We know that what we eat influences the microbial composition in our gut. However, it seems like it is not just WHAT we eat but also WHEN we eat. Believe it or not, but our bacteria also have some kind of wake-sleep cycle – a so-called circadian rhythm.
A healthy gut community fluctuates throughout the day and the expression of genes can differ drastically. After scientist discovered that our microbiome follows a circadian rhythm as we do, they ask the question, whether time-restricted feeding, so Intermittent fasting can restore or improve the natural cycle. After all, a healthy microbiome and intermittent fasting have a lot of things in common when it comes the health benefits:
improves insulin sensitivity
protects the brain
reduced risk for heart diseases
With these similarities, it makes sense to look how one can potentially affect the other. A study from 2014 looked into the effects of intermittent fasting on the microbiome. They divided mice into two groups. One group had a 24-hour access to food (FA) and the other group was restricted to an eating window of 12 hours (FT). The researchers then fed the mice an unhealthy, fattening diet and looked into the body health effects of it. The group of mice with the restricted feeding window had a slower weight gain, better glucose levels, and no fatty liver disease compared to the mice group on an unhealthy diet with 24-hours access to food.
Time-restricted feeding could also partially restores cyclical fluctuations of the gut bacteria populations. 
Another interesting study from 2017 found that alternate day fasting in mice leads to an elevated production of the short-chain fatty acid Acetate. Short-chain fatty acid are produced in our guts and have been shown to be very beneficial for our health, as they initiate fat loss and reduce inflammation levels in the body. 
Acetate is also the main component in Apple Cider Vinegar and is the reasons why it has so many health benefits.
Other mouse studies have found that intermittent fasting protects the gut against the negative impacts of stress, which include inflammation and that intermittent fasting even supports the clearance of pathogenic bacteria in infected mice via a similar process. [3, 4]
It is not completely understood why intermittent fasting improves the microbiome but one of the leading hypothesis is that many “bad” microbes rely on a constant flow of food to survive and thrive, and the “good” bacteria are more adjusted to periods without easily accessible nutrients. It makes sense in an evolutionary context, as the bacteria have adjusted to our ancestors who didn’t have access to food three times a day and sometimes even went without food for days.
Take Home Message: Intermittent Fasting has the potential to benefit our Microbiome but more research is needed!
Zarrinpar et al., Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome, Cell metabolism, 2014
Li et al., Intermittent Fasting Promotes White Adipose Browning and Decreases Obesity by Shaping the Gut Microbiota, Cell metabolism, 2017
M. Godínez‐Victoria et al., Intermittent Fasting Promotes Bacterial Clearance and Intestinal IgA Production in Salmonella typhimurium‐Infected Mice, Scandinavian journal of immunology, 2014
Lara-Padilla et al., Intermittent fasting modulates IgA levels in the small intestine under intense stress: A mouse model, Journal of Neuroimmunology, 2015