The importance of microbial associations to animals’ development, physiology, and fitness is widely recognized. In most animals, these microbial associations must be developed anew with every generation, making microbiome assembly a critical ecological and evolutionary process. To fully understand neonate microbial colonization, we need to study the interacting effects of neonate, parents, nest, and external environment. We propose an integrative approach based on the concept of the ‘nidobiome’, a new unit of microbiome–host interactions, which brings together these key elements. We discuss the contribution of each element on microbial colonization at different stages of host development, and we provide a framework based on key developmental events to compare microbiome assembly across animal species.

微生物关联对动物发育、生理和健康的重要性已得到广泛认可。在大多数动物中，这些微生物关联必须在每一代中重新发展，使微生物组组装成为一个关键的生态和进化过程。为了充分了解新生儿微生物定植，我们需要研究新生儿、父母、巢穴和外部环境的相互作用。我们提出了一种基于“nidobiome”概念的综合方法，“nidobiome”是微生物组与宿主相互作用的新单位，它将这些关键要素结合在一起。我们讨论了每个元素对宿主发育不同阶段的微生物定植的贡献，并提供了一个基于关键发育事件的框架来比较不同动物物种的微生物组组装。