Wednesday, March 29, 2023

Microbiome: The other ‘You’

Executive Summary

Our intestines, mouth, and nose host trillions of microorganisms, who live in a symbiotic relationship with our body. They manufacture many healthy nutrients, such as B–vitamins, vitamin K, and certain amino acids, for us while getting their food from what we eat.

The microbial composition in each of our bodies is unique, and is called our microbiota. That fragile universe, the microbiome, starts forming only after birth, and is defined by our DNA, age, food we eat, etc. The more diverse the microbiota, the healthier the person, in general.

An infant’s microbiome helps it develop a good immune system. It protects against asthma and allergies. Breast–fed babies and normal delivery babies have healthier microbiota.

Disturbance to the delicate balance of various species in microbiota are linked to digestive system disorders, auto–immune conditions, neuro–psychiatric conditions, cancer, diabetes, heart disease, and obesity.

Protect the microbial colonies in your intestine, just as you protect your body. Some ideas for that: Eat high–fiber foods and fermented foods. Avoid processed, sugary, and fried foods. Avoid artificial sweeteners. Avoid smoking, antibiotics, and NSAIDs. Reduce stress. Sleep adequately. Exercise. Use environmentally–friendly chemicals for cleaning your home.

Read the full article for explanation and medical references.

The discovery of a complex ecosystem inside our bodies could be the medical discovery of this century. This fragile system is called the Microbiome. And, it has ramifications in almost all aspects of our health.

Microbiota and microbiome

Our body is colonised by bacteria, fungi, archaea, protozoa, and viruses. They lurk in our mouth, nose, intestines, and many other organs. Most of them are useful, living in a symbiotic (mutually beneficial) way. Some are neutral, and a few are harmful.

These organisms are 30% more in number than the number of cells in our body. So there are more of ‘them’ inside us than we ourselves are. 🙂

These trillions of microorganisms are collectively called the Microbiota, and their ecosystem is called the Microbiome.

The most important place where these ‘guests’ reside is in our gastrointestinal tract, mainly, the intestines. Bacteria are the most common microbes.

Researchers are beginning to understand how our health is decided by these microbes. Their profound effects are getting noticed in various medical fields, such as endocrinology (diabetes), rheumatology, immunology, and neuro–psychiatry.

Genome and microbiome

The genome of an organism contains all of the information needed to build and maintain that organism. Thus, the human genome is the complete set of our DNA, including all its genes. Our genome has more than 3 billion DNA base pairs. Each of our cells that contain a nucleus, have a copy of this entire genome.

The bacteria and other organisms that reside in our bodies also have their own genomes. However, their symbiotic relationship with our body is so crucial that those genomes are now called our ‘other’ genomes.

These complex communities of bacteria and other parasites survive, thrive, and function based on the support of other organisms around them. They also need metabolic support from our bodies — from the food we eat, and the enzymes we secrete.

Uniqueness of microbiome

The microbiome for each individual is different, and somewhat unique. Just like you have a unique set of genes, or genome, you have a unique microbiome of your own.

Thus, your microbiome is like your fingerprints — unique, except that it keeps changing with time, diet, age, etc. But, there are certain common species. It is said that about 30% of the species in our microbiome are common.

Your genome decides the composition of organisms in your intestines. So, the ‘they’ part in your intestines is decided by the ‘you’ part in your body. That is why ‘they’ are called the other ‘you’. 🙂

Diversity in microbiomes

Some tribes in remote South America or Africa have microbiomes differing considerably from ours. It seems that their remoteness prevents them from sharing the genetic components of organisms that we share with others around us through contact.

Not only are the microbiomes in these tribes very different, they are also very rich in diversity. For example, there is a tribe in Tanzania, called Hadza. Their microbiomes have 40% more diversity than a typical western–country microbiome.

The more diverse the microbiome, the healthier the person is. There is less prevalence of heart disease, cancer, obesity, and asthma. The reason is not known, as yet.

It is said that a typical Hadza tribesman eats 600 different plants and animals in a year, with a lot of seasonal variation. In contrast, a typical western–country person eats only 50 different plants and animals in a year.

Perhaps, the variety of food sources offers this diversity to a microbiome, and confers health to that individual.

Infant microbiome

When a baby is in the womb, there are no microorganisms in its intestines. However, during birth, the infant gets exposed to the microorganisms, and its microbiome is formed.

Microbiome at birth

It seems that the organisms encountered by the baby during delivery in the birth canal take root in its intestines. A normal delivery baby’s microbiome is much healthier a the caesarean–section–born baby’s microbiome.

Breast–milk and breast–feeding

Breast milk has more than 200 types of complex sugars called Oligosaccharides. The babies cannot digest them. These oligosaccharides are used as food by the microbiota in the baby’s intestine.

The act of breastfeeding confers a set of good bacteria to the intestines of the baby. The microbiome of the babies who were fed formula milk was found to be different from those of the breast–fed babies.

Hygiene and infant microbiome

If you keep a child in a sterile environment, the good bacteria cannot thrive in its intestines. But, in their place, some undesirable but sturdier bacteria arrive and colonise.

You should leave your child to crawl on a slightly dirty floor. And, let it eat with those same hands without washing them, occasionally.

For more details about infant microbiome, read an article on this website: Infant microbiome: how decisions in infancy affect health for life.

Adult microbiome

As a baby grows up into an adult, its diet, antimicrobial practices, pollution, and other environmental exposures change its microbiome.

Digestive system and microbiome

Nutrient synthesis

The gut bacteria synthesize certain vitamins and amino acids. Our body synthesizes thousands of proteins using these amino acids.


All eight of the main B–vitamins are synthesized in the intestines by various gut bacteria.

The key enzymes needed to synthesize vitamin B–12 are not present in any plant nor animal. They are found only in certain bacteria, which can synthesize that vitamin. Thus, plants don’t have, nor can give you, vitamin B–12.

If your intestines have these bacteria, your body can get vitamin B–12 from them. If you take a dose of antibiotics, all parasites in your intestine, including these beneficial bacteria, will be killed. This leads to B–vitamin deficiency, especially that of vitamin B–12.

Vitamin K

Vitamin K is also synthesized in the intestines by the gut bacteria. Vitamin K helps in the production of blood clotting factors.

Amino acids and proteins

Different species of bacteria digest, or metabolise, many amino acids eaten through foods. Then, they form proteins that have a significant roles in our immunity and nervous system. So, one should eat adequate amounts of proteins.


The bacteria in the intestines ferment fibers and starches that our bodies cannot digest. They produce something called short chain fatty acids (SCFAs). The SCFAs help in muscle function.

Since the dietary fibers provide food for gut bacteria, they are called Prebiotics.

Gastrointestinal disorders

Recent studies have shown that SCFAs suppress inflammation in the intestines. Science is learning whether these SCFAs can prevent cancers, such as colorectal cancers.

Studies have shown that SCFA may be useful in the treatment of bowel disorders such as ulcerative colitis, Crohn’s disease, and antibiotic–induced diarrhea.

Some bacteria digest a few potentially toxic ingredients in our foods. Thus, they can protect us from harm.

Fecal Transplant

One of the strangest, and grossest, outcome of microbiome research is a treatment modality called fecal transplant.

Fecal transplant involves putting 500 cc of stools of a healthy person into the intestines of the patient, through a tube inserted either through the rectum, or the nose. That is what makes the idea gross.

Scientists are studying if fecal transplants can help in inflammatory conditions in the intestines such as inflammatory bowel disease (IBD), and irritable bowel syndrome (IBS). Small studies have found success rates of 36% to 78% in IBD, and 70% in IBS.

Immune system and microbiome

Proteins that help immunity

The bacteria synthesize many proteins using amino acids derived from our food. Read here for a very comprehensive coverage of this synthesis.

Some of these proteins are important components of our immune system. Nearly 70% of our immune system is in the lining of the gut.

Many strains of these bacteria in the gut compete for the same nutrients with harmful bacteria. The microbiota also digest some food toxins consumed.

Autoimmune conditions

Rheumatoid arthritis has been linked to the gut microbiome.

Two completely different autoimmune disorders, spondyloarthritis and inflammatory bowel disease (IBD), seem to have a similar type of bacterial profile.

Unfortunately, the exact role of the gut bacteria is still not understood.

Obesity and microbiome

Obesity has been shown to have an association with gut microbiota.

Neurology and microbiome

The intestines are considered to be our second brain. The microbiome secretes many chemicals that perform functions similar to that our nervous system does. Thus, the disturbances in microbiome can lead to several neurologic conditions.

Autism and autism spectrum disorders

Autism spectrum disorders may be associated with changes in the gut microbiota. GI disorders are also observed in such patients.

Alzheimer’s disease

A recent Alzheimer’s disease study was done on mice. In that, the scientists observed that long-term, broad-spectrum antibiotics decreased the plaques that contribute to Alzheimer disease.

Parkinson’s disease

A paper published in June 2019 in the journal Science showed that some bacteria digest levodopa in the intestines. Since levodopa is the medicine used in the treatment of Parkinson’s disease, such patients may not find any benefit of taking levodopa.

Other psychiatric conditions

Inflammatory changes are noted in the gut in schizophrenia, major depressive disorder, and bipolar disorder. They indicate a possible role of gut bacteria disturbance.

Microbiome summary

A healthy microbiome is the one that contains diverse species of bacteria that thrive simultaneously. If any act disturbs this balance, you get a microbiome in imbalanced state called Dysbiosis.

Poor sleep, poor diet, chronic stress, medications such as antibiotics, and too much alcohol adversely affect our microbiome. The effect is almost immediate. You can have up to 40% reduction in the diversity of microbiome within 2 weeks of eating a highly processed diet.

Scientists claim that people who eat healthy, whole–food diets are up to 40% more resilient to stress then their processed diet eating counterparts. They also have lesser chance of developing mental illnesses.

Medical conditions caused by disturbed microbiome

  • Allergies
  • Asthma
  • Autism
  • Autism spectrum disorders
  • Autoimmune diseases
  • Cancer
  • Cardiovascular disease
  • Celiac disease
  • Chronic fatigue syndrome
  • Depression
  • Type 1 and type 2 diabetes
  • Inflammatory bowel disease
  • Irritable bowel syndrome
  • Multiple sclerosis
  • Neurological diseases
  • Obesity
  • Osteoporosis
  • Cognitive and emotional health

For a comprehensive discussion on how our microbiome affects various systems in our body, read this article on this website: How your gut organisms affect your whole body.

Ideas for a healthy microbiome

Here are 20 ideas for maintaining, improving, and repairing gut organisms. Since many of them need further discussion, I have written a separate article on this website: 20 ideas for a healthy microbiome.

Increase fiber intake

Most of us have less than half the advised quantity of fiber a day. Read more on this website: Benefits of fiber.

Prebiotics, such as fiber, pass through our digestive system unchanged by our body. However, they are food for our gut bacteria. They convert fibers into nutrients in our intestines.

In general, fruits, vegetables, beans, and whole grains such as wheat, oats, and barley are all good prebiotics.

If you cannot easily eat high fiber foods, or you are some suffering from a digestive system ailment, take a prebiotic supplement.

Do not take your fiber supplement along with any medicines you are taking for blood pressure or other conditions. Leave a gap of at least 30 minutes, and preferably, of 2 hours.

Eat a variety of vegetables and fruits

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.

Eat fermented food

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

A locally available, fermented food is a good idea.

Research is conflicting about probiotic supplements, 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;
  • At old age;
  • After an event that reduces the gut bacteria, such as a course of antibiotics, or severe diarrhoea.

Avoid antibiotics

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

Some of them are normal food items and you may not want to live life without them. In my view, if you are suffering from a serious digestive system ailment, these foods are better avoided.

Avoid artificial sweeteners

Artificial sweeteners alter the gut bacterial variety. They encourage many unhealthy strains of bacteria.

Avoid genetically–modified food

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

Don’t be hygiene–obsessed

Repeated hand washing, overuse of antibacterial hand soaps and use of disinfectants in the house may be bad for your gut bacteria. It will not allow your immunity to strengthen.

Protect your home microbiome

Avoid harsh cleaning chemicals, disinfectants, deodorants, etc. Use as many environmentally friendly chemicals in your house as possible.

Sleep proper 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.

Reduce stress

Stress makes your brain damage your microbiome. Such damaged microbiome, in turn, affects your brain through intestinal inflammation and stress–related psychiatric disorders.

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.

Sports and exercise

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

Spend time with a lean person

The composition of the gut bacteria is 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.

Consider vaginal birth over caesarean section

Do consider staying off the caesarean path, unless medically needed.


Breast–feeding helps the baby get organisms 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

In general, avoid high fat, high sugar, or low–fiber diets. Avoid processed foods since they are high on emulsifiers, food additives, and preservatives.

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

Consider supplements of food products that are anti–inflammatory.

Increase intake of microbiome–friendly vitamins and minerals


B–vitamins, especially vitamins B–1, B–6, and B–12, have a big role in improving the damaged microbiome.

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.


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.

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. Eat high–fiber fruits and vegetables.

    Eat a large variety. Instead of a lot of one vegetable, a 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.

    Avoid processed and fried foods, simple sugars, trans fats, grains containing gluten, and deli meats.

  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 proteins, B–vitamins, iron, and magnesium.

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

Image credit: Gerd Altmann from Pixabay

First published on: 14th September, 2016


Please enter your comment!
Please enter your name here

This site uses Akismet to reduce spam. Learn how your comment data is processed.




Latest Articles