The gut microbiota of preterm infants develops predictably^{1,2,3,4,5,6,7}, with pioneer species colonizing the gut after birth, followed by an ordered succession of microorganisms. The gut microbiota is vital to the health of preterm infants^8,9, but the forces that shape these predictable dynamics of microbiome assembly are unknown. The environment, the host and interactions between microorganisms all potentially shape the dynamics of the microbiota, but in such a complex ecosystem, identifying the specific role of any individual factor is challenging^{10,11,12,13,14}. Here we use multi-kingdom absolute abundance quantification, ecological modelling and experimental validation to address this challenge. We quantify the absolute dynamics of bacteria, fungi and archaea in a longitudinal cohort of 178 preterm infants. We uncover microbial blooms and extinctions, and show that there is an inverse correlation between bacterial and fungal loads in the infant gut. We infer computationally and demonstrate experimentally in vitro and in vivo that predictable assembly dynamics may be driven by directed, context-dependent interactions between specific microorganisms. Mirroring the dynamics of macroscopic ecosystems^15,16,17, a late-arriving member of the microbiome, Klebsiella, exploits the pioneer microorganism, Staphylococcus, to gain a foothold within the gut. Notably, we find that interactions between different kingdoms can influence assembly, with a single fungal species—Candida albicans—inhibiting multiple dominant genera of gut bacteria. Our work reveals the centrality of simple microbe–microbe interactions in shaping host-associated microbiota, which is critical both for our understanding of microbiota ecology and for targeted microbiota interventions.

早产儿的肠道微生物群按照预测发展^{1,2,3,4,5,6,7} ，先锋物种在出生后定植于肠道，随后是有序的微生物序列。肠道微生物群对早产儿的健康至关重要^8,9 ，但塑造这些可预测的微生物组动态的力量尚不清楚。环境、宿主和微生物之间的相互作用都可能影响微生物群的动态，但在如此复杂的生态系统中，确定任何单个因素的具体作用都具有挑战性^{10,11,12,13,14} 。在这里，我们使用多界绝对丰度量化、生态建模和实验验证来应对这一挑战。我们对 178 名早产儿的纵向队列中细菌、真菌和古细菌的绝对动态进行了量化。我们发现了微生物的繁殖和灭绝，并表明婴儿肠道中的细菌和真菌负荷之间存在负相关。我们通过计算推断并在体外和体内实验证明，可预测的组装动力学可能是由特定微生物之间定向的、依赖于环境的相互作用驱动的。反映宏观生态系统的动态^15,16,17 ，微生物组中的后来者克雷伯氏菌利用先锋微生物葡萄球菌在肠道内站稳脚跟。值得注意的是，我们发现不同界之间的相互作用可以影响组装，单一真菌物种——白色念珠菌——抑制肠道细菌的多个优势属。 我们的工作揭示了简单的微生物与微生物相互作用在塑造宿主相关微生物群中的中心地位，这对于我们理解微生物群生态学和有针对性的微生物群干预措施至关重要。