In Silico Comparison Shows that the Pan-Genome of a Dairy-Related Bacterial Culture Collection Covers Most Reactions Annotated to Human Microbiomes

Abstract

<jats:p>The diversity of the human microbiome is positively associated with human health. However, this diversity is endangered by Westernized dietary patterns that are characterized by a decreased nutrient variety. Diversity might potentially be improved by promoting dietary patterns rich in microbial strains. Various collections of bacterial cultures resulting from a century of dairy research are readily available worldwide, and could be exploited to contribute towards this end. We have conducted a functional in silico analysis of the metagenome of 24 strains, each representing one of the species in a bacterial culture collection composed of 626 sequenced strains, and compared the pathways potentially covered by this metagenome to the intestinal metagenome of four healthy, although overweight, humans. Remarkably, the pan-genome of the 24 strains covers 89% of the human gut microbiome’s annotated enzymatic reactions. Furthermore, the dairy microbial collection covers biological pathways, such as methylglyoxal degradation, sulfate reduction, γ-aminobutyric (GABA) acid degradation and salicylate degradation, which are differently covered among the four subjects and are involved in a range of cardiometabolic, intestinal, and neurological disorders. We conclude that microbial culture collections derived from dairy research have the genomic potential to complement and restore functional redundancy in human microbiomes.</jats:p>

Bioactive Compounds Produced by the Accompanying Microflora in Bulgarian Yoghurt

“…parabuchneri, Lb. parafarraginis, Lactiplantibacillus plantarum, Lactococcus lactis, Leuconostoc mesenteroides, and Pediococcus acidilactici in both niches [35,36]. Our results partially confirmed these observations, because among autochthonic lactobacilli in Bulgarian artisanal yoghurts Lb.…”

OpenGenomeBrowser: a versatile, dataset-independent and scalable web platform for genome data management and comparative genomics

“…Annotation types can be customized, and ortholog-based features are optional. While the demo server only holds 70 genomes, the performance scales and is still outstanding even when hosting over 1400 microbial genomes [ 41 ].…”

“…The data used to generate the figures in this study are included in the published article Roder et al, 2020 [ 41 ] where the GenBank accession numbers are listed in Supplementary Table S 1 . 10.3390/microorganisms8070966.…”

OpenGenomeBrowser: A versatile, dataset-independent and scalable web platform for genome data management and comparative genomics

“…Annotation types can be customized, and ortholog-based features are optional. While the demo server only holds 24 genomes, the performance scales and is still outstanding even when hosting over 1'400 microbial genomes (40).…”