FeGenie: a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genomes and metagenome assemblies

Garber, A. I.; Nealson, K. H.; Okamoto, A.; McAllister, S. M.; Chan, C. S.; Barco, R. A.; Merino, N.

doi:10.3389/fmicb.2020.00037

Title: FeGenie: a comprehensive tool for the identification of iron genes and iron gene neighborhoods in genomes and metagenome assemblies

Journal Article · Fri Jan 31 00:00:00 EST 2020 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2020.00037· OSTI ID:1617279

Garber, A. I. ^[1]; Nealson, K. H. ^[2]; Okamoto, A. ^[3]; McAllister, S. M. ^[4]; Chan, C. S. ^[4]; Barco, R. A. ^[2]; Merino, N. ^[5]

Univ. of Southern California, Los Angeles, CA (United States); Univ. of Delaware, Newark, DE (United States)
Univ. of Southern California, Los Angeles, CA (United States)
National Inst. for Materials Science (NIMS), Tsukuba (Japan)
Univ. of Delaware, Newark, DE (United States)
Univ. of Southern California, Los Angeles, CA (United States); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Tokyo Institute of Technology (Japan)

Iron is a micronutrient for nearly all life on Earth. It can be used as an electron donor and electron acceptor by iron-oxidizing and iron-reducing microorganisms and is used in a variety of biological processes, including photosynthesis and respiration. While it is the fourth most abundant metal in the Earth’s crust, iron is often limiting for growth in oxic environments because it is readily oxidized and precipitated. Much of our understanding of how microorganisms compete for and utilize iron is based on laboratory experiments. However, the advent of next-generation sequencing and surge in publicly available sequence data has made it possible to probe the structure and function of microbial communities in the environment. To bridge the gap between our understanding of iron acquisition, iron redox cycling, iron storage, and magnetosome formation in model microorganisms and the plethora of sequence data available from environmental studies, we have created a comprehensive database of hidden Markov models (HMMs) based on genes related to iron acquisition, storage, and reduction/oxidation in Bacteria and Archaea. Along with this database, we present FeGenie, a bioinformatics tool that accepts genome and metagenome assemblies as input and uses our comprehensive HMM database to annotate provided datasets with respect to iron-related genes and gene neighborhood. An important contribution of this tool is the efficient identification of genes involved in iron oxidation and dissimilatory iron reduction, which have been largely overlooked by standard annotation pipelines. We validated FeGenie against a selected set of 28 isolate genomes and showcase its utility in exploring iron genes present in 27 metagenomes, 4 isolate genomes from human oral biofilms, and 17 genomes from candidate organisms, including members of the candidate phyla radiation. We show that FeGenie accurately identifies iron genes in isolates. Furthermore, analysis of metagenomes using FeGenie demonstrates that the iron gene repertoire and abundance of each environment is correlated with iron richness. While this tool will not replace the reliability of culture-dependent analyses of microbial physiology, it provides reliable predictions derived from the most up-to-date genetic markers. FeGenie’s database will be maintained and continually updated as new genes are discovered.

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Research Organization:: Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE National Nuclear Security Administration (NNSA)

Grant/Contract Number:: AC52-07NA27344

OSTI ID:: 1617279

Report Number(s):: LLNL-JRNL-791160; 989649

Journal Information:: Frontiers in Microbiology, Vol. 11; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 136 works

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