metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes

• DOI: 10.1093/bioinformatics/btab789
• Publication Date: 2021-11-14T20:06:46Z
• Authors: Thea Van Rossum; Paul I Costea; Lucas Paoli; Renato Alves; Roman Thielemann; Shinichi Sunagawa; Peer Bork
• Keywords: Subspecies; Identification; Human Microbiome Project

Abstract Summary Taxonomic analysis of microbial communities is well supported at the level species and strains. However, can contain significant phenotypic diversity strains are rarely widely shared across global populations. Stratifying between identify ‘subspecies’, which a useful intermediary. High-throughput identification profiling subspecies not yet in microbiome field. Here, we use an operational definition based on single nucleotide variant (SNV) patterns within to profile metagenomes, along with their distinctive SNVs genes. We incorporate this method into metaSNV v2, extends existing SNV-calling software support further SNV interpretation for population genetics. These new features analyses link profiles host phenotype or environment niche-specificity. demonstrate marine fecal metagenomes. In latter, analyze 70 7524 adult infant subjects, supporting common structure human gut illustrating some limits calling. Availability implementation Source code, documentation, tutorials test data available https://github.com/metasnv-tool/metaSNV https://metasnv.embl.de. Supplementary information Bioinformatics online.