Factors that Influence the Gut Microbiota

Factors that Influence the Gut Microbiota

A variety of outside factors can influence the trillions of microbes that live in your gut. The simple reality that our gut bacteria are easily influenced is actually a good thing because it allows us to change things that are under our control. 

Our gut microbes coexist with us in our bodies. They have the power to make us thin or fat, healthy or sick, happy or sad. That is why many researchers and doctors believe it is critical to maintain a healthy microbiome.

Modern lifestyles are threatening the health of our guts like never before, thanks in part to our unbalanced diets and lifestyle choices. In this blog, you will discover the different factors that influence our gut microbiota and how this could impact how your body works.

Factors Influencing the Gut Microbiota

The gut microbiota has many important functions in the body, including playing a role in digestion and metabolism, affecting the immune system, supporting resistance to pathogens, and affecting the behavioural and neurological functions of the host.

However, there are certain factors that affect and change the gut microbiota, including genetics, mode of birth, infant feeding, age, diet, hormones, geographical location, and ethnicity, exposure to pathogens, stress, physical activity, medications/antibiotics, alcohol consumption, and tobacco use. Let’s shed some light on each of these factors!

  • Genetics

Although genetics plays a minor role in shaping the gut microbiome, genes may negatively affect your gut. Heritability studies in twins and families have highlighted that human genetics contributes to gut microbial variation. According to a study from the MiBioGen consortium led by researchers at the University Medical Centre Groningen, at least two human genes have a significant impact on shaping our gut ecosystem:

  • The lactase gene (LCT) influences the abundance of lactose-digesting Bifidobacteria in adults.
  • The fucosyl transferase (FUT2) gene determines the abundance of Ruminococcus torques.
  • Mode of Birth

The mode of delivery affects the early-life development of the gut microbiota. The composition of the gut bacterial community is different in infants delivered by vaginal delivery from that of infants born by caesarean section. Researchers believe that C-sections could lead to dysbiosis of gut microbiota and may lead to c-section-related autoimmune and metabolic disorders. Research has also suggested that infants born by C-section are at a greater risk of developing obesity and/or diabetes than those born vaginally.

  • Infant Feeding

Following childbirth, bacteria from breast milk and the mother's skin enter the infant's body and play an important role in health. For infants, breast milk is the optimal food as it meets all their nutritional and physiologic requirements. It contains carbohydrates, protein, fat, and other necessary nutrients. Experts believe it is not sterile and contains as many as 600 different species of bacteria including beneficial Bifidobacterium and Lactobacillus. This creates a balanced microenvironment and the development of the local and systemic immune system.

  • Age

As we age, our gut microbes become relatively stable by early childhood, but there are plenty of opportunities for the community of microbes to change along the way. Around three years of age, the composition of the gut microbiota resembles that of an adult and remains stable. Upon ageing, declines in salivary function, dentition, digestion, and intestinal transit time may affect the gut microbiota. With regard to older people over the age of 70, immune activity and gut microbiota diversity weaken.

  • Diet

Diet is a very significant contributing factor that affects the composition of the gut microbiome. Animal-based diet microbiome (high fats and proteins and low fibres) or plant-based diet microbiome (low fats and proteins and high fibres) or any respective changes in the diet have demonstrated a shift in the function of the bacterial community. For example, an animal-based diet increases the abundance of bile-tolerant microorganisms (Alistipes, Bacteroides, and Bilophila). Plant-based diets have been found to be associated with healthy, diverse gut microbiota.

  • Geographical Location and Ethnicity

Your ethnicity and geographical location can also affect the composition and functioning of the gut microbiome. People from different parts of the world tend to have more diverse bacteria due to distinguishing factors like differences in diets, medical history, and living environments. Moreover, the moment you try to move and adapt to new environmental factors, your gut microbiota experience a shift almost immediately. Fortunately, we can manipulate our gut microbial composition through diet and lifestyle to maintain healthy gut flora.

  • Exposure to Pathogens

One of the most common causes of gut dysbiosis (imbalance of the gut composition) is infection. During an infection, changes in the gut microbiota occur as a result of changes in the host (gene expression, immunity such as inflammation), or environmental factors (diet or antibiotic). As a result, changes in the intestine's physiological (pH), metabolic, and nutritional environment occur. These changes may favour the growth of pathogenic microbes while inhibiting good bugs, thereby increasing the risk of pathogen colonisation and infection. Pathogenic bacteria dominate the altered gut microbial community, which aggravates the gut condition by inducing intestinal inflammation, which promotes pathogen growth.

  • Stress

Scientifically, stress is known as a state of fight-or-flight. This psychological response can induce numerous physiological changes in the gut. Stress signals travel along the gut-brain axis, which refers to a communication pathway between the central nervous system and the gastrointestinal tract; it uses signalling hormones and other fancy messengers to manage what we do and how we feel on a daily basis. According to research, stress alters the balance in our microbiome by favouring unhelpful bacteria, which can lead to feelings of anxiety and depression. Stress and depression can both increase permeability of the gut barrier. As a result of the “leaky gut,”bacteria enter the circulation and cause an inflammatory response. Prolonged stress has been linked to an increased risk of a variety of GI disorders, including IBD.

  • Physical Activity/Exercise

Contrary to other factors, physical activity or exercise enhances microbial diversity as it increases the number of beneficial microbial species. Increased frequency of moderate exercise on a daily basis is associated with greater diversity in Firmicutes species that contribute to a healthier gut environment. Exercise has the potential to improve the Bacteroidetes-Firmicutes ratio, which could contribute to weight loss, resulting in a lower incidence of obesity and metabolic diseases. It can also increase the good bugs, resulting in increased disease protection and improved barrier functions. It can stimulate specific bacteria known to produce substances such as short-chain fatty acids (SCFAs) that protect a person against gastrointestinal disorders and colon cancer. The SCFAs, such as butyrate, are the primary source of fuel for the cells of the gut lining, helping to maintain its integrity and prevent organic compounds from foods, metabolites, and toxins from entering the bloodstream.

  • Medications/Antibiotics

The use of antibiotics or other medications can have a major impact on gut microbiota composition. Antibiotics are a double-edged sword in that they kill both pathological and beneficial microbes indiscriminately, allowing for the loss of gut microbiota, or dysbiosis, and the growth of unwanted microbes. Antibiotics disrupt the competitive exclusion machinery, which is a fundamental mechanism by which microbiota eliminate pathogenic microbes. Studies have shown that certain medications, like proton pump inhibitors that relieve symptoms of acid reflux and are used to treat stomach ulcers, moderately increase the risk of small intestinal bacterial overgrowth.

  • Alcohol Consumption and Tobacco Use

Excessive alcohol consumption may result in dysbiosis, bacterial overgrowth, and the overall composition of the gut microbiome. It can inhibit the production of digestive enzymes and juices making it difficult for your body to breakdown, digest, and absorb nutrients from your food. Partially digested food can cause excessive fermentation in your gut resulting in bloating, gas and loose stools. Smoking appears to alter the composition of the gut microbiota, resulting in dysbiosis. The mechanisms by which smoke toxicants alter human intestinal microbiota are not well understood. Smoke components can benefit some bacteria populations by increasing intestinal pH or decreasing organic acid production, allowing some species to thrive and causing intestinal microbiota dysbiosis. Cigarette smoking increases the risk of intestinal disorders like peptic ulcers and Crohn's disease.


The gut microbiota has a profound effect on our day-to-day lives. While some factors are known to influence the gut microbiota, it is still unclear how exactly each factor influences its development. We hope that this blog post has helped you understand more about the factors that influence the gut microbiota.


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