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  • Scepanovic, PetarSwiss Federal Institute of Technology,Swiss Institute for Bioinformatics (SIB) (author)

A comprehensive assessment of demographic, environmental, and host genetic associations with gut microbiome diversity in healthy individuals

  • Article/chapterEnglish2019

Publisher, publication year, extent ...

  • 2019-09-13
  • Springer Science and Business Media LLC,2019
  • 1 s.

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  • LIBRIS-ID:oai:lup.lub.lu.se:ffcde02b-e547-4e05-a954-cb140865f988
  • https://lup.lub.lu.se/record/ffcde02b-e547-4e05-a954-cb140865f988URI
  • https://doi.org/10.1186/s40168-019-0747-xDOI

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  • Language:English
  • Summary in:English

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  • Subject category:art swepub-publicationtype
  • Subject category:ref swepub-contenttype

Notes

  • BACKGROUND: The gut microbiome is an important determinant of human health. Its composition has been shown to be influenced by multiple environmental factors and likely by host genetic variation. In the framework of the Milieu Intérieur Consortium, a total of 1000 healthy individuals of western European ancestry, with a 1:1 sex ratio and evenly stratified across five decades of life (age 20-69), were recruited. We generated 16S ribosomal RNA profiles from stool samples for 858 participants. We investigated genetic and non-genetic factors that contribute to individual differences in fecal microbiome composition. RESULTS: Among 110 demographic, clinical, and environmental factors, 11 were identified as significantly correlated with α-diversity, ß-diversity, or abundance of specific microbial communities in multivariable models. Age and blood alanine aminotransferase levels showed the strongest associations with microbiome diversity. In total, all non-genetic factors explained 16.4% of the variance. We then searched for associations between > 5 million single nucleotide polymorphisms and the same indicators of fecal microbiome diversity, including the significant non-genetic factors as covariates. No genome-wide significant associations were identified after correction for multiple testing. A small fraction of previously reported associations between human genetic variants and specific taxa could be replicated in our cohort, while no replication was observed for any of the diversity metrics. CONCLUSION: In a well-characterized cohort of healthy individuals, we identified several non-genetic variables associated with fecal microbiome diversity. In contrast, host genetics only had a negligible influence. Demographic and environmental factors are thus the main contributors to fecal microbiome composition in healthy individuals. TRIAL REGISTRATION: ClinicalTrials.gov identifier NCT01699893.

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  • Hodel, FlaviaSwiss Federal Institute of Technology,Swiss Institute for Bioinformatics (SIB) (author)
  • Mondot, StanislasINRA National Institute of Agricultural Research (author)
  • Partula, ValentinParis Diderot University,Centre of Epidemiology And Biostatistics Sorbonne Paris Cité Center (CRESS) (author)
  • Byrd, AllysonGenentech, Inc (author)
  • Hammer, ChristianGenentech, Inc (author)
  • Alanio, CécileUniversity of Pennsylvania (author)
  • Bergstedt, JacobLund University,Lunds universitet,Institutionen för reglerteknik,Institutioner vid LTH,Lunds Tekniska Högskola,Department of Automatic Control,Departments at LTH,Faculty of Engineering, LTH(Swepub:lu)cont-jan (author)
  • Patin, EtiennePasteur Institute,The French National Centre for Scientific Research (CNRS) (author)
  • Touvier, MathildeCentre of Epidemiology And Biostatistics Sorbonne Paris Cité Center (CRESS) (author)
  • Lantz, OlivierCurie Institute, Paris (author)
  • Albert, Matthew L.Genentech, Inc (author)
  • Duffy, DarraghPasteur Institute (author)
  • Quintana-Murci, LluisThe French National Centre for Scientific Research (CNRS),Pasteur Institute (author)
  • Fellay, JacquesSwiss Institute for Bioinformatics (SIB),Swiss Federal Institute of Technology,Lausanne University Hospital (author)
  • Swiss Federal Institute of TechnologySwiss Institute for Bioinformatics (SIB) (creator_code:org_t)
  • Milieu Intérieur Consortium

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  • In:Microbiome: Springer Science and Business Media LLC7:12049-2618

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