What is the microbiome and where does it come from?

The microbiome is an immense collection of microbial cells found on or in our body, but the majority of them are bacteria and reside in our gut. Despite the negative feeling the word ‘bacteria’ often evokes given their role in spreading some diseases, they are in fact crucial in allowing us to lead healthy lives: they help us digest things the body otherwise wouldn’t be able to, for example, and helpful bacteria outcompete “bad” bacteria within the intestine so they can’t establish themselves and do us harm.

But where do these bacteria come from and how did they become so suited to living in our bodies? I spoke with Ruth Ley, microbial ecologist at the Max Planck Institute, who’s been studying the co-evolution of humans and bacteria…

Ruth - When we're born, we're rather extraordinary in that we're an extremely large organism that is completely germ free. And this is an extraordinary thing to be because all large organisms are covered in microbes. But yet, when you develop in the womb, you're in this incredible protected space. Then, when you come out, you are colonised by microbes over several years, beginning at birth. But where these actually come from is your immediate environments. And what that really means is the people who are raising you or are around you as a child are the ones that are supplying you with the microbes that they have. And those microbes came from their parents and their families and your grandparents' microbes came from your great-grandparents and so on and so on. And then others, they might travel more widely between people and they might, for instance, spend time in water or in rivers and things like that and finally make their way into a human.

Chris - So they've evolved to be specifically part of our microbial passengers, then?

Ruth - It really does look like that. When you compare, for example, the microbes that we have to the ones that our great ape relatives have, you can see that there's a certain number of them that even share our evolutionary history. So, for instance, our closest relatives are the chimpanzees and then after that you have gorillas and orangutans and so on. We know how we're related to each other - who shares a common ancestor with whom and how far back that goes - and you can do the same for some of the species in the gut. So you can tell that they've been in our lineage so long that when we became human, our microbes followed us, if you will.

Chris - So it follows then that, if we have evolved to have this really close relationship with these microbial flora and fauna that come with us, that if they're not there or we upset the biological apple cart, we are presumably less healthy for it?

Ruth - Well, I think this is one of the questions. So we now know from recent work that when humans split off from our ancestors, with the chimpanzees, when we got the modern human lineages, a lot of them at that point were also lost. And so there's a lot that are in our great ape relatives that humans no longer have and that might be just fine because we have a different kind of digestive tract from them and a different kind of diet. And, we do very different things with our food: we cook our food. We might not need the suite of bacteria, for instance, that are good at breaking down the fibre in leaves because we don't eat as much leaf material as an ape, for instance. They're really folivores. So instead of relying on bacteria, we now rely on cooking and that's fine. We've culturally adapted to a new way of nourishing ourselves. But what's happening since we've taken that to a greater extreme is a little concerning. So what I mean by that is, with a more industrialised lifestyle and reliance on very fibre poor foods, it looks like we are losing even more. And that's where the concern's coming in.

Chris - I was gonna ask you because one of the words of the year that's going into the dictionary is 'ultra processed.' This whole field has really had a spotlight shone on it by Chris Van Tulleken writing his book about it. What impact does this modern ultra processed diet have on this assemblage of microbes?

Ruth - Well, I think it starves them. The biggest assemblage of microbes we have are in the large intestine, and they're there in order to break down fibre which is everything that reaches the large intestine. These ultra processed foods don't have any fibre in them at all. They're so highly pre-digested, if you will, that, when we eat them, we absorb sugars and fats and protein from them immediately. There's really nothing that happens in the small intestine and then there's no fibre left over for our gut microbes. The concern is that over time they disappear and then you can't get them back.

Chris - So what might be the health consequences of that?

Ruth - Well, I think this is what we're still trying to understand, but when you look at industrialised societies and their microbiomes compared to people who are living a lifestyle where they, at least with their nutrition, get much more fibre, they have a much more diverse microbiome, there's more species there and their species can do more things. There's a concern that we might be losing some of the beneficial functions that we take for granted, such as perhaps protecting us against pathogens, and being able to break down toxins that come in because we don't have those microbes anymore. Another one that's a bit more difficult to figure out, I think, is just how they interact with our immune systems and whether or not we are losing critical interactions with our immune systems such that then our immune systems might be doing things that work against us, such as the development of autoimmune diseases, for instance.

Chris - Researchers in Ireland in recent years have also shown that there may even be signals travelling between what's going on in a Mum's gut and her developing baby's brain. So could it be that by bending our microbiome through all the factors we're exposed to, we're not just impacting our own health, but we're potentially affecting the future health of a baby that hasn't even been born yet?

Ruth - That's entirely possible because when you look at what's in our blood, a lot of that is made up of molecules that are coming from the microbiome. And when you change the microbiome, you change this suite of molecules in the blood and those molecules do reach the developing baby through the placenta. That is the chemical environment that the baby then develops with. If that is radically changed because the mother's microbiome has been depleted, that can have knock-on consequences that we still need to understand but could be quite real.

Chris - So it definitely comes down to the saying 'you are what you eat,' I guess.

Ruth - You're not just what you eat, though. You are what you eat, and what your microbes have done with that. Yes.