Gut health: What is it and how does it affect your body?

woman cooking with her daughter to support gut health
(Image credit: Getty Images)

The gut contains trillions of microorganisms, including beneficial and harmful varieties. Collectively, these make up what is known as our "gut microbiome". Maintaining a healthy balance of microorganisms within the microbiome is crucial. Factors like diet, exercise, medications and even genetics can affect its composition and diversity, impacting various aspects of your health for better or worse. 

Gut health affects lots of different aspects of our wellbeing, from our mood to our immunity. But with all the hype surrounding gut health, separating fact from fiction can be confusing. That's why we've asked the experts what's really true when it comes to gut health, from the good to the bad.

What is gut health?

From the oesophagus to the bowel, gut health covers the health of the entire digestive system — the parts of our body responsible for breaking down our food into individual nutrients we use to run our bodies. 

Sue-Ellen Anderson-Haynes, a registered dietitian nutritionist and national spokesperson for the Academy of Nutrition and Dietetics, told Live Science that the gastrointestinal tract starts with digestion in the mouth.

"Then it continues to the stomach, small intestine and large intestine for further digestion and absorption, before leading to the end product where waste exits via feces," she said.

Sue-Ellen Anderson-Haynes, RDN
Sue-Ellen Anderson-Haynes

Anderson-Haynes is a registered dietitian nutritionist, certified diabetes care and education specialist and a nutrition and diabetes educator at Joslin Diabetes Center, Massachusetts. She obtained her Bachelors of Science in Food Science & Human Nutrition, Specialization Dietetics, with a minor in Health Science Education from the University of Florida, and her Masters of Science in Nutrition & Wellness from Andrews University, Summa Cum-Laude.

Microorganisms in the gut play a vital role in breaking down food, making it easy to digest. There is evidence that the gut microbiome may influence longevity, as suggested by the unique gut bacteria of people who live to be 100. Some gut microorganisms may also give athletes an edge.

Everyone's gut microbiome is unique, so foods that help one person to thrive may cause irritation in others.

illustration of colorful microbes in the intestinal tract


Why is gut health important?

According to Anderson-Haynes, the gut is responsible not only for digestion, but also for assisting functions such as hormone regulation and immune system activity. 

"Over 70% of immune cells are found in the gastrointestinal tract," she said.

Gut health is vital for immune function, suggests a 2019 review, published in Food Research International. The gut wall acts as a barrier to viruses, fungi, and harmful bacteria. Unfortunately, this barrier sometimes becomes permeable, known colloquially as "leaky gut", allowing these nasties to enter the bloodstream and make you sick. There's no one factor that contributes to leaky gut, rather a combination of factors, including diet, inflammation and antibiotic use, that come together to impact the integrity of your gut barrier.

Conditions such as irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), and celiac disease increase the chances of leaky gut, making people with these conditions more prone to infections. 

A 2014 review, published in the Journal of Medicinal Food, also suggests that gut health has a knock-on impact on mental health. This communication between the gut and brain is known as the gut-brain axis. Gut bacteria has the power to stimulate the nervous system, sending messages to your brain through the vagus nerve. Plus, microorganisms in the gut release neurotransmitters like serotonin, which can affect your mood.  

Signs of good gut health

So how do you know if you have a healthy gut? Cristy Dean, dietician and founder of Fettle and Bloom, based in Bath, England, told Live Science that there are several signs.

"Everybody is different, however, it is considered normal to pass a stool between three times a day and three times per week," she said. "Very slow or very fast transit time can indicate something isn't right with digestion. Stools should be medium to dark brown, smooth, sausage-like, and be passed without pain, excessive bloating or gas." 

Signs of bad gut health

It is estimated that 60-70 million Americans suffer from digestive problems, according to the National Institute of Diabetes and Digestive and Kidney Diseases The signs of an issue can include: 

  • Bloating
  • Loose stools
  • Constipation
  • Heartburn
  • Nausea and vomiting 

woman holding her stomach in pain

(Image credit: Getty Images)

Other, less obvious signs include: 

  • Fatigue and poor sleep: a 2020 review published in Sleep Medicine Reviews found that an imbalanced gut microbiome could lead to disturbed sleep and low energy. 
  • Skin irritation: Skin irritation can be a symptom of poor gut health, according to a 2019 review, published in the Microorganisms journal. 
  • Bad breath/halitosis: Since the mouth is the gateway to the gastrointestinal tract, bad breath can be a sign that something is off balance in the digestive system, suggested a 2020 review, published in the International Journal of Molecular Sciences

Dean added that changes in bowel habits can be a sign that something is wrong. These could include increased bloating, gas, diarrhea, heartburn, or waking in the night to pass a stool.

"Sleep disturbances, increased fatigue, skin irritation, food intolerances, and unintentional weight changes can all be linked to an unhealthy gut," she said.

If you experience symptoms, it is best to visit your doctor to discuss an appropriate intervention plan.

What factors affect gut health?

Optimal gut health is characterized by diversity and abundance of gut microbiota, with a balance in favor of beneficial strains. There are multiple factors that play a role in the gut microbiome composition. 

Mode of delivery

Did you know that gut health begins at birth? 

"Often overlooked factors include whether a child is born via vaginal delivery or cesarean section and whether they were breast or bottle fed," said Anderson-Haynes. "Research shows that infants who are born via vaginal delivery and who are breastfed have more gut diversity." 

The exact mechanism behind this is not known, but researchers believe that the birth canal exposes a newborn to the mother's vaginal bacteria first, before other environmental sources. They then drink maternal milk exclusively for a substantial proportion of their development, which further enriches their microbial community.


Diet has a significant impact on gut health.

"Overconsumption of ultra-processed foods can lead to a lack of microbiome diversity," said Anderson-Haynes. Ultra-processed foods are defined as being high in salt, sugar and saturated fat. 

She also said it's vital to consume "a variety of fiber-rich foods", including fruits, vegetables, wholegrains, legumes, nuts and seeds. Prebiotics (foods that fuel the good bacteria in the gut, including garlic, asparagus, and apples) and probiotics (live active cultures found in yogurt, tempeh, and sauerkraut) can also support gut health, she said.

A 2019 review, published in Frontiers in Nutrition, also found that a plant-based diet was linked to higher levels of beneficial bacteria like Lactobacillus and Bifidobacteria. This is likely because the diet is generally high in fiber, promoting the growth of these friendly bacteria. 


While they have the power to fight infections, antibiotics can compromise gut health. This is because they do not distinguish between beneficial and harmful bacteria, which depletes overall gut flora and reduces diversity.  

Lifestyle and environmental factors 

Genetic, lifestyle and environmental factors can negatively affect gut diversity, according to Anderson-Haynes. "These include exposure to toxins, inadequate sleep, uncontrolled stress, insufficient exercise, overuse of antibiotics, cigarette smoking, and alcohol consumption," she said. "This weakens the intestinal wall lining leading to a compromised immune system." 

This article is for informational purposes only and is not meant to offer medical advice.

Lou Mudge
Health Writer

Lou Mudge is a health writer based in Bath, United Kingdom for Future PLC. She holds an undergraduate degree in creative writing from Bath Spa University, and her work has appeared in Live Science, Tom's Guide, Fit & Well, Coach, T3, and Tech Radar, among others. She regularly writes about health and fitness-related topics such as air quality, gut health, diet and nutrition and the impacts these things have on our lives. 

She has worked for the University of Bath on a chemistry research project and produced a short book in collaboration with the department of education at Bath Spa University. 

With contributions from