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. 2022 Nov 11;17(11):e0277502.
doi: 10.1371/journal.pone.0277502. eCollection 2022.

Proof of principle study replicating microbial clusters in connection to birth mode and diet in the early life intestine

Patrick Schimmel  1 , Lennart Kleinjans  1 , Carl Vael  2 , Kristine Desager  3 , Jan Knol  1   4 , Clara Belzer  1
Affiliations

Proof of principle study replicating microbial clusters in connection to birth mode and diet in the early life intestine

Patrick Schimmel et al. PLoS One. .

Abstract

The human gut ecosystem starts developing at birth and is influenced by many factors during early life. In this study we make use of a Belgian cohort of 64 children, followed until the age of 6 years, to analyze different phases of microbiota development. We analyzed fecal samples taken before weaning (age 1 month), shortly after weaning (age 6 months), when milk feeding has been discontinued completely (age 1 year), and at the age of 6 years. We performed 16S rRNA gene amplicon sequencing on the collected fecal samples and analyzed the compositional data in relation to dietary metadata and birth mode. Human and formula milk feeding promotes a microbiota dominated by either Bacteroides or Bifidobacterium, respectively. Into later life stages, the microbiota composition follows distinct microbiota clusters, related to abundance dynamics of certain bacterial groups. Furthermore, it becomes apparent that a formula diet leads to early maturation of the infant gut microbiota. Despite other clinical variables within the infant cohort, they did not significantly contribute to the microbiota patterns we observed. Our data provide a proof of principle study of the importance of diet to the development of the microbiota in early life that replicates earlier findings in other cohorts.

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Conflict of interest statement

I have read the journal’s policy and the authors of this manuscript have the following competing interests: J.K. is an employee of Danone Nutricia Research. P.S., L.K., C.B. received funding from Danone Nutricia Research. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Figures

Fig 1
Fig 1. NTR3505 study setup.
Study setup & metadata (birth mode, feeding, age, prebiotic supplementation).
Fig 2
Fig 2. Principal component analysis.
Principal component analysis based on microbiota composition for all samples, labelled per timepoint.
Fig 3
Fig 3. Redundancy analysis (RDA).
RDA on all included samples based on microbiota composition, with the main variable: age on the X-axis.
Fig 4
Fig 4
(a) Principal Coordinates Analysis (PCoA). PCoA based on Weighted Unifrac; (b) PAM-clustering with 4 clusters; (c) area-plot showing age-distribution within the clusters.
Fig 5
Fig 5. Relative abundance boxplots.
Boxplots depicting bacterial difference (relative abundance) between the clusters.
Fig 6
Fig 6. Cluster metadata.
Birth mode metadata occurrence across the clusters.
Fig 7
Fig 7. Trajectory formulations.
Formulations and their occurrence rate across the infants.
Fig 8
Fig 8. Trajectory area charts.
Area charts showing the development of the relative abundances of the major bacterial groups across the major trajectories observed in this study.
Fig 9
Fig 9. Abundance area charts.
Area charts depicting relative abundance of major bacterial groups when separating infants into ‘early’ and ‘late’ maturation.
Fig 10
Fig 10. Maturation rates.
The differences in maturation rate between feeding mode and the expected values if it was random.
Fig 11
Fig 11. Maturation rate compared to expected values.
The differences in maturation rate between timing of weaning and the expected values if it was random.
Fig 12
Fig 12. Maturation rate and diet oligos.
The differences in maturation rate with our without oligos in the diet and the expected values if it was random.
See this image and copyright information in PMC

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