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Gut Health Diet: How to Restore Your Gut for Optimal Health

Sep 26, 2023
Gut Health Diet: How to Restore Your Gut for Optimal Health

Digestive issues, allergies, chronic fatigue, and frequent illness can all indicate your gut microbiome is not optimal. Your gut is home to trillions of microbes that contribute to your physical and mental health. Lifestyle changes and a gut health diet can improve your overall health.

The gut microbiome refers to the environment in which a community of microorganisms lives in your gut. Most of the microbiota reside in the distal colon, but there are colonies throughout the gastrointestinal tract. These 100 trillion bacteria, viruses, fungi, archaea, and other microbes are incredibly diverse and essential for overall human health.1

The gut microbiota assists in many human bodily functions, including:2,3

  • Harvesting energy from food, especially nondigestible carbohydrates
  • Producing vitamins
  • Metabolize bile
  • Regulating immune function
  • Strengthening the barrier lining the gut
  • Protecting against disease-causing bacteria
  • Interacting with the brain as part of the gut-brain axis

Microbial Health and Disease

Altered gut microbiota (dysbiosis) is associated with human disease, inflammation, obesity, immune dysfunction, and mood and brain function changes.2

Disorders associated with dysbiosis include:3

  • Some cancers
  • Respiratory diseases such as asthma and bronchitis
  • Diabetes mellitus
  • Brain disorders such as Parkinson’s disease, Alzheimer’s disease, and depression
  • Chronic kidney disease
  • Inflammatory bowel diseases such as Crohn’s disease and ulcerative colitis
  • Heart disease

Your gut microbiota co-evolves with you as you change your diet, lifestyle, exercise frequency, body mass index, cultural habits, and environment. Illnesses, antibiotic therapy, and changes in diet can cause major shifts in the gut microbiota.4,5

A Gut Health Diet

A gut-health diet provides nutrients to support a balanced and diverse gut microbiome. However, a well-balanced microbiome varies between people. Each person has a unique microbiome.5  This makes it difficult to understand what makes up a “healthy microbiome.”


A high-fiber, plant-based diet suppresses hunger and provides quality nutrients for your microbiome. Fiber increases stool bulk and motility. It can also lower cholesterol levels, modulate blood sugar, and reduce the risk of heart disease.

When microbiota bacteria ferment dietary fibers, the end product is short-chain fatty acids (SCFAs).

Research suggests that SCFAs may play a key role in preventing and treating metabolic syndrome, bowel diseases, and certain forms of cancer.

The average Western diet contains approximately 15 to 25 grams of fiber per day. Diets high in fruits and vegetables may reach 60 grams of fiber per day.6,7

Foods high in fiber include:

  • Legumes: lentils, beans, and peas
  • Whole grains: oats, brown rice, whole wheat pasta, quinoa
  • Fruits: pears, apples, berries, oranges, bananas
  • Vegetables: carrots, broccoli, spinach, Brussels sprouts, artichoke hearts
  • Nuts and seeds: pumpkin, chia and flaxseeds
  • Popcorn


Polyphenols are antioxidant compounds found in plants. Foods rich in these antioxidants support microbiome health.

Foods rich in polyphenols include:8

  • Fruits
  • Seeds
  • Vegetables
  • Tea
  • Cocoa products
  • Wine
Food rich in probiotics


Probiotics are live microorganisms that, when given in adequate quantities, can provide health benefits. Lactic acid-producing Bifidobacterium and Lactobacillus species are typically found in probiotic supplements and foods containing probiotics.

Populations that consume diets high in fresh fruit grown in good soil and fermented foods have plenty of probiotics in their diet.

Your gut microbiota’s response to probiotics varies depending on your current microbial profile, but the potential benefits of increasing probiotic-rich foods may include reducing diarrheal stools, decreasing inflammation, producing vitamins, reducing cholesterol, and enhancing immune function.9

Probiotics are typically trademarked by a brand rather than a bacterial strain, and formulations vary. This can make it challenging to know which ones effectively support the gut microbiome.10

Foods high in probiotics include:

  • Sauerkraut
  • Kefir
  • Kombucha
  • Yogurt
  • Raw and unpasteurized cheese
  • Tempeh
  • Kimchi
  • Natto
  • Olives
  • Pickles
  • Tamari
  • Buttermilk

Avoid cooking at high heat when preparing these foods, as this can kill the bacteria.


Prebiotics also promote bacterial growth. The most well-known prebiotics are inulin, fructo-oligosaccharides (FOS), lactulose, and galacto-oligosaccharides (GOS).3 They are not digested in the upper gastrointestinal tract, are fermented by the gut microbiota, selectively stimulate beneficial bacterial growth and diversity, and have a positive effect on human health.10

Foods high in prebiotics include:

  • Leeks
  • Garlic
  • Onions
  • Dandelion greens
  • Asparagus
  • Bananas
  • Jerusalem artichokes
  • Barley
  • Oats
  • Chickpeas
  • Lentils
  • Soybeans
  • Chia seeds
  • Flaxseeds
  • Wheat bran

To support your gut microbiome, consume a gut health diet high in fruits and vegetables. Consume foods high in probiotics and prebiotics, but ensure they have active cultures.

Some foods are soaked in vinegar but not fermented. Watch foods with added sugars and flavoring used to hide the taste of fermentation.

Foods high in prebiotics are part of a gut health diet

Unhealthy Gut Health Diet

Poor dietary choices cause shifts in the microbiome. Foods to avoid when building a healthy microbiome include:

  • Processed foods
  • Sugar and high-fructose corn syrup
  • Trans and hydrogenated fats
  • Antibiotic-infused foods
  • Alcohol
  • Caffeine
  • Artificial additives

To further support your gut, drink plenty of water to stay hydrated and keep your stool soft. Reduce stress and incorporate physical activity and exercise into your daily routine. Chronic stress reduces blood flow to your gut, which impairs digestive function and harms your microbiome. Exercise increases blood flow and gut motility.

The gut-brain axis is bidirectional. Diet, food intake, environmental factors, drugs, exercise, mood stress, social interaction, and cognitive behavior contribute to gut and brain health.3

Bacteria on a spoon

Vitamin B12 and the Microbiome

Certain bacteria and archaea in the gut synthesize vitamin B12. If there are imbalances in the gut microbiota, the gut microbiota will compete with your body for available vitamin B12. A healthy microbiome improves vitamin B12 absorption.

Disturbances in the microbiome can contribute to vitamin B12 deficiency. If you are experiencing symptoms of vitamin B12 deficiency, talk to an Invigor Medical specialist about vitamin B12 supplements to support your gut health until your gut microbiome is healthy again.

Get started today with a subscription for Vitamin B12.

Gut Health Diet: How to Restore Your Gut for Optimal Health
While we strive to always provide accurate, current, and safe advice in all of our articles and guides, it’s important to stress that they are no substitute for medical advice from a doctor or healthcare provider. You should always consult a practicing professional who can diagnose your specific case. The content we’ve included in this guide is merely meant to be informational and does not constitute medical advice.

Gut Health Diet: How to Restore Your Gut for Optimal Health

Leann Poston, M.D.

Dr. Leann Poston is a licensed physician in the state of Ohio who holds an M.B.A. and an M. Ed. She is a full-time medical communications writer and educator who writes and researches for Invigor Medical. Dr. Poston lives in the Midwest with her family. She enjoys traveling and hiking. She is an avid technology aficionado and loves trying new things.


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