Tuesday, 1 April 2014

Changes in the gut microbiota of Australian Fur Seals in response to age and diet

The microbial community dwelling within the gastrointestinal tract is integral to the health of any animal host. The gut microbiota helps in fermenting indigestible carbohydrates, vitamin synthesis, uptake and biotransformation of nutrients, immune system development, energy storage and embryonic development. Disturbances in the gut community can lead to chronic illnesses such as obesity, malnutrition or inflammatory bowel disease. Despite the clear importance of the gut microbiota, it remains largely undefined for most species, and the mechanisms that determine its composition remain largely unknown.

The healthy mammalian microbiota is dominated by three phyla: Firmicutes makes up around 80% of the gut community, Bacteroides stand at around 17%, whilst Actinobacteria are around 2-3%. However, few studies have focussed on marine mammals. Their drastically different lifestyles and diets to terrestrial mammals would suggest the potential for a radically different gut community.

This study focussed on an otariid, the Australian fur seal (or brown fur seal), who’s diet consists mostly of fish and cephalopods. Pups do not swim, they are terrestrial and survive on milk provided by their mothers, at 9 months they begin to dive and hunt. There was previously no information on how the change from a diet of milk to a diet of marine prey influences the gut microbiota. Therefore in this study, the diversity and dynamics of the fur seal gut community were compared between pups of 2 months, 6 months, 9 months and adult fur seals using fluorescent in situ hybridisation (FISH) and 16S rRNA gene pyrosequencing, to investigate how the microbiota of the gastrointestinal tract changes during development, as a consequence of a changing diet.

They found that, consistent with other mammal groups, the phylum Firmicutes was the dominant bacterial group for fur seals of all ages, followed by Bacteroides and Actinobacteria, despite the differences in habitat and diet. Many individual bacterial groups showed significant differences in their abundance between seals of different ages, however in most examples they did not linearly increase or decrease with age, for example Bacteroides represented 3.11%, 1.54% and 15.45% of the microbiota for the 2 months, 9 months and adult seals respectively. Many bacterial groups dipped or peaked during intermediate ages, perhaps this is because the transition from milk to fish diets causes a temporarily unstable microbial community during which relative abundances may shift radically. Firmicutes represented 22.14%, 38.83% and 67.33% of the community for the 2 months, 9 months and adult seals respectively, suggesting that they are less integral for milk-fed seal pups than for fish-fed pups and adults. Some individual phyla such as Cyanobacteria, Verrucomicrobia and  Fusobacteria were only present during one pup stage and absent for all other stages.

Ultimately in this study the authors have provided evidence that a species of marine mammal does indeed share similarities in its gut microbiota with terrestrial mammals. They have also shown how the gut community is affected by level of development and maturity, presumed to be a response to a changing diet. I think other factors associated with development could also affect the microbiota’s composition though, physiological changes due to developmental hormones, or behavioural changes such as a greater amount of time spent in the water could act as selection pressures that change the gut community throughout development.


  1. Hi Dave, this is an interesting paper investigating the microbiota of seals and their change throughout their lives. Have the authors also analysed the milk from the mother directly? It would be interesting to see what kind of bacteria would be present in the breast milk which is the primary food source for pups in the first months of their lives. Comparisons of the actual bacterial composition of the breast milk with the gut microbiota of the pup could help understanding which of these bacteria can become the initial colonisers of the gut since diet has been proven to be one main factor influencing the gut microbiota. I would imagine that the breast milk contains quite a large amount of LABs, and perhaps in general many beneficial bacteria that support the development of a healthy immune system. I think it would be important to investigate the microbial composition of the breast milk in order to understand the change of the gut microbiota better from pups to adult seals...although it might be difficult to get the samples from the mothers while they are feeding I reckon.

    1. It is interesting to think of breast milk as an inoculation of advantageous bacteria for immune and digestive function for the pups, nature's probiotic. Unfortunately I cannot find any studies on the bacterial composition of breast milk in seals (or any animals other than humans). Though the authors do state that long chain polyunsaturated fatty acids, such as those found in human milk, promote the growth of lactic acid bacteria, such as Bifidobacteria and Lactobacilli, and that fur seal milk has a high lipid content containing many PUFAs. Examining how the microbiota of the milk and the pup's gut overlap would show which ones have been selected for by the GI tract conditions, hinting at possible advantageous functions.

    2. That is exactly what I thought of when I read your summary. Yes, breast milk is obviously very important to the pups to provide them with enough fat and energy to ensure they survival and to provide the resource for their blubber. But I think there could also be a very important probiotic aspect of this breast milk that potentially introduces the autochthonous and beneficial bacteria into the gut microbiota of the pups. Like you said, there is a lot of evidence that this is the case for humans, and it has been proven that natural breast milk has a positive effect on the development of the immune system. It would make a lot of sense if this was also the case for other mammals such as seals. I will keep an eye out for upcoming research on this matter, I really think it should be investigated, also in order to understand the link between the change diet and resulting change in microbiota in more depth.