Gut bacteria are an ‘outside’ and an ‘inside’ job

Abstract

The gut of virtually every creature is packed with an army of microscopic helpers, mostly bacteria but also viruses and fungi. These microscopic lifeforms – which together constitute the gut microbiome – help with food digestion and with training the immune system of the creatures they inhabit. Given the fundamental role of these microorganisms in life support, scientists have been curious to understand how much of the variability in the composition and abundance of gut microbes comes from genetic differences of their inhabitants as opposed to environmental factors. Although work in humans has suggested that variability in gut flora is mostly influenced by our diet and lifestyle rather than our genetic makeup, an international group of scientists led by Laura Grieneisen and Ran Blekhman from the University of Minnesota, USA, suspected that the story could be more complex, and wondered whether one of our close relatives, baboons, could help us to discover whether our bacterial lodgers are kept within the family.Grieneisen and her colleagues collected over 16,000 fecal samples from 585 wild baboons over 14 years – which is a significant portion of the lifespans of most baboons – in Kenya's Amboseli National Park, to examine changes in their gut microbes. In addition, the team also knew the family relationships of each individual in each troop, their diet and their age when each fecal sample was collected, as well as how the local conditions were affecting them, so they could rule out similarities that were caused by the conditions that the animals were living in and identify true similarities owing to the baboons’ shared genes.The team's extensive work and dedication paid off: they found that the baboons inherited the majority of their gut microbiome communities (97%) from their predecessors. In addition, the researchers found that the similarity between family members’ gut microbiomes were closer during the dry season than during the wet season. This was probably because baboons consume a greater range of foods in the wet season when fruits, flowers and greens become abundant. How old each individual was also had an impact on how similar their gut microbiomes were, as they became increasingly more alike as the baboons aged, possibly because of changes in their dietary tastes over the course of the animal's life.Interestingly, the researchers found that the number of fecal samples available for each individual baboon – on average they collected 28 fecal samples per animal, rather than depending on one or two samples taken a single point during an animal's life – was an important factor that allowed them to reveal how heritable gut microbiomes are. When they collapsed their full dataset to only one fecal sample per individual baboon, to simulate the approach that scientists usually take, it incorrectly suggested that less than 5% of gut microbes were inherited. This goes to show how crucial it was to track the baboons over almost all of their entire lives, to bring out the true similarities between the individuals’ gut microbiomes.Grieneisen's study provides novel evidence about the role played by the genetics of the host animal in the regulation of their gut microbiome, challenging the concept that host genes are only bit players. These findings pave the way for novel and exciting research to try to identify the genetic code behind healthy human gut bacteria, which could help to improve the quality of our lives.