THE bacteria in our gut are vital to our health, but urbanisation and antibiotics mean that the rich diversity of the traditional human microbiome is being lost. Eric Alm wants to change this. A biologist at the Massachusetts Institute of Technology, he has set up the non-profit Global Microbiome Conservancy. The aim is to collect stool samples from indigenous and isolated peoples and build a repository of their intestinal inhabitants before they disappear.
Why create a library of gut bacteria?
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A lot of the biodiversity that is being lost today is housed within humans – in our gut microbiomes – and it could as more people living traditional lifestyles adopt industrialised ways of life. The time to act is now. What we are doing is taking a snapshot of the biodiversity of human gut microbes on Earth today, and then preserving that for future generations so that we always have the biodiversity that co-evolved with us stored somewhere.
How much does the gut microbiome differ from one person to the next?
It depends where you look. Across industrialised nations, there are some regional differences but they are relatively small compared with the differences between an urban North American, say, and someone living a non-industrialised lifestyle elsewhere in the world. When we look at some non-industrialised populations, many organisms we find don’t exist in urban North Americans.
Why do these differences matter?
We already know that there are many diseases of the modern world – inflammatory bowel disease, asthma, allergies, autoimmunity – that . Considering that these conditions are now rising in the developing world, the health crisis has already begun.
What will you do with the library once it has been built?
One of our foundational assumptions is that this biodiversity is quite valuable. The library is going to be valuable for indigenous peoples, who might want a reserve of their gut microbes that they can tap into and bring back if they need to, either for health reasons or for their traditional diets and lifestyles.
It is also going to be valuable for medicine, because these organisms co-evolved with humans over very long periods of time and may have metabolic functions that can be transformed into new therapies.
Just so we are clear: you are talking about collecting stool samples, right?
That is the first step. It isn’t the only step, though. We can’t just take poop, stick it in a freezer, and hope to get back the full picture of biodiversity if we thaw that out. We need to isolate the bacterial strains that are present, grow them up and then create master cell banks, for long-term storage, and working cell banks, for active research.
How many bacterial strains are you looking to collect?
Ideally, we want the whole spectrum of human-associated microbial diversity, but we don’t know what that is yet. We have set an initial target of 100,000 strains for the first few years, representing a few thousand strains each from 34 different countries – but we would like to get a lot more.
How is the collection going?
So far, we have collected samples from 19 distinct populations, including many indigenous populations living more traditional lifestyles, in Cameroon, Tanzania, Ghana, Rwanda, Arctic Canada, northern Finland and on a Northern Cheyenne reservation in Montana. We have isolated more than 4000 strains from those expeditions, and we anticipate getting many more. In addition, we have more than 7600 gut bacterial strains from people living in the Boston area whose stool we used to hone our methods of strain isolation.
Are people generally willing to participate?
We learned a lot on our very first trip, which was to the Northern Cheyenne reservation. We didn’t get as much enrolment as we had hoped. Then we went to the rainforests of south-eastern Cameroon, where we changed things logistically, spending time with the people while we were waiting for our supplies to arrive. Not in a structured way, we just hung out with them, chit-chatting, interacting. We realised this was key to gaining people’s trust.
You talk about poop, and everyone thinks it is funny, but you also get to explain what you are doing. Only towards the end of the visit do we now ask people to sign up – and they generally do so, eagerly.
They don’t find it strange that you want their faeces?
Well, they are almost always shocked that you want the entire stool sample! But there was this one woman, from the Baka people of Cameroon, who was very interested in that fact. This seemed like a really good idea to her, and she joked to us, “Hey, can you sign up my neighbour? He comes over every morning, walks across an entire field, and then he poops in front of my house.” This is in a village where people commonly poop outdoors, but usually in a secluded spot. So she asked, “Can you get him into your study, so he stops pooping in front of my house?”
And did you?
No, unfortunately. We couldn’t sign him up because he wasn’t part of the Baka community that we were sampling at the time.
Where are you off to next?
We’re going to Malaysia later this month to meet with different populations, including the Jahai people. They practice a hunter-gatherer lifestyle, which is pretty exciting because there aren’t that many isolated people that live this lifestyle anymore – and it may be that the hunter-gatherer lifestyle produces a microbiome that’s more closely adapted to the natural environment.
“People are almost always shocked that you want the entire stool sample!”
Have you analysed the samples that have been collected so far?
We are starting to perform tests on some of the bacterial strains that have been isolated from the samples, and we do see that they have some metabolic functions that are really rare or entirely absent from the organisms that we have cultured from North America. Not only are we seeing new functional genes, but we are finding that the rate at which genes can jump from one bacterial species to another is very different in industrialised and non-industrialised populations.
Who owns this collection of bacterial strains?
Every strain we isolate is owned by the people who contributed the stool samples. And although we don’t restrict who can work on those strains, we do have a clause that the material can’t be made into a commercial product. It is specifically disallowed. If a company takes a strain and wants to use that organism as a therapeutic agent, they need to go back to the owners of that organism and obtain a licence from the community.
