Intermittent Fasting and the Gut Microbiome

What is intermittent fasting?

Intermittent fasting refers to abstinence from food and drinks for a specific period of hours or days. It encompasses various regimens, including alternate-day fasting, several days of fasting, or daily fasting that restricts eating to a certain number of hours per day.1

The most common fasting periods are fifteen to eighteen hours, which allows for six to nine hours of eating time where all needed calories would be consumed. When you are fasting for more than one day, that does not mean that you break the fast with two days’ worth of calories. Alternate-day fasting is not recommended as a long-term regimen. Most individuals will practice one day of fasting a month or even every few months, with no food consumption for one full day followed by a well-rounded day of normal meals and snacks. Intermittent fasting is not a calorie-restrictive diet; instead, it allows you to include all needed calories and macronutrients within a shorter period of time.

But first, how does diet affect the gut microbiome?

Before reviewing the research that supports the potential benefits of fasting for the gut microbiome, it is important to recall how the diet drastically affects the composition of the gut microbiome. By first understanding how the gut microbiome changes from day to day—and even hour to hour—based on the foods we include, we will be able to better understand how fasting affects the gut microbiome.

Researchers have shown that a radical change in diet can quickly shift the gut’s microbial makeup and alter what gut bacteria are doing.2 It has been found that short-term, extreme changes in diet can alter the composition and population of microbes in the gut.3 Researchers confirmed this idea by assessing the population of study participants’ gut microbiomes via stool samples both before any interventions and again after changing their diets. The participants were split into two groups. One group followed a diet that only included animal-based foods (meat, cheese, and animal fat) and the other group followed a diet that included only plant-based foods (vegetables, fruit, beans, legumes, and plant fat). They then compared the bacteria composition of the participants’ stool samples before and during the diet change. They found that the composition of bacteria for each group looked similar to the participants following the same diet and extremely different from both the opposite group of participants and the initial stool samples.3

This study demonstrates not only that the inclusion of food and even specific food groups causes noticeable changes in the microbiome, but it also gives us reason to believe that fasting and abstaining from food can create similar effects.

What is known about the benefits of intermittent fasting on the gut microbiome?

After understanding that diet rapidly affects the microbiome, you can see how periods of fasting may have a similar effect. Because fasting encompasses a wide variety of time ranges, outlining the benefits and changes due to fasting can be challenging unless we clearly define the duration of fasting for each of the research articles we cite.

Let’s start with a fasting schedule that we can all understand: the sleep and wake cycle. During the day, most people eat several meals, often starting with breakfast and ending with an evening snack. Ideally, they then go to bed for eight hours, a period of unintentional fasting. During this time, the gut microbiome gets a much-deserved rest from its important role of breaking down food and producing a variety of important building blocks to keep our system functioning properly.

Research supports the connection between our circadian rhythms and our gut microbiomes. Not only does the sleep we get on a daily basis affect our microbes, but our microbes also affect our sleep cycle.4,5 This means that disrupted sleep affects the gut microbes.

The short period of fasting known as sleep is extremely important for maintaining the population and diversity of the gut microbiome. This foundational understanding can help build the case that increased duration of fasting may be more beneficial than the traditional fasting that happens while we sleep.

Is there any benefit to fasting longer than the natural 8–10 hours of fasting we get while sleeping? 

The simple answer is yes. Research has found that fasting periods ranging from several hours to a day support the health of the gut microbiome. One mouse study found that alternate-day fasting (twenty-four hours of eating regular meals that meet your calorie needs followed by twenty-four hours of fasting) promoted bacterial clearance.6 The process of bacterial clearance allows the gut to regain the ideal balance of bacteria. It was also found that during fasting, bad bacteria tend to starve more quickly than healthy bacteria, leaving more opportunity for good bacteria to colonize.

There has also been evidence to support that a sixteen-hour fasting window with an eight-hour feeding window has beneficial effects. Researchers divided mice into two groups and fed them the same chow; however, one group was restricted to an eight-hour feeding window while the other could eat as desired.7 The study found that although the mice were eating the same amount and type of foods, the group of mice that ate during all times of day gained weight. To connect the weight change to the microbiome, stool samples were collected every four hours to assess changes. The researchers found significant differences in the microbial composition of the two groups’ stool. This leads us to believe that our microbiome is connected to changes in weight and that the microbiome is significantly altered when there is no fasting window.

While both of the studies noted above are mouse studies, they offer valuable insight into how the human gut changes during feeding and fasting periods. Mouse studies give researchers the ability to measure changes faster and control environmental factors far better than with human studies.

Fasting research continues to support its beneficial effects on body composition, sleep cycles, blood glucose, longevity, and even chronic illness.8 As noted above, we are confident that fasting is also beneficial to our gut microbiome. Not only does fasting give the microbes a period of rest time, but it also improves and maintains the population of good bacteria and supports their ability to complete the variety of processes the human body needs them for.

Before Starting Intermittent Fasting

Now that we know fasting is beneficial for the gut microbiome, you may be wondering how to put it into practice. Here are a few tips.

  1. Talk to a physician or health professional before introducing extended fasting into your routine, especially If you are diabetic, an athlete, or need to take a medication with food.
  2. Review your current diet. Are you including a variety of foods that support health and a diverse gut microbiome? If you do not include several servings of fruits and vegetables, you may want to start with that diet shift first. A plant-based diet that is rich in fibrous foods will lay the foundation of a healthy gut microbiome.
  3. Start with a short duration. For example, start by fasting for twelve to thirteen hours (8 p.m. to 8 a.m., or 8 p.m. to 9 a.m.). Get into the habit of allowing a few hours before bed for food to digest and then waiting for hunger cues to start the next morning.
  4. Add longer fasting windows a few days a week. Consider adding one or two days of fourteen- to sixteen-hour fasting two or three times per week. Assess your intake on these days to ensure that you are hitting your calorie and macronutrient needs. If you find you are not meeting your calorie and nutrient requirements, increase your eating window.
  5. Listen to your body. You may hear recommendations to increase your fasting window to sixteen-plus hours, but although this works well for some individuals, it may not be best for everyone. It is important to listen to your hunger cues and continue to track your caloric intake when fasting.

Although additional research is needed to clearly define the benefits of fasting, as of right now, we are confident that fasting and intermittent fasting is beneficial to the gut because it allows time for rest and repopulation. It is also important to again note the positive impact of a gut-healthy diet and lifestyle. Before following a fasting routine, assess your current lifestyle, level of daily stress, diet, exercise, sleep, and mindfulness practices.

About the Author

Photo: Rachel Stuck, RDN

Registered Dietitian Nutritionist Rachel Stuck has a background in culinary arts and nutrition counseling. Rachel takes a positive approach to nutrition: she avoids recommending restrictive diets and instead focuses on helping people choose foods that promote health and well-being. She is passionate about empowering and assisting Ixcela members as they develop their unique, gut-healthy lifestyles.

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Interested in learning more about Ixcela? Check out Ixcela’s microbiome test, personalized nutrition and fitness plans, and other tools to help you optimize your health.


  1. “Intermittent Fasting.” Intermittent Fasting - an Overview | ScienceDirect Topics,
  2. PennisiDec, Elizabeth, et al. “Extreme Diets Can Quickly Alter Gut Bacteria.” Science, 10 Dec. 2017,
  3. David, Lawrence A., et al. “Diet Rapidly and Reproducibly Alters the Human Gut Microbiome.” Nature News, Nature Publishing Group, 11 Dec. 2013,
  4. Rosselot, Andrew E, et al. “Rhythm and Bugs: Circadian Clocks, Gut Microbiota, and Enteric Infections.” Current Opinion in Gastroenterology, U.S. National Library of Medicine, Jan. 2016,
  5. Wood, Matt. “The Microbiome and the Midnight Snack: How Gut Microbes Influence the Body's Clock.” Science Life, 29 Sept. 2017,
  6. Campos‐Rodriguez, R., et al. “Intermittent Fasting Promotes Bacterial Clearance and Intestinal IgA Production in Salmonella Typhimurium‐Infected Mice.” Wiley Online Library, John Wiley & Sons, Ltd, 20 Apr. 2014,
  7. Zarrinpar, Amir, et al. “Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome.” Cell Metabolism, U.S. National Library of Medicine, 2 Dec. 2014,
  8. Mattson, Mark P., et al. “Impact of Intermittent Fasting on Health and Disease Processes.” Ageing Research Reviews, Elsevier, 31 Oct. 2016,