Thursday, 20 March 2014

GI bacteria communities, and how they differ between species, habitat and trophic levels

This paper was all about examining the influence abiotic and biotic factors may have on the gut bacterial communities of fish from different taxa, trophic levels and habitats via phylogenetic and statistical analyses of 25 16S rRNA libraries.

They performed a meta-analysis of 16S rRNA gene sequence data of microbial communities, and the data was taken from a mixture of published (14) and unpublished (2) papers. In total, data from 19 different species was used, all of whom originated from the ray-finned fish class (Actinopterygii). It is worth noting that as this is a collection of previous work, not all microbial communities were sampled from the same place (e.g. samples could originate from the digestive tract, intestinal content, intestinal wall, intestinal mucus or faecal pellets.) Additionally these papers also used different methods to gather information about microbial communities (cultured or uncultured) – and cultivation-based studies have been shown to give a distorted picture of gut communities.

The data was used to build up phylogenetic trees, in order to discover the community structure of gut microbiota of the various fish. This data was further compared with microbial communities from the environment (free-living bacteria), vertebrate and non-vertebrate guts (e.g insect and mammalian guts).

·        Phylogenetic analysis revealed that most fish gut communities bear resemblance to those from invertebrate and vertebrate guts, with very few communities showing similarity to free—living environmental microbial assemblages – suggesting  most bacterial species in fish guts are specialised members of symbiotic communities rather than being free-living, environmental bacteria (which altogether hints at symbiont origins for gut microbe communities). In addition, most FW and SW gut communities correlated with bacteria found in FW and SW environments respectively – consistent with the idea that colonization of the host gut is made up of at least some environmental bacteria e.g Vibrio and Aeromonas. However this pattern is not followed by marine fish herbivores, who harbour few typical environmental marine bacteria, but show a close relatedness to bacteria from mammalian guts.
·        Freshwater fish were shown to harbour a greater proportion of Aeromonadales and Enterobacteriales species, the former of which was never detected in marine hosts. Marine fish communities had higher proportions of Vibrionales species (69.8%) compared to FW fish (3.6%).
·        Trophic levels (herbivorous, carnivorous or omnivorous) are also show to have an effect on the microbial community. For example, herbivorous fish were enriched with Clostridiales, Bacteroidales and Verrucomicrobiales while omnivorous fish were enriched with species from the Rhizobiales, Fusobacteriales and Planctomycetales. Interestingly, both carnivores and omnivores tended to have more Desulfovibrionales and Aeromonadales.
·        Comparison of fish gut bacterial communities with bacteria from other environments (lakes, soils, oceans and eukaryotic hosts) reveal that the fish gut bacteria can be quite distinct between different hosts. For example as a general rule the most dominant phylum inhabiting fish guts is that of Proteobacteria, which contrasts with the dominant phylum in mammals (Bacteroidetes and Firmicutes). Interesting this pattern does not hold true for 3/4 studied marine herbivores – who, like mammalian counterparts, show the greatest dominance of Bacteroidetes and Firmicutes. The authors discuss the idea that this could be due to the presence of short chain fatty acids in both herbivorous fish and mammals, suggesting that microbial communities of herbivorous fish and mammals undergo similar nutritional and digestive roles (e.g. in fermentation.) Additionally, the authors propose that this similarity could be used to form a hypothesis that fish may have served as the first vertebrate host for these shared microbes. This idea is based on the fact that fish were the first hosts with an adaptive immune system and therefore they came across these bacterium first, their guts serving as a ‘training ground’ for microbes that would later go on to colonise mammalian guts. However, they are quick to admit that these similarities between the gut microbial community could be due to convergent evolution

NB. Have attached one of the diagrams from the paper which I think gives a really cool view of how the bacterial community (in plyla) change between habitat salinity and diet. Really brings home the fact that Proteobacteria are the key players!

      Sullam, K. E., Essinger, S. D., Lozupone, C. A., O’CONNOR, M. P., Rosen, G. L., Knight, R. O. B., ... & Russell, J. A. (2012). Environmental and ecological factors that shape the gut bacterial communities of fish: a meta‐analysis. Molecular ecology21(13), 3363-3378.

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