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Author Notes:

Correspondence: M. A. Azcarate-Peril, Department of Cell Biology and Physiology, School of Medicine, University of North Carolina, 332 Isaac Taylor Hall, Campus Box 7545, Chapel Hill, NC 27599-7545, USA e-mail: azcarate@med.unc.edu

All authors contributed to study design and interpretation.

Amanda L. Thompson and Michelle L. Lampl acquired the samples.

Andrea Monteagudo-Mera and Maria B. Cadenas conducted DNA isolation and sample processing for sequencing.

Andrea Monteagudo-Mera and M. A. Azcarate-Peril conducted data analysis.

Amanda L. Thompson, Andrea Monteagudo-Mera and M. A. Azcarate-Peril drafted the manuscript.

All authors provided critical revision to the manuscript and have approved the final version.

All authors agree to take responsibility for accuracy and integrity of the research.

We are thankful to Allison McFadden for insightful scientific discussions.

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Research Funding:

The Microbiome Core Facility is supported in part by the NIH/National Institute of Diabetes and Digestive and Kidney Diseases grant P30 DK34987.

Funding for this analysis was provided in part by the University Research Council, University of North Carolina at Chapel Hill.

Amanda L. Thompson is supported by NIH NICHD grant K01 HD071948-01.

We thank the Carolina Population Center at the University of North Carolina at Chapel Hill (NIH 5 R24 HD050924) for general support.


  • infant gut microbiome
  • breastfeeding
  • metagenomics
  • daycare
  • feeding transitions

Milk- and solid-feeding practices and daycare attendance are associated with differences in bacterial diversity, predominant communities, and metabolic and immune function of the infant gut microbiome


Journal Title:

Frontiers in Cellular and Infection Microbiology


Volume 5


Type of Work:

Article | Final Publisher PDF


The development of the infant intestinal microbiome in response to dietary and other exposures may shape long-term metabolic and immune function. We examined differences in the community structure and function of the intestinal microbiome between four feeding groups, exclusively breastfed infants before introduction of solid foods (EBF), non-exclusively breastfed infants before introduction of solid foods (non-EBF), EBF infants after introduction of solid foods (EBF+S), and non-EBF infants after introduction of solid foods (non-EBF+S), and tested whether out-of-home daycare attendance was associated with differences in relative abundance of gut bacteria. Bacterial 16S rRNA amplicon sequencing was performed on 49 stool samples collected longitudinally from a cohort of 9 infants (5 male, 4 female). PICRUSt metabolic inference analysis was used to identify metabolic impacts of feeding practices on the infant gut microbiome. Sequencing data identified significant differences across groups defined by feeding and daycare attendance. Non-EBF and daycare-attending infants had higher diversity and species richness than EBF and non-daycare attending infants. The gut microbiome of EBF infants showed increased proportions of Bifidobacterium and lower abundance of Bacteroidetes and Clostridiales than non-EBF infants. PICRUSt analysis indicated that introduction of solid foods had a marginal impact on the microbiome of EBF infants (24 enzymes overrepresented in EBF+S infants). In contrast, over 200 bacterial gene categories were overrepresented in non-EBF+S compared to non-EBF infants including several bacterial methyl-accepting chemotaxis proteins (MCP) involved in signal transduction. The identified differences between EBF and non-EBF infants suggest that breast milk may provide the gut microbiome with a greater plasticity (despite having a lower phylogenetic diversity) that eases the transition into solid foods.

Copyright information:

© 2015 Thompson, Monteagudo-Mera, Cadenas, Lampl and Azcarate-Peril.

This is an Open Access work distributed under the terms of the Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/).
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