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Background  Host-associated microbiota is often acquired by horizontal transmission of microbes present in the environment. It is hypothesized that differences in the environmental pool of colonizers can influence microbiota community assembly on the host and as such affect holobiont composition and host fitness. To investigate this hypothesis, the host-associated microbiota of the invertebrate eco(toxico)logical model  Daphnia  was experimentally disturbed using different concentrations of the antibiotic oxytetracycline. The community assembly and host-microbiota interactions when  Daphnia  were colonized by the disturbed microbiota were investigated by inoculating germ-free individuals with the microbiota.    Results  Antibiotic-induced disturbance of the microbiota had a strong effect on the subsequent colonization of  Daphnia  by affecting ecological interactions between members of the microbiota. This resulted in differences in community assembly which, in turn, affected  Daphnia  growth.    Conclusions  These results show that the composition of the pool of colonizing microbiota can be an important structuring factor of the microbiota assembly on  Daphnia , affecting holobiont composition and host growth. These findings contribute to a better understanding of how the microbial environment can shape the holobiont composition and affect host-microbiota interactions.

Microbiota inoculum composition affects holobiont assembly and host growth in Daphnia