Factors That Influence The Gut Microbiome Diversity

by | Jun 25, 2023 | Life

The gut microbiome of your body appears to be a bustling city flooded with people rushing to work when seen under a microscope. This is actually the complex community of not only bacteria but fungi, parasites, and viruses residing in your intestine. For many of you, it must come up as a surprise that, the presence of bacteria makes your gut healthy. But it is true! The relationship between these good bacteria and human health has been recognized by various researchers. 

The normal human gut microbiome diversity mostly comprises two phyla, Bacteroidetes and Firmicutes. However, the gut microbiome distribution varies from the esophagus to the rectum all along the individual’s lifespan.

The gut microbiome is labeled a supporting organ because it performs smooth daily operations indispensable to its host namely, nutrient metabolism, drug metabolism, maintenance of structural integrity of gut mucosal barrier, immune modulation, and protection against foreign microbes. 

Despite so much value, there are a large number of factors influencing your gut microbiome diversity as you proceed with life. Along with these, several more aspects decide on the shaping of normal gut microbiomes since birth. These include the family genes; the mode of delivery, whether cesarean or vaginal; the diet during infancy; use of antibiotics since birth. Therefore, there is uniqueness among the microbiomes of different individuals. In your gut, each species of microorganisms have been assigned a specific task. 


Here, we are going to discuss the most important intrinsic and extrinsic factors influencing gut microbiome diversity in detail.


As per CDC, 32.2% of deliveries are performed by the caesarian section in the United States. This affects the composition of their gut microbiome diversity as it differs from those born by vaginal delivery. Studies have shown that infants born by caesarian delivery are more prone to developing obesity or diabetes than those born vaginally. This is because vaginal delivery infants are exposed to the mother’s bacteria at birth which influences the infant’s gut bacteria and stimulates the white blood cells along with components of the immune system. Hence, it contributes to a better immune system than cesarean-born infants.


The family members have been found to share similar gut microbiome communities than unrelated individuals. Thus, one can observe a resemblance in the metabolic and mental health of the host and one or more family members. But, it is still difficult to evaluate which human genes shape up the gut microbiome. Additionally, to investigate and assess the role of genetic background in determining the microbiome, the environmental effects have to be minimized.


Infant feeding is an important factor in determining the composition of the bacterial community in the gut of the host. The mother’s breast milk is the medium for potential probiotic bacteria which helps to shape up the infant’s gut bacteria. The human milk contains >700 species of bacteria and the median bacterial load is approx.106 bacterial cells/ml. Thus, ingesting up to 800 ml of breast milk every day can raise the bacterial cells 100 times higher than previous estimates. This clearly states that the gut microbiome diversity changes over the course of lactation. 

However, the composition of the gut microbiome differs in different lactating mothers. The gut microbiome is different and less diverse in the milk of obese mothers and mothers who underwent cesarean section. 


You all know about the role of gut microbiome in improving your immune response against foreign pathogens but the reverse is also true. A study conducted on the microbiome of mice has proven this fact. The mice microbiome was subjected to Citrobacter rodentium and an alteration in certain groups of bacteria was observed. It caused a reduction in the relative abundance of Lactobacillus causing dysbiosis of the whole gut.  Nowadays, these studies have encouraged us to use transplantation of the gut microbiome from healthy donors to infected patients as a part of the treatment regimen. In this, a fecal transplant is done and has shown success in an infection called Clostridium difficile and prevented it from coming back.


Antibiotics are the most common drugs that have saved millions of lives from infections. But their effect on the human gut microbiome is still unknown to many. The effect is rapid and may persist for long in some cases. The use of broad-spectrum antibiotics such as Clindamycin in infants and children has long-lasting and profound effects on the gut microbiome. They disrupt the gut microbial balance by decreasing the abundance of beneficial bacteria. 


Interventional studies show that the choice of diet results in substantial and rapid changes in the gut microbiome composition. A high-calorie diet is associated with obesity and type 2 diabetes, whereas probiotics and prebiotics consumption is believed to be beneficial to health. 

Probiotics naturally contain beneficial live microbiomes that uplift your gut’s microbiome. If not consumed as natural foods, they can also be taken as supplements. They are present in fermented foods such as kefir, yogurt, pickled vegetables, kombucha tea, kimchi, miso, and sauerkraut.

Prebiotics are present in high-fiber foods which particularly affects the type and amount of microbiome in the gut. When these undigested foods are broken down by the intestinal microbes, short-chain fatty acids are released. This lowers the pH level of the intestine, limiting the growth of some harmful bacteria like Clostridium difficile. They also help in maintaining normal levels of glucose and cholesterol. Prebiotics are abundantly present in raw versions of garlic, onions, asparagus, leeks, bananas, seaweed, and whole grains including wheat, oats, and barley. 


Research has improved our understanding of the environment as a major factor of variability in the human microbiome. The environment in the broad sense involves contextual, social, and environmental toxicants. Exposure to these factors has a direct impact on the human microbiome, implicated in human health and diseases. 


Environmental factors involve everything that affects everyday living and changes the natural ecosystem around us. The primary environmental factors are air, soil, water, noise and radioactive pollution; deforestation; solid waste pollution, and global warming. So, we all need to join hands to resolve these issues effectively.

  • Plant more trees
  • Prefer carpooling and public transport over personal vehicles
  • Use renewable and biodegradable sources
  • Recycling
  • Proper disposal of harmful wastes

Chronic stress is seen to have a direct link with reduced microbiome diversity and thereafter, compromising intestinal permeability. Thus, people suffering from long-term mental imbalance are more prone to gastrointestinal issues including irritable bowel syndrome and multiple inflammatory bowel diseases. This link between your gut and brain explains why you feel “butterflies in your stomach” whenever you are anxious. 

Taking this aspect into account, you can improve your gut diversity or have a better prognosis in case of gut disorders. So, you need to practice these methods to calm your overstressed mind.

  • Get enough physical activity on a regular basis like walking and running.
  • Take up exercises like Hatha or Iyengar yoga which focuses on alignment and posture to stay mindful.
  • Meditation exercises with deep breathing.
  • Do not reach for a cigarette or alcohol as a habit to lower your stress levels. These bad habits will further deteriorate the number of beneficial bacteria in your gut.
  • Get enough non-interrupted sleep.

Water is referred to as an essential nutrient required for good gut health. Studies conducted on people in the US and UK drinking high volumes of water a day have shown a lower abundance of gastrointestinal infection-causing bacteria, campylobacter. Other than this, staying dehydrated for a long will subject you to more risk of constipation. The long term constipation leads to disruption of the microbiome and contributes to diseases like diverticular disease. The presence of any of the symptoms including bloating, gassy, and stomach pain can be an alarming sign that it’s time to gear up your water intake. 

Bloating also becomes worse in summers

Fibrous foods are one reason. If you are upping the fiber, you need to take in more water or your stools will be extra dry and hard. Extra sweating in the high-temperature weather leaves you dehydrated. So, take an extra 500ml to stay regulated in the heat. Every mug of beer or caffeinated drink must also accompany a glass of water to compensate for the fluid loss.


The low diversity and uneven distribution of bacterial species need immediate action including diet and stress modulation. A healthy gut is the easiest way to support a healthy immune function which will in turn foster both mental and physical health. 

Download the JoyScore app and improve your health and lifestyle with simple steps.

Download on the Appstore

Get it on Google Play

Dr. Bob Singhal

Professor Bhupendra 'Bob' Singhal, has taught creativity by joy and right-brain thinking, is a renowned international architect, won major design competitions, has over 70 awards, publications, and media mentions, and served as President of the American Institute of Architects South Bay. In 2011, in his book Joy in Health and Happiness: Your Optimal Path to Success, Professor Singhal wrote about the transformative power of joy and helped readers learn to enhance their daily experience of it.


Download JoyScore App