Fish microbiomes vary in time and space

               

Microbial symbionts play an important role in the survival of multicellular organisms. Specifically, bacteria found in the gut are important for host nutrition, immune functions and behaviour. While gut microbiomes have been studied in terrestrial animals and economically valuable marine species, less attention has been paid to ecologically valuable marine species and our understanding of fish gut microbiomes is limited.

Most studies of fish microbiomes involve sampling faeces or simultaneously sampling the entire gastrointestinal track. These methods cannot discriminate between autochthonous and allochthonous microbes or assess spatial distribution; as diet has a strong influence on gut microbiomes and compartmentalisation has been seen in terrestrial species, these sampling methods are only telling us part of the story. Nielson et al. (2017) aimed to gather data on the gut microbiome of Siganus fuscescens (an ecologically important species in coastal ecosystems), while sampling in a way that allowed these factors to be considered.

The intestinal tract of four individuals were removed and separated into the midgut and hindgut; DNA was then extracted from the gut content and wall of these two sections separately. The V4 region of the 16S rRNA gene was then amplified using PCR; the OTUs produced were used to assess alpha- and beta- diversity of the bacterial community as well as taxa present. Species richness and species diversity (measures of alpha-diversity) were found to vary between individuals and were higher in the gut wall than the gut content. The authors suggest that the large variation between individuals is due to the variable diet of this species, a hypothesis supported by the larger individual variation seen in midgut content than other gut locations. Beta-diversity assessments showed that the midgut and hindgut contain different bacterial communities as do the gut wall and gut lumen.  The taxa present also changed between gut locations, which was suggested to be a result of whether the taxa are autochthonous or allochthonous and the environment in each gut location. For example, the Synechococcaceae family was only found in the midgut content, suggesting it is an autochthonous member of the microbiome, either from their diet or being ingested from the environment, while the enrichment of Desulfovibrio and Clostridium in the hindgut implies an anoxic, sulfate rich environment, indicating compartmentalisation due to host/environmental factors.

While the method used in this paper highlights the importance of spatial distribution of microbiome species along the gastrointestinal tract as well as the contribution of microorganisms obtained from the environment, there are limitations. A sample size of four individuals makes interpretations difficult; for example, species diversity of one individual was very different to the others, however with only four samples it is difficult to know how unusual this is. Such a small sample size also reduces statistical power, so some observed trends could not be supported statistically. There were also slight differences in sample collection which the authors suggest may have affected results. While the method used in this paper does allow greater insights into fish microbiomes, it is perhaps not such a widely-used method due to ethical considerations and difficulty in standardising sample collection; the use of faeces could be less invasive, allowing a larger sample size, and the use of whole gut analysis could make sample collection easier, especially in smaller species.

Reviewed Article:

Nielsen, S., Walburn, J. W., Vergés, A., Thomas, T., & Egan, S. (2017). Microbiome patterns across the gastrointestinal tract of the rabbitfish Siganus fuscescens. PeerJ, 5, e3317.

https://peerj.com/articles/3317/