Mounting evidence suggests that the richer and more diverse the community of microbes in your gut the lower your risk of disease. Diet is key to maintaining diversity and was strikingly demonstrated when an undergrad student went on a McDonald’s diet for ten days and after just four days experienced a significant drop in the number of beneficial microbes.
Similar results have been demonstrated in a number of larger human and animal studies.
Your gut microbiome is a vast community of trillions of bacteria that has a major influence on your metabolism, immune system and mood. These bacteria and fungi inhabit every nook and cranny of your gastrointestinal tract, with most of this 1kg to 2kg “microbe organ” sited in your colon (the main bit of your large intestine).
We tend to see the biggest diet-related shifts in microbes in people who are unhealthy with a low-diversity unstable microbiome. What we didn’t know is whether a healthy stable gut microbiome could be improved in just a few days. The chance to test this in an unusual way came when my colleague Jeff Leach invited me on a field trip to Tanzania, where he has been living and working among the Hadza, one of the last remaining hunter-gatherer groups in all of Africa.
My microbiome is pretty healthy nowadays and, among the first hundred samples we tested as part of the MapMyGut project, I had the best gut diversity – our best overall measure of gut health, reflecting the number and richness of different species. High diversity is associated with a low risk of obesity and many diseases. The Hadza have a diversity that is one of the richest on the planet.
The research plan was devised by Jeff who suggested I should have an intensive three days of eating like a hunter gatherer during my stay at his research camp. I would measure my gut microbes before heading to Tanzania, during my stay with the Hadza, and after my return to the UK. I was also not allowed to wash or use alcohol swabs and I was expected to hunt and forage with the Hadza as much as possible – including coming in contact with the odd Hadza baby and baboon poo lying about.
To help us record the trip I was accompanied by Dan Saladino, the intrepid presenter and producer of BBC Radio 4’s The Food Programme, who was preparing a Hadza microbe special.
After a long tiring flight to Mount Kilimanjaro Airport in Tanzania, we stayed overnight in Arusha, a city in the north of the country. Before setting off the next morning, I produced my baseline poo sample.
After an eight-hour journey in a Land Rover over bumpy tracks, we arrived. Jeff beckoned us to the top of a huge rock to witness the most amazing sunset over Lake Eyasi. Here, within a stones throw of the famous fossil site of Olduvai Gorge and with the stunning plains of the Serengeti in the distance, Jeff explained that we were never going to be closer to home as a member of the genus Homo, than where we were standing at that moment.
The Hadza seek out the same animals and plants that humans have hunted and gathered for millions of years. Importantly, the human-microbe tango that played out here for aeons probably shaped aspects of our immune system and made us who we are today. The significance of being in Hadza-land was not lost on me.
Unlike the Hadza, who sleep around the fire or in grass huts, I was given a tent and told to zip it up tight as there were scorpions and snakes about. I had to be careful where I stepped if I needed a nocturnal pee. After an interesting but restless night’s sleep, a large pile of baobab pods had been collected for my breakfast.
The baobab fruit is the staple of the Hadza diet, packed with vitamins, fat in the seeds, and, of course, significant amounts of fibre. We were surrounded by baobab trees stretching in the distance as far as I could see. Baobab fruit have a hard coconut-like shell that cracks easily to reveal a chalky flesh around a large, fat-rich seed. The high levels of vitamin C provided an unexpected citrus tang.
The Hadza mixed the chalky bits with water and whisked it vigorously for two to three minutes with a stick until it was a thick, milky porridge that was filtered – somewhat – into a mug for my breakfast. It was surprisingly pleasant and refreshing. As I wasn’t sure what else I would be eating on my first day, I drank two mugs and suddenly felt very full.
My next snacks were the wild berries on many of the trees surrounding the camp – the commonest were small Kongorobi berries. These refreshing and slightly sweet berries have 20 times the fibre and polyphenols compared with cultivated berries – powerful fuel for my gut microbiome. I had a late lunch of a few high-fibre tubers dug up with a sharp stick by the female foragers and tossed on the fire. These were more effort to eat - like tough, earthy celery. I didn’t go for seconds or feel hungry, probably because of my high-fibre breakfast. No one seemed concerned about dinner.
A few hours later we were asked to join a hunting party to track down porcupine – a rare delicacy. Even Jeff hadn’t tasted this creature in his four years of field work.
Two 20kg nocturnal porcupines had been tracked to their tunnel system in a termite mound. After several hours of digging and tunnelling – carefully avoiding the razor-sharp spines – two porcupines were eventually speared and thrown to the surface. A fire was lit. The spines, skin and valuable organs were expertly dissected and the heart, lung and liver cooked and eaten straight away.
The rest of the fatty carcass was taken back to camp for communal eating. It tasted much like suckling pig. We had a similar menu the next two days, with the main dishes including hyrax – a strange furry guinea-pig-like hoofed animal, weighing about 4kg – a relative of the elephant, of all creatures.
Harvested high from a baobab tree, our dessert was the best golden orange honey I could ever imagine – with the bonus of honeycomb full of fat and protein from the larvae. The combination of fat and sugars made our dessert the most energy-dense food found anywhere in nature and may have competed with fire in terms of its evolutionary importance.
In Hadza-land nothing is wasted or killed unnecessarily, but they eat an amazing variety of plant and animal species (around 600, most of which are birds) compared with us in the West. My other lasting impression was how little time they spent getting food. It appeared as though it took just a few hours a day – as simple as going round a large supermarket. Any direction you walked there was food – above, on and below ground.
Twenty-four hours later Dan and I were back in London, him with his precious audio tapes and me with my cherished poo samples. After producing a few more, I sent them to the lab for testing.
The results showed clear differences between my starting sample and after three days of my forager diet. The good news was my gut microbal diversity increased a stunning 20%, including some totally novel African microbes, such as those of the phylum Synergistetes.
The bad news was, after a few days, my gut microbes had virtually returned to where they were before the trip. But we had learnt something important. However good your diet and gut health, it is not nearly as good as our ancestors’. Everyone should make the effort to improve their gut health by re-wilding their diet and lifestyle. Being more adventurous in your normal cuisine plus reconnecting with nature and its associated microbial life, may be what we all need.
The world we occupy today is very different from the one occupied by our not-so-distant ancestors. As we enter a new geological epoch – the Anthropocene, in which the human footprint has left its mark – there is much concern about global deforestation, melting ice sheets and general biosphere degradation. But another, often overlooked, casualty of this new epoch is the diversity of microorganisms (including bacteria, viruses and fungi) that live on and in us. If our microbiome – the genetic diversity of these organisms – is a canary in the microbial coal mine, then my work with East African hunter-gatherers suggests that it is hanging upside down on its perch.
In the field I have watched a Hadza hunter skillfully butcher a baboon and share meat with others around a fire. Nothing goes to waste. Organs, including the brain, are consumed along with raw colon and stomach. By sterile Western standards, it is a gruesome sight for an evening meal. No matter how many times I watch Hadza carve up animals dispatched with a bow and arrow, I am always taken aback by the extraordinary exchange of microbes between this group and their environment. A microbial tango that probably characterised the entirety of human evolution.
Why is this important? Recent research has shown that disease is often associated with a fall in microbial diversity. What we don’t know is which way cause and effect runs. Does disease cause a drop in microbial diversity or does a drop in diversity cause – or precede – disease?
It’s still early days and a lot of work lies ahead. However, the idea that the microbes, and the diversity of microbes, that we carry may help us better understand and head off disease has spawned a level of optimism in medical research not seen since the introduction of antibiotics over 50 years ago.
Which brings me back to the Hadza.
Living and working among the Hadza makes me think of the intimate relationship humans have probably evolved with diverse groups of microbes. With each animal killed, microbes are given the opportunity to move from one species to the next. With each berry that is plucked from a bush or tuber dug from beneath the microbial-rich ground, each and every act of foraging keeps the Hadza connected to an extensive regional (microbial) species pool.
It is their persistent exposure to this rich pool of microorganisms that has endowed the Hadza with an extraordinary diversity of microbes; much greater than we see among people in the so-called developed world.
Viewed through the lens of ecology, the less diverse gut microbiome in the West can potentially be seen as either a result of a degraded regional species pool (all species available to colonise a local site) or an increase of environmental filters (things that thwart or limit the movement of microbes in the environment, or alter their composition). A combination of both is probably at play.
Much attention has been focused on environmental filters, such as diet, as the primary culprit for decreasing microbial diversity in the Western gut. Another environmental filter is the overuse of antibiotics. Each course of antibiotics can reduce the diversity of microbes in the host. Other filters may include too much time spent indoors, an increase in caesarean births and a decrease in breastfeeding rates, antimicrobial products such as handgels, small doses of antibiotics in the meat we eat, and modern hygiene.
But the contribution of the regional species pool gets little attention in microbial research. I suspect it has something to do with the difficulties in such large-scale sampling and, of course, cost and priorities. Given that regional species pools - though focused on macroorganisms (organisms large enough to see with the naked eye) - is a central theme in ecology, it would be beneficial if it was incorporated into more human-microbe research.
Considering our classic environmental filtering example of antibiotics, one wonders if someone who took an antibiotic and experienced a reduction in microbial diversity would not recover more quickly - to their pre-antibiotic state of microbial diversity - if he or she had exposure to a robust and diverse regional species pool, once the course of antibiotics was completed.
Surely more attention and better management of environmental filters would pay dividends in improving microbial diversity in humans. However, having a better understanding of how ecological degradation may be hitting a little closer to home (our own gut) than most of us previously imagined may provide the much-needed impetus that this generation needs to finally put the health of ecosystems, large and small, into perspective.
Importantly, all the buzz around the microbiome may be an opportune moment to mobilise a much-needed group of micro-environmentalists to better teach how to appreciate the importance of what’s happening to our shared biosphere.
In a previous version of this article, the following sentence contained an error: “…an increase in caesarean births and breastfeeding rates” should have read: “…an increase in caesarean births and a decrease in breastfeeding rates”.