美国波士顿儿童医院Seth Rakoff-Nahoum、Katharine Z. Coyte等研究人员合作揭示早产儿微生物组集合产生的生态驱动因素。相关论文于2021年2月24日在线发表在《自然》杂志上。

据研究人员介绍，早产儿的肠道菌群能够可预见地发展，其中先驱物种在出生后就在肠道内定殖，然后依次排列有序的微生物。肠道菌群对早产儿的健康至关重要，但是影响这些可预见的微生物组动力学的因素尚不清楚。环境、宿主和微生物之间的相互作用都可能影响微生物群落的动态，但是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是具有挑战性的。

研究人员使用多分类界的绝对丰度定量、生态建模和实验验证来解决了这一挑战。研究人员量化了178名早产儿的纵向队列中细菌、真菌和古细菌的绝对动态。研究人员发现了微生物的繁殖和灭绝，并表明婴儿肠道中细菌和真菌的负荷之间存在负相关。研究人员通过计算推断并在体外和体内实验中证明，可预测的集合动力学可能是由特定微生物之间有针对性的、背景相关的相互作用所驱动的。一种后来的微生物组成员克雷伯氏菌（Klebsiella）能够利用先到的微生物葡萄球菌在肠道内定植。

值得注意的是，研究人员发现不同分类界之间的相互作用会影响集合形成，而单个真菌物种——白念珠菌（Candida albicans）会抑制肠道细菌的多个优势属。这项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重要性，这对于人们理解微生物群生态学和针对性微生物群的干预都是至关重要的。

附：英文原文

Title: Multi-kingdom ecological drivers of microbiota assembly in preterm infants

Author: Chitong Rao, Katharine Z. Coyte, Wayne Bainter, Raif S. Geha, Camilia R. Martin, Seth Rakoff-Nahoum

Issue&Volume: 2021-02-24

Abstract: The gut microbiota of preterm infants develops predictably1,2,3,4,5,6,7, 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 infants8,9, 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 challenging10,11,12,13,14. 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 ecosystems15,16,17, 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.

DOI: 10.1038/s41586-021-03241-8

Source: https://www.nature.com/articles/s41586-021-03241-8