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Early Microbiota Colonization and Gut Metabolome

Written by
Dr Fathalla Ali, PHD Paediatrics


It’s believed that the status of our health in later life is associated with the first bacteria that colonize our gut. In a prospective, longitudinal cohort study, Bittinger et al (2020), investigated the gut microbiome, proteome and metabolome in 88 African American newborn infants during the first month of life. Infants included in this study were full term infants (>37 weeks gestation) and did not have any major congenital abnormalities. Findings from this study showed that:

  • Mode of delivery was associated with the bacterial and gene composition at 1 month but not at birth.
  • The increased composition in the number of Bacterial counts was due to the increased colonization rate of Bifidobacterium, Veillonella, Streptococcus, and Enterobacteriaceae.
  • Genes associated with carbohydrate fermentation (glycoside hydrolase genes) were significantly increased after 1 month of the infant’s life.
  • Continuous breastfeeding for the first month of life was associated with increased abundance of Bifidobacteria (non-pathogenic bacteria).
  • These bacteria were detected in samples collected after 1000 hours after birth.
  • The detection of bacterial DNA increased significantly with time since birth.
  • The transition from human DNA occurred earlier in samples collected from vaginal delivered infants than C-section delivered infants.
  • The likelihood of detecting bacterial DNA increased after 16 hours following birth. Samples collected after 16 hours showed higher bacterial-to-human DNA ratio than samples collected before 16 hours.
  • 16 hours after birth represented the cut off time after which the count of bacterial DNA exceeded the count of human DNA.
  • The functional analysis of the first bacterial colonizer showed that 45 metabolites were differentially abundant in samples with high bacterial DNA.
  • Amino acids such as serine and threonine, decreased with bacterial growth.
  • Metabolites associated with bacterial fermentation such as succinate and acetate increased with the detection of bacterial DNA.

Keywords: Microbiota, Mode of delivery, bacterial DNA, metabolite, gut metabolome reprogramming


Bittinger, K., Zhao, C., Li, Y., Ford, E., Friedman, E. S., Ni, J., Kulkarni, C. V., Cai, J., Tian, Y., Liu, Q., Patterson, A. D., Sarkar, D., Chan, S., Maranas, C., Saha-Shah, A., Lund, P., Garcia, B. A., Mattei, L. M., Gerber, J. S., Elovitz, M. A., … Wu, G. D. (2020). Bacterial colonization reprograms the neonatal gut metabolome. Nature microbiology, 5(6), 838–847. Click here


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