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Researchers Get Important Glimpse into Microbiome Development in Early Life

A team of researchers at the Children’s Hospital of Philadelphia (CHOP) has characterised how the gut microbiome develops in the first hours of infancy, providing a critical baseline for how changes in this environment can impact health and disease later in life. The findings were published online by the journal Nature Microbiology.

“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 study team focused on three species of bacteria – Escherichia coli, Enterococcus faecalis, and Bacteroides vulgatus – because to date those species have been observed in the highest number of babies. They analysed the genomes of these bacteria to determine why they are growing in infants. Additionally, the team characterised the proteins and metabolites, or small molecules, 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.

The study team found evidence that the initial environment of the gut microbiome is anaerobic, contrary to the prevailing model which holds that the gut becomes anaerobic only after bacteria grow and consume oxygen. The evidence came from observing the order in which amino acids were consumed by bacteria.

Analysis of the three bacterial species studied in these infants revealed that multiple strains of each bacterium were already emerging.

“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.”

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. Additionally, all 88 infants involved in the study are African American, a population for whom childhood obesity is a growing concern.

Paper: Bittinger K, et al. (2020). Bacterial colonization reprograms the neonatal gut metabolome. Nat Microbiol.;


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