Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease

Abstract

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.

Publication
Cell Host Microbe
Dr. Xin Zhou
Dr. Xin Zhou
Postdoc
Stanford University
Xiaotao Shen
Xiaotao Shen
Nanyang Assistant Professor

Metabolomics, Multi-omics, Bioinformatics, Systems Biology.

Dr. Si Wu
Dr. Si Wu
Research Scientist
AbbVie
Prof. Chao Jiang
Prof. Chao Jiang
Assistant Professor
Zhejiang University
Prof. Peng Gao
Prof. Peng Gao
Assistant Professor
University of Pittsburgh
Prof. Michael Snyder
Prof. Michael Snyder
Professor
Stanford University