Matthew D Di Guglielmo1,2, Karl Franke3, Courtney Cox2, Erin L Crowgey3. 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.
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.
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.
Entities:
Keywords:
Breast-feeding; Gut microbiome; Infants; Metagenomics; Next generation sequencing; Whole genome
Authors: Scott Schwartz; Iddo Friedberg; Ivan V Ivanov; Laurie A Davidson; Jennifer S Goldsby; David B Dahl; Damir Herman; Mei Wang; Sharon M Donovan; Robert S Chapkin Journal: Genome Biol Date: 2012-04-30 Impact factor: 13.583
Authors: Tanya Yatsunenko; Federico E Rey; Mark J Manary; Indi Trehan; Maria Gloria Dominguez-Bello; Monica Contreras; Magda Magris; Glida Hidalgo; Robert N Baldassano; Andrey P Anokhin; Andrew C Heath; Barbara Warner; Jens Reeder; Justin Kuczynski; J Gregory Caporaso; Catherine A Lozupone; Christian Lauber; Jose Carlos Clemente; Dan Knights; Rob Knight; Jeffrey I Gordon Journal: Nature Date: 2012-05-09 Impact factor: 49.962
Authors: S R Stockdale; R S Harrington; A N Shkoporov; E V Khokhlova; K M Daly; S A McDonnell; O O'Reagan; J A Nolan; D Sheehan; A Lavelle; L A Draper; F Shanahan; R P Ross; C Hill Journal: Sci Rep Date: 2022-06-02 Impact factor: 4.996
Authors: Matthew D Di Guglielmo; Karl R Franke; Alan Robbins; Erin L Crowgey Journal: Front Cell Infect Microbiol Date: 2022-03-04 Impact factor: 5.293