As the most diverse vertebrate group and a major component of a growing global aquaculture industry, teleosts continue to attract significant scientific attention. The growth in global aquaculture, driven by declines in wild stocks, has provided additional empirical demand, and thus opportunities, to explore teleost diversity. Among key developments is the recent growth in microbiome exploration, facilitated by advances in high-throughput sequencing technologies. Here, we consider studies on teleost gut microbiomes in the context of sustainable aquaculture, which we have discussed in four themes: diet, immunity, artificial selection and closed-loop systems. We demonstrate the influence aquaculture has had on gut microbiome research, while also providing a road map for the main deterministic forces that influence the gut microbiome, with topical applications to aquaculture. Functional significance is considered within an aquaculture context with reference to impacts on nutrition and immunity. Finally, we identify key knowledge gaps, both methodological and conceptual, and propose promising applications of gut microbiome manipulation to aquaculture, and future priorities in microbiome research. These include insect-based feeds, vaccination, mechanism of pro- and prebiotics, artificial selection on the hologenome, in-water bacteriophages in recirculating aquaculture systems (RAS), physiochemical properties of water and dysbiosis as a biomarker.

Antibiotics play a vital role in aquaculture where they are commonly used to treat bacterial diseases. However, the impact of antibiotic treatment on the gut microbiome and the development of antimicrobial resistance in Nile tilapia (Oreochromis niloticus) over time remains to be fully understood. In this study, fish were fed a single treatment of oxytetracycline (100 mg/kg/day) for eight days, followed by a 14-day withdrawal period. Changes in the distal gut microbiome were measured using 16S rRNA sequencing. In addition, the abundance of antimicrobial resistance genes was quantified using real-time qPCR methods. Overall, the gut microbiome community diversity and structure of Nile tilapia was resilient to oxytetracycline treatment. However, antibiotic treatment was associated with an enrichment in Plesiomonas, accompanied by a decline in other bacteria taxa. Oxytetracycline treatment increased the proportion of tetA in the distal gut of fish and tank biofilms of the treated group. Furthermore, the abundance of tetA along with other tetracycline resistance genes was strongly correlated with a number of microbiome members, including Plesiomonas. The findings from this study demonstrate that antibiotic treatment can exert selective pressures on the gut microbiome of fish in favour of resistant populations, which may have long-term impacts on fish health.

Edwardsiella ictaluri continues to pose a significant risk to the health and production of striped catfish (Pangasianodon hypophthalmus) in Vietnam. Whilst recent advances in genomic sequencing provide an insight into the global genomic diversity of this important fish pathogen, genome-wide analysis of Vietnamese isolates recovered over time is lacking. In this study, we used a whole-genome sequencing approach to compare the genomes of 31 E. ictaluri isolates recovered over a 20-year period (2001–2021) and performed comparative genomic analysis to explore temporal changes in genome diversity, population structure and mechanisms driving pathogenesis and antimicrobial resistance. Our findings revealed an open pan-genome with 4148 genes and a core genome (3 060 genes) accounting for over two-thirds of the genome. Moreover, we found the genomes sequenced to classify into two distinct lineages and estimated the ancestral origin of these lineages within Vietnam to date back to the 1950s. Plasmids were highly prevalent in Vietnamese E. ictaluri, with isolates harbouring up to four plasmids within their genome. Further, a diverse mobilome was observed with nine different plasmid types detected across the genome collection. Exploration of putative plasmids revealed a diverse set of antimicrobial resistance genes (ARGs) against key antibiotics used in Vietnamese aquaculture and virulence genes associated with protein secretion systems. Correlation analysis revealed the total number of ARGs detected in genomes to increase with isolate recovery time. Whilst the number of virulence genes remained relatively stable, temporal variation was noted in several virulence factors related to motility and immune system modulation. Findings from this study highlight the need for continued genomic surveillance to monitor changes in antimicrobial resistance and pathogenesis, to help inform the development of disease control and management strategies.

Aeromonas dhakensis and Aeromonas hydrophila cause significant economic losses within the global aquaculture sector, affecting numerous farmed fish species and posing a zoonotic threat to human health. In this study, we sequenced, assembled and analysed the genomes of seven and five A. dhakensis and A. hydrophila isolates, respectively, recovered from disease outbreaks in various fish hosts across Southeast Asia using a hybrid sequencing approach with Illumina and Oxford Nanopore technologies. To assess the relatedness of our isolates with those from the global aquatic environment, with particular reference to aquaculture-relevant systems, and compare their resistome and virulome profiles, we also conducted comparative genomic analysis with an additional 57 publicly available genomes of A. dhakensis and A. hydrophila , recovered from different aquatic sources. Findings from this study revealed large genomic variability across global Aeromonas populations, with a clear distinction in the pan-genome between Aeromonas species. In silico multi-locus sequence type analysis revealed a wide distribution of sequence types (STs) 656 and 251 in Asia in A. dhakensis and A. hydrophila , respectively, although the novel STs detected in Indonesia and the Philippines suggest local adaptation of populations circulating in these countries. Analysis of mobile genetic elements revealed plasmids, insertion sequences and genomic islands to be country- or host-specific. Exploration of resistome data revealed a high prevalence of multidrug resistance across Southeast Asia, with genomes frequently carrying resistance genes against antibiotic classes commonly used across the aquaculture sector, including potentiated sulphonamides and tetracyclines. However, several antimicrobial resistance genes were found to be country- or host-specific, suggesting local adaptation to anthropogenic or environmental conditions within specific regions. A diverse repertoire of virulence genes was also detected in this study, with A. hydrophila demonstrating greater diversity in virulence genes compared with A. dhakensis . Country-specific virulence pathways were also noted for several toxins and secretion systems, including aerA/act , rtx and type III and IV secretion systems. This work provides new insights into the genomic features and relatedness of Aeromonas spp. circulating within aquaculture systems in Southeast Asia. Further, findings from comparative genomic analysis highlight the influence of geographical or host pressures on the molecular drivers of antimicrobial resistance and pathogenicity, directly impacting animal health and aquaculture production.