Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States

Authors

Giorgio Casaburi, Evolve Biosystems, Inc.
Rebbeca M. Duar, Evolve BioSystems, Inc.
Heather Brown, Evolve Biosystems, Inc.
Ryan D. Mitchell, Evolve Biosystems, Inc.
Sufyan Kazi, Evolve Biosystems, Inc.
Stephanie Chew, Evolve Biosystems, Inc.
Orla Cagney, Evolve Biosystems, Inc.
Robin L. Flannery, Evolve Biosystems, Inc.
Karl G. Sylvester, Stanford University
Steven A. Frese, Evolve BioSystems & University of Nebraska - Lincoln & University of Nevada, RenoFollow
Bethany M. Henrick, Evolve BioSystems, Inc. and University of Nebraska-LincolnFollow
Samara L. Freeman, Evolve Biosystems, Inc.

Date of this Version

2021

Citation

Scientific (2021) 11:1472 | https://doi.org/10.1038/s41598-020-80583-9

Comments

2021 (Authors)

Abstract

The gut microbiome plays an important role in early life, protecting newborns from enteric pathogens, promoting immune system development and providing key functions to the infant host. Currently, there are limited data to broadly assess the status of the US healthy infant gut microbiome. To address this gap, we performed a multi-state metagenomic survey and found high levels of bacteria associated with enteric inflammation (e.g. Escherichia, Klebsiella), antibiotic resistance genes, and signatures of dysbiosis, independent of location, age, and diet. Bifidobacterium were less abundant than generally expected and the species identified, including B. breve, B. longum and B. bifidum, had limited genetic capacity to metabolize human milk oligosaccharides (HMOs), while B. infantis strains with a complete capacity for HMOs utilization were found to be exceptionally rare. Considering microbiome composition and functional capacity, this survey revealed a previously unappreciated dysbiosis that is widespread in the contemporary US infant gut microbiome.