It is now abundantly clear that the microbes that live in our bodies are critical parts of our lives and our health. The study of these microbes and their genes—the so-called microbiome—has never been more popular. It’s also very WEIRD.
That’s not to say it is odd or unusual. WEIRD is an acronym, which stands for Western, Educated, Industrialized, Rich, and Democratic. It means that scientists have largely analysed the microbes of volunteers from the richest parts of the world. Only a few studies have looked beyond the West, at places like Burkina Faso, Venezuela, Bangladesh, and Malawi.
This matters because we’re getting a very distorted view of the human microbiome—one based on an unrepresentative slice of humanity at large. It also matters because scientists are quickly realising that many aspects of modern life—from antibiotics, to Caesarean sections, to fatty foods—can shift our microbes towards communities that have been linked to conditions like obesity, allergies, diabetes, and more. Researchers are also developing ways of shifting these microbes towards healthier states.
But how can we do that if we don’t really understand what microbes look like in people who’ve never come into contact with Western lifestyles? Those communities aren’t necessarily healthier than ours, but they tell us about the full diversity of the bacteria that influence our lives. As I wrote in NOVA last year, “we are like conservationists who are trying to restore a forest when they have only ever seen deserts.”
Things are changing. Stephanie Schnorr from the Max Planck Institute for Evolutionary Anthropology and a team of international scientists have, for the first time, published the microbiomes of modern hunter-gatherers—27 Hadza people from Tanzania.
These Hadza don’t grow crops or keep animals. They get all their food from hunting and gathering, and their diet consists of tubers, fruit, foliage, honey, and meat from both big and small animals. They provide us with the closest approximation to (but not an exact replica of) the lives that our ancestors lived some 10,000 years ago. That’s what makes their microbiomes interesting.
The team found that bacterial communities in the Hadza guts were far more diverse than those in 16 Italian people whom they sequenced at the same time. This isn’t surprising—you see the same pattern in virtually every rural population that anyone has looked at so far.
But Schnorr also showed that Hadza men and women have slightly different sets of gut microbes, and that is new. These differences may reflect their varying lifestyles. Men spend their days travelling in search of game and honey, while women stay at a central camp to forage for plants and tubers. Everyone shares, but everyone also snacks on what’s at hand during the day. So, Hadza women have ended up with higher proportions of groups like Treponema that are good at breaking down the tough fibres found in plants.
Bizarrely, the Hadza have no Bifidobacteria—a group of bacteria that makes up to 10 percent of a Western gut population and is generally viewed as ‘healthy’. They’re the main microbes in infants and they seem to feed on special sugars in breast milk. As we get older, they lose their dominance but they still stick around, possibly because we continue to eat dairy foods. It makes sense that the Hadza, which don’t eat dairy and don’t keep livestock, would be missing these otherwise omnipresent bugs.
Meanwhile, they have high levels of other species that we normally view as opportunists—bacteria that are typically harmless but can cause serious diseases when our immune systems are compromised. The Treponema group, for example, also includes the species that causes for syphilis and yaws, but the Hadza have no trace of either disease. “When we see these bacteria in Western populations, they’re maybe a warning sign,” says Amanda Henry, who led the new study. “But Hadza have lots of these and seem to do just fine.”
Several of these so-called opportunists are also fibre-busting specialists, so it’s possible that the Hadza rely on them to extract more nutrients from their food. Still, their communities are slightly different to those of rural Africans from Burkina Faso who also eat mostly plants, so there may be something special about the Hadza diet that warrants a different cadre of fibre-busting microbes.
To Henry, these results show just how cautious we have to be before romanticising the Hadza’s lifestyle as being ancestral and, thus, healthier. They are often cited as inspirations for the Paleo diet. But Henry says, “They live in a wide region where there are pastoralists and agriculturalists. They’re visited by tourists and anthropologists. They’re still foraging, but they’re a modern people and they don’t exactly represent the ancestral state.”
Their lack of Bifidobacteria and their high levels of Treponema aren’t ‘unhealthy’, but their gut communities aren’t necessarily better than ours either. They eat local plants and animals, drink local water, and are covered in local soil. Their microbiomes have simply adapted to their own corner of the world.
There is one problem with the study: the team stored their Hadza stool samples in alcohol, which can seriously affect the proportions of different species found within them. This may explain why both the Hadza and Italian samples were dominated by bacteria from the Firmicutes group—a trend that has been linked to obesity in past studies. Maria Gloria Dominguez-Bello from New York University has run into this problem before, and had to repeat a lot of past work to correct for it. She has looked at the microbiomes of hunter-gatherers in Venezuela (as yet unpublished) and rural kids in Mexico, and neither group were dominated by Firmicutes.
“The conclusions about relative proportions of bacteria are likely not valid,” says Rob Knight, a microbiome scientist with expertise in technical issues. “Unfortunately there is no published reference for this yet; we’re working on one.” It’s not clear if this problem affects the study’s other conclusions, like the lack of Bifidobacteria.
Cecil Lewis Jr from the University of Oklahoma, says “I’m excited to see how their dataset compares to future microbiome studies of other hunter-gatherers.” He shouldn’t have to wait long. He and Dominguez-Bello are both looking at the microbiomes of Amerindian people, from Peru and Venezuela respectively.
Meanwhile, Knight and Dominguez-Bello are working on another project to sequence Hadza microbiomes, led by Jeff Leach from the Human Food Project. They have collected up to 500 samples so far, from the Hadza’s bodies, but also from their food and environment. They’ve also collected samples throughout the year, which matters because the Hadza diet changes dramatically between the wet and dry seasons. They get more plants in rainy months, and more meat in the drier ones.
“We expect some interesting insight into how free-living humans acquire microbes from the massive microbial metacommunity—plants, animals, water, etc.—that is east Africa,” says Leach. “The Hadza literally hunt the same animals (sans the megafauna), gather the same plants, and are covered in the same soil, blood, and feces that likely characterised much of hominin evolution. They represent a unique opportunity to test some interesting hypotheses.”
Reference: Schnorr, Candela, Rampelli, Centanni, Consolandi, Basaglia, Turroni, Biagi, Peano, Severgnini, Fiori, Gotti, De Bellis, Luiselli, Brigidi, Mabulla, Marlowe, Henry & Crittenden. 2014. Gut microbiome of the Hadza hunter-gatherers. Nature Communications http://dx.doi.org/10.1038/ncomms4654