On the Origins and Control of Community Types in the Human Microbiome

Microbiome-based stratification of healthy individuals into compositional categories, referred to as “enterotypes” or “community types”, holds promise for drastically improving personalized medicine. Despite this potential, the existence of community types and the degree of their distinctness have been highly debated. Here we adopted a dynamic systems approach and found that heterogeneity in the interspecific interactions or the presence of strongly interacting species is sufficient to explain community types, independent of the topology of the underlying ecological network. By controlling the presence or absence of these strongly interacting species we can steer the microbial ecosystem to any desired community type. This open-loop control strategy still holds even when the community types are not distinct but appear as dense regions within a continuous gradient. This finding can be used to develop viable therapeutic strategies for shifting the microbial composition to a healthy configuration.

基于微生物组将健康个体按组成特征划分为不同类别，即所谓的"肠型（enterotypes）"或"群落类型（community types）"，有望大幅推动个性化医学的发展。尽管具备这一潜力，但群落类型的存在性及其区分度一直广受争议。本研究采用动态系统分析方法，发现种间相互作用的异质性或强互作物种的存在足以解释群落类型的形成，且不受底层生态网络拓扑结构的影响。通过调控这些强互作物种的有无，我们可以将微生物生态系统引导至任意目标群落类型。即便群落类型并非截然分明，而是以连续梯度内的密集区域形式出现时，这种开环控制策略依然有效。该研究发现可用于开发可行的治疗策略，以将微生物组组成调整至健康状态。