The definitive guide to healing and regenerating your microbiome

Do you know that not all bacteria are harmful to the body? We often associate bacteria with illness, infections and poor health. The good news is there are good bacteria in your body, and you can start reaping the benefits of these bacteria! 

What is a microbiome? 

Your body contains trillions of cells that form tissues and organs. However, do you know that the population of bacteria in your body outnumbers your body cells’ population? Trillions of microorganisms currently reside in your skin, the intestines, mouth and the urogenital area. This might frighten you or make you wonder how the body can fend off these microorganisms that could cause havoc in your health and immunity. 

A microbiome is a collection of all microorganisms, such as viruses, bacteria and fungi [1]. In recent years, scientists have addressed the erroneous belief that all bacteria are harmful to the body. Today, it is well-accepted that there are commensals or good bacteria in the body. 

What is a microbiome? 

The microbiome in your body is a group of commensals that benefit the immune system, the skin, the digestive system and the urogenital system. For example, bacteria in the skin are essential in breaking down lipids, which can help moisturise your skin. Bacteria in your gut or digestive system digest cellulose and dietary fibre while producing vitamins and micronutrients the body needs. 

Microbiomes in the body are necessary to prevent pathogenic microorganisms from invading the skin or gut. Hence, while taking up residence in different parts of the body, the microbiome also acts as a shield against infectious organisms. 

What causes an imbalance in the population of microbiomes

The bacterial population in microbiomes varies between persons and across different systems in the body. Maintaining homeostasis is critical in promoting the overall health of the individual. However, certain factors can disrupt the body’s balance of good and bad bacteria. Here are some examples of factors that disturb the balance of microbiomes. 

  • Diet 
  • Cooking and processing of food 
  • Food additives 
  • Age 
  • Antibiotics 
  • Infant feeding 
  • Medication 

When there is an imbalance in the microbiome, this increases the risk of pathogenic organisms infecting the body. This also limits the ability of the gut microbiota to produce vitamins K and B, which are needed in the body for various physical functions and metabolism. Hence, restoring balance is necessary to promote overall health and longevity. 

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Repopulating the gut microbiota would require several strategies. Here are some proven ways to improve your gut microbiota: 

  • Eat prebiotic foods 

Several foods have been identified as prebiotics, meaning they can increase the population of good bacteria in the gut. These rich prebiotic foods include apples, asparagus, oats, bananas and artichokes [2]. These prebiotic foods are rich in fibre, which can stimulate the growth of many healthy bacteria in the gut and other body parts. 

  • Eat foods rich in polyphenols

Polyphenol compounds are naturally occurring compounds present in many plants and herbs. Some examples of polyphenols include curcumin, a compound present in turmeric plants [3]. Polyphenols are categorised as phytochemicals and have antioxidant and anti-inflammatory properties. These compounds protect the body from reactive oxygen species (ROS), which can destroy cells and tissues when present in massive amounts. The anti-inflammatory properties of polyphenols also protect the body against infections [3]. 

Eating fruits and vegetables rich in polyphenols can help stimulate the growth of healthy bacteria. These compounds are broken down by good bacteria in the gut and are used to increase the gut microbiota population. 

  • Limit artificial sweeteners intake 

Artificial sweeteners are found in colas and other beverages. These sweeteners could increase the population of Enterbacteriacea, which has been proven to increase blood glucose levels. Hence, it is necessary to limit artificial sweeteners in beverages to ensure that the Enterbacteriacea population in the gut are within appropriate ranges [4]. 

  • Increase intake of yoghurt and other fermented foods 

Fermented foods contain good bacteria, such as Lactobacilli. Eating fermented foods such as yoghurt can increase the Lactobacilli population in the gut, improving gut health and, indirectly, brain health [5]. 

Fermented food, yoghurt
  • Breastfeed infants for at least six months 

The benefits of breastfeeding have been well-documented in research studies. One use includes improving infants’ gut microbiome and increasing the diversity and population of good bacteria in the gut. Breastfed infants receive more Bifidobacteria than infants who only receive formula milk. Bifidobacteria produce metabolites that are necessary for improving overall health. These microorganisms are also beneficial since they help develop the immunity of infants. Hence, breastfed infants have more protection against infections than bottle-fed infants [6]. 

  • Increase intake of a plant-based diet 

Diet rich in dietary fibre from vegetables and fruits is necessary to improve gut microbiota diversity and increase the population of good bacteria. A study [7] has shown that a plant-based diet is associated with a reduced population of Escherichia coli  in the gut. These bacteria are responsible for infectious diarrhoea. Further, a plant-based diet is associated with reduced inflammation since plants are rich in antioxidants and have anti-inflammatory properties. Additionally, a vegetarian diet is linked with lower cholesterol in the body. 

  • Take antibiotics as prescribed

Antibiotics are highly beneficial in the body since they kill pathogenic microorganisms and promote healing and recovery from infectious diseases. However, prolonged intake of antibiotics can disrupt the balance between commensal and harmful bacteria. Constant intake of antibiotics has been demonstrated to reduce the diversity of the bacterial population and the population of good bacteria. 

  • Take a probiotic supplement 

Dysbiosis or disruption of the balance between good and harmful bacteria can occur during prolonged illness, intake of artificial sweeteners, or having a diet low in fibre. However, probiotic supplements can restore the gut microbiome to a healthy state. 

Probiotics are described as food rich in live, good bacteria. Some examples of probiotics include yoghurt, kefir and sauerkraut. 

How long does it take to repopulate the gut with good bacteria? 

Repopulating the gut with good bacteria would take time and depends on several factors:

  1. The diversity of gut microbiota is vast and depends on one’s diet, genes, environment and behaviour, such as whether one exercises.
  2. People with severe illnesses may take longer to recover and restore their populations of good bacteria than others.
  3. People taking antibiotics may need to recover from their illness before normal levels of their good bacteria are restored. 

A study [8] revealed that it takes at least two months for individuals who completed a short-term antibiotic course before their gut microbiota is restored to normal levels. However, it should be noted that this was a small study and only involved a short-term antibiotic course. 

Meanwhile, it is suggested that it would take at least six months before gut microbiota is restored to normal levels following a course of antibiotics [9]. However, this is another small study and could not be applied to a larger group of patients. 

The exact time at which the gut microbiota can be restored to normal levels needs to be better established. Since the population diversity of the microorganisms significantly differs between individuals, it is difficult to show how long repopulation of the gut with good bacteria to normal levels could be achieved. 

Despite the lack of consensus on the number of months or weeks needed to repopulate the gut microbiota, it is well-accepted that increasing the diversity of the microbiota is necessary for maintaining optimal health. 

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Eating a healthy diet of fruits and vegetables, exercising and limiting refined sugar from beverages are some strategies that could be done now to promote gut health and increase the population of good bacteria. 

Choosing the best probiotic supplements is also crucial in improving gut microbiota diversity. You can talk to your doctor to help determine the most appropriate probiotic supplement. 


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The information included in this article is for informational purposes only. The purpose of this webpage is to promote broad consumer understanding and knowledge of various health topics. It is not intended to be a substitute for professional medical advice, diagnosis or treatment. Always seek the advice of your physician or other qualified health care provider with any questions you may have regarding a medical condition or treatment and before undertaking a new health care regimen, and never disregard professional medical advice or delay in seeking it because of something you have read on this website.