US Study shows 90% of infants lack bacterial species needed for immune system development

Written by
Fathalla Ali, Bsc MSc, MPH and PHD student UNSW

A multiple states metagenomic cross sectional study revealed that the vast majority of American infants showed a significant deficiency in an important bacterial strain essential for human milk utilization and immune system development. The study was conducted on 127 healthy infants aged 0-6 months across five geographically diverse states (California, Georgia, Oregon, Pennsylvania and South Carolina). The aims of the study were: (1) characterize the gut bacterial composition of healthy infants during the 0-6 months; (2) determine the metabolic potential of different gut bacterial enterotypes to utilize Human Milk Oligosaccharide (HMO); and (3) to characterize the signature of Antibiotic Resistant Genes (ARGs) in infants across the five surveyed US states.

Findings from this study found that:

  • In general, more than 90% of the infant’s gut microbiota were represented by ten bacterial families. The majority were composed of potentially pathogenic species such as Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca, Enterobacter cloaceae and Streptococcus agalactiae which are associated with negative health outcomes such as Necrotizing Enterocolitis and Sepsis.
  • Non-pathogenic bacteria, specifically the bacterial family of Bifdobacteriaceae was found less abundant in all infants across the surveyed states.
  • The genera Bifidobacterium were less abundant than generally expected and the identified species were characterized by the limited capacity to utilize HMO.
  • Species with complete capacity for HMO utilization such B. infantis were rarely identified.
  • The microbiota structure of all infants in this study, regardless of location, diet or age were grouped into three distinct enterotypes which are Bifidobacteriaceae, Enterobacteriaceae and Bacteroidaceae.
  • The Enterobacteriaceae enterotype classified group of infants were characterized by the higher abundance of the potentially pathogenic bacteria (Enterobacteriaceae) and higher abundance of Antibiotic Resistance Genes (ARGs).
  • The Bifidobacteriaceae enterotype classified group of infants were characterized by the higher abundance of the potentially non-pathogenic bacteria (Bifidobacteriaceae) and lower abundance of Antibiotic Resistance Genes (ARGs)
  • About 325 unique Antibiotic Resistance Genes (ARGs) were identified in the microbiome of the surveyed infants across the five states, 20 of the identified ARGs were uniquely presented in infants from Southern California.
  • In conclusion, this study found that microbiome in infants in the US characterized by high abundance of pathogenic bacteria, high abundance of ARGs and the limited capacity to metabolize Human Milk Oligosaccharides from breast milk.

Keywords: Microbiome, Non-pathogenic bacteria, Pathogenic bacteria, Bifidobacterium, Antibiotic Resistance Genes, Human Milk Oligosaccharides


Casaburi, G., Duar, R.M., Brown, H. et al. Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States. Sci Rep 11, 1472 (2021).