Gut bacteria reflect diet and evolutionary past

Our bodies are rife with genes and the majority of them aren't even ours. We all have a strong sense of our own individuality, but the truth is that our bodies are hotels for a diverse array of microbes including bacteria and fungi. The numbers are simultaneously creepy and humbling. Tot up all the cells in our bodies and the microbial ones would outnumber our own by a factor of ten. The five feet of our large intestine houses the majority of these microorganisms and contain up to 100 trillion of them.

These single-celled tenants are known as the microbiota and they carry their own sets of genes. Some of these are incredibly important to us because they allow us to break down food and nutrients (including dairy products) that we couldn't digest by relying on our own genomes. They might even affect our bodyweight. Despite the importance of the microbiota, it's still unclear how unique our particular array of species is, how it has evolved over time and how it relates to our broad diets (that's broad in mammalian terms; I know some people only seem to ever eat fast food...)

Ruth Ley from the Washington University School of Medicine has started to answer that question by carrying out the first extensive comparison of the bacterial communities that live in the guts of different mammals. Her analysis found that these communities have co-evolved with their hosts and their members are strongly influenced by both diet and evolutionary history.

All the best jobs...

To do this, Ley had the glamorous task of taking dung samples from over 60 species of mammal. From flying fox faeces to panda poo, the samples covered over 13 orders of mammals including 17 species of our fellow primates. Many of the species were chosen because their ate unusual diets compared to typical members of their group. For example, the giant and red pandas made the list because their bamboo-only diet sticks out among the meat-based menus of their relatives.

The samples all came from either captive animals from zoos at San Diego or St Louis Zoo, or wild ones attracted to a waterhole in Namibia. Ley collected multiple samples and where possible, tried to supplement the ones with captive individuals with those from wild ones. Every sample of dung had to be oven-dried, blended and pulverised in a mortar and pestle - all in the name of science, kids.

The prize of all this labour was DNA, specifically thousands of sequences for a bacterial gene called 16S rRNA. The gene codes for part of the ribosome, the molecular machine that creates other proteins. This role is so important that the gene is the most unchanging in all cells, which makes it particularly suitable for identifying species of bacteria and the relationships between them.

Diet and evolution

These comparisons revealed both similarities and uniqueness within the microbiota of the different species. The majority (over 80%) of the sequences belong to two main groups of bacteria - the Firmicutes and, to a lesser extent, the Bacteroidetes. Both groups have previously been identified as the main lodgers in the guts of humans and mice. But every single mammal also harboured species that were unique to them and them alone.

The species of the host had the biggest influence on the make-up of the gut communities. Those from individuals of the same species were more closely matched than they were to those from other hosts, regardless of their backgrounds. For example, the sequences from two Hamadryas baboons were very similar even though one stool sample was collected from Namibia and another was taken from a captive resident of St Louis Zoo.

However, diet was also important and Ley found that the bacterial genes clustered into different groups according to whether the animals ate plants, meat or a mixture. The herbivores had the most diverse array of intestinal passengers. They carried over 14 distinct groups of bacteria in comparison to the 12 groups in omnivores and the measly 6 hosted by carnivores. There were some exceptions. The two pandas both had low microbiota diversity typical of their carnivore ancestors and quite atypical for their vegetarian diets.

Given that the last common ancestor of mammals was a carnivore, it could be that the extra groups in the guts of plant-eaters descended and diverged from the carnivore portfolio. But Ley's analysis disproved that idea and suggested instead that the early plant-eaters gained their extra complement of bacteria from the environment.

This new partnership was a massive step in the evolution of mammals. It allowed the early species to diverge to such an extent that today, 80% of all mammals feed on plants. The bacteria gave them the ability to break down complex carbohydrates like cellulose and starches, and their bodies responded in kind by lengthening their guts to provide the bacteria with extra room.

Ley's samples also included 17 humans. Despite their sizeable diversity in terms of age, place of birth and diet (one was a strict vegetarian), there was very little difference in their gut bacteria. And overall, their complement was wholly unremarkable for an omnivore.The development of agriculture and cooking may have contributed to our global success but in the microscopic passengers in our intestines have been largely unaffected.

I have no idea what this image means but presumably the science is happening where the circles are near each other :-)

Reference: Science 10.1126/science.1155725

Images: from Science/AAAS