Bacterial 16S Ribosomal Gene Fingerprints as a Tool to Diagnose and Mitigate Fish Larvae Gut Dysbiosis

Dysbiosis is associated with shifts in the diversity or relative abundance of beneficial versus harmful bacteria, leading to health issues in organisms. This study investigated gut bacterial dysbiosis associated with larval quality using 16S rRNA gene sequencing. The gut microbiome of gilthead sea bream and European sea bass, key commercial species and vertebrate models, was examined in high- and low-quality larvae batches from several European hatcheries. Larval quality, hatchery site and species influenced bacterial diversity in the gut. Individuals from larval batches that performed well had higher microbial diversity in the gut and individuals from batches that performed poorly had a gut microbiota dominated by pathogenic Vibrio (e.g., V. aestuarianus and V. cortegadensis). The bacterial dysbiosis index revealed a notable predominance of Fusobacteriota and Firmicutes phyla, Thermoanaerobacteria class and Lactobacillaceae, Moritellaceae, Clostridiaceae, Thiotrichaceae and Shewanellaceae families in good-quality larvae batches, and a prevalence of the Proteobacteria phylum, Gammaproteobacteria class, Sphingomonadaceae and Vibrionaceae families in the gut of individuals from poor-quality larvae batches. A positive dysbiosis index (cutoff > 0.4) was associated with a high risk of decreased larval performance and quality. Additionally, the abundance of Clostridium_sensu_stricto_15, Shewanellaceae_unclassified, Cetobacterium, Psychrilyobacter, Moritella and Latilactobacillus genera in the gut of good production batches, and the Vibrio genus in the gut of poor production batches, identified these genus as potential markers for diagnosing and mitigating bacterial dysbiosis in fish and potentially other vertebrates.