SNV-FEAST: microbial source tracking with single nucleotide variants.

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.

SUBMITTER: Briscoe L 

PROVIDER: S-EPMC10150486 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature