Is A High Protein Diet Ruining Your Gut Health?

You are 76% human. The rest is bacteria.

Sounds like a strange concept to many, but this area of research into the “microbiome” (which is the functions that these bacteria have), is strongly linking the composition of gut bacteria to health of the host.

Meaning you.

Research has shown, for example, that the guts of children eating traditional diets in Africa, which are high in complex carbohydrates, fibre and other non-digestible carbohydrates, and low in animal fat and protein, are different to European children eating the Standard Western Diet [“SWD”], high in total fat, saturated fat, animal protein, sugar, and with minimal fibre, vegetables, and other complex carbohydrates (De Filippo et al., 2010).

The difference is primarily a distinction between the prevalence of bacteria which specialise in the fermentation of non-digestible carbohydrates, which are abundant in the African populations studied (Ibid). The European kids, however, don’t have any of these bacteria, and their gut bacterial compositions reflected a composition that is associated with adverse health conditions, including obesity and inflammatory intestinal conditions (De Filippo et al., 2010; David et al., 2014). These same baseline differences have been found in adults, comparing African-Americans consuming the SWD with a group of native Africans consuming their traditional, high fibre and plant-based diet (Ou et al., 2013).

Why Is Fibre Important?

I’ve written about the importance of fibre here and here, but with this synopsis, I’ll focus on the role of fibre in relation to gut bacteria.

The term “fibre” is in fact broad, and refers to a wide range of structurally diverse carbohydrates that are indigestible to humans as we lack the necessary enzymes to break them down, and includes structures like resistant starch, non-starch polysaccharides, and other fibres which have a ‘prebiotic’ effect, meaning they reach the colon undigested and undergo fermentation by selective species of bacteria that are beneficial to our health (Brownawell et al., 2012). For the purposes of this post, I’m going to refer to all non-digestible carbohydrates as “fibre”.

A high intake of dietary fibre shifts the composition of your gut bacteria to by increasing populations of bacterial species and strains that ferment the fibre into short-chain fatty acids [SCFA’s]. Turns out SCFA’s are critical to the health of your digestive system. We derive up to 10-15% of our daily energy requirements from SCFA’s (Lopez-Legarrea et al., 2104), but more particularly than energy, SCFA’s are anti-inflammatory in the colon, and protect against cancer by prevent carcinogenic conversion and inhibiting tumour growth ((Ou et al., 2013;Lopez-Legarrea et al., 2104).

Yeah, SCFA’s are pretty awesome, and integral to your health.

The SWD and Gut Health

The comparative studies above were interesting, because they observed differences in the composition of the guts associated with diet. The next step for researchers was seeing what effect specific diets had on gut bacterial composition and health.

In one study, a controlled trial, feeding subjects an exclusively animal-based diet [subjects ate cured meats, cheeses, meat and consisted of 70% fat, 30% protein, 0% carbohydrates or fibre] for 6-days led to alterations in bacterial composition associated with intestinal inflammation, increased protein putrefaction, and inhibition of the growth of beneficial bacteria (David et al., 2014). Swapping and feeding an exclusively plant-based diet [subjects are wholegrains, squash, legumes, fruit, non-starchy vegetables], shifted their composition to increased levels of SCFA-producing bacteria (Ibid.).

In another study, the researches swapped the subjects’ diets: African-Americans consuming the SWD were put on the traditional diet, while the native Africans were fed the SWD (O’Keefe et al., 2015). The SWD contained 3-times the amount of fat and 2-times the amount of protein as their traditional diet, and within 2-weeks the microbiome of the native Africans had shifted composition to a pro-inflammatory environment associated with increased risk for colon cancer (Ibid.). The African-Americans had reduced levels of SCFA’s, compared to the abundant levels of SCFA-producing bacteria in the native Africans (Ibid.).

These studies, coupled with the massive popularity of higher protein diets due to their benefit to weight loss, have generated a suggestion that high protein diets are detrimental to our microbiome.

Are they?

A Closer Look At The Issue

One study specifically looked at the question of whether typical high protein, low(er) carbohydrate diets commonly used for weight loss negatively impact gut composition. Russell et al. (2011) fed subjects high protein diets [30% energy] with either 22g/d total carbs [the low-carb group] or 181g/d total carbs [the medium-carb group]. They noticed increased production of nitrogenous compounds associated with carcinogenesis, decreased production of SCFA’s and decreases in the bacterial populations associated with SCFA production.

Must be the protein, right? Wrong. The low-carb group consumed 8g/d fibre; the medium-carb group consumed 12g/d. This reflects average fibre consumption in the SWD, but it begs the question: is the issue the presence of protein or the absence of fibre?

In the study by David et al. (2014) in which the “animal-based” diet consisted of cured meats, cheese, and had absolutely no carbohydrate intake, the dietary fibre intake of the subjects in this phase was zero: 0g/d.

A better constructed study than that of Russell et al., was conducted some years before but provides an answer to this question. Brinkworth et al. (2009) fed both subjects higher protein diets [25-35% energy], with two differing carbohydrate levels. One group consumed 19g/d of which 13g was fibre. The other consumed 170g/d, of which 31g was fibre. While the expected negative effects were seen in the group consuming very low carb, the group consuming 31g fibre per day showed no change in SCFA levels, no evidence of increased toxic or carcinogenic metabolites, or evidence of deleterious byproducts of protein putrefaction (Brinkworth et al., 2009).

Comparing this with the study by Russell et al., in which a high protein intake was combined with essentially the same level of total carb intake (180g vs 170g), we can see that the real variable in the diets was fibre: 12g/d in one study corresponding to negative effects, against the protective effect of 31g/d in the study by Brinkworth et al.

The issue isn’t the presence of higher dietary protein, but the absence of the beneficial effects of dietary fibre at adequate levels.

Why Does This Matter?

Because for as much love as protein gets in the nutrition world, it also gets a lot of hate. Particularly the animal protein. And reading some of the research I’ve referenced above, you would be forgiven for thinking – as many have taken the deductive step – that ditching animal protein altogether from you diet and adopting a solely plant-based diet is the way to go.

Except, I’m not convinced that it is the way to go for optimal gut health. Protein foods are an excellent matrix for bacteria, and it’s not just carbohydrate fermentation that benefits human health: protein fermentation generates beneficial polyphenol compounds that exert anti-inflammatory, antioxidant, and anti-ageing effects (Compare et al., 2012). Protein intake increases levels of several beneficial bacterial strains (Lopez-Legarrea et al., 2014).

In addition, in comparing an omnivorous diet but one high in complex carbohydrates against exclusively vegetarians, the omnivores had higher levels of SCFA-producing bacterial strains and higher levels of SCFA than the exclusive vegetarians (Kabeerdoss et al., 2012).

I say this all the time: context matters in nutrition. Just because a diet is high in protein does not by implication mean it has to be low in fibre – or quality carbohydrates. The study by David et al., shovelling in salami and cheddar with not an ounce of plant foods, does not represent an “animal-based diet”: it reflects a shit poor diet. That people may eat that way isn’t protein’s fault.

These studies are touted as proof that “protein-rich” diets negatively impact gut health, when in fact the conclusion is erroneous: “fibre-poor” diets profoundly negatively impact gut health. There is nothing stopping having a higher protein, high fibre diet. Changes in the composition of the microbiome are primarily a function of the presence, or absence, of fibre (Walker et al., 2010).

In the context of adequate dietary fibre intake, the benefits to a higher protein intake stand.

What else do these studies show, that we shouldn’t be eating the SWD? Yeah, rocket science right there.

In sum: a higher protein intake per se is not an issue, the balance of other nutrients matters (as always). If you consume animal produce, be a plant-based carnivore.



Brinkworth, G., Noakes, M., Clifton, P. and Bird, A. (2009). Comparative effects of very low-carbohydrate, high-fat and high-carbohydrate, low-fat weight-loss diets on bowel habit and faecal short-chain fatty acids and bacterial populations. British Journal of Nutrition, 101(10), p.1493.

Brownawell, A., Caers, W., Gibson, G., Kendall, C., Lewis, K., Ringel, Y. and Slavin, J. (2012). Prebiotics and the Health Benefits of Fiber: Current Regulatory Status, Future Research, and Goals. Journal of Nutrition, 142(5), pp.962-974.


Compare, D., Coccoli, P., Rocco, A., Nardone, O., De Maria, S., Cartenì, M. and Nardone, G. (2012). Gut–liver axis: The impact of gut microbiota on non alcoholic fatty liver disease. Nutrition, Metabolism and Cardiovascular Diseases, 22(6), pp.471-476.

David, L., Maurice, C., Carmody, R., Gootenberg, D., Button, J., Wolfe, B., Ling, A., Devlin, A., Varma, Y., Fischbach, M., Biddinger, S., Dutton, R. and Turnbaugh, P. (2014). Diet rapidly and reproducibly alters the human gut microbiome. Nature, 505(7484), pp.559-563.

De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J., Massart, S., Collini, S., Pieraccini, G. and Lionetti, P. (2010). Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proceedings of the National Academy of Sciences, 107(33), pp.14691-14696.


Kabeerdoss, J., Shobana Devi, R., Regina Mary, R. and Ramakrishna, B. (2012). Faecal microbiota composition in vegetarians: comparison with omnivores in a cohort of young women in southern India. British Journal of Nutrition, 108(06), pp.953-957.

Lopez-Legarrea, P., Fuller, N., Zulet, M., Martinez, J. and Caterson, I. (2014). The influence of Mediterranean, carbohydrate and high protein diets on gut microbiota composition in the treatment of obesity and associated inflammatory state. Asia Pac J Clin Nutr., 23(3), pp.360-8.


O’Keefe, S., Li, J., Lahti, L., Ou, J., Carbonero, F., Mohammed, K., Posma, J., Kinross, J., Wahl, E., Ruder, E., Vipperla, K., Naidoo, V., Mtshali, L., Tims, S., Puylaert, P., DeLany, J., Krasinskas, A., Benefiel, A., Kaseb, H., Newton, K., Nicholson, J., de Vos, W., Gaskins, H. and Zoetendal, E. (2015). Fat, fibre and cancer risk in African Americans and rural Africans. Nature Communications, 6, p.6342.

Ou, J., Carbonero, F., Zoetendal, E., DeLany, J., Wang, M., Newton, K., Gaskins, H. and O’Keefe, S. (2013). Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans. American Journal of Clinical Nutrition, 98(1), pp.111-120.


Russell, W., Gratz, S., Duncan, S., Holtrop, G., Ince, J., Scobbie, L., Duncan, G., Johnstone, A., Lobley, G., Wallace, R., Duthie, G. and Flint, H. (2011). High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health. American Journal of Clinical Nutrition, 93(5), pp.1062-1072.


Walker, A., Ince, J., Duncan, S., Webster, L., Holtrop, G., Ze, X., Brown, D., Stares, M., Scott, P., Bergerat, A., Louis, P., McIntosh, F., Johnstone, A., Lobley, G., Parkhill, J. and Flint, H. (2010). Dominant and diet-responsive groups of bacteria within the human colonic microbiota. The ISME Journal, 5(2), pp.220-230.