Fasting And The Microbiome

Meal frequency, and fasting are easy ways to support gut health and our microbiome. Let’s explore some of the research in this topic.

Meal Frequency & Fasting

A regular meal pattern including breakfast consumption, consuming a higher proportion of energy early in the day, reduced meal frequency (i.e., 2–3 meals/day), and regular fasting periods may provide physiological benefits such as reduced inflammation, improved circadian rhythmicity, increased autophagy and stress resistance, and modulation of the gut microbiota.

The gut microbiome connection:

Recently it has been demonstrated that a chronic circadian misalignment in mice and a time shift jet–lag in humans induces a dysbiosis (imbalances in the microbiome); this dysbiosis has been demonstrated to be able to promote glucose intolerance and obesity in germ-free mice through fecal transplantation. On the other hand, maintaining a correct eating phase (i.e eating during the day) and increasing the fasting period (for example stopping eating by, say, 20:00) could positively affect the gut microbiome, reducing gut permeability and improving systemic inflammation.

The authors also created a great visual highlighting that the ketogenic diet, caloric restriction, and fasting have many pathways and targets in common as shown below:

Paoli et al., Nutrients 2019, 11(4), 719

How Does Fasting Affect The Microbiome?

In animal studies it has been shown that:

  • Water-only fasting could have a profound and long-lasting effect on gut microbiome.
  • However, juice fasting has a relatively limited effect on gut microbiome.
  • Water-only fasting could be a potential tool to reduce Fusobacterium.

It has also been found that:

Islamic fasting leads to an increased abundance of Akkermansia muciniphila

Cue leaky gut! Akkermansia is a bacteria that supports the health of the gut lining, and may be of benefit in cardio-metabolic health having been discussed in the context of diabetes and obesity . See my blog post on Akkermansia here.

Intermittent Fasting And Leaky Gut

The gut microbiome interacts with the intestinal wall and strongly influences its permeability and barrier function

Animal studies have demonstrated mixed results when it comes to the benefit of fasting on the integrity of the gut wall. In some studies, small intestine permeability has been shown to be normal (i.e no benefit from fasting), however in other studies the large intestine has been found to be hyper-permeable (aka leaky gut).

However a research paper discussing fasting in humans with rheumatoid arthritis states:

fasting may ameliorate the disease activity and reduce both the intestinal and the non-intestinal permeability in rheumatoid arthritis.

Interestingly in this study, when the participants went back on to lactovegetarian diet the intestinal permeability increased again. The study used the PEG-400 urine test which is the same test we use at Healthpath.

Interested in leaky gut testing?

Click Here.

A quote from a research discussing anorexia nervosa (AN) (in animals) states:

The microbiome in patients with AN appears to shift toward an increase of mucin-degrading Firmicutes and Verrucomicrobia and away from the carbohydrate-degrading species Bacteroidetes. This shift could increase digestion of the protective intestinal wall mucus and further weaken the intestinal wall barrier in the colon, allowing greater translocation of bacterial products and components, which might trigger immune and inflammatory responses.

So it could be that ‘well structured’ fasting, perhaps eve just 12 hours over night, is the safest approach. Extensive fasting, over extended periods of time, may induce leaky gut in the large intestine due to a negative impact on the microbiome. As many of you will be familiar with, dietary fibre and phytochecmicals from plants (vegetables, fruit etc) are thought to be essential for optimal microbiome diversity and gut health.

Summary – Is Fasting Good For Gut Health?

In summary fasting appears to be beneficial in reducing symptoms associated with certain autoimmune conditions, improving the microbiome with increases in kay bacteria such as Akkermansia, and improved cardio-metabolic health. However performing ‘safe’, ‘sensible’ and appropriate fasting regimes I think is important and it would appear we do not need extreme interventions to reap the rewards.

I would highly recommend listening to the episode of my podcast (click here) where I speak to Dr Joseph Antoun who works with one of the leading global researchers in the area of longevity – Professor Valter Longo.

So aim for a 12 hour eating window each day, for example having breakfast at 07:00 and finish eating dinner no later than 19:00.


Paoli (2019) The Influence of Meal Frequency and Timing on Health in Humans: The Role of Fasting, Nutrients, 11, 719

Fasting challenges human gut microbiome resilience and reduces Fusobacterium: click here.

The Impact of Starvation on the Microbiome and Gut-Brain Interaction in Anorexia Nervosa: click here.

Influence of fasting on intestinal permeability and disease activity in patients with rheumatoid arthritis: click here.

Share this post