Metagenomic Characterisation of the Gut Microbiome and Effect of Complementary Feeding on <i>Bifidobacterium</i> spp. in Australian Infants
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 intro...
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| Format: | Article |
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MDPI AG
2024-01-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/12/1/228 |
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| author | Kimberley Parkin Debra J. Palmer Valerie Verhasselt Nelly Amenyogbe Matthew N. Cooper Claus T. Christophersen Susan L. Prescott Desiree Silva David Martino |
| author_facet | Kimberley Parkin Debra J. Palmer Valerie Verhasselt Nelly Amenyogbe Matthew N. Cooper Claus T. Christophersen Susan L. Prescott Desiree Silva David Martino |
| author_sort | Kimberley Parkin |
| collection | DOAJ |
| description | 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 <i>Bifidobacterium infantis</i>. 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 <i>Escherichia</i> 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. |
| first_indexed | 2024-03-08T09:49:57Z |
| format | Article |
| id | doaj.art-9a4c2ce989df4719848880b48737e60b |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-08T09:49:57Z |
| publishDate | 2024-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-9a4c2ce989df4719848880b48737e60b2024-01-29T14:07:11ZengMDPI AGMicroorganisms2076-26072024-01-0112122810.3390/microorganisms12010228Metagenomic Characterisation of the Gut Microbiome and Effect of Complementary Feeding on <i>Bifidobacterium</i> spp. in Australian InfantsKimberley Parkin0Debra J. Palmer1Valerie Verhasselt2Nelly Amenyogbe3Matthew N. Cooper4Claus T. Christophersen5Susan L. Prescott6Desiree Silva7David Martino8Telethon Kids Institute, University of Western Australia, Nedlands, Perth, WA 6009, AustraliaTelethon Kids Institute, University of Western Australia, Nedlands, Perth, WA 6009, AustraliaTelethon Kids Institute, University of Western Australia, Nedlands, Perth, WA 6009, AustraliaTelethon Kids Institute, University of Western Australia, Nedlands, Perth, WA 6009, AustraliaTelethon Kids Institute, University of Western Australia, Nedlands, Perth, WA 6009, AustraliaSchool of Molecular Life Sciences, Curtin University, Bentley, Perth, WA 6102, AustraliaMedical School, University of Western Australia, Nedlands, Perth, WA 6009, AustraliaMedical School, University of Western Australia, Nedlands, Perth, WA 6009, AustraliaTelethon Kids Institute, University of Western Australia, Nedlands, Perth, WA 6009, AustraliaComplementary 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 <i>Bifidobacterium infantis</i>. 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 <i>Escherichia</i> 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.https://www.mdpi.com/2076-2607/12/1/228gut microbiomeshotgun metagenomicsbreastfeeding<i>Bifidobacterium</i>complementary feedingthe ORIGINS project |
| spellingShingle | Kimberley Parkin Debra J. Palmer Valerie Verhasselt Nelly Amenyogbe Matthew N. Cooper Claus T. Christophersen Susan L. Prescott Desiree Silva David Martino Metagenomic Characterisation of the Gut Microbiome and Effect of Complementary Feeding on <i>Bifidobacterium</i> spp. in Australian Infants Microorganisms gut microbiome shotgun metagenomics breastfeeding <i>Bifidobacterium</i> complementary feeding the ORIGINS project |
| title | Metagenomic Characterisation of the Gut Microbiome and Effect of Complementary Feeding on <i>Bifidobacterium</i> spp. in Australian Infants |
| title_full | Metagenomic Characterisation of the Gut Microbiome and Effect of Complementary Feeding on <i>Bifidobacterium</i> spp. in Australian Infants |
| title_fullStr | Metagenomic Characterisation of the Gut Microbiome and Effect of Complementary Feeding on <i>Bifidobacterium</i> spp. in Australian Infants |
| title_full_unstemmed | Metagenomic Characterisation of the Gut Microbiome and Effect of Complementary Feeding on <i>Bifidobacterium</i> spp. in Australian Infants |
| title_short | Metagenomic Characterisation of the Gut Microbiome and Effect of Complementary Feeding on <i>Bifidobacterium</i> spp. in Australian Infants |
| title_sort | metagenomic characterisation of the gut microbiome and effect of complementary feeding on i bifidobacterium i spp in australian infants |
| topic | gut microbiome shotgun metagenomics breastfeeding <i>Bifidobacterium</i> complementary feeding the ORIGINS project |
| url | https://www.mdpi.com/2076-2607/12/1/228 |
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