Maturation of the infant microbiome in time and space

Robert Bücking

MDC Berlin, ECRC, Robert-Rössle-Straße 10, 13125 Berlin [DE], robert.buecking@mdc-berlin.de

Author(s):
Robert Bücking, Víctor Hugo Jarquin Diaz, Georgina Sket, Claudia Buß, Dorothee Viemann, Sofia Forslund

The neonatal gut after birth is a vast empty habitat that provides a good model to investigate microbial colonization dynamics. While the number of published studies describing infant gut colonization is steadily rising, comparisons across cohorts, geographic locations and lifestyles are rare. The increasing number of available microbiome datasets enables meta-analyses to detect generalizable microbial dynamics across cohorts.
We aim to define a generalizable model of infant gut colonization that will provide insight into host-microbiome interactions and microbial ecological succession in a sterile environment. We analyzed published longitudinal 16S sequencing data of children up to two years of age from different cohorts, countries, and lifestyles. Our preliminary results based on 15,565 samples from 19 studies revealed a decline in cohort-specific effects with the inclusion of additional datasets. We identified key taxa predictive of host age across studies. We showed that lifestyle-specific models are more accurate than a global model.
The assembled dataset allows for a comprehensive analysis of variables influencing infant gut colonization. Our findings emphasize the importance of diverse datasets for deriving generalizable models for microbial dynamics. Next, our models will incorporate functional information from shotgun sequencing data. In the future, we aim to use these models to detect deviations from a healthy maturation.

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