Metagenomic Characterisation of the Gut Microbiome and Effect of Complementary Feeding on Bifidobacterium spp. in Australian Infants

Kimberley Parkin; Debra J Palmer; Valerie Verhasselt; Nelly Amenyogbe; Matthew N Cooper; Claus T Christophersen; Susan L Prescott; Desiree Silva; David Martino

doi:10.3390/microorganisms12010228

Metagenomic Characterisation of the Gut Microbiome and Effect of Complementary Feeding on Bifidobacterium spp. in Australian Infants

Microorganisms. 2024 Jan 22;12(1):228. doi: 10.3390/microorganisms12010228.

Authors

Kimberley Parkin^{1

2}, Debra J Palmer^{1

2}, Valerie Verhasselt^{1

3}, Nelly Amenyogbe¹, Matthew N Cooper¹, Claus T Christophersen^{4

5}, Susan L Prescott^{2

4

6

7

8

9}, Desiree Silva^{2

4

5

8

9}, David Martino^{1

10}

Affiliations

¹ Telethon Kids Institute, University of Western Australia, Nedlands, Perth, WA 6009, Australia.
² Medical School, University of Western Australia, Nedlands, Perth, WA 6009, Australia.
³ Larsson-Rosenquist Foundation Centre for Immunology and Breastfeeding, Medical School, University of Western Australia, Nedlands, Perth, WA 6009, Australia.
⁴ School of Molecular Life Sciences, Curtin University, Bentley, Perth, WA 6102, Australia.
⁵ School of Medical and Health Sciences, Edith Cowen University, Joondalup, Perth, WA 6027, Australia.
⁶ Joondalup Health Campus, Joondalup, Perth, WA 6027, Australia.
⁷ Nova Institute for Health, Baltimore, MD 21231, USA.
⁸ Department of Family and Community Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
⁹ The ORIGINS Project, Telethon Kids Institute, Nedlands, Perth, WA 6009, Australia.
¹⁰ School of Molecular Science, University of Western Australia, Nedlands, Perth, WA 6009, Australia.

Abstract

Complementary feeding induces dramatic ecological shifts in the infant gut microbiota toward more diverse compositions and functional metabolic capacities, with potential implications for immune and metabolic health. The aim of this study was to examine whether the age at which solid foods are introduced differentially affects the microbiota in predominantly breastfed infants compared with predominantly formula-fed infants. We performed whole-genome shotgun metagenomic sequencing of infant stool samples from a cohort of six-month-old Australian infants enrolled in a nested study within the ORIGINS Project longitudinal birth cohort. Infants born preterm or those who had been administered antibiotics since birth were excluded. The taxonomic composition was highly variable among individuals at this age. Predominantly formula-fed infants exhibited a higher microbiome diversity than predominantly breastfed infants. Among the predominantly breastfed infants, the introduction of solid foods prior to five months of age was associated with higher alpha diversity than solid food introduction after six months of age, primarily due to the loss of Bifidobacterium infantis. In contrast, the age at which solid food was introduced was not associated with the overall change in diversity among predominantly formula-fed infants but was associated with compositional changes in Escherichia abundance. Examining the functional capacity of the microbiota in relation to these changes, we found that the introduction of solid foods after six months of age was associated with elevated one-carbon compound metabolic pathways in both breastfed and formula-fed infants, although the specific metabolic sub-pathways differed, likely reflecting different taxonomic compositions. Our findings suggest that the age of commencement of solid foods influences the gut microbiota composition differently in predominantly breastfed infants than in predominantly formula-fed infants.

Keywords: Bifidobacterium; breastfeeding; complementary feeding; gut microbiome; shotgun metagenomics; the ORIGINS project.

Grants and funding

This study was funded by the Telethon Kids Institute Blue Sky Award. VV work was supported by the funding endowed by the Family Larsson-Rosenquist Foundation.