CANT-HYD: A Curated Database of Phylogeny-Derived Hidden Markov Models for Annotation of Marker Genes Involved in Hydrocarbon Degradation

Varada Khot; Jackie Zorz; Daniel A. Gittins; Anirban Chakraborty; Emma Bell; María A. Bautista; Alexandre J. Paquette; Alyse K. Hawley; Breda Novotnik; Casey R. J. Hubert; Marc Strous; Srijak Bhatnagar

doi:10.3389/fmicb.2021.764058

Frontiers in Microbiology (Jan 2022)

CANT-HYD: A Curated Database of Phylogeny-Derived Hidden Markov Models for Annotation of Marker Genes Involved in Hydrocarbon Degradation

Varada Khot,
Jackie Zorz,
Daniel A. Gittins,
Anirban Chakraborty,
Emma Bell,
María A. Bautista,
Alexandre J. Paquette,
Alyse K. Hawley,
Breda Novotnik,
Casey R. J. Hubert,
Marc Strous,
Srijak Bhatnagar

Affiliations

Varada Khot: Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
Jackie Zorz: Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
Daniel A. Gittins: Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
Anirban Chakraborty: Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
Emma Bell: Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
María A. Bautista: Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
Alexandre J. Paquette: Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
Alyse K. Hawley: Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
Breda Novotnik: Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
Casey R. J. Hubert: Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
Marc Strous: Energy Bioengineering and Geomicrobiology Group, Department of Geoscience, University of Calgary, Calgary, AB, Canada
Srijak Bhatnagar: Energy Bioengineering and Geomicrobiology Group, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada

DOI: https://doi.org/10.3389/fmicb.2021.764058
Journal volume & issue: Vol. 12

Abstract

Read online

Many pathways for hydrocarbon degradation have been discovered, yet there are no dedicated tools to identify and predict the hydrocarbon degradation potential of microbial genomes and metagenomes. Here we present the Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database of 37 HMMs of marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons. Using this database, we identify understudied or overlooked hydrocarbon degradation potential in many phyla. We also demonstrate its application in analyzing high-throughput sequence data by predicting hydrocarbon utilization in large metagenomic datasets from diverse environments. CANT-HYD is available at https://github.com/dgittins/CANT-HYD-HydrocarbonBiodegradation.

Published in Frontiers in Microbiology

ISSN: 1664-302X (Online)
Publisher: Frontiers Media S.A.
Country of publisher: Switzerland
LCC subjects: Science: Microbiology
Website: http://www.frontiersin.org/journals/microbiology

About the journal

Abstract

Keywords