Sequential Isolation of DNA, RNA, Protein, and Metabolite Fractions from Murine Organs and Intestinal Contents for Integrated Omics of Host–Microbiota Interactions

  • Pranjul Shah
  • Emilie E. L. Muller
  • Laura A. Lebrun
  • Linda Wampach
  • Paul WilmesEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1841)


The gastrointestinal microbiome plays a central role in health and disease. Imbalances in the microbiome, also referred to as dysbiosis, have recently been associated with a number of human idiopathic diseases ranging from metabolic to neurodegenerative. However, to causally link specific microorganisms or dysbiotic communities with tissue-specific and/or systemic disease-associated phenotypes, systematic in vivo studies are fundamental. Gnotobiotic mouse models have proven to be particularly useful for the elucidation of microbiota-associated characteristics as they provide a means to conduct targeted perturbations followed by analyses of induced localized and systemic effects. Here, we describe a methodology in the framework of systems biology which allows the comprehensive isolation of high quality biomolecular fractions (DNA, RNA, proteins and metabolites) from limited and/or heterogeneous sample material derived from murine brain, liver, and colon tissues, as well as from intestinal contents (fecal pellets and fecal masses). The obtained biomolecular fractions are compatible with current high-throughput genomic, transcriptomic, proteomic, and metabolomic analyses. The resulting data fulfills the premise of systematic measurements and allows the detailed study of tissue-specific and/or systemic effects of host–microbiota interactions in relation to health and disease.

Key words

Biomolecular isolation Host–microbe interactions Integrated omics Limited sample material Microbiota Mouse model Sample heterogeneity 



This work was supported by an ATTRACT fellowship (ATTRACT/A09/03), CORE grant (CORE11/BM/1186762) and a European Union Joint Programming in Neurodegenerative Diseases grant (INTER/JPND/12/01) to P.W., and Aide à la Formation Recherche (AFR) grants to L.W. (PHD-2013-1/BM) and E.E.L.M. (PRD-2011-1/SR), all funded by the Luxembourg National Research Fund (FNR). We are grateful to Anna Heintz-Buschart for SDS analysis and her valuable comments on the manuscript; Christian Jaeger and Karsten Hiller for GC-MS analysis; the LCSB mouse facility, especially, Djalil Coowar and Ludivine Treuillot for the provision of fecal pellets, and Manuel Buttini for the provision of mouse tissue samples.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Pranjul Shah
    • 1
  • Emilie E. L. Muller
    • 1
  • Laura A. Lebrun
    • 1
  • Linda Wampach
    • 1
  • Paul Wilmes
    • 1
    Email author
  1. 1.Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch-sur-AlzetteLuxembourg

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