Abstract Research on microbial communities colonizing animals has revealed that the microbiota, despite its typical containment to surfaces, influences virtually all organ systems of the host. In absence of a natural microbiota, the host’s development can be disturbed, but how developmental programs are affected by the microbiota is still poorly understood. Removing the microbiota from Hydra , a classic model animal in developmental biology, causes drastic developmental malformations and leads to polyps that temporarily lack the ability to bud. Recolonizing non-budding germfree Hydra with bacteria reverses this budding inhibition. Single-cell RNA sequencing and trajectory-based differential expression analysis showed that epithelial stem cell decision making is disturbed in non-budding polyps, whereby key developmental regulators are not expressed. This process is reversible by adding back bacteria. Transcriptionally silencing of one of the genes that failed to be activated in non-budding animals, GAPR1, led to polyps that have a significantly reduced budding capacity. The results show that maintaining a species-specific microbiota may enable the animal host to maintain its developmental program. Significance Statement Animal developmental programs work within the context of coevolved associations with microbes. Here, we provide mechanistic evidence of the involvement of the microbiota in maintaining the pattern formation program of Hydra with the asexual formation of buds in the lower part of the body column. We demonstrate that in the absence of bacteria key regulatory factors are not expressed, causing changes in stem cell trajectories that result in loss of budding capacity. This study provides a new perspective on the role that microbiota play during animal development and evolution. One Sentence Summary Microbiota interfere with Hydra ’s asexual reproduction via modulating its stem cell differentiation programs.

The microbiota affects stem cell decision making inHydra