A Comprehensive Review of the Habits that Affect Gut Health

By Molly Knudsen, MS, RDN, December 10, 2021

gut health woman coffee

Your body is your home. It’s also home to trillions of other living organisms. Trillions of microbes that is. And the composition of this microscopic community can have major implications on your wellness and performance. Fortunately, there are multiple steps you can take to support gut health and reap related benefits. Numerous habits, from meal timing, to sleep habits, to antioxidant consumption, can influence the makeup of your microbiome and its relationship with the rest of your body.

GUT HEALTH2A healthy gut is key for overall health and wellness

The gut microbiome is a complex system of living microorganisms (AKA microbes) found in the colon, a part of the large intestine. Over three trillion bacteria, consisting of 400-500 different species, call the gut microbiome home.[1,2] But not all of these microbes are beneficial to health—a healthy gut is one that has a rich diversity of beneficial bacteria.[3] And the benefits of a healthy gut microbiome impact every system in the body. Good gut health...

  • Helps maintain a healthy immune system [4]
  • Enhances digestion and absorption of food [4]
  • Improves vitamin production [2]
  • Balances hormones [2]
  • Mitigates inflammation [5]

InsideTracker recently announced the new Gut Health Goal, a set of personalized recommendations aimed at improving gut health based on hsCRP, cortisol, HDL cholesterol, triglycerides, glucose, and HbA1c (all of which are related to proper gut health). Sleep and exercise data can also contribute to the goal if you have an activity tracker

As with all things InsideTracker, the Gut Health Goal focuses on modifiable dietary, supplement, lifestyle, and exercise recommendations that influence gut health. Ultimately, even if your gut health is suboptimal in one way or another, there are steps you can take to change things in your favor. 

Gut health deep dive Image 1-04

How certain dietary choices and habits impact the gut microbiome

Establishing microbial diversity begins at an early age. Birth method (vaginal or cesarean) and infant feeding (breastmilk vs. formula) all influence the foundation of your microbial makeup.[6] Diet, genetics, exercise, and antibiotic treatments play a role in altering the gut microbiome for the better or worse throughout the course of your life.[6] So the trick is to make choices that tip the balance of good and bad microbes in your favor. 

Everything from meal timing, to sleep, to probiotics, to polyphenols, and sugar can affect gut health and the composition of gut microbiota. 


Intermittent fasting promotes healthy bacteria growth

Research on both intermittent fasting (IF) and the gut microbiome is still emerging—most of the research on this topic has been done in animals, and there’s a very limited number of well-controlled human trials on the topic.[7] But preliminary results show that IF does impact the daily fluctuations in the gut microbiome, including the abundance and metabolic activity of bacteria.[8.9] 

One of the few human studies published in 2019 evaluated the effects of Ramadan fasting, a version of time-restricted feeding, on intestinal microbiota composition.[10] This was a small study of only 9 people who fasted for 17 hours a day for 29 days. At the end of the month-long fast, stool samples showed a significant increase in the abundance of A. muciniphila and B. fragilis (healthy bacteria) compared to the beginning of the study. Blood samples also revealed a significant decrease in fasting glucose and total cholesterol levels in all study participants. 

Of course, there are many limitations to this study, including its small sample size and lack of control group for comparison. In addition, Ramadan fasting is unique in that fasting occurs during the day and eating occurs at night, which is the opposite of most non-religious IF practices (read more about IF here). Gut microbiota are connected to circadian rhythms, and it’s speculated that nighttime eating negatively impacts gut health.[11] However, this study was one of the first to show how IF may have positive impacts on the gut microbiome, despite these caveats. 


Not into intermittent fasting? It’s still beneficial to space out meals

Intermittent fasting isn’t for everyone, but that doesn’t mean that we should be constantly eating. Spacing out meals and snacks, even by just a few hours, can benefit digestion and gut health. The migrating motor complex (MMC) is a cyclic phenomenon that happens when you aren’t digesting food.[12] It’s often described as a housekeeping process that canvasses the digestive tract and cleans the small intestine after the previous meal or snack.[12] The MMC passes about two to three hours after finishing a meal, and the cycle can take around two hours to complete.[12,13] 

Spacing meals and snacks to allows the MMC to pass, helping to prep the body for better digestion at the next meal. Constant grazing or snacking during the day acts as an MMC suppressant, and disruptions in the MMC cycle have been associated with bloating, heartburn, nausea, and excess bacteria in the small intestine (known as small intestine bacterial overgrowth or SIBO).[13] 

However, if you’re hungry between meals, it’s extremely important to honor those cues. Read more about hunger and mindfulness here


Sleep and the gut microbiome are connected through the gut-brain axis

The gut and the brain are in constant communication through the gut-brain axis. This is a bi-directional relationship in which gut bacteria can influence mental states and behavior, and psychological states, including sleep, can impact gut health.[14] 

The gut microbiome experiences diurnal, or daily, variations that are related to food intake, diet composition, and circadian rhythms.[11] Ideally, the body’s internal clock works in tandem with microbial rhythms, but sleep deprivation, shift experience (night-shift workers), and even jet lag can impact a person’s circadian rhythm and the structure and diversity of gut microbes.[11] 

Gut health deep dive Image 2

In one study on sleep and gut health, researchers transplanted stool samples from two jet-lagged individuals (pre and post flight) into germ-free mice to measure the types and amounts of bacteria and any resulting metabolic changes.[15] Findings showed that a jet-lagged microbiome resulted in more weight gain, fat accumulation, and higher blood glucose levels in the mice. Though it represents very preliminary research, this study was one of the first to show this type of association. 

Just as poor sleep and misaligned circadian rhythms can negatively impact gut health, a healthy gut may be associated with better sleep. In a 2019 study published in PLos One, total microbial diversity was positively associated with sleep efficiency and total sleep time (as measured by a smart watch), and negatively associated with mid-sleep wakefulness.[14] The study also found associations between gut diversity and positive measures of immune system function. 


Probiotics positively impact gut health 

It’s no surprise that probiotics, live beneficial microbes, are good for gut health. Certain probiotic strains can help reduce blood glucose levels, help lower inflammation markers like hsCRP, support weight loss and maintenance, and even modulate mood and cognition.[16-19]

The exact mechanisms by which probiotics exert their benefit is still being studied, and different probiotic strains have different impacts on health. But here’s a short summary of what’s currently known about their mechanisms of action in the body.

Probiotics can:

  • Strengthen the gut lining (also called the epithelial barrier), which keeps the digestive tract contents from leaching into other body systems. A strong, healthy epithelial barrier contributes to good immune health and combats intestinal permeability that can lead to inflammation.[20]
  • Attach to the intestinal mucosa, allowing for the bacteria to interact with the gut and the host (you). This process helps exclude potentially harmful, or pathogenic, microbes from attaching to and colonizing the gut.[20]
  • Modulate the immune system by interacting with dendritic cells, monocytes/macrophages and lymphocytes.[20]

For more information on how to choose the right probiotic foods and supplements, check out this blog


Feed the good microbes with prebiotic and fibrous foods

Dietary and supplemental probiotics aren't imperative for gut health—you can also work to feed and nourish the good bacteria already in your gut with prebiotics and fiber-rich foods. 

Prebiotics are often fiber-rich foods that selectively feed the good bacteria in the gut and impart beneficial impacts.[21] Fibers are non-digestible carbohydrates, often classified as soluble or insoluble, that have a beneficial effect on human health. Foods high in prebiotics include chicory root, Jerusalem artichoke, onions, and asparagus. All fruits, vegetables, and whole grains are rich sources of fiber. 

Some of the beneficial impacts of prebiotics and fibers on the body include:

  • Producing short-chain fatty acids to provide energy to cells in the intestine and help strengthen the gut lining [22]
  • Helping to keep things moving through the intestinal tract, increasing stool frequency and bulk and may help alleviate constipation (specific to insoluble fiber)[23]
  • Increasing satiety [24,25] 
  • Stabilizing glucose and insulin responses[26]
  • Helping to lower cholesterol (specific to soluble cholesterol--read more about that here)[27]


Polyphenols from coffee, wine, and cocoa may impact growth of good gut bacteria

Polyphenols are a family of plant compounds that are active in the body and contribute to health. They often have antioxidant capabilities and contribute to reducing inflammation and oxidative stress.[28] Polyphenols are known to be poorly absorbed by humans, so it is largely up to microbes in the large intestine to break them down for absorption. Emerging data, mainly animal or cell studies, have shown that polyphenols may increase the amount of beneficial bacteria in the gut microbiome and even have protective effects against harmful types of bacteria.[29] However, there is human data to support the use of three commonly consumed (and loved) polyphenol-rich foods for gut health.

Coffee: Drinking coffee for gut health? You heard that right. Coffee is a potent source of polyphenols, and studies have tied it to digestive health, including antioxidant, anti-inflammatory, and antiproliferative effects on the gut lining.[30] A 2020 study of 145 people published in Nutrients found an association between regular long-term coffee consumption and higher levels of good groups of bacteria.[30] Another 2020 study found that coffee consumption was the largest contributor to overall polyphenol intake in American’s diets.[31] 

Wine: A systematic review of seven human intervention studies investigated the impact of wine and grape polyphenols on the gut microbiome. All of the studies in this review reported that polyphenols from these beverages modulated gut bacteria, contributing to a healthy microbial ecosystem.[29]

Cocoa: Rounding out this impressive list of polyphenol foods for gut health is cocoa. A 2020 intervention study published in Nutrients was the first of its kind to look at the impact of cocoa flavanols (compounds in the polyphenol family) on the growth of good bacteria in the gut.[32] Drinking a high-flavanol cocoa beverage (494 mg of flavanols) for four weeks significantly increased the growth of Lactobacilli and Bifidobacteral (good) populations and decreased Clostridia (bad) populations in the gut compared to the placebo drink. There were also significant reductions in plasma triglycerides and hsCRP levels. 

For reference, one tablespoon of cocoa powder provides around 370 mg of flavanols and 1 ounce of semi-sweet chocolate provides around 50.[33] The darker the chocolate, the higher the flavanol content will be. 



High sugar intake is not good for gut health 

Just because cocoa flavanols may benefit gut health doesn’t mean that all chocolate (especially white and milk) or other sweets do. A diet high in added sugars creates an imbalance of beneficial and harmful species of microbes in the gut, which can promote inflammation, harm the gut lining, and impact immunity.[34] 



Keeping the community of microorganisms that reside in the gut microbiome in balance is essential for optimal gut health and for overall health and performance. And the understanding of how certain foods and lifestyle habits directly impact the gut microbiome is evolving everyday through studies and human trials. What’s currently known to impact the gut microbiome and gut health is:

  • Six biomarkers evaluated by InsideTracker currently describe a healthy gut: hsCRP, cortisol, HDL cholesterol, triglycerides, glucose, and HbA1c
  • Intermittent fasting may increase counts of good bacteria in the gut, and spacing out meals primes the body for optimal digestion for the next.
  • Sleep can impact the gut microbiome, and the gut microbiome can impact sleep through the gut-brain axis. 
  • Probiotics play an important role in gut health by helping to maintain the gut lining, supporting the immune system, and preventing harmful bacteria from attaching to the gut. 
  • Prebiotics and fiber help nourish and diversify bacteria in the gut microbiome.
  • Polyphenols from coffee, wine, and cocoa have been shown to increase favorable types of bacteria in the gut.
  • High sugar intake feeds and increases counts of pathogenic bacteria, contributing to inflammation. 

Molly Knudsen1Molly Knudsen, MS, RDN
Molly is a Content Writer and Team Nutritionist at InsideTracker. As a Registered Dietitian, Molly enjoys connecting people to the food they eat and how it influences their biomarkers. When she’s not writing about the latest nutrition science, she’s likely in the middle of a yoga flow or at the beach with a good book.



[2] https://pubmed.ncbi.nlm.nih.gov/32398103/


[4] https://pubmed.ncbi.nlm.nih.gov/21401922/

[5] https://pubmed.ncbi.nlm.nih.gov/22254115/

[6] https://pubmed.ncbi.nlm.nih.gov/25651996/

[7] https://pubmed.ncbi.nlm.nih.gov/32731505/

[8] https://pubmed.ncbi.nlm.nih.gov/33530881/


[10] https://pubmed.ncbi.nlm.nih.gov/31854308/

[11] https://pubmed.ncbi.nlm.nih.gov/30568608/

[12] https://pubmed.ncbi.nlm.nih.gov/26660537/

[13] https://pubmed.ncbi.nlm.nih.gov/22837872/


[15] https://pubmed.ncbi.nlm.nih.gov/25417104/

[16] https://pubmed.ncbi.nlm.nih.gov/26161741/



















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