A phylogeny-based method in detecting the species-specialized genes in microbes and its application to a marine symbiont bacteriumn reveals habitat- and pathogen-specific bacterial iron interaction networks

Authors: Zhou X., Li W., Xie S., Xia K., Xiao M., Yang X., Li Z.A.

Journal: mBio

DOI: 10.1128/mbio.03566-24

Link: https://journals.asm.org/doi/10.1128/mbio.03566-24

Published: October 29, 2025

Document Type: Research Article

Abstract:

Different microbes possess special traits that enable adaptation to their specific niches, often through specialized genes. Beyond orphan genes, few methods identify homologous genes with unusual functional regions. To address this, we investigated the extreme recombination frequency of the marine symbiont Ca. E. kahalalidifaciens and developed an unbiased computational approach to detect genes deviating from phylogenetic expectations. This method identified Rec family genes as key contributors to the exceptional recombination capacity in Ca. E. kahalalidifaciens. Heterologous expression in Escherichia coli demonstrated that these gene variants significantly enhance recombination efficiency. These efficient Rec variants offer potential for improving genetic manipulation tools, while our pipeline provides a versatile strategy for microbial genome mining.