HELSEFORSKNING-HELSEFORSKNING

The bacteria in the human gut outnumber the total number of cells in the human body, and these microbes play important roles in health and disease. Establishment of the so-called gut microbiome begins during the birthing process and develops throughout infancy to eventually form a mature and stable ecosystem that provides vital services to the host. The infant gut microbiome is known to act as a reservoir for genes that can confer resistance to antibiotic drugs (ARGs), and the spread of such genes to pathogens is considered one of the main problems in global public health. However, we still lack basic knowledge of the gut microbiomes maturation process during infancy. IN this project we have a special interest in mapping the content of ARGs in the infant gut, and the potential that these genes have for spreading among different groups of bacteria. The main tools in the study are modern DNA sequencing technologies, e.g. metagenomic sequencing and single-cell sequencing techniques, combined with a range of bioinformatics tools. The project focuses on two cohorts of infants; 1. The BabyBiome cohort consisting of 12 healthy infants, born in the Oslo region, from whom near daily fecal samples were taken from birth until the first birthday. 2. The PreventADALL cohort (organized by Oslo University Hospital) which consists of several hundred infants sampled at 3, 6 and 12 months age, as well as samples from the mothers. The first cohort gives us a detailed picture of how the gene content in the infant gut changes as the child matures, while the second will give us a better understanding of how gene content is affected by antibiotic use, and the degree to which genes are transmitted from mother to infant. We have carried out deep metagenomic DNA sequencing of hundreds of samples from the BabyBiome cohort, conducting a large number of analyses of ARGs, virulence factors and genetic elements that confer mobility of genes to other bacteria. These results have been published, and demonstrate a general decline in the content of ARGs over the first year of life. Furthermore, the results show that total ARG carriage, as well as specific genes conferring resistance, are mostly associated with specific bacterial lineages, in particular a group known as the Gammaproteobacteria. Unlike most gut-associated species, many species in this group, for example E.coli, are able to exploit oxygen for energy production. Oxygen availability is especially elevated during the first weeks of life, before more typical gut species take over most of the ecosystem. When the amounts of Gammaproteobacteria vary over time, these variations are reflected in variations in ARG abundance, and infants with small amounts of these bacteria also tend to have low levels of ARGs. We saw these same patterns also for virulence factors, as these genes were tightly associated with resistance in the same lineages. In a separate analysis, which is to be published soon, we have looked specifically at so called plasmids. This is a type of mini-chromosome that exists and replicates outside of the main chromosome, where most genes are located, and they are especially important in dissemination of ARGs among bacteria. Studying plasmids in natural environments is very complicated, and we have devised a new method for reconstruction these molecules from metagenomic data. Our collaborators at the University of Amsterdam have also analyzed this data set, but with a focus on genomic evolution in gut bacteria. We have also sequenced hundreds of samples from the PreventADALL cohort, which have been put through many of the analysis described above. Analyses are still ongoing and more results are expected shortly.

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.