Microbiome Nonsense: response to “Chowing Down On Meat”

[Update 2023-11-18: Some changes made for readability; a few links on IBD added]

As the claim that animal protein and saturated fat is unhealthy becomes less and less tenable, those who have the intuition that animal-based nutrition must be bad for you are looking elsewhere.

There was great excitement at the end of 2014 about a study posted in Nature demonstrating the rapid changes in human gut microbes in response to animal-based vs. plant-based diets [1]. The paper is very interesting, and it has a lot of original data of a kind we’ve often wished for. The authors then go on to interpret their findings without apparent restraint.

A report on the study on NPR called Chowing Down On Meat, Dairy Alters Gut Bacteria A Lot, And Quickly gets right to the point:

“Looks like Harvard University scientists have given us another reason to walk past the cheese platter at holiday parties and reach for the carrot sticks instead: Your gut bacteria will thank you.”

and finally:

“”I mean, I love meat,” says microbiologist Lawrence David, who contributed to the study and is now at Duke University. “But I will say that I definitely feel a lot more guilty ordering a hamburger … since doing this work,” he says.”

That’s right. The excitement in the blog-o-sphere was not so much about the clear results — that the changes in the gut flora in response to diet are fast and large — but about the authors’ opinions that the observed changes support a link between meat consumption and inflammatory bowel disease (IBD).

We take exception to these claims, as they are not well-founded by the data in the study, or in any other study. The data to support them do not warrant the conclusion. We consider it irresponsible at best to suggest that a dietary practice is harmful to health when the evidence is weak, especially when one is in a position of authority and subject to high publicity.

Here are the points we address:

The Claims about Inflammatory Bowel Disease

Here are some quotes from the paper stressing the possible dangers of a carnivorous diet based on a supposed link to IBD — inflammatory bowel disease. Notice that they use language that implies the claims are proven, when as we will show, they are not.

From the abstract:

“[I]ncreases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease [6]”

Later, from figure 5, page 4.

“Bile acids have been shown to cause inflammatory bowel disease in mice by stimulating the growth of the bacterium Bilophila[6], which is known to reduce sulphite to hydrogen sulphide via the sulphite reductase enzyme DsrA (Extended Data Fig. 10).”

From the last paragraph, emphasis ours.

“Mouse models have also provided evidence that inflammatory bowel disease can be caused by B. wadsworthia, a sulphite-reducing bacterium whose production of H2S is thought to inflame intestinal tissue [6]. Growth of B. wadsworthia is stimulated in mice by select bile acids secreted while consuming saturated fats from milk. Our study provides several lines of evidence confirming that B. wadsworthia growth in humans can also be promoted by a high-fat diet. First, we observed B. wadsworthia to be a major component of the bacterial cluster that increased most while on the animal-based diet (cluster 28; Fig. 2 and Supplementary Table 8). This Bilophila containing cluster also showed significant positive correlations with both long-term dairy (P , 0.05; Spearman correlation) and baseline saturated fat intake (Supplementary Table 20), supporting the proposed link to milk-associated saturated fats[6]. Second, the animal-based diet led to significantly increased faecal bile acid concentrations (Fig. 5c and Extended Data Fig. 9). Third, we observed significant increases in the abundance of microbial DNA and RNA encoding sulphite reductases on the animal-based diet (Fig. 5d, e). Together, these findings are consistent with the hypothesis that diet-induced changes to the gut microbiota may contribute to the development of inflammatory bowel disease.”

This concern is prominent in the paper; they start with it and end with it. But notice the repeated citation. It is based on a single citation to a study in mice.

Reasons those claims are not warranted

Let’s look at that study (Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10−/− mice [2]):

Here’s the abstract (emphasis ours):

“The composite human microbiome of Western populations has probably changed over the past century, brought on by new environmental triggers that often have a negative impact on human health1. Here we show that consumption of a diet high in saturated (milk derived) fat, but not polyunsaturated (safflower oil) fat, changes the conditions for microbial assemblage and promotes the expansion of a low-abundance, sulphite-reducing pathobiont, Bilophila wadsworthia2. This was associated with a pro-inflammatory T helper type 1 (TH1) immune response and increased incidence of colitis in genetically susceptible Il10−/−, but not wild-type mice. These effects are mediated by milk-derived-fat-promoted taurine conjugation of hepatic bile acids, which increases the availability of organic sulphur used by sulphite-reducing microorganisms like B. wadsworthia. When mice were fed a low-fat diet supplemented with taurocholic acid, but not with glycocholic acid, for example, a bloom of B. wadsworthia and development of colitis were observed in Il10−/− mice. Together these data show that dietary fats, by promoting changes in host bile acid composition, can markedly alter conditions for gut microbial assemblage, resulting in dysbiosis that can perturb immune homeostasis. The data provide a plausible mechanistic basis by which Western-type diets high in certain saturated fats might increase the prevalence of complex immune-mediated diseases like inflammatory bowel disease in genetically susceptible hosts.”


They took some mice who were particularly susceptible to colitis, and also some regular mice, and fed them one of three different diets: a low fat diet (if we’re reading it correctly they used the AIN-93M Purified Diet from harlan, which is about 10% fat), or a diet with 37% fat which was either polyunsaturated, or saturated milk fat. They didn’t specify the amount of carbohydrate or protein, but we assume the diets were about 10-15% protein, leaving about 50% carbohydrate.

The mice who had the high milk-fat diet had a significant increase in the gut bacteria called Bilophila wadsworthia. The susceptible mice on the high milk-fat diet got colitis at a high rate (more than 60% in 6 months). The other susceptible mice, those on low-fat or polyunsaturated fat also got colitis, but at a lower rate (25-30%). The regular mice didn’t get colitis, even on the high milk-fat diet.

What’s the problem with knockout mice?

The mice that got colitis were susceptible because they were genetically manipulated to not function normally. Specifically, they couldn’t produce something called interleuken-10 (IL-10). IL-10 has many complex actions including fighting against inflammation in multiple ways.

The argument made by the scientists is that Bilophila wadsworthia must induce inflammation, and that colitis probably comes about in people who are less effective at fighting that inflammation, just like the knockout mice. This seems intuitive, but it is certainly not proven by the experiment.

Look at it this way:

Suppose we didn’t know the cause of phenylketonuria, a genetic disorder that makes the victim unable to make enzymes necessary to process the amino acid phenylalanine. We could knockout that gene in an animal, feed it phenylalanine, watch it suffer retardation and seizures, and conclude that phenylalanine must promote brain problems. This would be a mistake, of course. Phenylalanine is an essential amino acid occurring in breast milk. As far as we know, there is nothing unhealthy about it, as long as you don’t have a genetic mutation interfering with its metabolism.

It is, of course, possible that Bilophila wadsworthia inflames the colon. As a hypothesis, based on this study, it is not by itself objectionable.

What we object to is the leap to citing Bilophila wadsworthia as causing colitis, as in the second excerpt above, which we repeat here:

“Bile acids have been shown to cause inflammatory bowel disease in mice by stimulating the growth of the bacterium Bilophila[6], which is known to reduce sulphite to hydrogen sulphide via the sulphite reductase enzyme DsrA (Extended Data Fig. 10).” — from figure 5, page 4.

In fact, Bilophila did not appear to affect the normal mice at all!

There is no claim that the genetic mutation in the mice has any relation to genetic susceptibility to IBD in humans, yet it is implied that natural human susceptibility might work the same way.

Hydrogen Sulfide

In the knockout mice study, a second experiment was done to determine whether the Bilophila wadsworthia seen in the milk-fat condition came from a particular bile acid, taurocholic acid. They fed the knockout mice a low fat diet supplemented with either taurocholic acid (TC), or glycocholic acid (GC). They confirmed that Bilophila wadsworthia was increased by taurocholic acid and not by glychocholic acid.

What else do we know about taurocholic acid?

According to the authors of this study, it is “a rich source of organic sulphur, […] resulting in the formation of H2S [hydrogen sulfide]”. In one figure they even demonstrated the presence of Bilophila wadsworthia by the presence of H2S.

But H2S can be beneficial:

  • There is emerging evidence that H2S has diverse anti-inflammatory effects, as well as pro-inflammatory effects, possibly only at very high levels [3].
  • The levels needed for harm are probably higher than occurs naturally [4]
  • H2S levels in the blood are associated with high HDL, low LDL, and high adiponectin in humans [5], all considered good things.

Moreover, there is now evidence that colon cells in particular can actually use H2S as fuel, and lots of it. Other researchers have used a a similar argument in the opposite way. They claim that eating fiber is healthy, because of the butyrate generated from it in the colon, which colons cells then use as fuel. While we have problems with that argument, it shows a pervasive bias: Using it when it supports plants, but ignoring it when it doesn’t.

Taking all this into account, it is not at all clear that the higher levels of sulfite reducing bacteria seen in the meat and cheese eaters was unhealthy.

What would happen if a human sufferer of IBS or IBD went on an animal foods only diet?

It’s clear that these researchers are not studying IBS at all.

[Edit 2023-11-18: I meant to say they were not studying IBD, and in the remainder of this section I conflated the two, much to my embarrassment. This was pointed out immediately by a kind reader, and I was so demoralised by my mistake, I set it aside. When I eventually got back to it in a different post, I forgot to link it here. I'm leaving what I wrote about IBS, and just adding a short paragraph with that link.]

They were studying gut bacteria, found an association, and cherry-picked one study suggesting that what they found in the animal diet results might be unhealthy.

If they were studying IBS, they might have noticed reasons to hypothesise that a diet low in fiber [6], [7], carbohydrates [8], or fermentable carbohydrates [9] would help IBS sufferers. If humans who are susceptible to IBS are susceptible in the same way as the knockout mice in the cited study, then these results might be surprising. Instead, these results in combination with the animal diet paper, should further decrease our belief that the mice results have any relevance at all.

If they were studying IBD, they would have found the same thing, as I showed in this subsequent post on butyrate.

Moreover, unless the authors are advocating a diet of low-fiber, low-carb plants (can’t think of any plants like that off the top of my head…), they are encouraging IBS and IBD sufferers to eat foods that may worsen their condition.

We don’t know what would happen in an all meat trial for IBS/IBD, but we’d love to find out.

[2023-11-18: Note that improvements in constipation, diarrhea, and gas / bloating were reported as improved by a carnivore diet by many participants in a recent survey of 2029 people. See the supplemental materials for details.]

In Sum

The supposed link between the animal diet and inflammatory bowel disease is composed of a chain of weak links:

A kind of bacteria they found in those eating meat and cheese was also found in a mouse study that suggested a link between the bacteria and IBS.


  • It used animals that were genetically engineered to not function normally.
  • It did not and cannot establish causality between the observed gut bacteria changes and the increased level of disease.
  • It was merely an observation of the two coinciding along with a plausible mechanism, i.e. a clever story about how this might be a causal relationship.

This plausible mechanism is not as clean a story as it appears. Presenting it as such is downright misleading.



Diet rapidly and reproducibly alters the human gut microbiome
Lawrence A. David, Corinne F. Maurice, Rachel N. Carmody, David B. Gootenberg, Julie E. Button, Benjamin E. Wolfe, Alisha V. Ling, A. Sloan Devlin, Yug Varma, Michael A. Fischbach, Sudha B. Biddinger, Rachel J. Dutton & Peter J. Turnbaugh
Nature (2013) doi:10.1038/nature12820


Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10−/− mice
Suzanne Devkota, Yunwei Wang, Mark W. Musch, Vanessa Leone, Hannah Fehlner-Peach, Anuradha Nadimpalli, Dionysios A. Antonopoulos, Bana Jabri & Eugene B. Chang
Nature (2012) doi:10.1038/nature11225

3. Evidence type: review and non-human animal experiment

Hydrogen sulfide-releasing anti-inflammatory drugs.
Wallace JL.
Trends Pharmacol Sci. 2007 Oct;28(10):501-5. Epub 2007 Sep 19.

The notion of H2S being beneficial at physiological concentrations but detrimental at supraphysiological concentrations bears similarity to the situation with nitric oxide (NO), another gaseous mediator, which shares many biological effects with H2S. Also in common with NO, there is emerging evidence that physiological concentrations of H2S produce anti-inflammatory effects, whereas higher concentrations, which can be produced endogenously in certain circumstances, can exert pro-inflammatory effects [5]. Here, I focus on the anti-inflammatory effects of H2S, and on the concept that these effects can be exploited in the development of more effective and safer anti-inflammatory drugs.”

4. Evidence type: review and non-human animal experiment

Hydrogen sulfide-releasing anti-inflammatory drugs.
Wallace JL.
Trends Pharmacol Sci. 2007 Oct;28(10):501-5. Epub 2007 Sep 19.

(Emphasis ours)

“How much H2S is physiological?

“H2S is present in the blood of mammals at concentrations in the 30–100 m M range, and in the brain at concentrations in the 50–160 m M range [1–3]. Even after systemic administration of H2S donors at doses that produce pharmacological effects, plasma H2S concentrations seldom rise above the normal range, or do so for only a very brief period of time [24,27]. This is, in part, due to the efficient systems for scavenging, sequestering and metabolizing H2S. Metabolism of H2S occurs through methylation in the cytosol and through oxidation in mitochondria, and it is mainly excreted in the urine [1]. It can be scavenged by oxidized glutathione or methemoglobin, and can bind avidly to hemoglobin. Exposure of certain external surfaces andtissues to H2S can trigger inflammation [28], perhaps because of a relative paucity of the above-mentioned scavenging, metabolizing and sequestering systems. The highest concentrations of H2S in the body occur in the lumen of the colon, although there is some disagreement [29] as to whether theconcentrations of ‘free’ H2S really reach the millimolar concentrations that have been reported in some studies [30,31]. Although often alluded to [32,33], there is no direct evidence that H2S causes damage to colonic epithelial cells. Indeed, colonocytes seem to be particularly well adapted to use H2S as a metabolic fuel [4].

“There have been several suggestions that H2S might trigger mutagenesis, particularly in the colon. For example, one recent report [33] suggested that the concentrations of H2S in ‘the healthy human and rodent colon’ are genotoxic. Despite the major conclusion of that study, the authors observed that exposure of cultured colon cancer epithelial cells (i.e. transformed cells) to concentrations of Na2S as high as 2 mM for 72 hours did not cause any changes consistent with a genotoxic effect (nor cell death). It was only when the experiments were performed in the presence of two inhibitors of DNA repair, and only with a concentration of 2 mM, that they were able to detect a significant genotoxic signal. It is also important to bear in mind that the concentrations of H2S used in studies such as that described above are often referred to as those found in the ‘healthy’ colon. Clearly, if concentrations of H2S in the healthy colon do reach the levels reported, and if H2S has the capacity to produce genotoxic changes and/or to reduce epithelial viability, there must be systems in place to prevent the putative untoward effects of this gaseous mediator – otherwise, the colon would probably not be ‘healthy’”

5. Evidence type: observational

Relationship between hydrogen sulfide levels and HDL-cholesterol, adiponectin, and potassium levels in the blood of healthy subjects.
Jain SK, Micinski D, Lieblong BJ, Stapleton T.
Atherosclerosis. 2012 Nov;225(1):242-5. doi: 10.1016/j.atherosclerosis.2012.08.036. Epub 2012 Sep 10.

“Hydrogen sulfide (H2S) is an important signaling molecule whose blood levels have been shown to be lower in certain disease states. Increasing evidence indicates that H2S plays a potentially significant role in many biological processes and that malfunctioning of H2S homeostasis may contribute to the pathogenesis of vascular inflammation and atherosclerosis. This study examined the fasting blood levels of H2S, HDL-cholesterol, LDL-cholesterol, triglycerides, adiponectin, resistin, and potassium in 36 healthy adult volunteers. There was a significant positive correlation between blood levels of H2S and HDL-cholesterol (r=0.49, p=0.003), adiponectin (r=0.36, p=0.04), and potassium (r=0.34, p=0.047), as well as a significant negative correlation with LDL/HDL levels (r= -0.39, p=0.02). “

6 Evidence type: preliminary experiment

Clinical audit of the effects of low-fibre diet on irritable bowel syndrome
J. T. Woolner and G. A. Kirby
Journal of Human Nutrition and Dietetics Volume 13, Issue 4, pages 249–253, August 2000


Introduction High-fibre diets are frequently advocated for the treatment of irritable bowel syndrome (IBS) although there is little scientific evidence to support this. Experience of patients on low-fibre diets suggests that this may be an effective treatment for IBS, warranting investigation.

Methods Symptoms were recorded for 204 IBS patients presenting in the gastroenterology clinic. They were then advised on a low-fibre diet with bulking agents as appropriate. Symptoms were reassessed by postal questionnaire 4 weeks later. Patients who had improved on the diet were advised on the gradual reintroduction of different types of fibre to determine the quantity and type of fibre tolerated by the individual.

Results Seventy-four per cent of questionnaires were returned. A significant improvement (60–100% improvement in overall well-being) was recorded by 49% of patients.

Conclusion This preliminary study suggests that low-fibre diets may be an effective treatment for some IBS patients and justifies further investigation as a full clinical trial.”

7. Evidence type: Review

Fiber and functional gastrointestinal disorders.
Eswaran S1, Muir J, Chey WD.
Am J Gastroenterol. 2013 May;108(5):718-27. doi: 10.1038/ajg.2013.63. Epub 2013 Apr 2.


Despite years of advising patients to alter their dietary and supplementary fiber intake, the evidence surrounding the use of fiber for functional bowel disease is limited. This paper outlines the organization of fiber types and highlights the importance of assessing the fermentation characteristics of each fiber type when choosing a suitable strategy for patients. Fiber undergoes partial or total fermentation in the distal small bowel and colon leading to the production of short-chain fatty acids and gas, thereby affecting gastrointestinal function and sensation. When fiber is recommended for functional bowel disease, use of a soluble supplement such as ispaghula/psyllium is best supported by the available evidence. Even when used judiciously, fiber can exacerbate abdominal distension, flatulence, constipation, and diarrhea.”

8 Evidence Type: uncontrolled experiment

A very low-carbohydrate diet improves symptoms and quality of life in diarrhea-predominant irritable bowel syndrome.
Austin GL, Dalton CB, Hu Y, Morris CB, Hankins J, Weinland SR, Westman EC, Yancy WS Jr, Drossman DA.
Clin Gastroenterol Hepatol. 2009 Jun;7(6):706-708.e1. doi: 10.1016/j.cgh.2009.02.023. Epub 2009 Mar 10.


Background & Aims
Patients with diarrhea-predominant IBS (IBS-D) anecdotally report symptom improvement after initiating a very low-carbohydrate diet (VLCD). This is the first study to prospectively evaluate a VLCD in IBS-D.

Participants with moderate to severe IBS-D were provided a 2-week standard diet, then 4 weeks of a VLCD (20 grams of carbohydrates/day). A responder was defined as having adequate relief (AR) of gastrointestinal symptoms for 2 or more weeks during the VLCD. Changes in abdominal pain, stool habits, and quality of life (QOL) were also measured.

Of the 17 participants enrolled, 13 completed the study and all met the responder definition, with 10 (77%) reporting AR for all 4 VLCD weeks. Stool frequency decreased (2.6 ± 0.8/day to 1.4 ± 0.6/day; p<0.001). Stool consistency improved from diarrheal to normal form (Bristol Stool Score: 5.3 ± 0.7 to 3.8 ± 1.2; p<0.001). Pain scores and QOL measures significantly improved. Outcomes were independent of weight loss.

A VLCD provides adequate relief, and improves abdominal pain, stool habits, and quality of life in IBS-D.”

9. Evidence type: review

Low-FODMAP Diet for Treatment of Irritable Bowel Syndrome
Suma Magge, MD and Anthony Lembo, MDcorresponding author
Gastroenterol Hepatol (N Y). 2012 Nov; 8(11): 739–745.


A low-FODMAP diet appears to be effective for treatment of at least a subset of patients with IBS. FODMAPs likely induce symptoms in IBS patients due to luminal distention and visceral hypersensitivity. Whenever possible, implementation of a low-FODMAP diet should be done with the help of an experienced dietician. More research is needed to determine which patients can benefit from a low-FODMAP diet and to quantify the FODMAP content of various foods, which will help patients follow this diet effectively.”