A Blog by Ed Yong

Surprises Emerge As More Hunter-Gatherer Microbiomes Come In

The study of the human microbiome—the motley assortment of microbes that live in our bodies—has largely been the study of the Western microbiome. The research has been heavily biased towards people from Europe, North America, and other WEIRD countries—that is, Western, Educated, Industrialised, Rich and Democratic. It’s like trying to understand how cities work by studying London and New York, and ignoring Mumbai, Mexico City, Sao Paulo, Cairo, and others.

Recognising this problem, scientists are starting to catalogue the microbes of rural populations, including hunter-gatherers. Early last year, I wrote about attempts by Maria Gloria Dominguez-Bello and Cecil Lewis Jr to study the microbiomes of the Yanomami of Venezuela and the Matses of Peru, respectively. A few months later, I covered the first study looking at the microbiomes of Hadza hunter-gatherers from Tanzania. All of these studies found similar trends: rural guts usually harbour microbes that aren’t found in Western guts, and are generally more diverse.

The Hadza guts had a few striking differences. They contained almost no Bifidobacteria, a group that is generally viewed as ‘healthy’, and that makes up to 10 percent of a Western gut microbiome. They also had more Treponema, a group that includes the species responsible for syphilis and yaws. These differences aren’t necessarily unhealthy. They just reflect the conditions in that particular corner of the world, its food supplies, water, climate, and more.

Lewis has now published the results of his Peruvian work. His team also found that people who lead traditional lifestyles—both Matses hunter-gatherers and Tunapuco farmers—had higher levels of Treponema than a comparable group of Americans. By studying these strains in detail, the team showed that they are distinct from those that cause human diseases, and more closely related to those that help other animals to digest carbohydrates.

These Treponema strains are also found in the Hadza and non-human primates, but are totally absent from industrialised populations. As such, the team suggests that they “may represent a part of the human ancestral gut microbiome that has been lost through the adoption of industrial agriculture and/or other lifestyle changes.” In other words, they’re part of an ancient package of microbes that our ancestors shared, and that people from developed countries have somehow broken ties with.

This interpretation fits with the “missing microbes” idea espoused by Martin Blaser, which says that various facets of our modern lifestyles—antibiotics, over-sanitation, poor diets, and more—have left us with depleted microbiomes, bereft of species that once played important roles. This, perhaps, explains the rise of several “diseases of civilisation”, like allergies, asthma, obesity, inflammatory bowel disease, diabetes, and more.

Hold on, though. The Hadza and the Matses are not ancient people, and their microbes are not “ancient bacteria”, as one headline stated. They are modern people, carrying modern microbes, living in today’s world, and practicing traditional lifestyles. It would be misleading to romanticise them and to automatically assume that their microbiomes are healthier ones.

After all, we also have no idea what’s behind the characteristics of their communities. It could be their traditional lifestyles, like their diets or lack of antibiotics. But it could equally be something else like their genes, climate, or parasites. You can’t work out which of these factors is important by studying a few scattered groups. Ideally, you’d want to study several groups of people who lead traditional lifestyles, live close to each other, and vary in important traits like diet or genetics.

That is exactly what Elise Morton from the University of Minnesota has done. She and her colleagues sequenced the gut microbiomes of 64 people from four groups in Cameroon: Pygmy hunter-gatherers, Bantu farmers from two villages, and Bantu from a fishing population. All of them practice subsistence lifestyles—that is, they live off whatever they themselves catch or grow. All of them co-exist in rural areas that are close to tropical rainforests. The results have just been uploaded to the bioRxiv pre-print server.

The team found a lot of variation between the four groups, “indicating that there are multiple signatures of rural, unindustrialized microbiomes”. The Pygmy hunter-gatherers stood out. Compared to the Bantu, their guts had more Proteobacteria, Succinovibrio and Ruminobacter, and fewer Ruminococcus—the same pattern that others saw when comparing Hadza and Italian guts. These microbes “seem to be a specificity of hunter-gatherer populations, rather than reflecting a difference between industrialized European and rural African populations,” Morton wrote.

The team also found that one factor, above all others, heavily influenced the gut microbiomes of their Cameroonian groups. It wasn’t diet, ancestry, or location. It was the presence of Entamoeba, a parasitic amoeba. It had such a strong effect on the gut that the team could work out whether a person was infected with 79 percent accuracy, just by looking at their gut microbes.

In general, Entamoeba-infected guts have a greater diversity of bacteria, higher levels of Treponema, and lower levels of groups like Prevotella. The reasons behind these patterns aren’t clear. We know that our immune system affects the composition of our microbiome, so by triggering immune reactions, Entamoeba might indirectly dictate which species get to live in the gut and which do not. Alternatively, it might eat bacteria from dominant groups, creating vacancies that allow others to proliferate, and boosting the diversity in the gut. Or, it might prefer to colonise microbiomes that have already been altered by some other factor.

Regardless, these results throw up some interesting questions. Is the higher diversity of the hunter-gatherer microbiome down to the wider diets of their owners, or to a wider range of parasites? After all, Morton found that if the Cameroonians had a triple-bill of parasites, including a roundworm and a whipworm along with Entamoeba, their microbiomes were even more diverse. Diversity is generally seen as a good thing. Is it?

Likewise, when other groups see high levels of Treponema in the Hadza and Matses, does that just reflect a higher burden of intestinal parasites? Is that what they’re inadvertently talking about when they say “ancestral”? And speaking of Treponema, Morton found it in all four groups but at very low levels, including in the hunter-gatherers. If it’s really part of some ancestral microbiome that has been abandoned through agriculture and industrialisation, then why is it rare in the Pygmies?

We can only answer these questions by looking at the microbiomes of people from different regions around the world. That’s why studies of the Hadza, Matses, Yanomami, and Pygmies are important. But as results come in, we must be wary of concocting simple narratives to explain characteristics of hunter-gatherer microbes.

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9 thoughts on “Surprises Emerge As More Hunter-Gatherer Microbiomes Come In

  1. In dealing with microbiomes harboring the gut, a distinction has to be made whether they are parasites, commensals, symbionts, and whether they are helminthes or bacterial or protozoans.Those that produce vitamins for the body have to be distinguished from those that don’t. It is not easy to say that diversity in microbiome is good or bad. It depends on many variables. We cannot arrive at any tangible conclusion unless we examined food habits, age of the persons and their susceptibilities etc.

  2. Hi Ed, great post. I will say there’s a lot of content in our paper about these Treponema, in particular, their metabolic potential. That said, there is so much more to do. Our paper didn’t address parasitism. However, we did do parasite screening in collaboration with the Peruvian Institute of Health. Interestingly, the Matses samples had low levels of parasite detection (an unpublished tidbit), yet relatively high Treponema.

    [Hi Cecil, thanks for the comment! I’m aware that the paper contains a lot of work on these particular strains and that I didn’t have space to do this justice. The point about the low parasite burden and high Treponema levels is fascinating to me, and perhaps underscores the idea that the drivers of microbiome composition may vary with location, genetic background, and other local conditions. – Ed]

  3. Interesting post. About 30 years ago, as part of a study (vaccine trial) in rural Peru, I was asked to conduct parasitology exams on collected stool samples. What I found amazing was that virtually 100% of the study population had Entamoeba and hookworms. Obviously, we weren’t looking at microbiomes at the time, and it wasn’t even a parasitology study, so nothing about that was published. Looking back, I have to wonder what their microbiomes would look like compared to WEIRD countries.

  4. I am so grateful to all of you doing research on the microbiome. As a health practitioner I am convinced that the microbiome holds the key to unlocking many illnesses. Call it a gut feeling.

  5. Matsés are horticulturalists like all Pano speakers. This sentence straight from the paper: ” The Matses are traditional hunter-gatherers whose subsistence focuses primarily on gathered tubers (Manihot spp.) and invasive plantains (Musa spp.)” is completely contradictory.

  6. Have individuals been studied that live in WEIRD countries but that hunt and eat the meat from the hunted animals regularly? Have they been compared to individuals from the same WEIRD countries that eat only what they buy? Have they been compared against findings from studies on groups living traditional lifestyles as discussed in this piece? Just curious.

  7. Does the diversity of microbes in the guts of rural populations make them hardier people? For example can these microbes protect them from diseases associated with the digestive tract that would harm people from western countries? (15052789)

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