To understand the dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune, and clinical markers of microbiomes from four body sites in 86 participants over 6 years. We found that microbiome stability and individuality are body-site specific and heavily influenced by the host. The stool and oral microbiome are more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. We identify individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlate across body sites, suggesting systemic dynamics influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals show altered microbial stability and associations among microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease.

为了了解健康和疾病期间人类微生物组和宿主之间的动态相互作用，我们分析了 6 年来 86 名参与者的四个身体部位的微生物组的微生物组成、时间动态以及与宿主多组学、免疫和临床标记物的关联。我们发现微生物组的稳定性和个性是身体部位特异性的，并且深受宿主的影响。粪便和口腔微生物组比皮肤和鼻腔微生物组更稳定，这可能是由于它们与宿主和环境的相互作用。我们确定了个体特异性和共同的细菌类群，其中个体类群表现出更大的稳定性。有趣的是，微生物组动力学与身体各个部位相关，表明系统动力学受到宿主-微生物-环境相互作用的影响。值得注意的是，胰岛素抵抗个体表现出微生物稳定性以及微生物组、分子标记和临床特征之间关联的改变，表明它们在代谢疾病中的相互作用被破坏。我们的研究提供了多位点微生物动态及其与宿主健康和疾病关系的全面视图。