Evidence for a core gut microbiota in zebrafish

“Evidence for a core gut microbiota in the zebrafish”

In this paper by Roeselelers et al zebrafish were used in a study to examine in detail their host gut microbiota, this was achieved mainly by using 16srRNA sequencing. Comparisons were made between specimens from varied natural habitats and those raised domestically in laboratory conditions in order to acetate whether the communities are a selective decision or whether it is based on environmental or locality change.  An initial look at the gut microbiota of the zebrafish with in laboratory conditions, through DNA sequencing, shows that it is predominantly bacteria from the phylum proteobacteria, specifically  Firmicutes and Fusobacteria seemingly present during larva and adult stages.

Standard microbiological testing techniques were used in the methodology of this paper, they began with ensuring the laboratory conditions are standardised in order to maintain conformity across the board, vital for accurate results. Once samples were collected from the  Shutunga River in Mathabhanga subdivision of Cooch Behar district in the Indian state of West Bengal, Roeselers et al first began with DNA extraction using a classic blood/tissue DNA extraction followed by T-RFLP in order to analyse 16srRNA gene amplification, this in turn led to  sequencing of bacteria followed by standard phylogenic analysis to identify individual strains.

The results were quite interesting, firstly looking at the comparisons of the gut microbiota of domesticated (5 labs, multiple generations) and recently caught fish (using methods previously discussed) findings showed a significant similarity between communities. T-RFLP analysis also backed these results up, taxon based study was observed, the Shannon-weaver diversity index again showed significant similarities between the  domesticated and recently caught samples this was based on  OTU sequences defined by 97% pairwise sequence identity.

As well as the above Roestelers et al wanted to make phylogenetic comparisons, in order to achieve this they used the Uniifrac tree technique and supplemented 16srRNA sequences from the zebrafish against that of mammalian (mouse and human) samples as well as 7 other fish species in order to clear differences. Distinct clusters were seen, as expected the human and mouse libraries were clustering quite distinctively, denoting the obvious difference between mammalian species and fish species gut microbiota.

When analysing the fish libraries a distinct cluster was also seen with all the zebra fish samples and the yellow cat fish alike, further follow up studies subjecting 16srRNA gene sequences to PCoA, similarly to previous tests,  it showed a high similarity between recently caught zebrafish and the yellow cat fish. Interestingly two bacterial classes were found consistently in the gut of the zebrafish (both domesticated and terrestrial) these two classes were ƴ-proteobacteria and Fusobacteria, this could suggest that these classes have become  adapted for life in the fish intestine and utilising this as a niche environment.

One last study was looking at the change in community structure from different aquaculture laboratories, results demonstrated that the fish with in the same labs displayed similar community microbial communities but differed from that of other laboratories, this could be that they are displaying historical connections between bacterial communities and individual locations. The difference can be seen when looking at the 3 lab samples 525 OTU’s were discovered but only 21 were found in all 3, not displaying a high enough quantity to be significant.

I think that this is an interesting paper, perhaps a little wordy in the methods section, as most people who study microbiology are familiar with these techniques. As far as the study is concerned I found it a very interesting area, it could be particularly beneficial for the aquaculture industry and a further increase study could be expanded to other farmed fish such as salmon or tuna to help in the eradication of harmful bacteria released in fish fecal matter. It would also help in ornamental aquaculture industries as many fish are of muti-generations and these bacteria may be transferred during cross breeding from various other fish farms.

There is much more information in the paper, what I have talked about is only about two thirds of its depth, those interested in aquaculture may find it interesting so have a read I will put the paper below. Hope it makes sense and thanks for reading.   

 Roeselers, Guus, et al. "Evidence for a core gut microbiota in the zebrafish." The ISME journal 5.10 (2011): 1595-1608.