Intestinal microbial species composition in Atlantic cod

The intestinal microbial community provides a variety of crucial functions for their vertebrate hosts. However, the microbiota in individual is influenced by host-specific selection and it has been shown that a selective group of microbiota is common across different host of the same species. This concept of core microbiota, although it is widely studied in mammals, few studies have been done on fishes. The core microbiota is said to be the key which provides a minimal functionality in the healthy gut and the colonisation factors appear to be conserved among wide range of vertebrates, including fish. The diversity of fish lineages provides the opportunities to investigate the factors that influence the composition of the vertebrate intestinal microbiota. In this study, Star et al. (2013) describe microbial intestinal communities of eleven individual Atlantic cod (Gadus morhus) caught at a single location and quantify a core microbiota based on an extensively 454 sequenced 16S rRNA library of the V3 region.

Using high throughput sequencing, they identified 573 operational taxonomic units (OTUs) from a total of 280447 sequences and found that 10 OTUs are shared at 97% sequence similarity among the 11 individual Atlantic cod. They found that the shared OTUs is dominated by the orders of Vibrionales (50%), which is prevalent in the Atlantic cod intestinal microbiota, followed by variable numbers of Bacteroidales (17%), Erysipelotrichales, Clostridiales, Altermonadales and Deferribacterales. Furthermore, they found that the intestinal microbiota is dominated by a few abundant OTUs, while the majority of OTUs is present at rare frequency. This pattern is similar to intestinal composition in zebrafish or humans.    

However, the utility of the core microbiota concept at a taxonomic level has raised questions due to limited evidence of universally abundant species in humans. Additionally, the authors stated that the number of shared OTUs identified in the paper may be an overestimation. This is because the fishes were kept in the same tank, and thus experience the same environmental conditions before sampling. They assumed that similar environment is more likely to homogenize microbial communities, rather than promote individual differences. Therefore, a different experiment would be required to investigate is the shared OTUs are due to environmental factors or are species specific.

In conclusion, individual variations in the OTUs in wild-caught Atlantic cod suggest that a complex combination of factors influences the gut microbiota composition. However, such variation has gone unobserved in previous studies of natural populations of teleost, which may affect estimates of the number of shared OTUs among hosts.   

Star, B., Haverkamp, T. H., Jentoft, S. and Jakobsen, K. S. (2013) Next generation sequencing shows high variation of the intestinal microbial species composition in Atlantic cod caught at a single location. BMC Microbiology. 13: 248.