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

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. T...

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Autores principales:	Giorgio Casaburi, Rebbeca M. Duar, Heather Brown, Ryan D. Mitchell, Sufyan Kazi, Stephanie Chew, Orla Cagney, Robin L. Flannery, Karl G. Sylvester, Steven A. Frese, Bethany M. Henrick, Samara L. Freeman
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/98c8513e1de341c28667530bcbc7f34b
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spelling	oai:doaj.org-article:98c8513e1de341c28667530bcbc7f34b2021-12-02T13:57:05ZMetagenomic insights of the infant microbiome community structure and function across multiple sites in the United States10.1038/s41598-020-80583-92045-2322https://doaj.org/article/98c8513e1de341c28667530bcbc7f34b2021-01-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-80583-9https://doaj.org/toc/2045-2322Abstract 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.Giorgio CasaburiRebbeca M. DuarHeather BrownRyan D. MitchellSufyan KaziStephanie ChewOrla CagneyRobin L. FlanneryKarl G. SylvesterSteven A. FreseBethany M. HenrickSamara L. FreemanNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Giorgio Casaburi Rebbeca M. Duar Heather Brown Ryan D. Mitchell Sufyan Kazi Stephanie Chew Orla Cagney Robin L. Flannery Karl G. Sylvester Steven A. Frese Bethany M. Henrick Samara L. Freeman Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States
description	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.
format	article
author	Giorgio Casaburi Rebbeca M. Duar Heather Brown Ryan D. Mitchell Sufyan Kazi Stephanie Chew Orla Cagney Robin L. Flannery Karl G. Sylvester Steven A. Frese Bethany M. Henrick Samara L. Freeman
author_facet	Giorgio Casaburi Rebbeca M. Duar Heather Brown Ryan D. Mitchell Sufyan Kazi Stephanie Chew Orla Cagney Robin L. Flannery Karl G. Sylvester Steven A. Frese Bethany M. Henrick Samara L. Freeman
author_sort	Giorgio Casaburi
title	Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States
title_short	Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States
title_full	Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States
title_fullStr	Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States
title_full_unstemmed	Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States
title_sort	metagenomic insights of the infant microbiome community structure and function across multiple sites in the united states
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/98c8513e1de341c28667530bcbc7f34b
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Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States

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