BabyBiome: Antimicrobial resistance gene dynamics in the infant gut microbial ecosystem



About the Project

The adult human gastrointestinal (GI) microbiome is a stable and complex ecological community comprised of trillions of microorganisms that play vital roles in health and disease. Establishment of this community in the infant is widely recognized a fundamental developmental process with lasting Health effects. It is noteworthy that the infant GI microbiome acts as a reservoir for antimicrobial resistance genes (ARGs). The spread of antimicrobial resistance is considered one of the main threats to global public health. The proposed project will provide essential knowledge on the temporal Dynamics of ARGs in the developing infant.

As part of a recently concluded project funded by the Research Council of Norway, we have analyzed the microbiota of nearly 2700 fecal samples from 12 Norwegian infants during the first year of life. In terms of temporal resolution this sample set is by far the densest of its kind, and our analysis has produced the most detailed picture to date of the human gut colonization process on the microbial population level.

There remains, however, a knowledge gap concerning the normal infant gut microbiome maturation process. For example, we still do not understand the ecological mechanisms causing increased ARG carriage in infant microbiomes compared with adults. Our proposed project will drastically extend current knowledge by creating a detailed, time-resolved characterization of the developing infant gut microbiome during the first year of life. To accomplish this, we will employ community level shotgun metagenomic sequencing coupled with emulsion-PCR based techniques.

The goal will be to develop conceptual and statistical modes of this vital developmental process with a particular focus on ARG dynamics. Furthermore, we will analyze a large subset of fecal samples (>100) from the comprehensive Norwegian PreventADALL study in order to map natural variability in the timing of key events during early development.


1. To identify classes of antimicrobial resistance genes enriched in the GI microbiome during specific developmental stages.

2. To evaluate causes and consequences of strain level replacement events in the developing infant GI microbiome.

3. To identify taxonomic groups that act as hubs in the accumulation and transmission of ARGs in the developing GI microbiota.


Currently, we do not have good models describing the dynamics of ARGs associated with developmental stages during early childhood. This type of knowledge is of great value to clinicians, as it would allow them to make more informed decisions about the kind of drugs that are most suitable for administration to children during specific age windows. Project results will enhance understanding of the spread of ARGs in the public health context and help provide a framework for more appropriate and accurate use of antibiotics.


This Project is funded by the Research Council of Norway (RCN)

RCN project number: 300948 (Project data bank at RCN)

UiO project number:145014


01.05.2020 - 31.10.2024


Published Nov. 30, 2020 11:03 AM - Last modified Feb. 2, 2021 10:01 AM