8 factors that can cause microbiome imbalance

Do you know that not all bacteria cause infection and diseases? There are trillions of different kinds of bacteria residing in your body. Many of these are pathogenic, but some are not. Those that are not pathogenic are named good bacteria and are crucial in producing substances that protect your body and promote overall health. For example, bacteria in the large intestine produce vitamins K and B. 

The microorganisms living in the body, whether bacteria, viruses or fungi, are called the microbiome [1]. These organisms can exist in a particular environment, such as the skin, mouth, urogenital and gastrointestinal tract. 

These organisms are dynamic and respond to changes in the environment, such as the following: 

  • Diet
  • Medication 
  • Exercise 
  • Other exposures 

What are the benefits of the microbiome in the body? 

  • Bacteria that live in the gut help in food digestion 
  • Bacteria present in the skin help break down lipids, providing natural moisturiser for the skin 
  • Microbiota or microbiome stimulate the immune system 
  • Breaks down potentially toxic compounds 
  • Synthesise certain amino acids and vitamins 

Maintaining an appropriate balance of the microbiome is essential in promoting the individual’s overall health. However, imbalances can occur, which then can have an impact on one’s health. Here are eight factors that cause microbiome imbalance: 


Diet is long recognised to dramatically modulate gut microbiota (microbiome) composition [2]. In studies conducted amongst athletes [2], findings revealed that the microbiota’s actions are similar to that of endocrine organs. The microbiota was responsible for secreting neurotransmitters such as dopamine and serotonin. However, these studies reiterated that the athletes’ diet was a concern since this was low in plant polysaccharides. The latter is necessary for increasing the functionality and diversity of the gut microbiota. The higher the plant polysaccharides in the diet, such as plants rich in glycogen, chitin, cellulase, hyaluronic acid, and starch, the more diverse the gut microbiota. 

When applied to non-athletes, consumption of a diet low in plant polysaccharides or a diet low in fruits and vegetables can alter the balance of the microbiome. This could reduce the production of neurotransmitters needed for signalling between neurons or nerves. When this occurs, this could impact the body’s ability to regulate mood. For example, the body needs neurotransmitters such as serotonin to help improve mood, focus, and emotional stability. When serotonin levels are low, this is associated with depression [3]. 

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Food additives 

Food additives are used to prolong the shelf-life of foods and beverages. These additives include salt, vinegar and commercial additives that aim to extend a food’s lifespan. Some of these additives can alter the gut microbiota by interacting directly with the microorganisms in the digestive system, disrupting the microbiome’s balance. Some additives might act as allergens and cause stomach upset or allergic reactions. When this occurs, this can reduce populations of good bacteria, thereby disrupting the level of good bacteria in the gut. 

Cooking and processing of food 

Processing and cooking most of the food we eat are essential in maintaining their safety and taste. A review of studies [4] revealed that depending on the food that is cooked, the type of cooking method is associated with an increase or decrease in the population of good bacteria. For example, foods such as bread and banana, when cooked in intense heat such as grilling and roasting, can decrease levels of healthy bacteria. In addition, eating processed meat or red meat could increase the risk of developing colorectal cancer partly because of the interaction between carcinogens and the gut microbiome [4]. 


Micronutrients are critical in optimal body functioning and health. Although the body needs only tiny amounts of micronutrients, these are necessary for growth and development. Diets that are poor in micronutrients, such as Western diets, are associated with gut dysbiosis. Gut dysbiosis results from an imbalance in the good and bad bacteria in the gut microbiome. 

Meanwhile, dietary habits can alter the gut microbiome. For example, specific medications can reduce the population of healthy bacteria, leading to reduced production of vitamins and micronutrients in the gut, such as vitamins B and K. 


Carbohydrates are essential macronutrients of the body. Carbohydrates are categorised as organic compounds that are composed of carbon, hydrogen, and oxygen. It has broad biological functions and chemical structures [4]. Less complex carbohydrates are easily absorbed in the body. However, certain carbohydrates, such as cellulose, which are components of the cell walls of plants, could not be absorbed in the small intestine. Instead, this carbohydrate is taken to the large intestine, where colonic bacteria metabolise it. These carbohydrates are also called microbiome-accessible carbohydrates (MAC). 

MAC in the gut is necessary to reduce colon cancer risk. Another type of MAC important in maintaining the population of good bacteria includes human milk oligosaccharides (HMO). MAC and HMO are necessary to prevent bacterial pathogens’ adhesion in the gut. Both also guide the gut microbiome’s maturation, which in turn could improve human health. 

When diet is poor in dietary fibre and infants are not fed with HMO, this would lead to an imbalance of the gut microbiome. In adults, reduced levels of good bacteria are associated with an increased risk of colon cancer. When infants are not fed with HMO, this would also result in poor gut microbiome maturation, resulting in decreased immunity. 


The gut microbiota is developed in utero or fetal age and is established at about three years old [5]. Following birth, vaginal birth or the mode of delivery affects the gut microbiota’s early development. Newborns who are delivered through vaginal birth exhibit high levels of Prevotella and Lactobacillus, which are taken from the mother’s microbiota in the vagina. 

In contrast, caesarean delivery increase the population of Propionibacterium, Streptococcus, and Corynebacterium in infants born through this type of delivery [5]. These bacteria are abundant in the mother’s skin. These bacterial populations evolve and become more diverse until the age of three when the children’s microbiota become similar to adults’ microbiota. 

Imbalance in the population of bacteria during infancy and early childhood may be due to the mode of delivery and the type of diet the child has. 

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Antibiotics are essential medicines in combatting bacterial infections. However, large doses of antibiotics can decrease the population of good bacteria in the gut. The effect of antibiotics on the gut microbiota may be persistent and rapid. For example, broad-spectrum antibiotics have been shown to reduce the diversity of bacteria in the gut [6]. 

Infant feeding 

Infant feeding is another essential factor in establishing the microbiome of the infant’s gut. Since the mother’s milk is not sterile, it is a source of potential probiotic and commensal bacteria that influence the gut bacteria development of the infant [6]. 

It is now known that human milk contains more than 700 species of bacteria. The amount and diversity of bacteria ingested from human milk vary as the infant ages. In infants who are 0 months old, the predominant bacteria include Leuconostoc, Weissella, Streptococcus, Staphylococcus, and Lactococcus [6]. These bacteria are also the main components of human colostrum. Infants 1 to 6 months old has high levels of Prevotella, Leptorichia, and Veillonella. 

The mother’s body weight and body mass index also play a role in the type and amount of bacteria present in human milk. Mothers who are obese pass on less diverse bacteria to their infants compared with mothers with average body mass index. 

Breast milk is also recognised as a rich source of IgA antibiotics, which are needed to boost the immune system and protect the infant from infections. 

An imbalance in the gut microbiota could occur when infants are fed formula milk. However, some formula milk fortified with probiotics appears to benefit infants since this would increase the population of the good bacteria in the infant’s gut microbiota. 

Promoting a sufficient balance between good and bad bacteria is necessary for promoting the overall health of adults and infants. Increasing good bacteria in the body would help reduce the risk of different types of cancer, such as colon cancer. A healthy population of good bacteria also improves an individual’s brain health and overall health [6]. 

Due to the importance of maintaining commensal and good bacteria in the body, it is crucial to examine if one’s diet is appropriate for increasing the population of good bacteria. When diet is insufficient, taking probiotic supplements could increase your protection against certain forms of cancer while also boosting your immune system. 

Since there is a gut-brain connection, improving the population of good bacteria in the intestine could help mental acuity and improve memory and critical reasoning. 

Identifying the factors that could tip the balance of good and bad bacteria and avoiding these factors could improve overall health. 

Examining the probiotic supplementation most effective for you is necessary for good health and well-being. Talking to your doctor about available probiotic supplementations and which ones are most appropriate for your lifestyle and habits would take you on the right path towards health and wellness. 

[1] https://www.genome.gov/genetics-glossary/Microbiome 
[2] https://www.tandfonline.com/doi/full/10.1186/s12970-016-0155-6 
[3] https://www.nature.com/articles/s41380-022-01661-0 
[4] https://www.frontiersin.org/articles/10.3389/fnut.2021.644138/full#B135 
[5] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6699480 
[6] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5483960/ 

Photograph: sdecoret/Shutterstock
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