Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort
Open accessAbstract
BACKGROUND: The gut is the most extensively studied niche of the human microbiome. The aim of this study was to characterise the initial gut microbiota development of a cohort of breastfed infants (n = 192) from 1 to 24 weeks of age. METHODS: V4-V5 region 16S rRNA amplicon Illumina sequencing and, in parallel, bacteriological culture. The metabolomic profile of infant urine at 4 weeks of age was also examined by LC-MS. RESULTS: Full-term (FT), spontaneous vaginally delivered (SVD) infants' microbiota remained stable at both phylum and genus levels during the 24-week period examined. FT Caesarean section (CS) infants displayed an increased faecal abundance of Firmicutes (p < 0.01) and lower abundance of Actinobacteria (p < 0.001) after the first week of life compared to FT-SVD infants. FT-CS infants gradually progressed to harbouring a microbiota closely resembling FT-SVD (which remained stable) by week 8 of life, which was maintained at week 24. The gut microbiota of preterm (PT) infants displayed a significantly greater abundance of Proteobacteria compared to FT infants (p < 0.001) at week 1. Metabolomic analysis of urine at week 4 indicated PT-CS infants have a functionally different metabolite profile than FT (both CS and SVD) infants. Co-inertia analysis showed co-variation between the urine metabolome and the faecal microbiota of the infants. Tryptophan and tyrosine metabolic pathways, as well as fatty acid and bile acid metabolism, were found to be affected by delivery mode and gestational age. CONCLUSIONS: These findings confirm that mode of delivery and gestational age both have significant effects on early neonatal microbiota composition. There is also a significant difference between the metabolite profile of FT and PT infants. Prolonged breastfeeding was shown to have a significant effect on the microbiota composition of FT-CS infants at 24 weeks of age, but interestingly not on that of FT-SVD infants. Twins had more similar microbiota to one another than between two random infants, reflecting the influence of similarities in both host genetics and the environment on the microbiota..
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There is divergence in intestinal microbiome assembly between different birth modes, between breast- and formula-fed infants, and between preterm and full-term infants, with implications for the associated microbial metabolite profile.
“There is also a divergence in intestinal microbiome assembly between different birth modes (Bokulich et al., 2016), between breast-and formula-fed infants (Clarke et al., 2014a), and between preterm and full-term infants, with implications for the associated microbial metabolite profile (Hill et al., 2017).”
From Gut reactions: Breaking down xenobiotic–microbiome interactions (2019) · cites this paper as Hill et al., 2017
Microbial colonization of the intestinal tract is a successive process throughout the course of life.
“Microbial colonization of the intestinal tract is a successive process throughout the course of life.”
From Diet and the Microbiota–Gut–Brain Axis: Sowing the Seeds of Good Mental Health (2021) · cites this paper as [232]
In the first years of life the microbial community is dynamic and some bacteria that become part of the adult microbiota already colonize the gut during the first months of life.
“Especially in the first years of life the microbial community is dynamic and some bacteria that become part of the adult microbiota already colonize the gut during the first months of life (230-232).”
From Diet and the Microbiota–Gut–Brain Axis: Sowing the Seeds of Good Mental Health (2021) · cites this paper as [232]
The composition of gut microbiota is dynamic throughout the lifespan, undergoing rapid changes from birth until about 3 years of age, after which greater stability is established.
“The composition of gut microbiota is shown to be dynamic throughout the lifespan, undergoing rapid changes from birth until ~ 3 years of age, after which greater stability is established [11, 12].”
From Gut Microbiota Contribute to Age-Related Changes in Skeletal Muscle Size, Composition, and Function: Biological Basis for a Gut-Muscle Axis (2018) · cites this paper as [12]
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The connection between microbiome and schizophrenia
Golofast, B., & Vales, K. (2020) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2019.12.011 · Cited by 92 · see citing works
Mills, S., Lane, J. A., Smith, G. J., Grimaldi, K. A., Ross, R. P., & Stanton, C. (2019) · Nutrients · doi:10.3390/nu11071468 · Cited by 88 · see citing works
Self-citationOu, Y., Belzer, C., Smidt, H., & de Weerth, C. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2038853 · Cited by 54 · see citing works
Between Dysbiosis, Maternal Immune Activation and Autism: Is There a Common Pathway?
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Mancabelli, L., Tarracchini, C., Milani, C., Lugli, G. A., Fontana, F., Turroni, F., van Sinderen, D., & Ventura, M. (2020) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2020.08.028 · Cited by 39 · see citing works
O’Connell Motherway, M., O’Brien, F., O’Driscoll, T., Casey, P. G., Shanahan, F., & van Sinderen, D. (2018) · Scientific Reports · doi:10.1038/s41598-018-29034-0 · Cited by 29 · see citing works
Samarra, A., Cabrera-Rubio, R., Martínez-Costa, C., & Collado, M. C. (2024) · Gut Microbes · doi:10.1080/19490976.2024.2357176 · Cited by 25 · see citing works
Scanlan, P. D., Hill, C. J., Ross, R. P., Ryan, C. A., Stanton, C., & Cotter, P. D. (2018) · Parasitology · doi:10.1017/s0031182018000033 · Cited by 14 · see citing works
Self-citation
- Authors
- Hill, C. J., Lynch, D. B., Murphy, K., Ulaszewska, M., Jeffery, I. B., O’Shea, C. A., Watkins, C., Dempsey, E., Mattivi, F., Tuohy, K., Ross, R. P., Ryan, C. A., O’ Toole, P. W., & Stanton, C.
- Affiliations
- University College Cork (IE)
- Teagasc - The Irish Agriculture and Food Development Authority (IE)
- Fondazione Edmund Mach (IT)
- Cork University Hospital (IE)
- Corresponding author
- Stanton, Catherine
- ORCID
- Venue
- Microbiome
- Published
- 2017-01-17
- Volume
- 5
- Issue
- 1
- Pages
- 4-4
- ISSN
- 2049-2618 (ISSN-L)
- PMC
- PMC5240274
- OpenAlex
- W2574079157
- Cited by
- 573
- References
- 60
- Citations by year
- 2026: 27 · 2025: 56 · 2024: 52 · 2023: 58 · 2022: 70 · 2021: 88 · 2020: 69 · 2019: 66 · 2018: 51 · 2017: 35 · 2016: 1
- FWCI
- 24.67
- Type
- journal article
- Language
- en
- Update notices
- correction (2017-02-14)
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Microbiome (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Arrow@dit (Dublin Institute of Technology) (acceptedVersion)
- T-Stór (Teagasc) (acceptedVersion)
- Iris (University of Trento) (submittedVersion, cc-by)
- CINECA IRIS Institutional Research Information System (Fondazione Edmund Mach) (submittedVersion, cc-by)
- Arrow@dit (Dublin Institute of Technology) (submittedVersion, cc-by)
- Arrow@dit (Dublin Institute of Technology) (submittedVersion, cc-by-nc-sa)
- Cork Open Research Archive (University College Cork, Ireland) (submittedVersion, cc-by)
- T-Stór (Teagasc) (submittedVersion, cc-by-nc-sa)
- Lenus, The Irish Health Repository (Dr Steevens Hospital Library) (submittedVersion)
- Funders
- Department of Agriculture, Food and the Marine (10FDairy INFANTMET)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Keywords
- gut microbiota development, infant gut microbiota, breastfeeding, mode of delivery, cesarean section, preterm infants, gestational age, urinary metabolome, tryptophan metabolism, tyrosine metabolism, bile acid metabolism, fatty acid metabolism, twins
- MeSH terms
- Gastrointestinal Microbiome, Bacteria, Breast Feeding, Cesarean Section, DNA, Bacterial, DNA, Ribosomal, Feces, Female, Humans, Infant, Newborn, Phylogeny, Pregnancy, RNA, Ribosomal, 16S, Urine, Sequence Analysis, DNA, Premature Birth, Metabolomics
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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