Animals and microorganisms often establish close ecological relationships. However, much of our knowledge about animal microbiomes comes from two deeply studied groups: vertebrates and arthropods. To understand interactions on a broader scale of diversity, we characterized the bacterial microbiomes of close to 1,000 microscopic marine invertebrates from 21 phyla, spanning most of the remaining tree of metazoans. Samples were collected from five temperate and tropical locations covering three marine habitats (sediment, water column and intertidal macroalgae) and bacterial microbiomes were characterized using 16S ribosomal RNA gene sequencing. Our data show that, despite their size, these animals harbour bacterial communities that differ from those in the surrounding environment. Distantly related but coexisting invertebrates tend to share many of the same bacteria, suggesting that guilds of microorganisms preferentially associated with animals, but not tied to any specific host lineage, are the main drivers of the ecological relationship. Host identity is a minor factor shaping these microbiomes, which do not show the same correlation with host phylogeny, or ‘phylosymbiosis’, observed in many large animals. Hence, the current debate on the varying strength of phylosymbiosis within selected lineages should be reframed to account for the possibility that such a pattern might be the exception rather than the rule.

动物和微生物经常建立密切的生态关系。然而，我们关于动物微生物组的大部分知识来自两个深入研究的群体：脊椎动物和节肢动物。为了了解更广泛多样性的相互作用，我们对来自 21 个门的近 1,000 种微型海洋无脊椎动物的细菌微生物群落进行了表征，这些微生物跨越了大部分剩余的后生动物树。从覆盖三个海洋生境（沉积物、水柱和潮间带大型藻类）的五个温带和热带地点收集样本，并使用 16S 核糖体 RNA 基因测序对细菌微生物组进行了表征。我们的数据表明，尽管它们体型庞大，但这些动物体内的细菌群落与周围环境中的细菌群落不同。远亲但共存的无脊椎动物往往共享许多相同的细菌，这表明微生物公会优先与动物相关，但与任何特定的宿主谱系无关，是生态关系的主要驱动力。宿主身份是塑造这些微生物组的一个次要因素，它们与许多大型动物中观察到的宿主系统发育或“系统共生”没有显示出相同的相关性。因此，目前关于选定谱系中系统共生强度不同的辩论应该重新构建，以解释这种模式可能是例外而不是规则的可能性。宿主身份是塑造这些微生物组的一个次要因素，它们与许多大型动物中观察到的宿主系统发育或“系统共生”没有显示出相同的相关性。因此，目前关于选定谱系中系统共生强度不同的辩论应该重新构建，以解释这种模式可能是例外而不是规则的可能性。宿主身份是塑造这些微生物组的一个次要因素，它们与许多大型动物中观察到的宿主系统发育或“系统共生”没有显示出相同的相关性。因此，目前关于选定谱系中系统共生强度不同的辩论应该重新构建，以解释这种模式可能是例外而不是规则的可能性。