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The Persistent Gut Microbiota in Infancy and it’s Origin

Scientifically reviewed by
Dr Fathalla Ali, PhD (Paediatrics)


During and after birth, the gut of a newborn baby is rapidly colonized with microbiota. This early gut colonization plays an important role in the baby’s immune system development. Factors such as premature birth, cesarean section delivery and antibiotic exposure have been identified to disrupt the colonization process and contributed to the increased risk of developing chronic diseases in later life, such as asthma, and metabolic disorders.

In a recent study published in Cell Reports Medicine, Jillian and her colleagues followed 23 full-term infants and 19 preterm infants for 1 year to understands the persistent gut microbiota and the origin of this microbiota. A total of 402 samples from infants and their mothers were collected and subjected to deep metagenomic sequencing. Infants’ samples were assigned into seven groups based on the age of children at the time of sample collection (at birth, 1 month, 2 months, 3 months, 4 months, 8 month and 1 year). The mothers’ samples were collected at the time of delivery and used to identify the transmission of microbiota between the infant and the mother’s gut microbiota.

Findings from this study found that:

    • Early bacterial colonization represented about 47% of bacteria that colonized the gut during the first 2 months of life.
    • Only 11% of the early bacterial colonizers persisted through the first year of baby’s life. However, this small percentage of early persisted colonizers have the ability to shape the pattern of the developing microbiota, and significantly impact on the developing immune system.
    • Bacteroides and Bifidobacteria were among the early colonizers and more likely to persist than were other bacteria.
    • The persistence of Bacteroides was attributed to the maternal gut origin of this bacteria.
    • The persistence of Bifidobacteria was attributed to the availability of specific enzymes that have the ability to degrade polysaccharides. 
    • The percentage of the persisted early colonizers was higher among full-term infants than preterm infants. This could be due to various factors related to premature birth such as gestational age, early antibiotic exposure and prolonged hospital stay.
  • Bacteroides vulgatus and Bifidobacterium breve were the most persisted microbiota in full-term babies.
  • Bacteroides uniformis and Escherichia coli were the more persisted microbiota in preterm babies.
  • Preterm infants were less likely to share bacterial strains with other preterm infants.
  • The gut microbiota of preterm infants was found to diverged from full-term between 1-3 months of age.
  • Similarity in the gut microbiota between full-term and preterm infants was identified to begin at 3 month and accelerate between 4-8 months of age.


In conclusion, early gut microbiota colonization plays an important role in determining the persistent microbiota throughout the first year of life.

Keywords: Persistent microbiota, Full-term infants, Preterm infants, Bifidobacteria, Bacteroidetes 


Lou, Y. C., Olm M. R., Diamond S., et al. (2021), Infant gut strain persistence is associated with maternal origin, phylogeny, and traits including surface adhesion and iron acquisition, Cell Reports Medicine, 2 (9),

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