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

Authors

Matthew D. Di Guglielmo, Thomas Jefferson University; Nemours Alfred I. duPont Hospital for ChildrenFollow
Karl Franke, Nemours Alfred I. duPont Hospital for Children
Courtney Cox, Nemours Alfred I. duPont Hospital for Children
Erin L. Crowgey, Nemours Alfred I. duPont Hospital for Children

Document Type

Article

Publication Date

6-1-2019

Comments

This article has been peer reviewed. It is the author’s final published version in Human Microbiome Journal, Volume 12, June 2019, Article number 100057.

The published version is available at https://doi.org/10.1016/j.humic.2019.100057. Copyright © Di Guglielmo et al.

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 under- standing the adult gut microbiome, and the pathogenesis of obesity.

Recommended Citation

Di Guglielmo, Matthew D.; Franke, Karl; Cox, Courtney; and Crowgey, Erin L., "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" (2019). Department of Pediatrics Faculty Papers. Paper 87.
https://jdc.jefferson.edu/pedsfp/87

Creative Commons License

This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.

Language

English