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

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…

• SU
  Stanford University
• LM
  Leona M. and Harry B. Helmsley Charitable Trust

  Awards: G-2004-03820, P30AG059307
• KT
  Kennedy Trust for Rheumatology Research
• KM
  Kennedy Memorial Trust
• NI
  National Institutes of Health

  Awards: R01_DK110186, S10_OD020141, U54_DK102556, TR001085, P30AG059307, R01 AT010232-04, UL1 TR001085, S10_OD023452, P30_DK116074, U54_DE0237891
• NI
  National Institute on Aging

  Awards: K08 ES028825, P30AG059307, 1F32DK126287, K01AG070310
• CF
  Common Fund