🔬Diet Signatures in the Gut Microbiome Across 21,561 Individuals

Please take a look at the corresponding Substack episode.

The future of health might be less about restriction and more about strategic abundance

We've been having the wrong conversation about food. For decades, the debate has endlessly revolved around what we should eliminate—meat, dairy, carbs, fat, gluten, sugar. 

We've turned eating into a game of nutritional Jenga, carefully removing blocks and hoping our health doesn't fall apart. But what if the most effective intervention isn't about removing things at all? 

An extensive study examining the gut microbiomes.

Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals

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Transcript

0:25

Welcome to the deep dive. Today, we're really getting into it, looking inside the human gut. We wanna figure out how the big three diets, omnivore, vegetarian, vegan, actually change the microbes living inside us.- Yeah, our mission here is to basically break down the results from this huge, huge microbiome study. We're trying to map out the specific microbial fingerprints, if you like, that each diet leaves behind. Not just trends, but like species level stuff. And when you say huge, you really mean it, right? This data comes from over 21,000 people. 21,561 individuals, yeah. across five different groups, different countries. So it's not some small, isolated thing. It's more like a gut census. It really lets you see robust patterns. Okay, so a massive study. What did it find right off the bat? Well, the first big takeaway confirms what a lot of people figured. Yeah. Your diet creates a really unique microbial signature. They used machine learning and found these signatures were actually very good at telling the diets apart. How good? Like, give us a number. How accurate are we talking? Pretty accurate. They used this score called Area Under the Curve, or AUC. Overall was 0.85. You can sort of think of that like the microbiome as a fingerprint. based just on the bacteria present, they could guess the diet correctly 85% of the time. Wow, 85% is, that's really high for something this complex. And I bet the contrast was clearest between the extremes. Exactly. When they tried to separate omnivores from vegans, the score jumped to 0.90 AUC. So the diet with the most restrictions versus the least restrictive one, they produce microbial signals that are almost impossible to mix up. Now, before we dive into the specific bacteria, the study didn't just take people's word for what they ate, did they? They used something called the Healthy Plant-Based Diet Index, the HPDI. Right, yeah, that was smart. They needed to know, like, are we talking about someone eating loads of healthy plants or a junk food vegan? The HPDI scores basically confirmed what you'd expect. vegans scored highest on healthy plant foods, then vegetarians, then omnivores. So they were comparing actual dietary quality, which is key. Okay, great context. Let's get into those signatures then. Starting with the omnivores, the least restrictive group, what's driving that microbial profile? The analysis really pointed a finger at red meat consumption. That seems to be a major driver. And the bacteria that thrive there, they're sort of built to handle higher amounts of protein and fat. Okay, so who are the main players on the omnivore team? Give us the names. All right. The key ones highlighted were Ruminococcus torx, Bilophila wadsworthia, and Allostipes putridinus. Functionally, you can see why. Allos hippies putridinus, for instance, is known for helping with protein fermentation. Makes sense for meat eaters. Yeah, and bilofila wadsworthia. It's linked to handling bile acids better, which you need more of when you're digesting a lot of animal fat. Okay, but wasn't there one that raised a bit of a red flag? Ah, yes. That would be rheumatococcus torx. It's described as a mucolytic indicator. Basically, it can eat away at the protective mucus layer in your gut. It sort of thins out your gut's natural shield against inflammation. Oh, wow. Not good. No. And it's been linked pretty strongly before to things like inflammatory bowel diseases. So, yeah, the omnivore gut seems optimized for breaking down animal stuff, but maybe sometimes at a cost to the gut barrier itself. That paints a really clear picture. So if the omnivore gut is like a disassembly line for animal products, what about the plant powerhouse? the vegan profile. It's almost the functional opposite, really. The vegan signatures, dominated by microbes that are really good at breaking down fiber. We're talking about those valuable short-chain fatty acid producers, SCFAs, names like Loch Nose Birisi, der Uruchococcus, Rosaberea hominis. Ah, the good guys, the ones making butyrate, right? The stuff that actually feeds our colon cells and keeps them healthy. Exactly, they specialize in fermenting those complex plant fibers that our own bodies just can't handle. And the SCFAs they produce. That's fundamental for a strong, healthy, non-inflamed gut lining. It helps keep everything in balance.

Okay, that leads us nicely to the group in the middle: 4:36

Vegetarians, they avoid meat, just like vegans. So what's the main thing that sets their microbiomes apart from vegans? Dairy. It really boils down to dairy consumption. When the researchers compared the microbes between vegetarians and vegans, the bacteria showing the biggest difference were overwhelmingly linked to dairy products. So like the bacteria you find in yogurt and cheese, are these guys actually living there long term or just passing through? Well, that's the interesting part. It seems to be a bit of both. You see species like Streptococcus thermophilus, which is, you know, a super common starter culture in yogurt and cheese having the biggest difference. Okay. And other lactic acid bacteria like Lactobacillus, Acidophilus, Lactococcus. acus lactis, they pop up too. It really suggests that eating or not eating these microbes often live in fermented dairy is a major factor shaping the vegetarian gut differently from the vegan one. Even if someone is visiting, their presence or absence changes the whole neighborhood. Right. So the diet labels definitely create distinct microbial communities. Let's connect this to health. What about cardiometabolic health, heart disease, diabetes risk, that sort of thing? What did the data show? This is where it gets really interesting, yeah. The study used the ZOEMB health ranks. Basically, a score closer to zero means lower risk for those kinds of cardiometabolic problems. And where did the omnivore microbes fall on that scale? Not great, unfortunately. The microbes associated with the omnivore signature consistently link to less favorable health outcomes. Their average ranks were around 0.53 and 0.58 in different comparisons. That's not just a small blip. It's a statistically significant difference compared to the plant-based groups. Okay, a noticeable difference. And the plant-based signatures, how did they fare? Much better. The vegan-associated bacteria had the most favorable scores, averaging around 0.38. and importantly even when you compared vegans directly vegetarians the vegan microbes tend to have slightly more favorable rankings though both plant-based groups were clearly doing better than the omnivore profile in this regard so the species tell one story what about their jobs the functional pathways what are these different microbial communities actually doing day to day based on the The functional analysis lined up perfectly with the species data, really. In omnivores, the overrepresented pathways are all about processing animal nutrients. Things like breaking down specific amino acids that are abundant in meat and dairy, elthronine, elserine, glycine metabolism. They're geared up for that kind of fuel. Yeah, exactly. And they also showed more machinery for salvaging essential cofactors that you get a lot of from animal foods. Think of vitamin B12 precursors, folate precursors. Their whole system is kind of optimized for an animal-based supply chain. Okay. And the vegan and vegetarian pathways, what are they busy doing? They're set up to tackle plant stuff. Complex fibers, bioactive compounds you find in plants. So you see enrichment in pathways for converting simple plant sugars like D-galactose or breaking down things like myo-inositol. Inositol. Yeah, it's a type of sugar alcohol, very common in plants, especially fruits and grains. It's a big carbon source in plant environments. So the microbes thriving in these guts, they're built to pull energy directly out of the plant structures themselves. This mostly sounds like the diet selects for the microbes that can best use it. But you mentioned something about acquisition too, like microbes jumping straight from the food into the gut. Yes, exactly. The food to gut acquisition idea. They found that the biggest factor influencing which species were shared between food and the gut wasn't actually the overall diet label, but specific types of food. And guess which food group showed the most sharing? Let me guess. Dairy. You got it. Dairy products had the highest transfer rate, which again helps explain some of the differences Yes. between vegetarians, omnivores and vegans. Because the dairy eaters are constantly getting these microbes from their food. Precisely. Vegetarians and omnivores had more of these food associated microbes and in higher amounts compared to vegans. The researchers think many of these dairy microbes are probably just passing through transients derived directly from the food, not necessarily permanent residents selected by the gut environment itself. But vegans had their own unique acquisition source too, didn't they? Something linking them to soil. They did! It's fascinating! Vegans showed a noticeably higher amount of microbes that are commonly found on plants and even in soil. Things like nitrogen-fixing bacteria, enterobacterhormice, klebsil, and ammonia. What's really cool here is that it suggests agricultural practices, how food is grown, maybe how much soil is still clinging to fresh produce when it's eaten, might actually play a distinct role in shaping the vegan gut microbiome. That is incredible. So the journey of the food right from the farm is literally reflected in the gut microbes. We really are eating the whole ecosystem. Yeah, it connects our internal world back to the agricultural environment in a way we're really just starting to fully grasp. Okay, let's shift to maybe the most practical point from all this. We've talked about the strict diet labels, omnivore, vegetarian, vegan, but how much does that HPDI score, the quality of the plant foods, cut across those labels? This is, I think, the key takeaway for most people. The study found that the amount and quality of healthy plant foods someone ate often mattered more than their overall diet category. Wait, really? So let's say I'm an omnivore, but I make a serious effort to pack my meals with diverse veggies, fruits, legumes, whole greens. Does my microbiome start looking a bit more like vegetarians or vegans in terms of the good microbes? Absolutely. The link between a high HPDI score and those beneficial microbes like the SCFA producers we talked about held true across all three diet groups. If eating more healthy plants boosted good bugs in a vegan, it did the same thing in an omnivore. So the microbes don't really care what label you put on your diet. Not really, though. They just care about the fuel you give them, specifically high-quality plant fuel. Seems that way. It really raises an important point. An omnivore who focuses on getting lots of diverse, high-quality plant foods... can potentially nudge their microbiome towards sharing some of those health-promoting features. Now, the study did point out the caveat. Which is that, in reality, the omnivores in this study did generally eat significantly fewer healthy plant foods than the vegetarians or vegans. So while the potential is there, it often goes untapped in practice. Okay, this has been incredibly insightful, a really deep dive. The findings seem pretty clear. Our dietary choices have a massive impact on our gut microbiome. They shape which species live there. Yeah, from the meat specialists, sometimes linked to inflammation. To the fiber chompers linked to better cardiometabolic health. And it also shapes what those microbes are actually doing, their metabolic functions. And we saw it's a mix of selection, feeding the microbes that thrive on your diet, and direct acquisition, like getting microbes from yogurt or even from soil on your veggies. Right. Which leaves us with a final thought for you, the listener, to consider. Given that the quality and diversity of plant foods that HPDI score seems so strongly linked to beneficial gut microbes, regardless of whether you call yourself vegan, vegetarian, or omnivore, Maybe the most powerful first step isn't necessarily about eliminating entire food groups like meat or dairy. Maybe it's more about strategically adding. Focusing first on packing as much diversity of healthy fruits, vegetables, legumes, nuts, seeds, and whole grains into every meal you eat. starting right now. That proactive addition, rather than just restriction, might just be the most effective lever you can pull for changing your gut microbiome for the better. It certainly gives you something powerful to focus on. Thank you for joining us on this deep dive. We'll see you next time.