Sea breams got guts!

Aquaculture is the most sustainable source of protein based on the feed conversion ratio. Global demand for food is increasing, increasing aquacultures already high economic significance. Mediating disease and developing techniques to reduce cost and increase productivity, e.g. the use of probiotics, are important. So far, many fish gastro-intestinal (GIT) microbiota studies focus on disease and probiotics without fully understanding natural GIT microbiota. Gut microbiota have an influence on the host nutrition and immunity through symbiotic interactions; some genes have importance for virulence, antibiotic resistance and xenobiotic metabolism. Fish GIT’s remain largely understudied with the majority of previous studies based on bacterial cultivation techniques and archaea often completely missed.

Sea bream (Sparus aurata) is an economically important species from the Mediterranean which is fished and produced in aquaculture conventionally and organically. Organic sea bream production requires international standards and certification. Although organic production is significantly less than conventional, 1300 tons of sea bass and sea bream production compared total 275,000 tons in 2012, production is thought to increase as expectations for food sustainability and quality increase.

This study used tag pyrosequencing of 16s rRNA to compare the intestinal structural diversity of bacteria and archaea on wild (fed on a variety of prey e.g. molluscs, crustaceans, and fish), organic (fed sustainable certified fish meal and fish oil: 45% protein and 14% fat) and conventionally- reared sea bream (fed a commercial diet of 46% protein and 17% fat). Gut tissue was removed from 3 fish in each group and washed in sterile, particulate free seawater before DNA extractions.

This study is the first using next generation sequencing (NGS) techniques for the study of the gut microbiome of sea bream. Analysis of communities showed wild and organic sea bream to have higher bacterial diversity compared to conventionally- reared sea bream suggesting organic rearing simulates natural conditions better than conventional methods. Proteobacteria were prominent (above 50% of abundance), a finding that coincides with high abundance at phylum level previously reported in culture experiments. Four operational taxonomic units (OTUs) were found across all individuals. Dominant species were most closely related to genus: β-Proteobacteria Diaphorobacter, a denitrifier known to degrade polyaromatic hydrocarbons; γ-Proteobacteria Acinetobacter; known to metabolise amino acids, aromatic compounds and short-chain fatty acids and; Flavobacterium Cloacibacterium, commonly found in waste water. Only one sample within each group held enough Archaea for amplification, showing very low numbers across all treatments. Those identified were mainly Euryarchaeaota of the methanomicrobia.

This study is difficult to compare to earlier work which uses conventional techniques rather than NGS due to the much higher taxonomic resolution of NGS. Further study is needed to increase our knowledge of the microbiome to make it more comparable and identify differences within the gut e.g. difference between gut tissue, contents and faeces. I have difficulty fully accepting this paper due to its small sample size and confused discussion, with few high resolution studies this study is a start but more in depth analysis is required to increase statistical significance and investigate mechanism of transfer and microbial function within the gut.

Kormas, K. A., Meziti, A., Mente, E., Frentzos, A. (2014) Dietry differences are reflected on the gut prokaryotic community structure of wild and commercially reared seabream (Sparus aurata). Microbiology Open. 3(5): 718-728. 

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4234263/