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.