Signatures of dysbiosis in fish microbiomes in the context of aquaculture

Abstract

Fish microbiome plays an important role in maintaining host homeostasis, with many bacterial functions directly linked to host fitness. Fish microbiome research is advancing fast, especially in the context of aquaculture where several stressors are known to disrupt stability of host‐associated bacteria, prompting dysbiosis. Therefore, understanding the signatures of dysbiosis in different fish mucosae and their association with such stressors is fundamental to set up efficient health‐monitoring strategies, as well as sound and objective working hypothesis for future research. Herein, we reviewed studies that employed culture‐independent approaches to assess the effects of disease, chemotherapeutics and water quality changes on several diversity metrics of gut, skin and gill microbiomes. We conclude that increases in abundance of potential pathogens and changes to bacterial community structure are reliable indicators of dysbiosis in fish. The gut microbiome emerged as being highly susceptible to salinity changes and chemotherapeutics, whereas external microbiota seems to be more susceptible to dysbiosis caused by disease and temperature changes. Our analysis showed that treatments with tetracyclines and florfenicol are more likely to elicit severe dysbiosis compared to quinolones and disinfectants that cause lesser disturbance to fish microbiome. Bacterial diseases also frequently elicit severe dysbiosis (enteritis in particular), whereas parasitic diseases are far less deleterious. Regarding impacts on water quality, only changes to salinity and temperature are reasonably studied. Recent developments in metagenomics, that include a fast turn‐around time of results, can be used to detect changes to fish homeostasis during critical periods of fish production, assisting aquaculture management.

Effects of two common antibiotics on the skin microbiome of ornamental reef fishes: Implications for manipulative experiments in microbial dynamics

“…This suggests a lower effect of this antibiotic in disrupting fish skin microbiome compared to Nitrofurazone but could also be indicative of a resistance against this antibiotic. These results are in accordance with the review of Xavier et al (2024), who found that despite the low number of existing studies, quinolones do not frequently alter the alpha-diversity of fish microbiomes. Moreover, they are consistent with results of Zheng et al, 2014).…”

“…Moreover, they are consistent with results of Zheng et al, 2014). Indeed, increases in Vibrio and other Vibrionaceae are frequently reported in studies investigating the effects of quinolones in fish microbiomes (Xavier et al, 2024).…”

Spatio-temporal fish gill microbiota analysis as indicators in estuarine fish health monitoring

“…Many studies have dealt with the in uence of abiotic stress on the gut and skin microbiota in sh, usually under arti cial rearing conditions (Bell et al, 2024). However, despite its huge potential for health monitoring, gill compositions are largely overlooked (Sehnal et al, 2021;Xavier et al, 2024), especially along physicochemical gradients in an estuarine system.…”

Oral administration of a new copper (I) complex with coumarin as ligand: modulation of the immune response and the composition of the intestinal microbiota in Onchorhynchus mykiss

“…Another problem of excessive use of antibiotics, reported in recent years, is the effect on the composition of the intestinal microbiota of salmonids. Antibiotics generate dysbiosis in the intestine of fish, which causes changes in various biological processes, including the immune response ( Donati et al, 2022 ; Huyben et al, 2023 ; Xavier et al, 2023 ). The problem of excessive use of antibiotics has been recognized by Chilean salmon producers, so in 2019, the salmon farming sector and the Monterey Bay Aquarium launched the Chilean Salmon Antibiotic Reduction Program (CSARP) with the aim of reducing the use of antibiotics by 50% by 2025.…”