Wednesday, March 29, 2023

How your gut organisms affect your whole body

Your gut health affects many systems in your body. Its role in your nervous and immune systems is significant.

Executive Summary

The organisms in our intestines live in a symbiotic relationship with us. Our food provides nutrients to them and they, in turn, product nutrients that help our body.

The gut bacteria product B–vitamins, vitamin K, various amino acids, and proteins. They metabolise fibers that our bodies cannot digest, and produce short chain fatty acids, which help our muscle function.

The gut organisms produce proteins that help our immune system. Disturbed microbiome can lead to Leaky Gut Syndrome. Some expert think that leaky gut is the root cause of many autoimmune conditions.

Some beneficial gut bacteria prevent overgrowth of bad bacteria. A few other strains digest and neutralise some food toxins.

Obese people have different microbiome than that of lean people.

Our microbiome secretes chemicals similar to what our nervous system does. Those bacteria can communicate with our brain. A disturbed microbiome is suspected to be the cause of many neuro–psychiatric conditions.

Read the full article for more details.

Our gut hosts trillions of microorganisms, who live in a symbiotic relationship with our body. They manufacture nutrients, such as B–vitamins, vitamin K, and certain amino acids that help us. In turn, they 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 genetic makeup, age, and foods we eat.

Disturbance to this delicate microbiota can lead to digestive system disorders, auto–immune conditions, neuro–psychiatric conditions, cancer, diabetes, heart disease, and obesity.

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

This article discusses how our microbiome affects many other systems in our body.

Digestive system and microbiome

Nutrient synthesis

The gut bacteria are known to 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. Some of them produce only a few of the B–vitamins.

Some gut bacterial species actively exchange B–vitamins with other species, which do not produce them. So, not only are the gut bacteria in a symbiotic (mutually beneficial) relation with the host (us), but also with one another.

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


Scientists have noticed that laboratory white rats demonstrate a strange behaviour called Refection, when they were not given B–vitamins in their diet.

These rats eat their own feces. Why would an animal eat what it eliminated from its own body? The reason is the B–vitamins that are synthesized by the bacteria in the rats’ guts.

We are too sophisticated for that, and so we may suffer severe a B–vitamin deficiency, post–antibiotics.

Vitamin K

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

Newborn babies have no microbiota in their intestines. So, they cannot synthesize their own vitamin K. Therefore, to prevent the risk of bleeding, newborns are given vitamin K injections.

Amino acids and proteins

Gut bacteria also synthesize certain amino acids and proteins.

Different species of bacteria digest, or metabolise, many amino acids eaten through foods, forming proteins that have a significant role in our immunity and nervous system.

So, for proper functioning of those systems, one should eat adequate amounts of proteins. Prominent such proteins are those containing amino acids, such as tryptophan, glutamine, methionine, and branched–chain amino acids.

Don’t get stuck on the specifics of the proteins. The purpose of mentioning them is to point out that proper protein intake is essential to keep gut bacteria healthy.


Our body can digest simple sugars, and a few complex carbohydrates. Post–digestion, these carbohydrates get quickly absorbed in the early part of the intestines.

But, digesting most of the fibers, and some complex carbohydrates such as starches is not easy. These undigested food items pass through the small intestines and reach towards our colon.

The bacteria in the intestines have enzymes to digest, or break down, these carbohydrates. The bacteria ferment these fibers and starches, and form something called short chain fatty acids (SCFAs). The SCFAs help in muscle function. They can be absorbed in the colon and used as nutrients.

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

Gastrointestinal disorders

2005 Nobel Prize

In 2005, Drs Barry Marshall and Robin Warren won the Nobel Prize in Medicine. They had showed that the bacteria in the stomach can cause peptic ulcers or gastric cancers. This showed that our microbiota can lead to diseases.

Colorectal cancer is supposed to be caused by certain harmful bacteria in the intestines. Their action is further enhanced by the high level of inflammation in the intestines, created by altered microbiota.

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.

Not all end–products of microbial digestion are healthy. Some bacteria produce secondary bile acids, which can lead to cancer.

Fecal Transplant

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

Can taking a part of the microbiota of a healthy person and putting it in an unhealthy one, make the latter healthy? The answer happens to be, yes, in some situations.

But, it is not a good idea to open the intestines of the healthy person, and extract his microbiota. A simpler way is to take his excreted microbiota, or stools.

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

If the suffering individual has certain intestinal infections, such as C. difficile, the antibiotics work only 80% of the times. On the rest 20% occasions, the symptoms, and infection, recur. In such people, fecal transplant is shown to work 90% of the times.

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

1908 Nobel Prize

Nearly 100 years before the 2005 Nobel Prize was awarded for the microbiome’s role in gastrointestinal disorders, another Nobel Prize was awarded to a scientist, Dr Metchinikoff, for his pioneering work in cellular immunology. While that Nobel Prize was not for microbiome–related immunity, he had also highlighted the microbiome’s role in maintaining health.

Proteins that help immunity

The bacteria digest many amino acids derived from the proteins in our foods. For example, tryptophan, glutamine, methionine, and branched–chain amino acids such as valine, leucine, and isoleucine.

The bacteria synthesize many proteins using these amino acids. Read here for a very comprehensive coverage of this synthesis.

Some of these proteins are important components of our immune system. Thus, our microbiota helps our local immune system. It also affects our adaptive immune response. 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. This prevents the overgrowth of those bad bacteria. Those good bacteria also prevent harmful bacteria from attaching to the mucus membranes of the intestines, where antimicrobial proteins are produced.

The microbiota also digests some food toxins consumed. Some organisms that come through contaminated food or drinks are edged out by the gut microbiota.

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. However, many autoimmune conditions are said to be caused by something called Leaky Gut Syndrome.

Damage to gut microbiome leads to increased permeability of the intestines, which has been implicated in certain autoimmune conditions.

Leaky gut syndrome is a massive subject and I will keep it for another article in future.

Obesity and microbiome

In our intestines, there are two dominant species of beneficial bacteria — the Bacteroidetes and the Firmicutes.

A study compared the gut microbiota of obese and lean people, and studied these two species. In obese people, the relative proportion of Bacteroidetes is decreased compared to that in the lean people. This proportion increased with weight loss.

Thus, obesity showed an association with gut microbiota. Of course, we don’t know whether obesity changed the microbiota, or it was the other way round.

Neurology and microbiome

In the recent years, the intestines are considered to be the second brain. The microbiome is found to secrete many chemicals that perform similar functions in the body that our nervous system does. ‘Your gut feeling’ may have a physiological origin, after all.

The microbiome can communicate with the brain indirectly, either hormonally or using the immune system. Some bacteria in the gut release neurotransmitters that stimulate the vagus nerve. This way, they directly communicate with the brain.

As a result, the disturbances in microbiome can lead to several neurological conditions.

Autism and autism spectrum disorders

Autism spectrum disorders may be associated with changes in the gut microbiota. GI disorders are 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.

Could certain bad strains of bacteria in the gut be contributing to that disease? Did the plaques reduce, once those bacteria were killed by antibiotics?

Parkinson’s disease

Parkinson’s disease is a condition where the person develops tremors and finds difficulty in movement. One culprit is a neurotransmitter in the brain, called Dopamine.

A medication, called Levodopa, is used for the treatment. It is metabolised in the brain to form dopamine, giving immediate improvement in the symptoms. However, some people don’t find any benefit. The scientists did not know why.

Research published in Jun 2019 in the journal Science showed that some bacteria digest levodopa in the intestines. So, addressing this might help in improving Parkinson’s treatment.

Other psychiatric conditions

Inflammatory changes in the gut are noticed in schizophrenia, major depressive disorder, and bipolar disorder. These 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, in a symbiotic manner.

If any act disturbs this balance, you get a microbiome wherein only a few organisms dominate many other, beneficial organisms. This imbalanced state of microbiome is called Dysbiosis.

A dysbiosed microbiota (that was a mouthful; a better phrase would have been ‘damaged gut bacterial colony’) has only a few strains of good organisms, with less quantity and diversity.

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 than their processed diet–eating counterparts. They also have lesser chances of developing mental illnesses.

Medical conditions caused by disturbed microbiome

There are many medical conditions, besides the ones discussed above, which are caused by a damaged microbiome. Here is a compilation of conditions:

  • 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

Actionable tips

  1. Avoid antibiotics, as far as possible.

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

  2. Eat adequate protein daily.

    Eat at least 1 g protein per kg of body weight.

  3. Increase dietary fiber intake, or take a fiber supplement.

    Aim for 25 g fiber for women, and 38 g for men.

  4. Ensure adequate sleep.

    Sleep at regular times.

  5. Reduce processed foods in diet.

    Eat more vegetables.

  6. Reduce chronic stress.

    Use mindfulness or yoga techniques.

  7. Reduce or stop alcohol consumption.

    If you are vegan or vegetarian, take a B–vitamin supplement.

  8. Reduce intestinal inflammation.

    Eat anti–inflammatory foods or supplements such as fish oil, garlic, ginger, and turmeric.

First published on: 7th August, 2019

Image credit: Gerd Altmann from Pixabay


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