Metagenomic Characterisation of the Gut Microbiome and Effect of Complementary Feeding on Bifidobacterium spp. in Australian Infants
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Approval and Consent to Participate
2.2. Study Participants
2.3. Questionnaires and Operational Definitions
2.4. Laboratory Processing and Bioinformatics Profiling
2.4.1. Stool Sample Collection
2.4.2. DNA Extraction
2.4.3. Library Preparation
2.4.4. Sequencing
2.4.5. Metagenomic Sequencing Data Quality Control (QC)
2.4.6. Quantification of Microbial Species, Gene, and Pathway Abundances
2.5. Statistical Analyses
2.5.1. Community Composition
2.5.2. Diversity Analysis
2.5.3. Differential Abundance
2.5.4. Plots
3. Results
3.1. Cohort Description
3.2. Metagenomic Characterisation of Faecal Samples
3.3. Infant Gut Microbiome Taxonomy Is Highly Variable between Individuals and Primarily Defined by Feeding Method
3.4. Age of Solid Food Introduction Influences Alpha Diversity in Breastfed Infants Only
3.5. Age of Solid Food Introduction Affects Differential Abundance of Different Species in Breast versus Formula-Fed Infants
3.6. Functional Potential
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Level | n (%) | Missing Data (%) | |
---|---|---|---|
n | 170 | ||
Sex | F | 90 (52.9) | 0 (0) |
M | 80 (47.1) | ||
Milk-based diet at six months of age | Predominantly formula-fed | 58 (34.1) | 0 (0) |
Predominantly breastfed | 93 (54.7) | ||
Mixed-fed | 19 (11.2) | ||
Delivery method | Emergency caesarean | 35 (20.6) | 0 (0) |
Planned caesarean | 40 (23.5) | ||
Vaginal | 95 (55.9) | ||
Age of solid food introduction | <5 months | 38 (22.4) | 6 (3.5) |
5–6 months | 114 (67) | ||
>6 months | 12 (7) |
Age of Solid Food Introduction | |||||
---|---|---|---|---|---|
Level | <5 Months of Age (%) | 5–6 Months of Age (%) | >6 Months of Age (%) | p-Value | |
n | 38 | 114 | 12 | ||
Sex | F | 13 (14.9) | 68 (78.2) | 6 (6.9) | 0.024 |
M | 25 (32.5) | 46 (59.7) | 6 (7.8) | ||
Milk-based diet at six months of age | Predominantly formula-fed | 17 (29.8) | 37 (64.9) | 3 (5.3) | 0.595 |
Predominantly breastfed | 17 (19.3) | 63 (71.6) | 8 (9.1) | ||
Mixed-fed | 4 (21.0) | 14 (73.7) | 1 (5.3) | ||
Delivery method | Emergency caesarean | 5 (15.2) | 27 (81.8) | 1 (3.0) | 0.038 |
Planned caesarean | 9 (22.5) | 24 (60.0) | 7 (17.5) | ||
Vaginal | 24 (26.4) | 63 (69.2) | 4 (4.4) |
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Parkin, K.; Palmer, D.J.; Verhasselt, V.; Amenyogbe, N.; Cooper, M.N.; Christophersen, C.T.; Prescott, S.L.; Silva, D.; Martino, D. Metagenomic Characterisation of the Gut Microbiome and Effect of Complementary Feeding on Bifidobacterium spp. in Australian Infants. Microorganisms 2024, 12, 228. https://doi.org/10.3390/microorganisms12010228
Parkin K, Palmer DJ, Verhasselt V, Amenyogbe N, Cooper MN, Christophersen CT, Prescott SL, Silva D, Martino D. Metagenomic Characterisation of the Gut Microbiome and Effect of Complementary Feeding on Bifidobacterium spp. in Australian Infants. Microorganisms. 2024; 12(1):228. https://doi.org/10.3390/microorganisms12010228
Chicago/Turabian StyleParkin, Kimberley, Debra J. Palmer, Valerie Verhasselt, Nelly Amenyogbe, Matthew N. Cooper, Claus T. Christophersen, Susan L. Prescott, Desiree Silva, and David Martino. 2024. "Metagenomic Characterisation of the Gut Microbiome and Effect of Complementary Feeding on Bifidobacterium spp. in Australian Infants" Microorganisms 12, no. 1: 228. https://doi.org/10.3390/microorganisms12010228