SNV-FEAST: microbial source tracking with single nucleotide variants

Leah Briscoe; Eran Halperin; Nandita R Garud

doi:10.1186/s13059-023-02927-8

SNV-FEAST: microbial source tracking with single nucleotide variants

Genome Biol. 2023 Apr 30;24(1):101. doi: 10.1186/s13059-023-02927-8.

Authors

Leah Briscoe¹, Eran Halperin^{2

3

4

5

6}, Nandita R Garud^{7

8}

Affiliations

¹ Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA. leahpbriscoe@gmail.com.
² Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA.
³ Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
⁴ Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
⁵ Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
⁶ Institute of Precision Health, University of California Los Angeles, Los Angeles, CA, USA.
⁷ Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA. ngarud@ucla.edu.
⁸ Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA. ngarud@ucla.edu.

Abstract

Elucidating the sources of a microbiome can provide insight into the ecological dynamics responsible for the formation of these communities. Source tracking approaches to date leverage species abundance information; however, single nucleotide variants (SNVs) may be more informative because of their high specificity to certain sources. To overcome the computational burden of utilizing all SNVs for a given sample, we introduce a novel method to identify signature SNVs for source tracking. Signature SNVs used as input into a previously designed source tracking algorithm, FEAST, can more accurately estimate contributions than species and provide novel insights, demonstrated in three case studies.

Keywords: Microbiome; Single nucleotide variants; Source tracking; Strains; Transmission.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
High-Throughput Nucleotide Sequencing
Microbiota*
Nucleotides
Polymorphism, Single Nucleotide

Substances

Nucleotides