Systematically investigating and identifying unmodified bacteriocins in the human gut microbiome

Abstract

Unmodified class II bacteriocins are naturally occurring antimicrobial peptides that are synthesized by bacteria. When produced by human gut bacteria, these bacteriocins not only protect against harmful pathogens, but also play a role in regulating host physiology. However, the limitations of current bioinformatic tools impede the comprehensive investigation of their biosynthesis in the human gut microbiome, leaving these natural products largely elusive. Here, we introduce IIBacFinder, an analysis pipeline dedicated to identifying unmodified bacteriocins, which outperforms existing tools. Through large-scale bioinformatic analysis of bacterial genomes and experimental validation of novel bacteriocin sequences, we demonstrate the widespread distribution of unmodified bacteriocins across the bacterial tree of life, which are generally niche-specific and enriched in the human microbiome. Analyzing over 200,000 bacterial reference genomes from the human gut microbiome, we reveal the vast potential of gut bacteria to produce diverse unmodified bacteriocins. Guided by meta-omics analysis, we chemically synthesized 26 hypothetical bacteriocins from primary gut commensal species such as Bacteroides and Prevotella, with 16 showing inhibitory activities against bacterial pathogens and human gut commensal bacteria. Our study uncovers the underappreciated biosynthetic potential of unmodified bacteriocins in the human gut microbiome, paving the way for elucidating their biological functions and relationship to human health.