Gut Instinct: Why Microbial Diversity Matters – a talk by Professor Kevin Foster at Meeting Minds 2025, Oxford University

I don’t think it will come as a surprise to many manual therapists out there that we are absolutely crawling with microbes (just to get clear on the wording: the word microbe is shorthand for, (and basically interchangeable with), micro-organism. The word micro-organism, in turn, is shorthand for microscopic organisms, i.e., a living creature so tiny it can only be seen with a microscope).

The human microbiome, i.e., the entire genetic content of all the microbes that live on us, has become a hot topic over the last few years. As this was billed as something of an introduction to the subject, I thought I would know it all, but Professor Foster actually presented me with things I didn’t already know and gave me a new perspective on bacteria in general. It was a really fascinating insight.

How long have we known about the microbiome?

It’s nearly 350 years since Antonie van Leeuwenhoek, a draper from Delft, scraped a bit of plaque from his teeth, stuck it under a microscope, and pronounced that it consisted of little animals. He called them animalcules. But it seems to have taken us a long time to figure out that they are not just bad germs, come to cause disease, but they also have numerous positive effects on our health.

How many are there?

We have about 100 trillion of these little critters, a similar number to the number of actual cells of our body. They particularly like to live in the large intestine. Luckily they’re much smaller than cells, or we’d walk around like giant bee swarms. However they outstrip us in genetic diversity.

How do they behave?

They form an ecological system, interacting with each other. Professor Foster is well versed in looking at systems like this. He started out in zoology and his PhD was in understanding social systems in insects, particularly wasps and hornets. (Among the valuable insights he gained while doing his research was that bee suits do not protect you from wasps.)

Bacteria love to fight

One thing that came through strongly in his talk — and it’s so obvious it’s easy to forget — is that bacteria are astonishingly competitive. They fight on an individual and a collective level. They are mean. They can be vicious. They love to fight. They have an amazing arsenal of weaponry. They have contact weapons, they have diffusion weapons. They can even fire tiny molecular spear guns full of toxins into neighbouring cells, like poisoned harpoons (the Type VI Secretion System). Professor Foster was so taken with their attack modes that he showed us a game he designed in partnership with the Oxford University Museum of Natural History, called Gut Wars, in which you can pit different bacteria against each other to see who wins.

Why don’t they just overpower us then?

Well, vicious as they can be, only a fraction of all bacteria are actually toxic to us. They have quite a narrow spectrum of enemies, as a rule. So you find them mostly in competition with each other, fighting for their own little niche. Most of their toxins actually target very closely related strains. And many of them have good effects on us, helping our digestion and immune system amongst other things.

Are antibiotics a problem?

Diversity of species is the key to colonisation resistance. And if you take antibiotics, you risk losing the protection of the microbiome. Interestingly, Alexander Fleming, on receiving the Nobel Prize in 1945, was already warning against the potential for antibiotic resistance. He didn’t call it that, but he didn’t pull his punches when he said

The thoughtless person playing with penicillin treatment is morally responsible for the death of the man who finally succumbs to infection with the penicillin-resistant organism

Resistance is already having major impacts. It is currently linked to more deaths than HIV and malaria. There is a relatively short list of species which are causing these problems, but many are gut-based. I was scribbling hard but only caught a few which were

• salmonella (nothing to do with salmon fish, but named after Dr Daniel Salmon who discovered it)
• shigella
• klebsiella

As a result, there is currently an effort to make microbiome-friendly antibiotics.

What is nutrient blocking?

Well, it seems that if you can’t use antibiotics, what you need to do is to starve these creatures of their essential nutrients. So what you can do is introduce strains which compete for the same food, basically. There is an effort to design custom microbiome communities and give them prophylactically. So, for example, if you have an unfriendly strain of E Coli, you can add a friendly strain of E Coli. You can use their incredible aggression to suppress the more pathogenic strains. It’s all about harnessing the power for positive ends. This is a developing area.

Are ultra-processed foods bad for your microbiome?

Talking about the dangers of ultra-processed foods is maybe even more fashionable than talking about the health benefits of the microbiome right now. The problem, apparently, for the microbiome, is that ultra-processed foods contain fairly simple nutrients without complex carbohydrates. Yet over 50% of our species are bacteroidales, which absolutely love to dine on fibre (a complex carbohydrate). If you eat highly processed bread, it might taste yummy to you but it will not feed your microbes. You will feed yourself, or the wrong guys, rather than the microbes you want to nurture and thrive.

Do probiotics work?

Sorry not to be more definite, but the verdict on this is – maybe… for some. Now I don’t think anything will stop me feeling virtuous when I eat my natural yoghurt, nor will I convince my father in law that it is not his cherished Actimel pots keeping him in good health, but the evidence base for commercial probiotics is mixed. It’s a shame, and I would have liked to know more about this. Does it mean yoghurt? Or are we talking about tablets, such as Bio-kult and acidophilus, which I have periodically taken for at least 20 years?

Many probiotics do nothing, for sure, said Professor Foster, but some work for some people for some conditions. It’s disappointing, but the evidence is currently highly variable and their effects are weaker than the companies that sell them would have us believe. Professor Foster kindly pointed me towards a nice review from a few years back that summarises many of the issues: it is chattily titled Probiotics: If It Does Not Help It Does Not Do Any Harm. Really? It indicates that not only probiotics might not work well, there can also be adverse effects associated with taking them. (There might be a future blog based on this paper, in fact…)

Does a better diet improve your microbiome?

Well, he was generally positive on this, but expressed some caution. All other things being equal, generally an increase in fibre and fermented food should lead to a shift for the better in microbiome terms. However, all things are not equal. And the results are variable. Changing the diet should work for most, but it is not guaranteed.

Should we wash less?

Well, overly aggressive washing is bad, but if you don’t wash you really could invite a build up of the bad stuff. Don’t be a total soap-dodger, but don’t smother yourself head to toe in hand sanitizer 3 times a day either.

Why don’t vultures get sick?

This is not a question that has ever occurred to me. But it’s interesting. Vultures, as we know, feast on all sorts of disgusting and decaying material. The reason they don’t get sick is partly because they have a formidable number of even nastier bugs which reside in their guts. (They also have a few other tricks up their sleeves, such as having an intensely acidic stomach.)

Do faecal transplants work?

I had heard about these. And I thought they sounded like a good idea. Transplant someone’s more healthy microbiome into your own large intestine, and hey presto! you have a fantastically healthy colony! Intuitive and perfect!

The professor didn’t go into any detail about how faecal transplants practically work, and for that I was fairly grateful – I’d had a late lunch – but disappointingly, they do not seem to have as broad an application as was initially hoped. They have proved very effective in fighting C. difficile, and are widely used for that, but the effects are more variable with other diseases. We may find quite a few things they are useful for, but we need more evidence.

What next? Well, that’s the exciting thing. It seems there is plenty to research and discover. Certainly there is a lot of potential and we still seem to be at the start of learning how to harness the power of the microbiome.

If you want to know more about Professor Foster, and Oxford Univerity’s Fosterlab, do visit his surprisingly funky website here. You can play ‘gut wars’ and peruse their list of 135 publications (some of these look quite fun: Are sperm spiteful? Is there such a thing as zombie hornets? How many sexual partners do wasp queens actually have?). There are also pictures of the 17 brainy scientists on the team, and even their Glastonbury stall.

Thanks for reading.

Many thanks to Professor Kevin Foster for checking through the accuracy of this information. It was an incredibly stimulating talk.