Key takeaways
- Years on a carnivore diet did not wipe out gut bacteria diversity in the one cross-sectional study of long-term carnivores, but it did change what those bacteria were doing, including pathways tied to inflammation and constipation.
- The study sampled ten healthy people who had eaten only animal foods for about three years on average and compared them with hundreds of omnivores.
Years on a carnivore diet did not wipe out gut bacteria diversity in the one cross-sectional study of long-term carnivores, but it did change what those bacteria were doing, including pathways tied to inflammation and constipation. The study sampled ten healthy people who had eaten only animal foods for about three years on average and compared them with hundreds of omnivores. Because it is a single snapshot, it shows an association, not proof that the diet caused the changes.
What does a carnivore diet do to the gut microbiome over years?
The honest answer: the carnivore diet gut microbiome keeps its diversity but changes its job. In the one study of long-term carnivores, the bacteria were still there in similar variety, but their predicted metabolism had shifted a long way. That is the short version. Here is the long one.
Here’s what they did. The researchers looked at ten healthy people following a carnivore diet for an average of 36 months, against 874 confounder-matched controls. They sequenced stool samples and compared what was living there and what it was predicted to be doing. Diversity scores? No significant difference between the groups. One richness score, Chao1, actually came out higher in the carnivores. Didn’t see that one coming.
Sit with that for a moment. Most people assume fiber is what keeps the gut crowded. This paper says the long-term all-meat eaters did not lose their crowd. What changed was the work the crowd was doing.
Which gut bacteria changed on a long-term carnivore diet?
Two small groups of bacteria grew the most. But the bigger story is function, not names. Look at the numbers: Synergistetes and Desulfobacterota were 90 and 9 times more abundant in carnivores than in omnivores. Both are low-abundance phyla. Big jump, small numbers. Think one guy at the party becoming ninety guys at the party.
Zoom in further and the same paper reports significant differences in 56 genera and 12 species, and only two species were more abundant in carnivores, one being Phascolarctobacterium faecium. Translation: most of the named bacteria that differed got scarcer on meat. Not more. Fewer.
Now the part that matters: over 300 metabolic pathways and 13 functional modules differed, covering amino acid breakdown, vitamin B synthesis, energy metabolism, gut barrier integrity and protein fermentation. And here’s the kicker: modules linked to cytotoxicity, inflammation and constipation went up. The authors read it both ways: certain animal-food nutrients may feed bacteria, and there may be long-term risks. Good news, bad news. Same envelope.
Achieving Ketosis Carnivore Diet: Challenges and Insights
What happens when fiber disappears from your diet?
Simple. The microbes stop fermenting plants and start fermenting protein and fat. An earlier study found that an animal-based diet in ten people over five days shifted the gut from plant-fermenting taxa toward bile-tolerant taxa that ferment protein and fat. Days. Not years. Days.
Then there’s a review of the carnivore and gut health research. It says cutting out fiber affects microbiome composition and short-chain fatty acid production, which poses risks to mucosal integrity. Flip it over, though, and the same review notes some case reports of IBD and IBS symptoms improving, possibly because there are fewer fermentable carbohydrates. Two sides, same coin.
Here’s the real problem. A five-day study and a years-long snapshot measure different things. Neither one tells you which gut you’ll end up with. Your gut didn’t read the paper.
Can a cross-sectional study prove the carnivore diet caused these changes?
No. A cross-sectional study takes one snapshot, so it can show that carnivores’ bacteria differ, not that the meat made them differ. The authors adjusted for activity, stress and perceived health. They report that those extra covariates did not change their conclusions. Adjustment helps. It is not a before-and-after.
Here is the test I would want. Sample the same people before they go all-meat, then again a year later, then again three years in. Nobody has published that. Ten people who chose this diet and stayed on it are also a self-selected group: anyone whose gut fell apart probably quit, and never got sampled.
The setting matters too. The paper states that the work ran at a privately owned gut microbiome centre in Zagreb that offers paid analyses to customers. That does not make it wrong. It is one more reason to read it as a first look, which is exactly how I read our own carnivore evidence round-up.
How does Dr. Mike's burger month fit the long-term bacteria picture?
The film shows the short end of this story, and the paper shows the long end. In the 600-burger month Dr. Mike ate 20 plain Burger King patties a day for 30 days, with no bun, no condiments and water only. There was no stool sequencing, so I cannot tell you what his bacteria did. I can tell you what his body did. I covered the day-by-day bathroom report in the constipation post, so I won’t repeat it.
What the book documents beyond the gut: Dr. Mike’s HRV was cut in half within a week and was a little over halfway back to baseline by Day 19. He wrote of dizzy spells, nausea and losing interest in eating, to the point of setting alarms to remind himself to eat. His fitness was tested at baseline, on Day 14 and on Day 29, and Dr. Mike wrote on Day 29 that his ARX numbers were record lows for him and his mile was his worst “since maybe middle school”.
The film suggests, and this is my interpretation, that a gut under stress does not stay a gut problem. One more detail no paper can give you: I tried to have the patties analysed and every lab refused or quoted a five-figure minimum, so the meat itself was never lab-tested. If you aren’t testing, you’re guessing, and on that point we had to guess.
Is the carnivore diet right for your gut?
Nobody can answer that for you without testing you, and the long-term evidence is ten people deep. Individual results vary. That is not a hedge. It is the one finding everything here agrees on.
Case in point: a single-person case study of a healthy 32-year-old carnivore found no differences in diversity or functional capacity compared with control groups. The larger follow-up then found big functional differences. Same lab, two answers, as the sample grew.
In my experience, the person who does best is the one who measures before, during and after. After the burger month came a keto-pescatarian reset month in which Dr. Mike recovered. A later month of grass-finished beef brought another decline, though a smaller one. The book concludes he does best on vegetation with some fish. My own view is that I do well on grass-fed beef with organs, but that is my software, not yours. If you go all-meat, read our vitamin C checklist first.
Frequently asked questions
What are signs of an unhealthy gut microbiome?
No single symptom diagnoses one. Bloating, constipation or diarrhoea, and pain after meals are common complaints, but they have many causes. Stool sequencing describes which bacteria are present and what they are predicted to do. It does not give you a verdict. Anyone with ongoing gut symptoms should see a clinician rather than read a bacteria report on their own.
No single symptom diagnoses one. Bloating, constipation or diarrhoea, and pain after meals are common complaints, but they have many causes. Stool sequencing describes which bacteria are present and what they are predicted to do. It does not give you a verdict. Anyone with ongoing gut symptoms should see a clinician rather than read a bacteria report on their own.
How long does it take to lose 20 pounds on carnivore?
None of the gut research here measured weight loss, so it cannot answer that. In the burger month, Dr. Mike wrote on Day 8 that a scan showed his weight about where it started. Eating only meat does not guarantee weight loss. How much you eat, and how long you keep it up, still counts.
None of the gut research here measured weight loss, so it cannot answer that. In the burger month, Dr. Mike wrote on Day 8 that a scan showed his weight about where it started. Eating only meat does not guarantee weight loss. How much you eat, and how long you keep it up, still counts.
Why did Joe Rogan quit carnivore?
I can’t speak for anyone else’s reasons, and I won’t guess. The useful question for you is what your own body does on the diet. That means a baseline, bloodwork and a symptom log before you start, then the same checks partway through and again at the end. Without that, any celebrity’s result tells you nothing about yours.
I can’t speak for anyone else’s reasons, and I won’t guess. The useful question for you is what your own body does on the diet. That means a baseline, bloodwork and a symptom log before you start, then the same checks partway through and again at the end. Without that, any celebrity’s result tells you nothing about yours.
The Bottom Line
Years of meat did not empty the gut in this study. They changed what it does, and the snapshot design means nobody can yet say whether the diet caused that change or whether it lasts. Ten people is a start, not an answer. If you’re considering going all-meat, test before you start, test while you’re on it, and bring the numbers to your own clinician.
What happened to Dr. Mike’s body at the end of the 30 days is what the film is for. I won’t give it away here. Watch The Keto Project on Prime Video to rent or buy, or see where to watch. Then answer the question only you can answer: what will you test first?
Sources
- Long-term adherence to the carnivore diet and its impact on the gut microbiota: a cross-sectional study (DOI)
- Long-term adherence to the carnivore diet and its impact on the gut microbiota (Microbiota and Host)
- The gut microbiome without any plant food? A case study on the gut microbiome of a healthy carnivore
- The Carnivore Diet and Gut Health: Mechanisms, Benefits and Risks
This article is for information only and is not medical advice. Individual results vary. Speak to a qualified clinician before changing how you eat.
The whole experiment is in the film. 600 burgers, 30 days, every blood test — and the ending we never post.
Watch The Keto Project on Amazon