@article{GierseMeeneSchultzetal.2020,
  author    = {Laurin Gierse and Alexander Meene and Daniel Schultz and Theresa Schwaiger and Claudia Karte and Charlotte Schr{\"o}der and Haitao Wang and Christine W{\"u}nsche and Karen Methling and Bernd Kreikemeyer and Stephan Fuchs and J{\"o}rg Bernhardt and D{\"o}rte Becher and Michael Lalk and Tim Urich and Katharina Riedel},
  title     = {A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and Function},
  series   = {Microorganisms},
  volume    = {8},
  number    = {12},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2076-2607},
  doi       = {https://doi.org/10.3390/microorganisms8121887},
  url       = {https://nbn-resolving.org/urn:nbn:de:gbv:9-opus-42014},
  year      = {2020},
  abstract  = {Swine are regarded as promising biomedical models, but the dynamics of theirgastrointestinal microbiome have been much less investigated than that of humans or mice. The aimof this study was to establish an integrated multi-omics protocol to investigate the fecal microbiomeof healthy swine. To this end, a preparation and analysis protocol including integrated samplepreparation for meta-omics analyses of deep-frozen feces was developed. Subsequent data integrationlinked microbiome composition with function, and metabolic activity with protein inventories, i.e.,16S rRNA data and expressed proteins, and identified proteins with corresponding metabolites.16S rRNA gene amplicon and metaproteomics analyses revealed a fecal microbiome dominated byPrevotellaceae,Lactobacillaceae,Lachnospiraceae,RuminococcaceaeandClostridiaceae.Similar microbiomecompositions in feces and colon, but not ileum samples, were observed, showing that feces can serveas minimal-invasive proxy for porcine colon microbiomes. Longitudinal dynamics in composition,e.g., temporal decreased abundance ofLactobacillaceaeandStreptococcaceaeduring the experiment,were not reflected in microbiome function. Instead, metaproteomics and metabolomics showed arather stable functional state, as evident from short-chain fatty acids (SCFA) profiles and associatedmetaproteome functions, pointing towards functional redundancy among microbiome constituents.In conclusion, our pipeline generates congruent data from different omics approaches on the taxonomyand functionality of the intestinal microbiome of swine.},
  language  = {en}
}