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How Intermittent Fasting Affects Your Microbiome

January 28, 2020

The trillions of microbes inside your body come in all shapes and sizes and inhabit various parts of your body, particularly your digestive tract. We know that what we eat feeds this colony of bacteria, viruses, fungi, and amoebae. Based on what you give your gut bugs, they can change how you digest and metabolize food and can even tell your brain when you’re hungry and full.

But it turns out that when you eat might be just as important: You might be giving your gut microbes too much food at the wrong times of day, and intermittent fasting could be just what you need to take your gut health to the next level.

What is intermittent fasting?

Intermittent fasting (I.F.), also called time-restricted feeding, is an eating pattern that involves eating food only during a specific window of hours each day. You get a “feeding window” and a “fasting window.”

During the fasting window, you can’t consume anything that has calories. You can drink water, black coffee, and zero-calorie herbal teas. Some, but not all, I.F. experts say you can also drink zero-calorie sports beverages and other beverages sweetened with artificial sweeteners (but we know artificial sweeteners are bad for your gut).

Most people use I.F. as a weight-loss strategy, but this popular eating pattern actually holds much more promise than that: I.F. can lead to improved fat-burning, improved insulin sensitivity, lowered blood sugar levels, and improved heart health.

Those things all influence our gut in one way or another, but the real kicker is that I.F. itself may improve gut health. Here’s how.

Fasting gives your overworked gut a break

When you eat frequently throughout the day — always grabbing a handful of whatever snack is in the office — you never give your body a chance to stop digesting food. Previously, scientists thought that this led to greater weight loss, because it takes energy (calories) to digest food. That’s called the thermic effect of food. That makes sense in principle, but we now know that the amount of energy it takes to digest food is insignificant compared to the calories you burn doing other everyday activities.

When you keep stuffing your digestive tract full of food every few hours, it can’t efficiently digest the new food because there’s still food from a previous meal waiting to be digested. That remains true even overnight. If you allow your body to fully digest all of the food you eat, your gut can start fresh and allocate all its energy and resources, such as digestive enzymes, to the new food.

Compare this to how you feel when you get six hours of sleep versus your usual eight. You feel okay, but you know you could feel better. You’re operating at 75 percent. That’s what happens to your gut when you don’t give it time to properly digest the food you eat.

Fasting helps your gut adhere to its circadian rhythm

Your 24-hour cyclic clock is important for more than just adequate and quality sleep. You might be surprised to learn that your gut microbes also perform better when they’re in line with their circadian rhythm — they are living organisms, after all.

Your circadian clock helps your body know when to enter the appropriate metabolic state based on nutrient availability, such as burning fats instead of sugars during sleep. If you eat in ways that go against your body’s natural clock, you can force your body into a less efficient metabolic state rather than a more efficient one.

For example, as night approaches, your body prepares itself for rest and your gut microbes stop working as hard. If you task your gut with digesting a large meal late at night, your body won’t digest that food as efficiently or completely as it would during the day.

Remember: Humans evolved for millions of years without 24-hour access to food. So while it may feel unnatural at first to oust your late-night snack, you’re actually doing the more natural thing. Research suggests that eating in line with your biological clock can improve insulin sensitivity, lower insulin levels, and decrease appetite.

Fasting can help you lose weight

The theory behind I.F. makes sense. When you eat, your body breaks down food using enzymes in your gut. Any food you eat eventually ends up as molecules in your bloodstream, either as nutrients or harmful substances like HDL cholesterol. Your body quickly breaks down carbohydrates, especially refined carbohydrates, into sugar, which your cells use for fuel.

If your body doesn’t use all of the fuel that comes from a meal, it stores it in your cells as fat. However, this process can only happen with insulin, a hormone that brings sugar into fat cells and essentially locks it in them.

If you snack all day long, that process is continual and you may end up with excess body fat and, eventually, insulin resistance. But if you allocate your meals to only a few hours each day, your insulin levels go down and your body taps into your fat cells to release the stored sugar as energy. Basically, instead of constantly feeding your body new fuel, it’s forced to use what’s already there, which can lead to fat loss.

3 simple ways to try intermittent fasting

If you think I.F. sounds hard, you’re not alone. Most of us are used to eating small meals or snacks every few hours. But just like your body adapts to exercise, your body can also adapt to an eating pattern. To help you get started, here are a few of the most popular I.F. protocols you can try:

The 16:8 protocol: One of the most popular I.F. methods, you eat all of your food in an 8-hour window and fast for the remaining 16 hours of the day. This is a great protocol for beginners because the fast isn’t terribly long, and for 7-8 of those 16 fasting hours, you should be asleep.

The Warrior Diet: This protocol involves fasting for 20 hours and seriously feasting during a 4-hour window at night. It’s best for people with some experience fasting and people who don’t have a history of binge eating disorder.

Alternate-day fasting: Alternate-day fasting is exactly what it sounds like — you eat normally on one day, fast on the next, and so on. This method is a little different because you’re allowed 500-600 calories on your fasting days.

A word from Dr. G

The interplay of calorie intake, meal timing, and meal frequency may very well influence our guts in profound ways. We need more research in humans to be sure and to truly understand these mechanisms, but for now, we have reason to believe I.F. can be the cherry on top of a gut-friendly diet (let’s not forget that what you eat matters: Don’t use I.F. as an opportunity to eat gut-damaging foods). Always consult your doctor before starting an eating program or diet if you have any existing health conditions.

Learn more: 7 lifestyle mistakes to avoid for better gut health


Become the expert of your own health and nutrition. Lose weight, gain energy and never worry about dieting again. Jared Koch, the founder of Clean Plates, put 15 years of research and insights from helping over 1 million people live happier, healthier lives into developing The Clean Plates Approach program. Click here to learn more and get 75% off for being part of our community!

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