Structure and Diversity of Microbiomes Associated with the Gastrointestinal Tracts of Wild Spiny Lobsters and Profiling Their Potential Probiotic Properties Using eDNA Metabarcoding

Abstract

Microbial communities have been documented as playing many pivotal roles, and contributing to the growth or health performance of animal hosts. Thus, many studies are currently looking for potential beneficial bacteria “probiotics” from diverse environments, including wild species. The present study aimed to investigate the diversity and potential metabolic functions of bacterial communities in the gastrointestinal tract of wild spiny lobsters. The gastrointestinal (GI) tracts of two wild lobster species (Panulirus ornatus and Panulirus homarus) were dissected aseptically and analyzed through high-throughput sequencing, followed by PICRUSt analysis. The results exposed that the most dominant phyla inhabiting both lobster species at the post-puerulus and juvenile stages were Proteobacteria, Firmicutes, Bacteriodota, Patescibacteria, and Verrucomicrobiota, while at the genus level, the GI tracts were mostly dominated by Photobacterium, Candidatus Bacillopora, Vibrio, and Catenococcus at the post-peurulus stage, and Vibrio, Catenococcus, Acanthopleuribacter, Acinetobacter, Pseudoalteromonas, Grimontia, and Photobacterium at the juvenile stage. Further metagenomic prediction analysis discovers many potential probiont properties indicated by the detection of marker genes corresponding to many important metabolic activities, such as antimicrobial compounds (streptomycin, vancomycin, carbapenem, tetracycline, novobiocin, penicillin, cephalosporin, ansamycines, butirosin, and neomycin), antioxidants (e.g., flavonoids and carotenoids), and several important digestive enzymes (e.g., lipase, protease, and amylase). These results suggest that GI tracts of wild spiny lobsters are potential sources to discover novel probionts for aquaculture purposes. Further studies, such as the isolation of the natural product-producing bacteria, or cloning of the beneficial compound-identified genes, are highly recommended to develop novel probiotic strains for aquaculture purposes.