The microbiota and T cells non-genetically modulate inherited phenotypes transgenerationally

The host-microbiota relationship has evolved to shape mammalian physiology, including immunity, metabolism, and development. Germ-free models are widely used to study microbial effects on host processes such as immunity. Here, we find that both germ-free and T cell-deficient mice exhibit a robust sebum secretion defect persisting across multiple generations despite microbial colonization and T cell repletion. These phenotypes are inherited by progeny conceived during in vitro fertilization using germ-free sperm and eggs, demonstrating that non-genetic information in the gametes is required for microbial-dependent phenotypic transmission. Accordingly, gene expression in early embryos derived from gametes from germ-free or T-cell deficient mice are strikingly and similarly altered. Our findings demonstrate that microbial and immune-dependent regulation of non-genetic information in the gametes can transmit inherited phenotypes transgenerationally in mice. This mechanism could rapidly generate phenotypic diversity to enhance host adaptation to environmental perturbations. To investigate transcriptomic, transgenerational differences in the presence of an altered microbiome, we performed several sequencing experiments comparing tissues from mice derived from conventionally raised (CR) parents, germ-free (GF) parents, and/or a GF male parent crossed to a CR female parent. We performed mRNA sequencing on F0 and F1 sebaceous glands, F1 and F2 back skin, F1 small intestine, F1 liver, and 4 cell and morula stage embryos. To further investigate the influence of the immune system on RNA expression in gametes and embryos, we performed mRNA sequencing on embryos derived from WT eggs fertilized with RAG knockout sperm.