Vagococcus changpingensis sp. nov., a Fly-Associated Bacterium with Human Gut Metagenomic Representatives: Genomic and Metagenomic Insights into Its Ecological Distribution

Abstract

The genus Vagococcus comprises Gram-positive bacteria with a broad ecological distribution, yet its diversity and potential links between animal and human habitats remain underexplored. Here, we report two novel fly-associated strains, CY52-2T and CY62-2, isolated from a retail market in Beijing, China. Polyphasic taxonomic analyses demonstrated that they represent a novel species, for which we propose the name Vagococcus changpingensis sp. nov. Large-scale mining of 805 public metagenomes identified two human gut-derived genomes that share > 99.3% ANI with V. changpingensis, extending the known distribution of this species from insects to the human gastrointestinal tract at the genomic level. Pangenome analysis revealed an open pangenome and uncovered niche-specific gene sets. These findings highlight the power of targeted metagenomics to reveal the potential ecological breadth of newly described species and provide a genomic framework for future investigations of the genus Vagococcus.