Midgut Bacterial Microbiota of 12 Fish Species from a Marine Protected Area in the Aegean Sea (Greece)

Comparative study of gut content microbiota in freshwater fish with different feeding habits: A case study of an urban lake

The gut microbiota plays a crucial role in various physiological functions of the host and can be modulated by numerous factors, including feeding habit or trophic level. In this study, the impact of host feeding habits on the gut microbiota of freshwater fish was explored. Ten fish species, classified into four feeding habit categories (herbivorous, omnivorous, planktivorous, and carnivorous) were sampled from West Lake, a renowned urban scenic lake, and their gut content microbiota was analysed using 16S ribosomal RNA gene sequencing. A total of 2531 operational taxonomic units, belonging to 34 bacterial phyla, were identified, with 33.4% shared across all feeding habits. Firmicutes and Proteobacteria were the predominant phyla. However, at the family level, Peptostreptococcaceae and Clostridiaceae_1 were the most dominant. Microbiota composition diversity was highest in herbivorous fish, followed by omnivores, carnivores, and planktivores. Statistically significant differences in microbiota diversity were found between different feeding categories, except for the omnivores, which did not differ from the carnivores or planktivores. The most abundant predicted metabolic pathways across all feeding habits were similar, with amino acid metabolism, carbohydrate metabolism, metabolism of cofactors and vitamins, and metabolism of other amino acids being dominant. However, comparing the relative abundance of gene functions between different feeding habits revealed notable variations across most comparisons. Co-occurrence network analysis for each feeding habit revealed that all networks were dominated by the strong positive correlation among pairs of bacterial genera abundances, while the basic properties varied, implying differences in gut microbiota interactions based on the feeding habit. In conclusion, these results confirmed that the feeding habit could affect the structure and composition of the gut content microbiota but also changed their functions and interactions.

The Marine Fish Gut Microbiome as a Source of Novel Bacteriocins

The marine environment is the largest ecological habitat on Earth, albeit one of the least explored, particularly in terms of its microbial inhabitants. The marine fish gut is host to a diverse microbial community from which diverse bioactive molecules can be sourced. Due to the unique environmental pressures these microbial communities experience, the bioactive molecules they produce often evolve unique adaptations that give them diverse structures and activities, differentiating them from terrestrial homologues. Of particular interest, due to their structural and functional diversity, are the ribosomally-synthesized antimicrobial peptides (bacteriocins). With increasing pressure from emerging antibiotic-resistant disease and industrial demand for novel therapeutics, the marine fish gut microbiome represents a relatively untapped resource of novel bacteriocins that could prove beneficial to human health and aquaculture. This review presents an overview of the marine fish gut microbiome and explores its potential as a source of bacteriocins for human health with considerations for applications and future research in this area.

The gills and skin microbiota of five pelagic fish species from the Atlantic Ocean

The gills and skin microbiota and microbiome of wild fish remain far more under-investigated compared to that of farmed fish species, despite that these animal-microbe interactions hold the same ecophysiological roles in both cases. In this study, the gills and skin bacterial microbiota profiles and their presumptive bacterial metabolisms were investigated in five open-sea fishes: bullet tuna (Auxis sp.), common dolphinfish (Coryphaena hippurus), Atlantic little tunny (Euthynnus alletteratus), Atlantic bonito (Sarda sarda) and Atlantic white marlin (Kajikia albida). Gills and skin tissues were collected from two to three individuals per species, from specimens caught by recreational trolling during summer of 2019, and their bacterial 16S rRNA gene diversity was analysed by high-throughput sequencing. The gills bacterial communities among the five species were clearly different but not the skin bacterial microbiota. The dominant operational taxonomic units belonged to the Moraxellaceae, Pseudomonadaceae, Rhodobacteraceae, Staphylococcaceae and Vibrionaceae families. Despite the differences in taxonomic composition, the presumptive bacterial metabolisms between the gills and skin of the five fishes investigated here were ≥ 94% similar and were dominated by basic metabolism, most likely reflecting the continuous exposure of these tissues in the surrounding seawater.

The intestinal digesta microbiota of tropical marine fish is largely uncultured and distinct from surrounding water microbiota

Studying the gut microbes of marine fishes is an important part of conservation as many fish species are increasingly threatened by extinction. The gut microbiota of only a small fraction of the more than 32,000 known fish species has been investigated. In this study we analysed the intestinal digesta microbiota composition of more than 50 different wild fish species from tropical waters. Our results show that the fish harbour intestinal digesta microbiota that are distinct from that of the surrounding water and that location, domestication status, and host intrinsic factors are strongly associated with the microbiota composition. Furthermore, we show that the vast majority (~97%) of the fish-associated microorganisms do not have any cultured representative. Considering the impact of the microbiota on host health and physiology, these findings underpin the call to also preserve the microbiota of host species, especially those that may be exposed to habitat destruction.