A large-scale, multi-year microbial community survey of a freshwater trout aquaculture facility

Abstract

Aquaculture is an important tool for solving growing worldwide food demand, but infectious diseases of the farmed animals represent a serious roadblock to continued industry growth. Therefore, it is essential to understand the microbial communities that reside within the built environments of aquaculture facilities to identify reservoirs of bacterial pathogens and potential correlations between commensal species and specific disease agents. Here, we present the results from three years of sampling a commercial rainbow trout aquaculture facility. We observed that the microbial communities residing on the abiotic surfaces within the hatchery were distinct from those residing on the surfaces at the facility's water source as well as the production raceways, despite similar communities in the water column at each location. Also, a subset of the water community seeds the biofilm communities. Lastly, we detected a common fish pathogen, Flavobacterium columnare, within the hatchery, including at the source water inlet. Importantly, the relative abundance of this pathogen was correlated with clinical disease. Our results characterized the microbial communities in an aquaculture facility, established that the hatchery environment contains a unique community composition, and demonstrated that a specific fish pathogen resides within abiotic surface biofilms and is seeded from the natural source water.

Aquaculture ecosystem microbiome at the water-fish interface: the case-study of rainbow trout fed with Tenebrio molitor novel diets

“…In line with other recent studies [34], the overall composition of the water community from the natural source spring through to the outflow from the farm was stable and not significantly different despite variations in water quality parameters among sampling dates. Overall, water showed astounding microbial diversity compared to host-associated and feed samples, and considering all the alpha diversity metrics tested, water samples, in particular inlet water, had the highest alpha diversity, followed by tank biofilm samples.…”

“…Despite an array of studies evaluating fish gut microbiomes and health, there is a lack of information on how the microbiome of the built environment contributes to fish health and aquaculture system equilibrium. The built environment encompasses all the environments that humans have constructed, including buildings, cars, public transport, other human-built spaces [ 14 ], and aquaculture plants [ 11 , 34 ]. Built environments harbor unique microbial communities, different from those found in other environments on Earth.…”

Slowing Alzheimer’s disease progression through probiotic supplementation

“…The Illumina MiSeq generated 16S rRNA V4 gene sequence data, which were demultiplexed using BaseSpace 1 . The paired-end data was then imported into QIIME 2 (version 2018.8 2 ) for further analysis ( Testerman et al, 2022 ). The reads were filtered, denoised, and dereplicated using the DADA2 denoise-paired plugin ( Callahan et al, 2016 ).…”

Preparation and Evaluation of a Dosage Form for Individualized Administration of Lyophilized Probiotics

“…Lactobacilli, when used for prevention and treatment, are stored in established microbial banks [ 26 , 27 , 28 ] and could be used when needed [ 29 , 30 ]. In addition, this could be applied to the microorganisms present in trout aquaculture [ 31 ]. In particular, Lactobacillus plantarum R2 Biocenol™ has shown antimicrobial susceptibility, and this was evaluated based on the guidelines issued by the European Food Safety Authority (EFSA).…”