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

Robin L Flannery,Sufyan Kazi,Steven A Frese,Heather Brown,Bethany M Henrick,Giorgio Casaburi,Orla Cagney,Samara L Freeman,Rebbeca M Duar,Ryan D Mitchell,Karl G Sylvester,Stephanie Chew

doi:10.1038/s41598-020-80583-9

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.

Highlights

The neonatal period represents a unique stage of life when critical foundations of lifelong health are established[1,2]
Illumina sequencing led to an average of 28 million PE reads per sample (± SD 6.4 million), of which 4.6% (± SD 12%) per sample on average were discarded as human reads
A total of 367 classified bacterial species belonging to 119 genera, 53 families, 25 orders, 15 classes, and 7 phyla were identified across the samples (Supplementary Table 2)

Summary

Introduction

The neonatal period represents a unique stage of life when critical foundations of lifelong health are established[1,2]. It is well established that gut microbiome perturbations characterized by the overrepresentation of potentially pathogenic taxa are implicated in mediating persistent pathophysiological and immune abnormalities, including heightened risk for immunological disorders later in life and acute chronic inflammation[3,5,6,7] These gut microbial perturbations, conceptually referred to as dysbiosis, are strongly associated with the absence of infant-associated Bifidobacterium that encode key functions required for the metabolization of human milk oligosaccharides (HMOs) in the infant[8]. The above criteria were used to classify microbiomes as dysbiotic or not, based on the concept of ecosystem s ervices[24] adapted to evaluate the benefits infants receive from functions provided by their gut m icrobiomes[8] Overall, this survey revealed that, on average, infants in the US have a low abundance of Bifidobacterium, a high abundance of potentially pathogenic bacteria carrying high levels of ARGs, as well as limited capacity of metabolizing HMOs from breast milk. This survey offers a new perspective when considering infants in the context of a healthy microbiome and the acute and long-term consequences it implies

Objectives

Methods

Results

Conclusion