Liles, M. R. | bioRxiv Science

bioRxiv2026

Comparative genomics and microbiome profiling reveal a conserved Vibrio rich mucus microbiota of the Florida false coral (Ricordea florida)

Mucus is a critical interface between marine invertebrates and their environment and plays key roles in host defense. Despite its ecological importance, little is known about the microbial communities associated with mucus-producing corallimorpharians. Here, we used a multi-omics approach to characterize the mucus microbiome and immune repertoire of the Florida false coral, Ricordea florida. Culture-dependent and culture-independent analyses revealed that R. florida mucus harbors a bacterial community distinct from surrounding seawater and consistently dominated by Vibrio species. Whole-genome sequencing of 13 cultured Vibrio isolates representing nine distinct lineages revealed substantial taxonomic diversity, including several highly divergent strains that may represent undescribed species. Comparative genomic analyses identified enrichment of genes associated with carbohydrate acquisition, glycoside hydrolysis, and host colonization, including multiple components of the Tad/Flp adhesion system, suggesting adaptation to the mucus microenvironment. To investigate host factors that may shape microbial associations, we assembled and annotated a host transcriptome from healthy and immune-challenged polyps. This analysis identified a diverse innate immune repertoire, including Toll-like receptors, NOD-like receptors, lectins, scavenger receptors, complement-associated proteins, antiviral defense pathways, and membrane attack complex/perforin domain-containing effectors. Together, these findings demonstrate that R. florida supports a conserved, Vibrio-rich mucus microbiome and possesses a complex innate immune system capable of mediating host-microbe interactions at the mucosal surface. This study provides a foundation for understanding microbial colonization, immune defense, and holobiont function in an understudied cnidarian lineage.

microbiology↗

bioRxiv2025

Paenitracins, a novel family of bacitracin-type nonribosomal peptide antibiotics produced by plant-associated Paenibacillus species

The growing threat of antimicrobial resistance necessitates the discovery of novel antibiotics with activity against drug-resistant pathogens. Members of the genus Paenibacillus are a rich source of nonribosomal peptides (NRPs), including well-known antibiotics such as polymyxins, paenibacterin and tridecaptins. Here we use a targeted Mass-QL-based mass spectrometry approach to identify the NRPs produced by a collection of 227 taxonomically diverse plant-associated Paenibacillus strains, providing detailed insights into their NRP-producing potential. Using MassQL to zoom in specifically on NRPs containing basic amino acids, we discovered a novel family of bacitracins, which we designated paenitracins. The paenitracins are the first bacitracin-type peptides reported in Paenibacillus, and are distinguished from canonical bacitracins by three previously unseen amino acid substitutions. The paenitracins exhibit potent activity against Gram-positive pathogens, including vancomycin-resistant Enterococcus faecium E155. Our work provides a novel metabolomics- and genomics-guided workflow for the discovery of bioactive NRPs as a strategy to prioritize natural product chemical space and accelerate antibiotic discovery. IMPORTANCEMembers of the genus Paenibacillus play an important role in soil ecology, producing a range of important nonribosomal peptides (NRPs) that protect their eukaryotic host. A collection of plant-associated Paenibacillus spp. was analyzed for their phylogenetic and metabolic diversity. We developed a novel discovery pipeline that combines feature-based molecular networking with MassQL queries to systematically prioritize bioactive NRPs containing basic amino acids. Thus we provide a comprehensive genus-wide inventory of NRPs produced by Paenibacillus spp. We thereby identified the paenitracins, a new subfamily of bacitracins active against multidrug-resistant Gram-positive pathogens. Our pipeline enables the discovery of novel peptidic natural products to accelerate the prioritization of chemical space for antibiotics.

microbiology↗