Bacteria is not a word we commonly associate with anything good. That is about to change. The relatively new microbiome science is working to uncover the effects of an unseen and very difficult to study ecosystem made up of trillions of microorganisms that live inside the human gut.

Freaky as this may sound it is really not bad. Research shows that all these bacteria, collectively, act like an extra vital organ. Studying them helps us understand some things better like mental and physical health, disease, the immune system, athletic performance, the metabolic rate in the human body and obesity and why it happens at all.

There are a couple of things to keep in mind: First, microbiome science is really young. It dates back to 2005, to the moment next generation genetic sequencing was invented and metagenomics, which allows us to study genetic material recovered directly from environmental samples, was born. Second, while microbiome science is advancing rapidly and new studies are coming out all the time, it is really difficult to study communities of bacteria inside the living human gut. It is even harder to test theories about them as ethical questions of patient discomfort and even harm have to be taken into account.

So, first the absolute basics. The colonies of bacteria that live in our gut are in a symbiotic relationship with us. That means that when they are in a homeostatic balance with the body they work hard to keep us alive. Here are some of the basic things we do know about them:

  • There are 500 to 1,000 different strains of bacteria that live inside us. The exact combination of all these strains is different for each person but the way they combine constitutes a bacterial “fingerprint” that can identify an individual as uniquely as the swirls at the tip of our fingers.
  • The gut bacteria is actually called microbiota and the term covers all the micro-organisms and viruses associated with the human gastrointestinal tract. The microbiome refers to the genetic make-up (the genes from all the all the bacteria, eukaryotes, archaea and viruses that live inside us) of the microbiota. It’s a bit like talking about the DNA of the bugs in our gut.
  • There are about 39 trillion bacterial cells in the human body which means that there are as many bacterial cells in our gut as there are cells in the human body (approx. 37.2 trillion cells). The bacterial cells are smaller and lighter and in total, in an average 70kg person, weigh about 200g.
  • The microbiome each individual has is partly inherited from their mother during birth but its composition (i.e. the number of each different strain of bacteria and its size) that forms the unique microbial fingerprint of each individual is shaped by a host of environmental and lifestyle factors which means we can take steps to improve it.
  • The bacteria in our gut secrete a large number of different hormones. Hormones are chemical messengers that travel throughout the body turning on and off different processes. Cortisol, to mention just one as an example, controls stress but it also controls blood sugar levels, regulates metabolism, helps reduce inflammation, and assists with memory formulation. Cortisol is a chemical messenger used by gut bacteria. The suggestion here, backed by current evidence, is that the bacteria in our gut plays a key role in anything that is affected by hormones which pretty much includes everything.

How The Microbiome Works

The sugar contained in our diet, the fiber found in the fruit and vegetables we eat, the protein meat is made of and the carbohydrates in bread and pasta are all broken down and used by the microbes in our gut. In fact everything we think of as food is processed by the bacteria in our gut. Some of it is broken down into nutrients which we can then be used by other organs in the body and some is consumed by the bacteria themselves so they can grow in number.

What studies have shown is that the microbiome depends on the food we eat and, in a complex feedback loop, secretes chemical messages that signal our brain to create cravings and make us pine for specific foods at specific times. This is why we can get the ‘munchies’ in the middle of the night and reach for a sugar-rich snack.

During pregnancy the female microbiome undergoes specific changes in preparation for birth when some of its strain is passed onto the newborn child. Pregnant women, famously, experience cravings for particular foods and, until now, there was no real idea why. Changes in the bacterial colonies in the gut that happen during pregnancy, apparently, change the balance of the bacterial populations. Larger bacterial populations become dominant and can then demand whatever type of foodstuff that particular bacterial strain processes which leads to food cravings.

Here are some of the things we do know about the way the microbiome works:

  • Different types of gut bacteria process different types of food. Paradoxically the food we eat also affects the types of gut bacteria that thrive in our gut. Because the gut bacteria then produces the fundamental chemicals that drive our metabolism and muscles the food we eat is linked directly to our mental, psychological and physical health.
  • The wrong type of food can turn good bacteria into bad. For instance refined sugar gives rise to the bacteria called Candida that weakens the lining of the gut. This allows bacteria to leak into the bloodstream and travel to other parts of the body where they have no business being there. Inflammation of the heart and blood vessels (cardiovascular disease), allergies and specific mental problems (like depression) have been linked with the condition.
  • Gut bacteria are ultimately responsible for the chemicals that create glycolysis (the breaking down of carbohydrates) and the production of adenosine triphosphate (ATP) that powers each of our cells, generates muscle power and fuels our metabolism which in turn controls how our body handles food, stores fat and generally remains aline. In order for the gut to be able to produce the many different chemicals necessary to do all this there has to be a good level of diversity in the bacterial colonies in our gut. This requires variety in the food we eat (more about this a little further down this article).
  • A healthy microbiome is associated with better emotional control, more energy, optimized cognitive functions, slower aging, better cardiovascular health, better quality of sleep and, overall, a better quality of life. Just like the live yeast that’s used to make bread the microbiome has a regular, cyclical rhythm in its activity and we feel that when at different times during the day we experience an ebb in our energy flow, feel fatigued and experience brain fog.
  • Like every other vital organ in our body the microbiome can be damaged by antibiotics, pesticides, environmental pollutants, radiation (like that received in medical treatments) and a nutritionally poor diet.

The Microbiome and our Health

New studies are uncovering the central role that the microbiome plays in our health and the ways in which imbalances it experiences can make us sick. One area in particular, which affects hundreds of thousands of individuals, is Irritable Bowel Syndrome (IBS) which is a disorder that covers many types of illness and has many different symptoms. Analysis of fecal matter in individuals that suffer from IBS showed consistent abnormalities in the microbiota it contained[1].

The activity of our gut bacteria is linked to our psychological and emotional state. Stress is an emotional response which expresses itself in physical symptoms all of which are rooted in hormones. Stress can harm the body by derailing the immune system. One study seeking to prove the link between gut bacteria and emotional states, like stress, which then affect behavior transplanted fecal microbiota from patients suffering with IBS to mice. The mice then went on to exhibit the same symptoms of anxiety[2], stress and faster transit of food through the body that the IBS patients suffered from.

The study makes mention of several red flags raised by imbalances in the bacterial populations[3] in the gut and suggests that many common modern diseases may be traced directly to these imbalances once more studies are performed.

Here are some of the ways the microbiome directly affects our health:

  • The microbiome not only controls our appetite but, as studies have shown, it can direct us on the type of food we need to eat to satisfy its needs. This raises the possibility that in situations where a person is overweight, remodeling the microbiome can lead to weight loss [4] [5]
  • Learning, memory and decision making can be impaired by changes in the composition and diversity of the microbiome. Changes that are beneficial can lead to improved cognitive health while changes that adversely affect the physiology of the brain can impair many of its critical functions, particularly as we age [6] [7]
  • Cell repair, the rate at which healing occurs and inflammation in tissues and organs of the human body are all governed by the surge and ebb of specific bacterial populations in our gut. The way that the microbiome affects healing[8] is being studied with a view to find ways to help accelerate it when trauma occurs.
  • Research suggests that the microbiome also plays a central role in the ageing process (itself part of the pathways that control the metabolism) with specific microbiome modulation leading to longevity in both human and animal trials[9]
  • Recent research shows that endurance exercise and high intensity workouts elicit a number of adaptive responses from the body that include the correction of electrolyte imbalance, a decrease in glycogen storage and the increase of oxidative stress, intestinal permeability, muscle damage, and the systemic inflammatory response. This, in turn, modifies our gut bacteria and produces a number of positive microbiome changes [10].  In addition, the microbiome itself, through specific types of gut bacteria appears to influence the VO2 max of individuals, directly affecting their cardiorespiratory fitness [11]

Factors that Affect the Health of the Microbiome

Much as the gut bacteria affect the human body at a physical, mental and psychological level they are affected, in turn, by a number of human-initiated factors.

In 2015 15,096 fecal, oral, and skin samples of bacteria provided by 11,336 people across the United States, United Kingdom, Australia, and 42 other countries were analyzed using genomic sequence that allowed the researchers to look for specific genetic markers. The action was the result of the American Gut Project set up by Rob Knight, Ph.D., from the University of California, in 2012 and its express purpose was to use new technologies to examine the impact of gut bacteria on physical and mental health.

The findings, published in the journal mSystems and reported in Medical News Today, strengthen what other studies have also indicated. Namely that a healthy microbiome requires bacterial diversity and for that to happen we have to eat up to 30 different types of plants each week. Because modern food production methods make use of pesticides and antiobiotics which affect the balance of the microbiome, diets that consist of organic food deliver measurable results in gut bacteria health and diversity.

In addition exercise[12] seems to also play a role in changing the microbiome both in composition and function. The findings affect both lean and overweight humans [13]

Symptoms of an unhealthy microbiome

A large number of people suffer from an imbalance in their microbiome but the symptoms are not debilitating enough to warrant serious concern so most of us ignore them and learn to live with the discomfort. If it remains untreated long enough (and it may take years) it will lead to more serious health problems and diseases, obesity, premature aging and deep depression. If your microbiome can no longer do what it is supposed to do (produce the necessary hormones and protect your immune system) you may require medication to do it for you in the future.

If your microbiome has been damaged by poor diet and/or by a course of antibiotics you may experience the following symptoms.

  • Difficulty losing weight.
  • Chronic fatigue, inability to concentrate, brain fog.
  • Irritability and/or depression.
  • Digestive problems - chronic bloating, diarrhea and/or constipation.
  • Bad skin, eczemas.
  • Susceptibility to infection.

How to Fix an unhealthy microbiome

A gut microbiome is a living organism, it is a pool of bacteria both good and bad. In a body with a balanced microbiome the good bacteria outnumbers the bad and there is diversity in the type of bacteria overall. One way to fix a damaged microbiome is to use strong antiobiotics for a period of time to completely sterilize the gut and then to introduce new bacterial cultures there via a fecal transplant (that is exactly what it sounds like) which builds a more balanced bacterial culture, from scratch. Thankfully, there are various other methods to achieve this in a home environment without having to resort to such measures.

Try Intermittent Fasting. It affects the microbiome [14] and lowers blood pressure, cholesterol and inflammation in the body. It helps accelerate cell repair, helps with weight loss [15] and even appears to contribute to longevity.

Eat organic, whenever possible. Buying organic food is pricey so the next best thing is to peel your fruit and vegetables whenever possible to remove some of the pesticide residue. Also choose more fruit and vegetables from what is known as the clean 15, foods that naturally contain lower levels of pesticides due to the lower pesticide use in their intensive farming process:

    • Avocado
    • Sweet Corn
    • Pineapple
    • Cabbage
    • Onion
    • Sweet Peas
    • Papaya
    • Asparagus
    • Mango
    • Eggplant
    • Honeydew
    • Kiwis
    • Cantaloupe
    • Cauliflower
    • Broccoli

Whenever budget allows buy the following fruit and vegetables from the organic section of your supermarket as their non-organic counterparts have shown to contain higher amounts of pesticides:

      • Strawberries
      • Spinach
      • Nectarines
      • Apples
      • Grapes
      • Peaches
      • Cherries
      • Pears
      • Tomatoes
      • Celery
      • Potatoes
      • Sweet Bell Peppers

Add probiotic and prebiotic foods into your diet. It can help modify gut bacteria populations and increase the diversity of types of bacteria in the gut [16].  This helps the microbiome remain healthy.

Avoid relying on probiotics in pill form as they’ve been shown to have mixed results and instead opt-in for more natural sources [17]. The best sources of natural probiotics are fermented foods with live bacteria already present. Most store-bought products have already been pasteurized to increase shelf-life. Unfortunately pasteurization removes all bacteria, beneficial or otherwise, so they do not contain probiotics (probio means “live”).

The best way to add live, good cultures to your microbiome (which will then help the existing ones multiply and thrive) is to make your own in a home environment. The two easiest ones to make is kefir and sauerkraut (recipe). You will need kefir seeds or live starter cultures (they can be purchased online - you can also ask a local dairy shop to give you some) to make kefir at home through fermentation of milk. Sauerkraut is made by fermenting cabbage with a use of salt and several days of fermentation at room temperature. Other well-known probiotics include: kimchi, yogurt, cheese, kombucha and miso. All probiotics have to be made at home in order to preserve the cultures that they inhabit. Commercial food health guidelines require the pasteurization of these products otherwise they cannot be sold.

All foods high in fiber are prebiotic (prebios means “before life”). They serve as the best type of food for your microbiome and it helps the “good guys” multiply and thrive. Here are some of the best prebiotics you can consume on a daily basis for a healthy gut:

        • Leek, garlic and onion
        • Apples and under-ripe bananas
        • Tomatoes, cucumbers and carrots
        • Oats, barley and buckwheat
        • Beans and lentils
        • Flaxseeds and pumpkin seeds
        • Pop corn

Note: raw fibrous fruit and vegetables are always better as they will contain more fiber compared to the cooked state - nonetheless, even cooked, these foods will aid your gut health.

Drink filtered water. Avoid drinking water straight from the tap as it contains traces of chlorine which can damage the balance of your gut flora. Filtered water also seems to be better for a healthy microbiome[18] helping reduce bowel inflammation and maintain healthy, regular bowel movements.

Reduce alcohol intake. It is a factor that helps the microbiome recover[19] from alcohol-induced imbalances in its population of bacteria, which then allows it to maintain a more efficient immune system.

Reduce non-organic animal product intake. Recent studies showed that livestock that consumes antibiotics on a regular basis (even when the animals are not sick) grow bigger and get fatter. It’s more profitable to grow larger animals in a shorter time. Unfortunately, there are traces of the same antibiotics the animals receive in the meat we buy. When we consume the meat we also receive, in lower doses, the same bacteria-killing antibiotics that were given to the animals. The suggestion here is that these lower doses of antibiotics, cumulatively, will also affect us in a similar way, making us bigger and fatter. Certified organic meat, dairy and eggs are not budget-friendly so simply replacing like-for-like in the same quantity may be unrealistic. So, it can be a good idea to simply limit the amounts of meat, dairy and eggs we consume and see if it makes a difference in how we feel.

Eat 30+ different types of food every week. Eating a wide variety of different foods will help to cultivate a diverse gut flora. It is recommended to eat a minimum of 30 different varieties every week to maintain a healthy and balanced microbiome. Focus primarily on high fiber foods - vegetables, fruit and grains and make sure to include all food groups. The only type of food that should be limited is sugar. Also limit or completely exclude any food that has been overly processed as it lacks the nutritional value of its organic equivalent and will only starve your microbiome: supermarket bread and snacks, breakfast cereals, canned foods, ready meals, ham and sausages, sugary drinks and ketchup are some examples to avoid. Make your meals at home with food that is as close to its natural state as possible.

Get enough sleep. Sleep deprivation and poor quality sleep have been cited as causes of disturbance of the balance of the microbiote in a number of studies [20] and have shown that this impacts the way the body handles insulin, puts on weight and fights off disease. Poor quality sleep has also been implicated in the rise in populations of bad bacteria in the gut and the incidence of chronic fatigue[21]. Getting sufficient hours of good quality sleep is of direct benefit to the mind and body as they both use the time to repair their basic structures, replenish their store of energy and refresh the connections that make them function correctly.

Exercise. High intensity exercise produces adaptation responses throughout the body and affects us at a cellular level. It also helps the microbiome achieve greater diversity of bacterial populations[22] by inhibiting the growth of bad bacteria in the gut and promoting the growth of bacteria that is more beneficial to us. Even moderate levels of exercise have been found to affect the microbiome which then releases hormones that affect the way the heart functions[23].

The Big Picture Regarding the Microbiome

It is clear that the microbiome is the missing link between health and nutrition and the reason why so many of our mental and psychological functions can become impaired with time. The evidence links an organic food diet and intense exercise with a diverse and healthy microbiome. It is however, far from simple. The causal links are not always linear or immediately obvious, they are however impossible to ignore.


1.Faecal biomarker patterns in patients with symptoms of irritable bowel syndrome
2. Transplantation of fecal microbiota from patients with irritable bowel syndrome alters gut function and behavior in recipient mice
3. Irritable bowel syndrome: a gut microbiota-related disorder?
4. Commensal bacteria and essential amino acids control food choice behavior and reproduction
5. Microbiome remodelling leads to inhibition of intestinal farnesoid X receptor signalling and decreased obesity
6. Microbiota-gut-brain axis and cognitive function
7. Age Drives Distortion of Brain Metabolic, Vascular and Cognitive Functions, and the Gut Microbiome
8. Pathogenic shifts in endogenous microbiota impede tissue regeneration via distinct activation of TAK1/MKK/p38
9. You Are What You Host: Microbiome Modulation of the Aging Process
10. Exercise Modifies the Gut Microbiota with Positive Health Effects
11. The Association between Cardiorespiratory Fitness and Gut Microbiota Composition in Premenopausal Women
12. Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans.
13. Exercise training-induced modification of the gut microbiota persists after microbiota colonization and attenuates the response to chemically-induced colitis in gnotobiotic mice
14. Effect of intermittent fasting on physiology and gut microbiota in presenium rats
15. Diet and Feeding Pattern Affect the Diurnal Dynamics of the Gut Microbiome
16. The Impact of Diet and Lifestyle on Gut Microbiota and Human Health
17. Influence of diet on the gut microbiome and implications for human health
18. Microbiome profiling of drinking water in relation to incidence of inflammatory bowel disease.
19. The Gastrointestinal Microbiome: Alcohol Effects on the Composition of Intestinal Microbiota.
20. Gut microbiota and glucometabolic alterations in response to recurrent partial sleep deprivation in normal-weight young individuals
21. Sleep quality and the treatment of intestinal microbiota imbalance in Chronic Fatigue Syndrome
22. High-intensity exercise training increases the diversity and metabolic capacity of the mouse distal gut microbiota during diet-induced obesity
23. Moderate-Intensity Exercise Affects Gut Microbiome Composition and Influences Cardiac Function in Myocardial Infarction Mice
There are 37.2 Trillion Cells in Your Body
Revised Estimates for the Number of Human and Bacteria Cells in the Body
More than half your body is not human
Glycolysis for the Microbiome Generation
Mechanisms Linking the Gut Microbiome and Glucose Metabolism
Gut microbiome and aging: Physiological and mechanistic insights
Role of the Microbiota in Immunity and Inflammation
Revised Estimates for the Number of Human and Bacteria Cells in the Body
NIH Human Microbiome Project defines normal bacterial makeup of the body
The Epidemiology of Obesity: A Big Picture
The Obesity Epidemic: Challenges, Health Initiatives, and Implications for Gastroenterologists
The Epidemiology of Obesity
Gut bacteria and the brain: Are we controlled by microbes?
American Gut: an Open Platform for Citizen Science Microbiome Research
Evidence of different metabolic phenotypes in humans
Human metabolic phenotype diversity and its association with diet and blood pressure
Human genetics shape the gut microbiome
An introduction to the analysis of shotgun metagenomic data
Microbial regulation of microRNA expression in the amygdala and prefrontal cortex
When Good Bacteria Go Bad
Microbiome Research Is Becoming the Key to Better Understanding Health and Nutrition
Microbiome Research is Changing Medicine

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