6084/m9.figshare.19186294.v1 The current record is supplemented by this dataset	dataset	January 2022