Calculating fast differential genome coverages among metagenomic sources using micov
Breadth of coverage, the proportion of a reference genome covered by at least one sequencing read, is critical for interpreting metagenomic data, informing analyses from genome assembly to taxonomic profiling. However, existing tools typically summarize coverage breadth at the whole-genome or aggregate-sample level, missing informative variation along genomes and between sample groups. Here we introduce MIcrobiome COVerage (micov), a tool that computes and compares per-sample breadth of coverage across many genomes and samples. micov offers two key advances: (1) rapid cumulative coverage breadth calculations specific to each sample type, and (2) detection of differential coverage breadth along genomes. Applying micov to three metagenomic datasets, we show that it identifies a genomic region in Prevotella copri that explains variation in community composition independent of host country of origin, uncovers dietary association with a partially annotated region in an uncharacterized Lachnospiraceae genome, enabling hypothesis generation for genes of unknown function, and improves sensitivity in low-biomass settings by detecting a single genomic copy of enteropathogenic Escherichia coli (EPEC) in wastewater and distinguishing Mediterraneibacter gnavus across specimen types.
Authors
- Hiutung Chu (ORCID: https://orcid.org/0000-0001-7489-0446)
- Se Jin Song (ORCID: https://orcid.org/0000-0003-0750-5709)
- Suzanne Devkota (ORCID: https://orcid.org/0000-0001-5575-9362)
- Evguenia Kopylova (ORCID: https://orcid.org/0000-0003-0225-3223)
- Rodolfo A. Salido (ORCID: https://orcid.org/0000-0003-0631-2817)
- Caitlin Guccione (ORCID: https://orcid.org/0000-0002-0446-1635)
- Daniel McDonald
- Andrew P. Bartko (ORCID: https://orcid.org/0000-0002-1237-2747)
- Rob Knight (ORCID: https://orcid.org/0000-0002-0975-9019)
- Gregory D. Sepich‐Poore (ORCID: https://orcid.org/0000-0002-3443-3715)
- Jeff Hasty (ORCID: https://orcid.org/0000-0003-1673-0473)
- M. Omar Din (ORCID: https://orcid.org/0000-0003-4012-4182)
- Kit Curtius (ORCID: https://orcid.org/0000-0002-2678-0960)
- Renee Oles (ORCID: https://orcid.org/0000-0001-5945-0215)
- Yuhan Weng (ORCID: https://orcid.org/0009-0005-3453-1402)
Institutions
- Northwestern University (US)
- Cedars-Sinai Medical Center (US)
- University of California San Diego (US)
- Claritas Genomics (United States) (US)
- VA San Diego Healthcare System (US)
- La Jolla Bioengineering Institute (US)
Publication Details
- Journal
- Communications Biology
- Published
- 2025-11-20
- DOI
- https://doi.org/10.1038/s42003-025-09007-6
- Citations
- 5
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 4.03
Funders
- U.S. Department of Veterans Affairs
- AGA Research Foundation
- Northwestern University
- Danone
- Cedars-Sinai Medical Center
- Danone Nutricia Research
- Yuhan
- Chiba University
- National Institutes of Health
- Centers for Disease Control and Prevention
- University of California, San Diego
- Feinberg School of Medicine
- Veterans Affairs San Diego Healthcare System
- National Institute of Diabetes and Digestive and Kidney Diseases