While researchers understand the important connection between the many species of bacteria in the gut microbiome and human health, how these species emerge in infancy and what functions they serve are not fully understood.
In the current study, published online by the journal Nature Microbiology, a team of researchers from Children's Hospital of Philadelphia (CHOP) analysed the bacteria present in 88 African American infants - a population for whom childhood obesity is a growing concern.
"Eventually, the gut in children will hold hundreds of different species of bacteria, but at birth, there might only be 10 or fewer species," said Kyle Bittinger, PhD, the analytics core director of the Microbiome Center at CHOP and first author of the study.
"We wanted to understand why those particular bacteria are the first to emerge and what they are doing in those first hours of life."
The team focused on three species of bacteria - Escherichia coli, Enterococcus faecalis, and Bacteroides vulgatus - because those have been observed in the highest number of babies.
They analysed the genomes of these bacteria to determine why they are growing in infants and characterised the proteins and metabolites that were present in the microbiome at this stage of development.
One of the challenges for collecting this information is that for the first several hours of life, any DNA collected from a stool sample is not from the bacteria but from the infant itself. The researchers did not see bacteria emerge in detectable concentrations until the infants were about 16 hours old.
By observing the order in which amino acids were consumed by bacteria the team concluded that the initial environment of the gut microbiome is anaerobic, contrary to the previous understanding that the gut becomes anaerobic only after bacteria grow and consume oxygen.
The researchers also observed that metabolite levels were generally consistent with the detection of bacteria - Molecules typically produced by gut bacteria, like acetate and succinate, went up in samples where bacteria were detected.
Additionally, the levels of select proteins went down in samples containing bacteria, suggesting that bacteria might have been consuming those proteins to promote growth.
Analysis of the three bacterial species studied in these infants revealed that multiple strains of each bacterium were already emerging.
The microbiome and weight gain
The researchers hope to use the study findings to determine how the development of the gut microbiome may influence excess weight gain. The infants involved in this study will be followed through the first two years of life.
"With the information we have, as we continue to follow these infants, we can track them and see how long these early strains of bacteria linger," Bittinger said. "We can then see the consequences of this initial chemical activity in later samples and hopefully pinpoint early changes that might impact health later in childhood."
Babette Zemel, PhD, director of the Nutrition and Growth Laboratory at CHOP, and senior co-author of the study, added: "There are remarkably few studies that have looked at infant growth patterns in African Americans.
"With this important first piece in the puzzle, we can follow these healthy term infants and learn what a normal growth pattern looks like so that, in the future, we may be able to intervene when changes in the microbiome can adversely affect children."
Source: Nature Microbiology
Bittinger. K., et al
"Bacterial colonization reprograms the neonatal gut metabolome."