Host- specific communities of active bacteria found in the gut of Rainbow Trout (Oncorhynchus mykiss)

Intestinal bacteria have previously been shown to be important to the wellbeing and nutrition of fish and contribute to important functions of the host. Previous studies have investigated gut microbiota of rainbow trout using culture-independent methods and reported that the gut can be dominated by many different bacterial groups. A previous study; as discussed in Sophie’s blog post below showed that lactococcus, Citrobacter, Kluyvera, Obesumbacterium and Shwanella dominated intestinal microbiota. These studies were useful as they showed the composition of the gut microbiota but they do not look at what may have lead to composition they observed. Many factors can influence this composition including environmental factors such as temperature as well as factors such as gut structure and developmental stage of the fish.

Host genotype is expected to be a factor influencing the individual’s intestinal microbiota but this is yet to be proven. As diet has been shown to be a main contributing factor to gut microbiota composition this must be controlled before the influence on genes can be assessed.

The aim of this study was to use molecular techniques to assess the extent to which genes of the host and the effect of inclusion of vegetables products in the diet. For the purpose of the investigation into the role of genetics, siblings from a single breeding pair from 4 different rainbow trout families were used. 

Principal component analysis (PCA) of the temporal temperature gradient gel electrophoresis (TTGE) bands showed that the main variations in host microbiota could be attributed to the host rather than the diet. The composition of microbiota varied greatly among different families and specific association was observed between certain families and bacterial groups although there was some cross over in the microbial communities observed which indicates that the host has some influence on gut microbiota composition.  The response of the microbial communities to different feed types depended on the host i.e. the 4 families responded differently to the different diets; some phyla of bacteria disappeared on the introduction of vegetable products.  Each family provides unique habitat and selects for specific microbial community. The microbial community composition was studied using DNA and RNA analysis to provide a comparison between the two techniques. It was found that RNA analysis was more informative than DNA analysis because more bands were recovered from RNA analysis.

Other studies have not taken into account genetic background of fish used for their experiment therefore I feel that this experiment is important as it assesses the role of individual genetic/fish internal environments therefore providing a new insight into this complex subject. This study provides a good base for further work because the actual host factors likely to be involved in shaping the bacterial composition of the gut are still unknown. This study also identified that RNA based analysis was a better approach than DNA-based analysis for the study of these bacterial populations which could be an important finding for future work.

Navarrete et al. 2012 PCR-TGGE Analysis of 16S rRNA from Rainbow Trout (Oncorhynchus mykiss) Gut Microbiota Reveals Host-Specific Communities of Active Bacteria PLoS One; 7(2): e31335

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3290605/