Antibiotic-induced alterations and repopulation dynamics of yellowtail kingfish microbiota

Abstract

Background: The use of antibiotics in aquaculture is a common infection treatment and is increasing in some sectors and jurisdictions. While antibiotic treatment can negatively shift gut bacterial communities, recovery and examination of these communities in fish of commercial importance is not well documented. Examining the impacts of antibiotics on farmed fish microbiota is fundamental for improving our understanding and management of healthy farmed fish. This work assessed yellowtail kingfish (Seriola lalandi) skin and gut bacterial communities after an oral antibiotic combination therapy in poor performing fish that displayed signs of enteritis over an 18-day period. In an attempt to promote improved bacterial re-establishment after antibiotic treatment, faecal microbiota transplantation (FMT) was also administered via gavage or in the surrounding seawater, and its affect was evaluated over 15 days post-delivery. Results: Antibiotic treatment greatly perturbed the global gut bacterial communities of poor-performing fishan effect that lasted for up to 18 days post treatment. This perturbation was marked by a significant decrease in species diversity and evenness, as well as a concomitant increase in particular taxa like an uncultured Mycoplasmataceae sp., which persisted and dominated antibiotic-treated fish for the entire 18-day period. The skinassociated bacterial communities were also perturbed by the antibiotic treatment, notably within the first 3 days; however, this was unlike the gut, as skin microbiota appeared to shift towards a more 'normal' (though disparate) state after 5 days post antibiotic treatment. FMT was only able to modulate the impacts of antibiotics in some individuals for a short time period, as the magnitude of change varied substantially between individuals. Some fish maintained certain transplanted gut taxa (i.e. present in the FMT inoculum; namely various Aliivibrio related ASVs) at Day 2 post FMT, although these were lost by Day 8 post FMT. Conclusion: As we observed notable, prolonged perturbations induced by antibiotics on the gut bacterial assemblages, further work is required to better understand the processes/dynamics of their re-establishment following antibiotic exposure. In this regard, procedures like FMT represent a novel approach for promoting improved microbial recovery, although their efficacy and the factors that support their success requires further investigation.

Dead or alive: microbial viability treatment reveals both active and inactive bacterial constituents in the fish gut microbiota

“… 2020 ; Legrand et al . 2020c ). In this study, we first investigated whether the microbial communities of digesta samples were different to those associated with mucosal samples.…”

“…The exposed mucosa was then collected using a sterile glass microscope slide as described previously (Legrand et al . 2020c ) and placed in a 50‐ml falcon tube. Gloves were used and changed between the collection of each sample type to avoid contamination.…”

“… 2020a ; Legrand et al . 2020c ). Alternative methods that assess microbial viability of gDNA in samples can also be utilized, such as molecular viability testing (MVT) and viability PCR (vPCR) (Cangelosi and Meschke 2014 ).…”

Intestine and spleen microbiota composition in healthy and diseased tilapia

“…Mycoplasma was the most dominant genus in the spleens of healthy fish, the third most dominant in the spleens of diseased fish, much less abundant in the intestine of diseased fish and nearly negligible in the intestine of healthy fish (Table 2 ). According to Legrand et al [ 40 ], Mycoplasma was identified in the intestines of a variety of fish species but not always with association to disease. Bozzy et al [ 19 ], who studied the intestinal microbiota of healthy and diseased Atlantic salmon, reported that Mycoplasma was more dominant in healthy fish compared to the diseased fish.…”

An examination of the use of antibiotics as a method to experimentally perturb the microbiota of suspension‐feeding bivalves

“…were shown to perturb their gut microbiomes and lead to states of dysbiosis, with increased abundances of opportunistic pathogens (Kim et al, 2019;Legrand et al, 2020). Carlson et al (2017) showed that 1 week of exposure to an antibiotic caused significant perturbation of the gut mucosal microbiome in mosquitofish (Gambusia affinis), and 1 week of recovery was not sufficient to return the community to the undisturbed state.…”