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. We show that 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.