My final blog post-I'll sign off with some gastrointestinal bacteria from turbot, lovely.

The gastrointestinal (GI) tract of fish is very complex, containing up to 107-108 colony-forming units (A unit used to measure the number of viable bacteria). The GI tract composition for farmed adult turbot Scophthalmus maximus hasn’t been previously studied using metagenomics (Xing et al., 2013). Xing et al., (2013) therefore looked into this, using metagenomics alongside 16S rRNA analysis, aiming to characterize taxonomic distribution and metabolic potential of the S.maximus microbiome, assess the bacterial diversity and see how the microbiome is related to the environment.

Xing et al., (2013) used 10 adult S.maximus alongside water samples from China. The GI tract of each fish was removed, and the contents squeezed out. The mucus was also collected, along with the bacteria present in the seawater. The genomic DNA was extracted and metagenomics and 16S rRNA were carried out to assess the taxonomic composition and functional diversity of the microbiome.

They found that both the GI tract and mucus samples of the fish were largely made up of Protebacteria (a major bacterial group) and Firmicutes. It was also found that the GI tract might possess bacteria that are initially associated with the seaewater. Both quorum sensing and biofilm formation were found to be overabundant when compared to other metagenomes. The genes associated with these were found to be mainly in species within the group Vibrio. The species also showed an overrepresentation of the systems associated with protein folding and stress responses. Alongside this, the genes related to human activity, such as antibiotic and heavy metal resistance were also detected. Therefore, it can be inferred that humans are affecting the GI microbiome in marine aquaculture species. (Xing et al., 2013)

Being one of the very early pieces of research using metagenomics on a farmed species, I feel this study is clearly of huge importance both in the present and for the future of aquaculture. It gives a clear idea of the bacteria that are associated with the fish, in this case, a high level of Vibrio. Also showing a detection of the genes associated with antibiotic resistance shows that the fish microbiome in aquaculture is being compromised by humans. Xing et al., (2013) suggest that aquaculture may effect the microbiome of the fish. Finding this out has huge implications in terms of being able to manage aquaculture to give the healthiest fish and the best yield. I feel using metagenomic profiling in the GI tract of fish holds potential for giving an insight into the bacteria associated with it and so may be of great use in the future of aquaculture. However, the number of samples and species that this is conducted on needs to be hugely increased in order to give broader, more applicable results.

Reference:

Xing, M., Hou, Z., Yuan, J., Liu, Y., Qu, Y., Liu, B. (2013). Taxonomic and functional metagenomic profiling of gastrointestinal tract microbiome of the farmed adult turbot (Scophthalmus maximus). FEMS Microbiology Ecology. 86, 432-443.