The fish gut microbiome under a fisheye lens

Ghanbari et al., (2015) portray how the development of Next Generation Sequencing (NGS) has been pivotal to our understanding of the fish gut microbiome. The relationship between gut microbiota and physiology is complex and influenced by lots of external factors affecting the host. Fish are an excellent model to study the factors affecting intestinal bacterial community due to the diversity of their physiology, ecology and natural history. It is important to understand the dynamics of microbial communities as they are so influential to the host’s physiology.  A comprehensive understanding of the fish gut microbiome will be beneficial for future aquaculture developments. This review highlights the need for a shift from taxonomic to functional profiling of microbial communities through the use of ‘meta’ data.

Recently, NGS technologies are being used for metabarcoding studies to characterize the fish gut – microbiome. This has paved the way for gut microbial analysis as the composition of densely populated microbial communities can be determined rapidly and at a low cost. However, NGS technologies are still limited; for instance, short reads can cause issues with assembling and mapping sequences however longer reads are prone to error readings which may overestimate richness estimates. The caveats listed in the review highlight the complexities of interpreting NGS data.

NGS based studies have used 16S rRNA sequencing to describe the diversity of bacterial taxa associated with the fish gut. Studies have demonstrated that despite high bacterial density, it has an unusually low diversity. This is due to the core gut microbiota concept; the presence of similar fish gut bacteria from different populations that are integral to gut functionality.

In addition to the core gut microbiota, other environmental and host related factors influence bacterial communities. The reviewed studies used a combination of pyrosequencing and metagenomics to assess the origin of bacteria and found that colonization from the surrounding water and sediment is a primary recruitment mechanism. However, other studies, again through 16S rRNA pyrosequencing, have revealed the presence of species-specific microbiota irrespective of environment and life history. These specialized bacteria are selected for by the host and retrieved sequences suggest they benefit the host via vitamin production and food digestion.

In addition, the interaction of feeding habit, diet and genetic factors can also impact bacterial composition. NGS based studies have revealed a trend in bacterial diversity between feeding strategies, as planktivorous fish were found to have a significantly higher diversity than that of omnivorous and herbivorous species. As well as this, diet composition and origin of ingredients were shown via pyrosequencing to significantly influence the abundance of specific taxa. Furthermore, the effect of diet on the abundance of OTUs was significantly different betwen male and female fish. Likewise, one study found an inverse and sex dependent relationship between the allelic diversity of an immune system related gene and bacterial diversity. Interestingly this study suggests that contrary to expectations adaptive immunity constrains bacterial communities.

Lastly, specific treatments can be applied to promote beneficial bacteria, for instance, probiotic and prebiotic supplements. One study demonstrated the use of a prebiotic carbohydrate significantly decreased bacterial diversity, but improved growth performance and boosted immune responses. These recent NGS tools have allowed the modification of diets and treatments to be utilised in aquaculture.

The reviewed studies have largely used 16S rRNA pyrosequencing to assess the effect of factors on the taxonomic profile of the microbial community and highlight the complex relationship between the host, gut microbiome and environment. Future studies should use meta-omic approaches in a high – throughput fashion to address issues regarding metabolic potential and functional impact. This review is important as despite advances in technology it is essential to simultaneously reflect on and develop the approaches being used.

Reviewed paper:

Ghanbari, M., Kneifel, W., & Domig, K. (2015). A new view of the fish gut microbiome: Advances from next-generation sequencing. Aquaculture, 448, 464-475.

http://dx.doi.org/10.1016/j.aquaculture.2015.06.033