Tuesday, October 3, 2023

20 ideas for a healthy gut microbiome

There are many simple things one can do to maintain, improve, and even repair the intestinal microbial flora.

Executive Summary

For a healthy gut microbiome, follow these 20 tips:

Increase your intake of fruits and vegetables, prebiotics (dietary fibers), and probiotics, such as yogurt.

Avoid antibiotics and painkillers (NSAIDs).

Avoid simple sugars, highly processed foods, GMO foods, and artificial sweeteners. Eat at regular times.

Reduce use of harsh chemicals, disinfectants, and cleansers in your home. Don’t be overobssessed with hygiene.

Get adequate sleep. Reduce stress. Exercise and participate in sports.

Get pets. Spend time with lean people.

Choose normal delivery over C–section, if possible. Breastfeed babies physically.

Stop smoking. Reduce gut inflammation with anti–inflammatory foods and supplements.

Increase intake gut healthy vitamins and minerals, such as B–vitamins, iron, and magnesium. Take a natural–source multivitamin, multimineral supplement.

Read the full article to know more about each of the tips above.

Our intestines host trillions of microorganisms, who live in a symbiotic relationship with our body. They manufacture nutrients that help us. They, in turn, get their food from what we eat.

The microbial composition in each of our bodies is unique, and is called our Microbiota. That fragile universe, called Microbiome, is determined by our DNA, age, and food we eat.

Disturbance to this delicate balance between various species in microbiota is linked to various disorders.

To learn more, read this comprehensive article on this website: Microbiome: the other ‘You’.

This article discusses ideas for maintaining, improving, and repairing the population and the diversity of healthy gut microbes.

Increase fiber intake

Men are advised 38 gm of fiber, or prebiotics, per day, while women should take 25 gm daily. But, our modern diet is highly processed, with fiber removed to a large extent. As a result, most of us have about 10–15 gm of fiber a day.

Read more on this website: Benefits of fiber.

Prebiotics are indigestible carbohydrates and fibers such as inulin, resistant starches, gums, pectins, and fructo–oligosaccharides. They pass through your digestic system unchanged by your body.

However, they are food for your gut bacteria. Those microorganisms convert fiber into nutrients in your intestines, and your body can benefit from that.

Prebiotic food

Eat foods which are high in fiber.

Plants with high levels of a water–soluble fiber, called Inulin, are a good start. Examples are onions, garlic, artichokes, and leeks. In general, fruits, vegetables, beans, and whole grains such as wheat, oats, and barley are all good prebiotics.

Eat a variety of plants and vegetables. Eating a lot of a single fibrous vegetable is very different from eating a little bit of a lot of different vegetables. The more the dietary variety, the more the bacterial variety in microbiota, making it a healthier microbiome.

Don’t blindly consume vegetables assuming they have fiber. Lettuce has almost no fiber, nor any nutrient value.

Don’t increase your intake of prebiotics rapidly. Till your gut gets used to it, prebiotic foods can increase gas production (flatulence) and bloating. Your tolerance to prebiotics will increase with time and usage.

Prebiotic supplements

If you cannot easily eat high fiber foods, or you are some suffering from a digestive system ailment, you may need to take a prebiotic supplement. These are dried fiber powders that are to be mixed with water and consumed.

Do not take your fiber supplement along with any medicines you are taking. The fiber may hold some of the medication in suspension and won’t allow your body to absorb it. Leave a 2–hour gap before or after taking the fiber supplement for medications.

Eat a variety of vegetables and fruits

The microbiota is better if it is made up of diverse species of bacteria. Not just the bacterial numbers, but also the variety of the species makes a healthier microbiota.

The more variety of fruits and vegetables you eat, the more diverse the bacterial flora is.

Eat fermented food

Fermented foods are typically high in beneficial bacteria. They are called probiotics — foods that increase the biological diversity and quantity of gut bacteria.

Probiotic foods

Depending on the country or ethnicity you belong to, there are many choices for probiotic foods. Generally, a locally available fermented food is a good idea. Just make sure it is not too sweetened.

  • In most countries, unsweetened yoghurt, with live, active culture, and pickled vegetables;
  • If you are from Korea: Kimchi, a Korean dish made from garlic, cabbage, and chilli;
  • If you are from Japan: Kombucha tea, and soybean-based products such as soy sauce, tempeh, miso, and natto;
  • If you are from eastern europe or russia: Kefir, which is a sour milk drink with five times as many microbes as yoghurt;
  • If you are from europe: raw milk cheeses, which have a lot of bacteria;
  • If you are from northern, central and eastern europe: Sauerkraut, which is finely cut raw cabbage fermented by bacteria.

These days, you get foods from global origin in many countries. Check your local shops.

Probiotic supplements

Research on the benefits of probiotic supplements is conflicting, as is always the case with dietary supplements. Read on this website for how to correctly interpret results trials on of dietary supplements.

However, probiotic supplements are helpful in three situations, for sure:

  • At young age, when the microbiome is not fully formed;
  • At old age, when the microbiome is relatively weaker, due to various factors such as lower nutrient intake;
  • After an event that reduces gut bacteria, such as a course of antibiotics, or severe diarrhoea.

In all other situations, use the probiotics supplements as a second line of defence, if you suspect some problem of intestinal origin.

Avoid antibiotics

Antibiotics are non–specific killer guns. In the process of eliminating harmful microorganisms from the body, they simply kill all organisms. This destroys intestinal flora significantly. Such a person develops deficiencies of B–vitamins and vitamin K since they are produced by the intestinal bacteria. This deficiency persists till the intestinal flora builds again.

However, the research shows that it can take months, and sometimes as much as three years, for the gut microbiota to get restored after a course of antibiotics.

Another problem is the new bacterial flora that would take root may not be identical to the original one. There may be many new strains that are unhealthy.

Avoid NSAIDs

Non–steroidal anti–inflammatory drugs (NSAIDs), such as aspirin and ibuprofen, help as pain–killers. However, they change the intestinal permeability in less than 24 hours of taking them.

Most NSAIDs lead to inflammation in the intestines, along with increased intestinal permeability. These two conditions together can lead a medical condition called Leaky Gut Syndrome. This condition is considered the prime cause of many auto–immune conditions, such as rheumatoid arthritis and psoriasis.

Discussion on leaky gut will need a very long article in itself. So I will take it up in a separate article. You can read this article about leaky gut caused by ibuprofen, for more information.

Avoid simple sugars and processed foods

These foods are best avoided to keep the bacterial flora in tact. Of course, some of these are normal food items and you may not want to live life without them. Also, you may have been advised to take some of those, in a different dietary context.

So, the advice to avoid these is only for having a healthy microbiota. Judge your situation and take a call. In my view, if you are suffering from a serious digestive system ailment, these foods are better avoided. Their harm would be worse than their benefits. Avoid:

  • Processed and fried foods.
  • Artificial sweeteners.
  • Sugars.
  • Fruit juices.
  • Starchy fruits and vegetables, such as bananas, potatoes, peas, and corn.
  • Trans fats.
  • Hydrogenated vegetable oil fats.
  • Deli and cured meats.
  • Eggs and dairy. Butter and ghee are fine.
  • Peanuts and soy. Chickpeas are fine.
  • All grains containing gluten, such as wheat, barley, rye, and oats. Rice, millet, and sorghum are fine.
  • Foods containing yeast.
  • Dried fruit.

Avoid artificial sweeteners

To avoid sugars, many people consider artificial sweeteners, such as aspartame and sucralose. Artificial sweeteners are considered safe for human consumption (are certificated as such, by the Food and Drug Administration, USA).

However, they may not be so good for healthy living. Artificial sweeteners alter the gut bacterial variety. They encourage many unhealthy strains of bacteria.

Read on this website: Artificial sweeteners are toxic to your body.

Avoid genetically–modified food

Many plants fall victim to pests, reducing the crop yield. So, strong pesticides are sprayed on them. However, some strains of plants cannot withstand such harsh chemicals. So, specialised strains called GMO, or genetically–modified organisms, are developed that can withstand toxic pesticides such as glyphosates.

As a result, GMO plants have far more glyphosates sprayed on them than normal. If you consume them without proper cleanup, your gut bacteria get disturbed causing inflammation, intestinal permeability, and then leaky gut.

Organic foods will not be GMO–based. So, consider plants and other foods from organic sources, though they may be expensive.

Eat at regular times

Our body has a 24–hour circadian cycle. It is a natural, internal system that regulates feelings of sleepiness and wakefulness. Based on our sleeping pattern, we also have a feeding schedule — the times when we eat.

The gut bacteria also have their circadian cycles. Since they depend on us for their nutrients, their circadian cycle is synchronised to ours.

If we eat at irregular hours, the bacteria don’t get nutrients are regular intervals. This causes their circadian clock to go haywire, and makes our microbiome unhealthy.

Don’t be hygiene–obsessed

Repeated hand washing and use of antibacterial hand soaps and disinfectants in the house may look like hygienic habits. But, overdoing them may be bad for your gut bacteria. They will not allow your immunity to strengthen.

Playing in mud is not bad for health, unless that mud is in a bio–hazard area, such as a garbage dump, a hospital, or a chemical manufacturing zone.

Protect your home microbiome

Microbiome is a delicate, symbiotic ecosystem of organisms. By that definition, even the microbial setup in your house will be a microbiome. We can call that ecosystem your home’s microbiome.

Since your body’s microbiome will be in harmony with that of your home, protect your home’s microbiome.

Avoid harsh cleaning chemicals, disinfectants, deodorants, etc. Use as many environmentally friendly chemicals in your house as possible. You don’t have to do that out of love for the environment. Do it for the love of your gut bacteria and your health.

Pest control is a very risky operation. To save on costs, people hire non–qualified, cheap workmen in some countries, including mine. Be wise and careful. The toxic fumes of pest control sprays, on inhalation, can disrupt a healthy microbiome.

Sleep for adequate hours at regular times

People, who sleep irregularly, have been found to have disturbed microbiota. Sleeping properly is shown to help improve the gut bacteria.

Your body, and many of its vital organs, run on a circadian rhythm. Levels of many hormones in your body wax and wane in this cycle.

Your wake–and–sleep cycle is intricately linked to your circadian rhythm. Any disturbance in it, due to irregular sleeping hours, blue lights, or foreign travel, affects your circadian rhythm.

Since the gut bacteria depend on the food you eat, their own circadian rhythm is synchronised to yours. If you follow an irregular schedule, your gut bacteria suffer, and the microbiome is ruffled.

Reduce stress

Your microbiome communicates with your brain through your immune system via chemicals secreted by bacteria, tryptophan signalling, and gut hormones signalling. Thus, problems with your brain affect your microbiome, and resulting problems with your microbiome, in turn, affect your brain.

Due to this, stress causes your brain to damage your microbiome. The damaged microbiome, in turn, affects your brain through intestinal inflammation and stress–related psychiatric disorders.

Reduce stress to stop this vicious cycle.

Sports and exercise

Exercise and sports increase the diversity of gut microbes. They are shown to raise the population of beneficial bacteria.

Get pets

While pets can help you reduce stress, they are also found to reduce allergies and obesity in children who were exposed to them in the childhood. This is assumed to be because pets can offer more biodiversity to your gut microbiota.

Of course, go a bit carefully about this. You don’t want your child to get asthma attacks because of a new furry pet you brought home. Discuss with experts. Possibly, you may want a pet that does not shed much of feathers or hair.

Spend time with a lean person

This one is a bit weird. As the scientists have found, the composition of the gut bacteria in a lean person is different from that in an obese person.

If you are in contact with a lean person, some of those bacterial strains are shown to pass across to you, keeping you leaner and healthier. However, this is quite strange an advice to implement.

Consider vaginal birth over caesarean section

No, I am not talking about your birth. But, if you are planning on having children, do consider staying off the caesarean–section path, unless medically needed.

There is a technique called vaginal seeding that some hospitals perform. Discuss with your doctor for a caesarean baby.

This aspect and other infant microbiome related issues are discussed in an article on this website: Infant microbiome: how decisions in infancy affect health for life.


Breast–feeding helps the baby get organisms present on mother’s body and prepare its immune system. Also, the breast–milk has ingredients that help the baby’s microbiome.

Stop smoking

Smoking changes the composition of your gut microbiota. A study found that smoking changes your gut microbiota to the one that resembles of obese people or people with inflammatory bowel disease.

Reduce gut inflammation

One sure sign of a disturbed microbiome is the level of gut inflammation. While you cannot objectively measure it through a simple laboratory test, it is present in almost all the medical conditions that are caused by damaged microbiota.

Anti–inflammatory foods

On a presumptive basis, you should consider anti–inflammatory diet. Avoid high–fat, high–sugar, or low–fiber diets.

Avoid processed foods since they are high on emulsifiers, food additives, and preservatives. They thin out the intestinal mucus layer, increase gut permeability, and damage healthy bacteria in the intestine.

Use healthy oils (olive oil, instead of butter), lean meat (instead of cured or red meat), and herbs for flavouring (instead of salt).

Read on this website: Inflammatory diets: what foods to avoid.

Anti–inflammatory supplements

If you cannot get enough anti–inflammatory foods, consider supplements of food products that are anti–inflammatory. This is especially true if you are suffering from a serious digestive system problem.

Foods supplements that are anti–inflammatory are:

  • Omega–3 fish oils (EPA and DHA)
  • Garlic (allicin and diallyl disuphide)
  • Ginger (gingerol)
  • Turmeric (curcumin)
  • Grapes and blueberries (resveratrol)
  • Spirulina
  • Oranges and cherries (vitamin C)
  • Coffee (caffeine)
  • Fruits and vegetables (quercetin)
  • Guggul (boswellia)
  • Gamma–linolenic acid (GLA)
  • Alpha–lipoic acid (ALA).

Increase intake of microbiome–friendly vitamins and minerals


B–vitamins have a big role in improving the damaged microbiome.

  • Alcoholics have low levels of vitamin B–1. Since vitamin B–1 helps in eliminating toxic, foreign substances from the microbiome, alcoholics may need to supplement with vitamin B–1.
  • Vitamin B–6 protects the body from the inflammation in the intestines.
  • Vitamin B-12 is found only in animal fats and dairy. So, vegans should take supplements of it.

For a comprehensive article on B–vitamins, read on this website: Are dementias and B–vitamin deficiencies related?


Many gut bacteria compete for iron that you get from food. Some bacteria may take up most of the iron that you consume, leaving your body with very little.

If you have a digestive system problem, consider taking iron supplements. Once your gut becomes normal, you can continue with iron intake through foods only.


Magnesium deficiency damages gut bacteria, and can lead to depression–like behaviour. Magnesium also increases bio–availability of vitamin B–6.


Molybdenum works with four enzymes in the intestines, and helps cells to produce energy.

In my view, rather than worrying about what to eat for each of the above nutrients, taking a simple natural multivitamin, multimineral supplement may be a simpler strategy.

Actionable Tips

  1. Take prebiotics.

    Eat high–fiber foods, or take fiber supplements.

  2. Increase intake of fruits and vegetables.

    Eat a variety. Instead of a lot of one vegetable, little bit of many vegetables is better.

  3. Take probiotics.

    Eat fermented foods, or take probiotic supplements.

  4. Avoid antibiotics, when possible.

    Don’t pop in an antibiotic at the first sign of fever.

  5. Avoid NSAIDs.

    Check with your doctor, for an alternative.

  6. Avoid simple sugars and highly processed foods.

    Do this, especially if you have a digestive system ailment.

  7. Avoid artificial sweeteners.

    Stevia, xylitol, and erythritol seem to be OK.

  8. Eat at regular times.

    Be consistent in your times of eating, whatever they are.

  9. Avoid GMO foods.

    Choose organically grown fruits and vegetables, if financially possible.

  10. Don’t use harsh chemicals, cleansers, and disinfectants at home.

    Don’t be overly obsessed with hygiene.

  11. Get adequate sleep.

    Sleep at regular sleeping time.

  12. Reduce stress.

    Use mindfulness or yoga techniques.

  13. Exercise regularly.

    Participate in a sport or physical activity on a regular basis.

  14. Get a pet.

    Avoid furry or feathery pets, if you are allergic.

  15. Spend time with lean people.

    Interact enough that some germs on their body may transfer onto to you. Admittedly, tough!

  16. Choose vaginal delivery instead of C–section.

    Discuss vaginal seeding with your obstetrician.

  17. Breastfeed an infant.

    Physical act of breastfeeding is important.

  18. Stop smoking.

    Consumption of tobacco is equally bad.

  19. Reduce gut inflammation.

    Consume anti–inflammatory foods and food supplements.

  20. Eat microbiome–friendly nutrients, such as B–vitamins, iron, and magnesium.

    Take a plant–based, natural multivitamin, multimineral tablet.

First published on: 6th August, 2019

Image credit: skeeze from Pixabay


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