Genomic insights intoLactobacillaceae: Analyzing the “Alleleome” of core pangenomes for enhanced understanding of strain diversity and revealing Phylogroup-specific unique variants

Abstract

The Lactobacillaceae family's significance in food and health, combined with available strain-specific genomes, enables genome assessment through pangenome analysis. The Alleleome of the core pangenomes of the Lactobacillaceae family, which identifies natural sequence variations, was reconstructed from the amino acid and nucleotide sequences of the core genes across 2,447 strains of 26 species. It comprised 3.71 million amino acid variants in 29,448 core genes across the family. The alleleome analysis of the Lactobacillaceae family revealed key findings: 1) In the core pangenome, amino acid substitutions prevailed over rare insertions and deletions, 2) Purifying negative selection primarily influenced core gene variations in the family, with diversifying selection noted in L. helveticus. L. plantarum core alleleome was investigated due to its industrial importance. In L. plantarum, the defining characteristics of its core alleleome included: 1) It is highly conserved; 2) Among 235 isolation sources, the primary categories displaying variant prevalence were fermented food, feces, and unidentified sources; 3) It is predominantly characterized by conservative and moderately conservative mutations; and 4) Phylogroup-specific core variant gene analysis identified unique variants (DltX, FabZ1, Pts23B, CspP) in phylogroups I and B which could be used as identifier or validation markers of strain or phylogroup.