Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease.
Document Type
Article
Publication Date
4-10-2024
Original Citation
Zhou X,
Shen X,
Johnson J,
Spakowicz D,
Agnello M,
Zhou W,
Avina M,
Honkala A,
Chleilat F,
Chen S,
Cha K,
Leopold S,
Zhu C,
Chen L,
Lyu L,
Hornburg D,
Wu S,
Zhang X,
Jiang C,
Jiang L,
Jiang L,
Jian R,
Brooks A,
Wang M,
Contrepois K,
Gao P,
Rose S,
Binh Tran T,
Nguyen H,
Celli A,
Hong B,
Bautista E,
Dorsett Y,
Kavathas P,
Zhou Y,
Weinstock E,
Weinstock GM,
Snyder M.
Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Cell Host Microbe. 2024;32(4):506-26 e9.
Keywords
JGM, Humans, Core Stability, Microbiota, Skin, Host Microbial Interactions, Biomarkers
JAX Source
Cell Host Microbe. 2024;32(4):506-26 e9.
ISSN
1934-6069
PMID
38479397
DOI
https://doi.org/10.1016/j.chom.2024.02.012
Grant
This work was funded by National Institutes of Health (NIH) Common Fund Human Microbiome Project U54_DE0237891, NIH U54_DK102556, NIH R01_DK110186, NIH S10_OD020141, NIH R01 AT010232-04, NIH UL1 TR001085, NIH P30_DK116074, S10_OD023452. We are also sincerely grate- ful for the generous support from Leona M. and Harry B. Helmsley Charitable Trust (grant no. G-2004-03820), the Innovative Medicines Accelerator (grant no. IMA-1051) grant, and the RAMBAM-Stanford International Collaboration grant at Stanford University. We acknowledge the fellowship support received by X. Zhou from the Stanford Aging and Ethnogeriatrics (SAGE) Research Cen- ter under NIH/NIA Resource Centers for Minority Aging Research grant P30AG059307, S.M.S.-F.R. from the NIH K08 ES028825, A.W.B. from 1F32DK126287, D.J.S. from NIA-K01AG070310, and J.S.J. from the Kennedy Trust for Rheumatology Research. Some of the icons in the summary figure were created with Biorender.com.
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.