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Di Guglielmo MD, Franke K, Cox C, et al. Whole genome metagenomic analysis of the gut microbiome of differently fed infants identifies differences in microbial composition and functional genes, including an absent CRISPR/Cas9 gene in the formula-fed cohort. Hum Microb J. 2019;12doi: 10.1016/j.humic.2019.100057.
Di Guglielmo, M. D., Franke, K., Cox, C., & Crowgey, E. L. (2019). Whole genome metagenomic analysis of the gut microbiome of differently fed infants identifies differences in microbial composition and functional genes, including an absent CRISPR/Cas9 gene in the formula-fed cohort. Human microbiome journal, 12. https://doi.org/10.1016/j.humic.2019.100057
Di Guglielmo, Matthew D, et al. "Whole genome metagenomic analysis of the gut microbiome of differently fed infants identifies differences in microbial composition and functional genes, including an absent CRISPR/Cas9 gene in the formula-fed cohort." Human microbiome journal vol. 12 (2019). doi: https://doi.org/10.1016/j.humic.2019.100057
Di Guglielmo MD, Franke K, Cox C, Crowgey EL. Whole genome metagenomic analysis of the gut microbiome of differently fed infants identifies differences in microbial composition and functional genes, including an absent CRISPR/Cas9 gene in the formula-fed cohort. Hum Microb J. 2019 Jun;12. doi: 10.1016/j.humic.2019.100057. Epub 2019 May 25. PMID: 34278055; PMCID: PMC8281965.
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Hum Microb J. 2019 Jun;12. doi: 10.1016/j.humic.2019.100057. Epub 2019 May 25.

Whole genome metagenomic analysis of the gut microbiome of differently fed infants identifies differences in microbial composition and functional genes, including an absent CRISPR/Cas9 gene in the formula-fed cohort.

Human microbiome journal

Matthew D Di Guglielmo, Karl Franke, Courtney Cox, Erin L Crowgey

Affiliations

  1. Division of Gastroenterology and Nutrition, Department of Pediatrics, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States.
  2. Department of Pediatrics, Nemours/Alfred I. duPont Hospital for Children, Wilmington, DE, United States.
  3. Biomedical Research Department, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, United States.

PMID: 34278055 PMCID: PMC8281965 DOI: 10.1016/j.humic.2019.100057

Abstract

BACKGROUND: Advancements in sequencing capabilities have enhanced the study of the human microbiome. There are limited studies focused on the gastro-intestinal (gut) microbiome of infants, particularly the impact of diet between breast-fed (BF) versus formula-fed (FF). It is unclear what effect, if any, early feeding has on short-term or long-term composition and function of the gut microbiome.

RESULTS: Using a shotgun metagenomics approach, differences in the gut microbiome between BF (n = 10) and FF (n = 5) infants were detected. A Jaccard distance principle coordinate analysis was able to cluster BF versus FF infants based on the presence or absence of species identified in their gut microbiome. Thirty-two genera were identified as statistically different in the gut microbiome sequenced between BF and FF infants. Furthermore, the computational workflow identified 371 bacterial genes that were statistically different between the BF and FF cohorts in abundance. Only seven genes were lower in abundance (or absent) in the FF cohort compared to the BF cohort, including CRISPR/Cas9; whereas, the remaining candidates, including autotransporter adhesins, were higher in abundance in the FF cohort compared to BF cohort.

CONCLUSIONS: These studies demonstrated that FF infants have, at an early age, a significantly different gut microbiome with potential implications for function of the fecal microbiota. Interactions between the fecal microbiota and host hinted at here have been linked to numerous diseases. Determining whether these non-abundant or more abundant genes have biological consequence related to infant feeding may aid in understanding the adult gut microbiome, and the pathogenesis of obesity.

Keywords: Breast-feeding; Gut microbiome; Infants; Metagenomics; Next generation sequencing; Whole genome

Conflict of interest statement

Declaration of Competing Interest None of the authors has a conflict of interest to report.

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