Colonization resistance in human gut microbiome samples

We used an anaerobic gut microcosm system (described in Baumgartner et al. PLoS Biology, 2020) to investigate how the microbiome sampled from healthy human donors suppresses the invasion of an opportunistic pathogen. Our aim was to elucidate if community composition is the driving force of colonization resistance or if changes in the environment also play an important role in suppressing an invading strain. Our results showed that changes in community composition coincided with stronger suppression of the invading strain but strength of suppression was dependent on the state of the environment. The sequences deposited here are 16S rRNA amplicons from our microcosm system. We sequenced each human donor sample before inoculation (n=3) and each microcosm with microbiome samples after 72h (n=9).