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Conclusions
Despite the limited sample variety, this study provides a novel perspective on microbiota-host interactions
in the infant gut during a critical time of immune system maturation. Our results add a dynamic perspective
to host-microbe interactions, suggesting that gut permeability and immune system responses in healthy
infants may fluctuate in association with the microbial stimuli, which is likely important in the maintenance
of gut homeostasis. We observed a change in the nature of microbe-host interactions from apparent
immune tolerance at 6 months toward more tight regulation at 12 months. IAP activity, measured by the
Quanti-Blue assay, and muc2, measured by ELISA, emerged as potentially important regulators of gut
microbiota in infants. The study demonstrates the utility of biomarker and bacteria profiling from daily
stool samples as a potent tool for analysing in vivo associations between the immune system and the gut
microbiota.

DECLARATIONS

Authors’ contributions
Made substantial contributions to the conception and design of the study and performed data analysis and
interpretation: van Beek N, Korpela K
Performed data acquisition, as well as providing administrative, technical, and material support: Katavisto I,
van Beek N, Korpela K, Lehto M, Kolho KL, de Vos WM, Salonen A

Availability of data and materials
The data that support the findings of this study, the taxonomic tables and biomarker concentrations, are
available as supplementary data.

Financial support and sponsorship
This work was supported by ERC Starting Grant 101039583 - MICROECO.

Conflicts of interest
All authors declared that there are no conflicts of interest.

Ethical approval and consent to participate
The research was approved by the Helsinki University Hospital Ethics Committee (HUS/2346/2016).
Informed consent was obtained from the parents of the study subjects.

Consent for publication
Not applicable.

Copyright
© The Author(s) 2024.

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