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The early life determinants for Gut Dysbiosis

Written by
Dr Fathalla Ali, PhD (Paedatrics)


The gastrointestinal tract is the home for the most diverse and populated bacterial community known as microbiota. Ideally, the gut microbiota lives in a mutually symbiotic relationship with the human body. Whilst the gut provides the well-adapted shelter, the microbiota provides the physiological benefits to the host such as help the development and function of the immune system through the fermentation of indigestible carbohydrates. Homeostasis or the balance in the growth and development of gut microbiota plays an important role in maintaining this relationship. However, dysbiosis or microbial imbalance often develops and negatively effect on this mutual symbiotic relationship. Dysbiosis is the result of a loss of overall diversity, a loss in beneficial bacteria, or a gain of pathogenic bacteria, often associated with disease development such as asthma, obesity, coeliac disease, inflammatory bowel disease, and irritable bowel syndrome. Among the most important factors that are associated with dysbiosis are delivery methods, infant feeding, antibiotic exposure and the exposure to household pets.

  • Delivery methods

Mode of delivery is one of the most important determinants for gut microbiota development during the first 4-6 months of infant’s life. Caesarean section delivery could contribute to gut dysbiosis in early infancy which consequently impact on immune system development. Infants delivered by caesarean section have delayed contact to their mother, delayed start of breastfeeding and at risk of developing hospital microbiota, which has been associated with risk of developing respiratory diseases.

  • Antibiotic use

Gut dysbiosis is also caused by the exposure to antibiotic after, during or after birth. For example, infants sometimes get exposed to antibiotics indirectly through the administration of antibiotic to the mother during delivery. This early exposure has been found to have a stronger impact on newborn gut microbiota than the impact of caesarean section delivery. A single dose of antibiotic to newborn infants could contribute significantly in decreased the abundance of good bacteria, particularly Bifidobacterium, and increased the abundance of pathogenic bacteria.

  • Feeding

Breast milk is composed of essential components that play a vital role in shaping the gut microbiota which is essential in the development of the immune system.

The gut microbiota of breast-fed infant is relatively less diverse than the gut microbiota of formula-fed infants due to the higher abundance of Bifidobacterium species, including Bifidobacterium breve, Bifidobacterum bifidum, and Bifidobacterium longum, which are essential for the digestion of Human Milk oligosaccharides (HMOs).

Solid food introduction has been identified to influence the diversity of gut microbiota through stimulating the development of bacteria essential in the digestion of complex carbohydrate. Among these bacteria are Bacteroides and Firmicutes species


  • Household Pets 

Contact with household pets prenatally and postnatally could promote a more gut microbiota diversity in young children, which is known to protect against atopy and obesity.

Keywords: dysbiosis, breastfeeding, mode of delivery, antibiotics, pets, microbiota


Parkin, K., Christophersen, C. T., Verhasselt, V., Cooper, M. N., & Martino, D. (2021). Risk Factors for Gut Dysbiosis in Early Life. Microorganisms, 9(10), 2066. MDPI AG. Retrieved from

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