Xiaoqian Lin

Microbes use signaling molecules to regulate multiple physiological processes and mediate chemical interactions. Decoding these chemical languages is instrumental in comprehending microbial regulatory mechanisms within complex microbiota. Here, we discover previously unidentified autoinducing peptides (AIPs) derived from the plant probiotic bacterium Paenibacillus polymyxa , identified as Pp-AIPs. Omics analyses coupled with genetic manipulations revealed that Pp-AIP1 could effectively modulate the production of multiple antimicrobial secondary metabolites at nanomolar concentration, expanding known AIP functions. Furthermore, through inoculating P. polymyxa in the natural rhizosphere microbiome and analyzing its antagonistic interactions against root microbes, we suggest that Pp-AIPs may influence the microbial community composition through modulating the antimicrobial spectrum. Global analysis of biosynthetic gene clusters (BGCs) reveal widespread co-occurrence of uncharacterized AIPs with secondary metabolite BGCs. This study underscores the unreported roles of AIPs in antibiotic regulation and the microbiome interactions, advancing knowledge of quorum-sensing mechanisms in microbial ecosystems.

The Lachnospiraceae family holds promise as a source of next‐generation probiotics, yet a comprehensive delineation of its diversity is lacking, hampering the identification of suitable strains for future applications. To address this knowledge gap, we conducted an in‐depth genomic and functional analysis of 1868 high‐quality genomes, combining data from public databases with our new isolates. This data set represented 387 colonization‐selective species‐level clusters, of which eight genera represented multilineage clusters. Pan‐genome analysis, single‐nucleotide polymorphism (SNP) identification, and probiotic functional predictions revealed that species taxonomy, habitats, and geography together shape the functional diversity of Lachnospiraceae. Moreover, analyses of associations with atherosclerotic cardiovascular disease (ACVD) and inflammatory bowel disease (IBD) indicated that several strains of potentially novel Lachnospiraceae species possess the capacity to reduce the abundance of opportunistic pathogens, thereby imparting potential health benefits. Our findings shed light on the untapped potential of novel species enabling knowledge‐based selection of strains for the development of next‐generation probiotics holding promise for improving human health and disease management.