Metagenomic strain detection with SameStr: identification of a persisting core gut microbiota transferable by fecal transplantation.

ABSTRACT:

Background

The understanding of how microbiomes assemble, function, and evolve requires metagenomic tools that can resolve microbiota compositions at the strain level. However, the identification and tracking of microbial strains in fecal metagenomes is challenging and available tools variably classify subspecies lineages, which affects their applicability to infer microbial persistence and transfer.

Results

We introduce SameStr, a bioinformatic tool that identifies shared strains in metagenomes by determining single-nucleotide variants (SNV) in species-specific marker genes, which are compared based on a maximum variant profile similarity. We validated SameStr on mock strain populations, available human fecal metagenomes from healthy individuals and newly generated data fro

SUBMITTER: Podlesny D 

PROVIDER: S-EPMC8951724 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature