The long-term genetic stability and individual specificity of the human gut microbiome

Lifelines Cohort Study, Lianmin Chen, Daoming Wang, Sanzhima Garmaeva, Alexander Kurilshikov, Arnau Vich Vila, Ranko Gacesa, Trishla Sinha, Eran Segal, Rinse K Weersma, Cisca Wijmenga, Alexandra Zhernakova*, Jingyuan Fu*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

By following up the gut microbiome, 51 human phenotypes and plasma levels of 1,183 metabolites in 338 individuals after 4 years, we characterize microbial stability and variation in relation to host physiology. Using these individual-specific and temporally stable microbial profiles, including bacterial SNPs and structural variations, we develop a microbial fingerprinting method that shows up to 85% accuracy in classifying meta-genomic samples taken 4 years apart. Application of our fingerprinting method to the independent HMP cohort results in 95% accuracy for samples taken 1 year apart. We further observe temporal changes in the abundance of multiple bacterial species, metabolic pathways, and structural variation, as well as strain replacement. We report 190 longitudinal microbial associations with host phenotypes and 519 associations with plasma metabolites. These associations are enriched for cardiometabolic traits, vitamin B, and uremic toxins. Finally, mediation analysis suggests that the gut microbiome may influence cardiometabolic health through its metabolites.

Original languageEnglish
Pages (from-to)2302-+
Number of pages26
JournalCell
Volume184
Issue number9
Early online date4-Apr-2021
DOIs
Publication statusPublished - 29-Apr-2021

Keywords

  • FAECALIBACTERIUM-PRAUSNITZII
  • ANTIMICROBIAL RESISTANCE
  • METABOLIC PATHWAYS
  • METACYC DATABASE
  • LEVEL ANALYSIS
  • MULTI-OMICS
  • MELATONIN
  • NETWORKS
  • DYNAMICS
  • DISEASE

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