Evidence for a core gut microbiota in the zebrafish

Many studies analysing microbial communities of the gut and their interactions with the host are conducted on domesticated animals bred for generations in laboratory facilities, and therefore may not give a true representation of naturally occurring relationships. Zebrafish have been used for this purpose since the 1960s, however no research had been conducted to determine if such husbandry had impacted the biology of the fish. This study aimed to compare the structure and composition of gut microbiota between wild and domesticated zebrafish.

Wild zebrafish were caught from the Shutunga River in India and kept in a static tank for 32 days during transportation and quarantine before the experiment was conducted. Samples of fish were also collected from five laboratory facilities in America. Intestinal DNA from the fish was isolated and amplified, then used to create 16S rRNA clone libraries and phylogenetic analysis was conducted.

16S rRNA gene T-RFLP profiles showed no significant difference between the structure and composition of gut bacterial communities of recently caught and domesticated zebrafish. As this method only sequences diversity at a small range of sites, Sanger chemistry was also used to create 16S rRNA clone libraries from the intestinal samples from each location. This showed a similar diversity in the gut microbiota of all samples, suggesting the origination of the host has little influence on the gut bacterial community richness and diversity.

UniFrac metric, a method that uses phylogenetic information to calculate the distance between organismal communities, was used to compare the intestinal bacterial communities from each location. Data from this study was combined with 16S rRNA clone libraries from intestines of humans, mice and other teleost fish. This demonstrated two separate clusters of mammals and fish. The fish divided into two clusters of marine and freshwater fish, the latter of which was the largest cluster and compromised of zebrafish and yellow catfish. Principle coordinate analysis further demonstrated large similarities between the composition and structure of gut bacterial communities in the recently caught and domesticated zebrafish.

T-RFLP profiles were then used to determine if there was any significance between the composition of microbiota in individuals of each sample. This revealed strong similarities between domesticated fish from different locations, probably due to the laboratory facilities used in the study originating from the same institute. The differences between the recently caught and domesticated fish were not much different from this.

Roche GS-FLX pyrosequencing revealed more bacterial phylotypes present at lower abundances, with the overall bacterial classes being very similar for all samples and 21 operational taxomony units being shared by all. Such similarities suggest there may be core microbionts found in the intestines of zebrafish.

Despite the bacterial taxa dominating the recently caught and domesticated fish being very similar, the genus Edwardsiella was only found in recently caught zebrafish and wild yellow catfish. Therefore, these may be natural members of the zebrafish intestinal microbiota, but have been excluded in the laboratory bred fish.

Although there are strong similarities in the bacterial communities of both groups of fish, the authors note that the collection from the wild, transport and subsequent quarantine for 32 days could have prompted a rapid change in the microbiota of the wild zebrafish. On the other hand, the similarities could be due to the fish acquiring a common gut bacterial community, and thus the shared features of the intestinal habitat means this results in a similar composition of bacteria regardless of differences in the host origin and the local environment.

This study demonstrates that the structure and composition of intestinal bacterial communities are very similar in wild and domesticated zebrafish, suggesting those bred in the laboratory are suitable models to represent the relationships between host and microbes in their natural environment. Nonetheless, the mechanisms of selective pressures that result in core gut microbiota are still unknown and further studies are required to determine this, potentially enabling the manipulation of gut microbial communities to enhance research of human and animal health.

Guus Roeselers, Erika K Mittge, W Zac Stephens, David M Parichy, Colleen M Cavanaugh, Karen Guillemin and John F Rawls

http://www.nature.com/ismej/journal/v5/n10/full/ismej201138a.html