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...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2021-01-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-020-80583-9 |
| _version_ | 1818851294749655040 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-19T07:02:45Z |
| format | Article |
| id | doaj.art-98c8513e1de341c28667530bcbc7f34b |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-19T07:02:45Z |
| publishDate | 2021-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-98c8513e1de341c28667530bcbc7f34b2022-12-21T20:31:22ZengNature PortfolioScientific Reports2045-23222021-01-0111111210.1038/s41598-020-80583-9Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United StatesGiorgio Casaburi0Rebbeca M. Duar1Heather Brown2Ryan D. Mitchell3Sufyan Kazi4Stephanie Chew5Orla Cagney6Robin L. Flannery7Karl G. Sylvester8Steven A. Frese9Bethany M. Henrick10Samara L. Freeman11Evolve BioSystems, Inc.Evolve BioSystems, Inc.Evolve BioSystems, Inc.Evolve BioSystems, Inc.Evolve BioSystems, Inc.Evolve BioSystems, Inc.Evolve BioSystems, Inc.Evolve BioSystems, Inc.Department of Surgery, Stanford UniversityEvolve BioSystems, Inc.Evolve BioSystems, Inc.Evolve BioSystems, Inc.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.https://doi.org/10.1038/s41598-020-80583-9 |
| spellingShingle | 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 Scientific Reports |
| title | 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_short | 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 |
| url | https://doi.org/10.1038/s41598-020-80583-9 |
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