What Dieting Does to the Gut Microbiota

Taking into consideration not only weight loss outcomes, but aiming to create a virtuous cycle

Photo by Brooke Lark on Unsplash

There is another pandemic rumbling below the surface. The burden of obesity has tripled since 1975 and the last WHO figures, in 2016, showed 39% of adults were overweight and 13% obese globally. The Covid-19 lockdowns only made matters worse.

There are genetic factors to obesity, but they only explain a few per cents of the variability. The second genome could have a greater role. Indeed, we now know there is a microbial component to weight. Fecal transplants from twins discordant for obesity to germ-free mice showed the mice receiving the microbiota from a lean donor stayed lean, while the recipient from an obese donor gained weight rapidly, confirming a causative effect of gut microbes on weight and metabolism. Specific mechanisms underlying these effects have even been described.

While exercise seems to exert positive effects on the gut microbiota, the impacts of diets is not so clear. When a diet increases the Firmicutes/Bacteroidetes ratio or stimulates the bacteria converting choline to trimethylamine, it could contribute to a vicious cycle leading to later weight gain and promote atherosclerosis. A reduction of gut microbiota diversity or butyrate producers could also contribute to a pro-inflammatory setting and higher risks of inflammatory bowel diseases, depression, or colorectal cancer, to name a few. For this reason, I propose a short review of typical weight loss diets and their impacts on the microbiota.

What does the science have to say about the impacts of dieting on the microbiota?

1. Ketogenic diet

The ketogenic diet, a diet very rich in fats and deprived of carbohydrates that has become increasingly popular in the past few years, strongly impacts the microbiota. A review by Paoli and colleagues in 2019 showed the frame as a complex one, however the diet is marked by a reduction in Bifidobacteria (an anti-inflammatory group), E. rectale (a butyrate producer), Firmicutes, total bacterial abundance and diversity, while E. coli (a group including good, bad and ugly individuals), Desulfovibrio (contributing to hydrogen sulphide production, not desired in abundance), Bacteroidetes & Parabacteroidetes (exposing to increased risks of metabolic syndrome) and Akkermansia (considered a good guy especially in the context of obesity) rise.

Overall, this diet can reduce the production of short chain fatty acids and stimulate putrefactive metabolism to the detriment of fermentative metabolism, generating pro-inflammatory conditions and increased insulin sensitivity.

Figure illustrates the effects of the keto diet on the microbiota and metabolism, from Paoli et al., open acces on MDPI.

2. Low calorie diet

The first trial conducted to evaluate the impact of a weight loss diet on the gut ecosystem was published over 15 years ago. It showed that neither low-fat nor low-carbohydrates affected the bacterial diversity in the gut, but dieting led to a surge in Bacteroidetes, thus a reduction in the Firmicutes/Bacteroidetes ratio, which correlated with the weight loss outcome.

Diets or lifestyle changes able to reduce the Firmicutes/Bacteroidetes ratio are levers to activate the virtuous cycle of weight loss: as you can find explained here, the gut bacteria in this setting will harvest and provide you with less calories from the diet.

3. Very low calorie diet

A recent study by Peter Turnbaugh’s group showed that 8 weeks very low calorie diet (800 calories) did lead to rapid weight loss but this was accompanied by a loss in bacterial load and a dramatic depletion in butyrate-producers.

The authors also highlighted an enrichment in Clostridium difficile, a finding certainly not trivial given the life-threatening infections this pathogen can cause.

An exciting finding of this study is that weight loss is transmissible through the microbiota: mice were transplanted with stool samples collected from donors pre-diet and post-diet, and the post-diet recipient mice lost 12% of their body mass within 2 days of colonization: this is extreme for a mouse!

This microbiota could contribute to weight loss by decreasing the efficiency of dietary energy absorption. If questions around the healthfulness of this microbiota could be solved, I would expect to see weight loss centers offering fecal microbial transplants in the future.

4. Very low calorie, high protein and low carbs diets

In a recent French study including 263 volunteers on a weight loss program (low calorie at 800 calories for women and 1000 for men, high protein, low carb, supplemented with vitamins and minerals, with or without probiotics), the impact of the diet on the microbiota was not clear when looking at the whole cohort, but when stratifying according to the type of microbiota at baseline, discrimination of effects was possible.

The participants characterized by a Bact2 enterotype (an enterotype dominated by Bacteroides, and characterized by a low level of diversity — a signature associated with obesity, inflammatory bowel diseases, depression and multiple sclerosis) at baseline tended to see an enrichment of their microbiota during the trial.

The consumption of the probiotics blend helped reduce the proportion of Bact2 enterotypes and led to a significant decrease in Bacteroides vulgatus, Bacteroides fragilis and a surge in Faecalibacterium prausnitzii (Fprau), one of the main butyrate producers in the gut. Prebiotics for 3 months also helped increase Bifidobacteria and Fprau.

These results are not easy to interpret, as some good bacteria were increased, but others were reduced. The researchers conclude that the stratification by enterotype is useful to predict the benefits of a diet, which opens the door to personalized nutrition efforts — with higher benefits in this study for individuals starting with a low-diversity Bact2 enterotype, although this finding contrasts with the results from Cotillard et al. who found that dietary intervention seemed less efficient in individuals with lower bacterial gene richness.

A useful conclusion from this trial is that the diet potentially negative impacts on the microbiota can effectively be mitigated by probiotics and prebiotics during the program.


The microbiota associated with overweight and obesity is not the perfect example of health, although as highlighted by Le Chatelier and colleagues there is heterogeneity: some people with obesity have comorbidities, and others don’t. A screening of the second genome could be used to identify the individuals that would most benefit from a weight loss intervention.

As highlighted by Dr. Francesco Di Pierro, interventions such as extreme diets (very low calorie diet and keto diet) are instruments that should be placed only in capable hands and for very limited periods of time given their negative effects on the microbiota.

Seganfredo also concludes in his review on weight loss interventions and impacts on the microbiota that diets for weight loss like high protein low fiber contribute to intestinal inflammation, oxidative stress and genotoxicity, with an increased risk of colorectal cancer, contrarily to interventions with probiotics and prebiotics.

Healthcare professionals, dietitians, nutritionists and weight loss programs would thus benefit in taking into account the effects of their interventions on their patients’ microbiota, a key component of their health and future stabilization of weight status.

You just read another post from In Fitness And In Health: a health and fitness community dedicated to sharing knowledge, lessons, and suggestions to living happier, healthier lives.

If you’d like to join our newsletter and receive more stories like this one, tap here.



Get the Medium app

A button that says 'Download on the App Store', and if clicked it will lead you to the iOS App store
A button that says 'Get it on, Google Play', and if clicked it will lead you to the Google Play store
Nina Vinot

Nina Vinot

My Education is in Biology, Agronomy and Nutrition My Career is in Health-Promoting Bacteria My Passion is to Benefit Life, Happiness and the Planet