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Abstract

Animals are colonized by complex bacterial communities. The processes controlling community
membership and influencing the establishment of the microbial ecosystem during development are
poorly understood. Here we aimed to explore the assembly of bacterial communities in Hydra with
the broader goal of elucidating the general rules that determine the temporal progression of
bacterial colonization of animal epithelia. We profiled the microbial communities in polyps at various
time points after hatching in four replicates. The composition and temporal patterns of the bacterial
communities were strikingly similar in all replicates. Distinct features included high diversity of
community profiles in the first week, a remarkable but transient adult-like profile 2 weeks after
hatching, followed by progressive emergence of a stable adult-like pattern characterized by low
species diversity and the preponderance of the Betaproteobacterium Curvibacter. Intriguingly, this
process displayed important parallels to the assembly of human fecal communities after birth. In
addition, a mathematical modeling approach was used to uncover the organizational principles of
this colonization process, suggesting that both, local environmental or host-derived factor(s)
modulating the colonization rate, as well as frequency-dependent interactions of individual bacterial
community members are important aspects in the emergence of a stable bacterial community at the
end of development