Gut (Microbiota) Therapy

Today’s Microbiome Science is saying that diverity of the Microbiome (MB) is more important that it’s balance, assuming that the more diversified it is, the more balance there will be. In this Page, I will first question this above-mentioned claim (Section A) and thereafter, I will review a few techniqus that can help the Gut to be more diversified in the good critters and flourishing in an abundance of homeostasis. (Section B)

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Section A

Section B


What we eat has a great effect on our gut bacteria [R]. If the good bacteria species in foods or supplements do not have the appropriate fuels or conditions to grow in your gut, they may not colonize. Therefore, diet has a larger effect on the gut microbiota composition than probiotic supplementation.

Dietary changes can account for up to 30 – 60% of gut microbiota changes, whereas genes account for no more than 12% [RR].

People who eat a lot of animal fat or protein have more Bacteroides, whilethose who eat a lot of carbohydrates have more Prevotella. Firmicutes are associated with fiber-rich diets [RR].

The western diet is high in red meat, animal fat, and sugar and low in fiber. This increases Bacteroides [R].

Prevotella are the most abundant bacteria in vegetarians [R].

Short-term dietary modifications change microbiota rapidly but also reversibly. Long-term dietary change, however, can cause irreversible alterations to gut microbiota [R].

A study looked at what happens when people eat either plant- or animal-based diets exclusively for 5 days. Their bacteria changed within the first day. However, bacteria also reverted to the original state 2 days after the diet was over [RR].

Long-term consumption of a Mediterranean diet increases butyrate producers(these have many health benefits) [R].

  • Fruits, vegetables, and grains in general (fiber-containing foods) [RR]
  • Apples [R]
  • Pomegranate [R]
  • Blueberries [R]
  • Blackcurrant [R]
  • Black raspberries [R]
  • Nuts (almonds, pistachios, walnuts) [RRRR]
  • Yogurt [RRRR] and fermented milk (kefir) [RRR]
  • Kimchi [R]
  • Red wine [RR]
  • Cocoa [RR]
  • Coffee [R]
  • Oatmeal [R]
  • Soy and fermented soymilk [RR]
  • Rice bran [R]
  • Olive oil with thyme [R]
  • Lion’s Mane [R]
  • Capsaicin (more beneficial for people on meat- and fat-rich diets) [RR]
  • Retinoic acid [R]

Foods with Negative Effects on Gut Bacteria

  • Artificial sweeteners [R]
  • Sugars in excess [R]

Foods with Complex Effects on Gut Bacteria

  • Long-chain saturated fatty acids [RR]

Prebiotics: Plant Fiber and Resistant Starch

Prebiotics are basically non-digestible plant fiber (complex carbohydrates). They have the following characteristics [R]:

  • They are resistant to stomach acidity and digestive enzymes
  • reach the colon undigested
  • In the colon, they are fermented by gut microbiota
  • They promote the growth and activity of ‘good bacteria’

Prebiotics include oligo- and polysaccharides, inulin, resistant starch, and pectin.

Prebiotics increase the growth of beneficial bacteria, such as Bifidobacteria and Lactobacilli in humans [RRRRR].

They also increase butyrate-producing bacteria [RR].

In 19 subjects, fiber increased overall microbiota richness and stability [R].


They tend to increase the levels of ‘good bacteria’ such as Lactobacilli and Bifidobacteria in the gut while decreasing the levels of potentially harmful microbes [RRRRRRRRRRRRRR].

Probiotics also increase SCFA levels (such as butyrate) [RRRR].

They also help restore gut microbiota after a course of antibiotics or illness [RR].

2) Stress

Stress can disturb gut microbiota, and this can, in turn, cause various disorders and diseases.

A study addressed the effects of stress in pregnancy (measured as self-reported stress, elevated cortisol levels or both). Of the 56 infants observed in the study, those born to mothers who were stressed during pregnancy had disturbed gut microbiota. They had more harmful bacteria, and lower levels of ‘good bacteria’, such as lactic acid bacteria and Bifidobacteria. They were also more prone to gut disorders and allergic reactions [R].

A similar situation was found in animals, where stress in pregnancy altered the gut microbiota of the offspring [R, R, R].

Stress negatively changed gut microbiota in mice. They end up having increased intestinal permeability and became prone to drug-induced gut injury [R].

3) Exercise

Exercise can increase the number of ‘good’ bacteria and enrich the gut microbial diversity [R].

A study showed that elite rugby players (40 subjects) had richer gut microbiota compared to carefully chosen non-athlete controls (46 subjects). In particular, there was a greater diversity of Firmicutes (including the beneficial Faecalibacterium prausnitzii) [R].

Another study compared 40 active and sedentary women. Active women had more health-promoting bacteria (including F. prausnitziiRoseburia hominis, and Akkermansia muciniphila) [R].

When a study compared 39 healthy subjects with various degrees of fitness, fit individuals had more butyrate-producers [R].

A high abundance of Prevotella (≥2.5%) was associated with the duration of exercise during an average week in 33 cyclists [R].

Exercise also improves gut microbiota in animals [R, R].

Interestingly, early-life exercise in rats was more beneficial compared to exercise in adulthood [R].

IMPORTANT: while low-intensity exercise is beneficial, endurance exercise can have a negative effect [R].

Military-type training had a negative impact on gut microbiota and it increases gut inflammation in 73 young soldiers [R].

In mice with IBD, voluntary wheel running improved symptoms. Forced treadmill running, on the other hand, worsened gut inflammation [R].

4) Sleep

Lack of sleep and low sleep quality disturb gut microbiota.

Nine people had increased Firmicutes/Bacteroidetes ratio after two days of partial sleep deprivation. Sleep deprivation caused a shift in gut bacteria associated with metabolic disturbances (that can lead to metabolic syndrome and diabetes) [R].

Chronic sleep fragmentation reversibly altered gut bacteria in mice (by decreasing beneficial Lactobacilli) [R].

Interestingly, dietary prebiotics improved both gut microbiota and sleep quality in rats [R].

Shift work increases the risk of obesity, metabolic syndrome, and type 2 diabetes, and perturbations in gut bacteria are one of the main suspects in this relationship [R].

5) Jet Lag

Jet lag disturbs the daily fluctuations of gut microbiota (yes, gut bacteria have daily rhythms) causing microbial imbalance also known as dysbiosis. Germ-free mice that received gut bacteria from jet-lagged mice developed glucose intolerance and obesity [R].

6) Medications

Antibiotics, proton pump inhibitors, antidepressants, statins and other commonly used drugs alter our microbiota in specific ways. As a consequence, commonly used drugs could affect how the gut microbiota resist infection, promote or decrease gut inflammation, or change the host’s metabolism [R].


Antibiotics are used to treat or prevent infection. However, they can cause unintended damage by depleting beneficial gut bacteria [R].

Antibiotics can dramatically decrease the richness of the gut community [R].

In some cases, after prolonged antibiotic treatment, full restoration of the gut microbiota is no longer possible [R].

A 7-day therapy with clindamycin, which has a strong and broad activity, decreased the diversity of Bacteroides in 4 subjects, compared to another 4 people who didn’t take the drug. The diversity was not restored to its original level even two years after therapy [R].

These effects can also be transferred to the next generation. In a study of 606 infants, depleted microbiota was found in infants born to mothers treated with antibiotics [R].

Furthermore, ‘bad bacteria’ can take advantage of the disturbance caused by antibiotics and multiply [R].

To minimize the risk of gut dysbiosis, it is best to use narrow-spectrum antibiotics whenever possible [R].

Finally, in some conditions where gut microbiota is already disturbed, antibiotics can actually help. They can restore gut microbial balance by decreasing ‘bad bacteria’.

For example, in 2 DB-RCTs with a total 211 IBS patients, rifampin helped by preventing the overgrowth of bad bacteria [RR].

Proton Pump Inhibitors (PPIs)

The overuse of PPIs shifts the gut microbiome towards a less healthy state. It may increase the risk of gut infections. PPIs also seems to favor Streptococcal growth – these are harmful bacteria that may cause ulcers [R].

In a study of 1815 individuals, 211 PPI users had lower bacterial diversity and 20% of their bacteria was significantly altered compared to non-users [R].


NSAID cause small intestine damage and ulcers. The damage may be worse in those with imbalanced gut bacteria.

In a DB-RCT with 20 healthy volunteers, probiotics decreased NSAID-induced gut damage, presumably by improving the composition of gut bacteria [R].


Metformin is a drug that improves type 2 diabetes symptoms. It increases beneficial bacteria such as A. muciniphila (a butyrate-producer) and Lactobacilli [R, R].

However, a study of 199 diabetic patients showed that metformin also increased Escherichia, which can be harmful [R].

7) Smoking

Smoking changes the gut microbiome.

Tobacco smokers have lower gut microbial diversity and lower levels of Bifidobacterium (20 subjects) [R].

When people stop smoking, their gut microbiota changes once again. Basically, their microbiota becomes more similar to that of obese people. This may partly explain the weight gain which happens after smoking cessation [RR].

In rats, cigarette smoke decreased SCFAs (acetic acid, propionic acid, and butyric acid – produced by good bacteria). It also lowered the levels of beneficial bacteria such as Bifidobacterium [R].

8) Pollution

Pollutants can disturb gut microbiota and impair gut microbiota-related metabolic processes [R].

Mice exposed to airborne pollution had an altered gut microbiome. They had decreased butyrate levels and developed acute and chronic gut inflammation [R].

Similarly, polychlorinated biphenyls (PCBs) decreased the abundance of gut bacteria in mice [R].

9) Gastric Bypass Surgery

A meta-analysis of 22 studies and a total of 562 patients showed that gastric bypass surgery changes gut microbiota. After the surgery, it resembles the microbiota of leaner people [R].

However, there are also possible side effects. A study of 51 patients showed that gastric bypass surgery increased TMAO by two-fold [R]. TMAO is a bacterial product that increases the risk of heart disease.

10) Fecal Microbiota Transplantation

Fecal microbiota transplantation is a relatively new procedure. It transfers gut bacteria from a healthy person into a patient with a disease/disorder. The goal is to completely restore a healthy gut microbiome [R].

There is a limited number of studies but the results so far are promising.

This procedure has been successful in 15 out of 16 patients with a Clostridium difficile infection [R].

Promising results were also observed in IBD. According to a meta-analysis of 9 studies, 22% of patients with ulcerative colitis and 60% of patients with Crohn’s disease were symptom-free after the procedure [R].

11) Geography

People in different parts of the world have different bacteria [R]. However, most of these differences can be attributed to their diets.

Prevotella dominate in in Malawi, Venezuela, Peru, India, Tibet, Indonesia, Thailand, and Korea [RRRR].

Bacteroides dominate in USA, China, Denmark, Spain, France, and Jamaica [RR].

Eubacterium dominates in Russia. Russian people, in general, have more bacteria that can degrade resistant starch [RR].

Japanese have more Bifidobacteria and Clostridium. They also have gut bacteria that can break down carbohydrates from algae. This are not found in other people [RRR].

People from Burkina Faso eat a high-fiber diet. They have four times higher butyrate and propionate compared to Europeans [R].

Hadza nomadic tribes of Tanzania have less inflammatory factors in their gut microbiota than Italians [R].

Isolated Amerindians, who had no previous contact with Western people, have the highest diversity of gut bacteria ever reported [R].

12) Urban vs. Rural Environment

People living in rural environments tend to have richer (and healthier) microbiota. This is also mostly diet-related [R].

For example, children from rural Thailand have more lactic acid bacteria than children from urban Singapore [R].

13) Birth and Breastfeeding

A study following 24 newborns, showed that infants delivered by C-section had depleted microbiota. They had lower Bacteroidetes compared to vaginally delivered children (24 children) [R].

Infant microbiota resembles their mothers’ in 72% of vaginally delivered babies. In C-section delivered babies this resemblance is reduced to 41% [R].

A study in 60 children showed that the differences in microbiota between vaginally and C-section delivered babies persists up to 7 years of age [R].

Finally, in a study of 606 infants, formula-fed infants had lower Bifidobacteriacompared to breastfed infants [R].

14) Having Older Siblings

People with older siblings have higher gut microbial diversity in early childhood (a study of 114 infants) [R].

15) Infections

Infections change our gut microbiota. This is true for bacterial infections, viral infections, such as influenza or HIV, or helminth infections [RRRRRRR].

These infections can cause long-term changes in gut bacteria, that persist long after the infection has been cleared [R].

Post-infection gut dysbiosis can result in other disorders, such as IBS or insulinresistance.

For example, H. pylori-infected mice have altered gut microbiota and often develop insulin resistance as a result [R].

16) Sex Hormones

The composition of our gut bacteria is sex-specific [R].

Gender differences in gut bacteria emerge during puberty.

In mice, gut microbiota undergoes a change in males but not in females. Castrating mice during puberty eliminates sex differences in adult mice. This shows the role of testosterone in organizing gut microbiota [R].

Interestingly, if females in puberty receive gut bacteria from adult males, they develop masculine microbiota. They also end up with elevated testosterone levels [R].

Finally, in animals, microbial communities exhibit high variability in females. This suggests a possible contribution of pulsatile estrogens [R].


For individual case analysis and personalized recommendations, you can book a consultation with one of our consultants.

Disclaimer: Nothing in this Educational post should be construed as medical advise.

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