TY  - JOUR
U1  - Zeitschriftenartikel, wissenschaftlich - begutachtet (reviewed)
A1  - Gierse, Laurin
A1  - Meene, Alexander
A1  - Schultz, Daniel
A1  - Schwaiger, Theresa
A1  - Karte, Claudia
A1  - Schröder, Charlotte
A1  - Wang, Haitao
A1  - Wünsche, Christine
A1  - Methling, Karen
A1  - Kreikemeyer, Bernd
A1  - Fuchs, Stephan
A1  - Bernhardt, Jörg
A1  - Becher, Dörte
A1  - Lalk, Michael
A1  - Urich, Tim
A1  - Riedel, Katharina
T1  - A Multi-Omics Protocol for Swine Feces to Elucidate Longitudinal Dynamics in Microbiome Structure and Function
JF  - Microorganisms
N2  - 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.
KW  - biomedical model swine
KW  - gastrointestinal microbiome
KW  - integrated multi-omics
KW  - 16S rRNA gene-sequencing
KW  - metaproteomics
KW  - metabolomics
Y1  - 2020
UN  - https://nbn-resolving.org/urn:nbn:de:gbv:9-opus-42014
SN  - 2076-2607
SS  - 2076-2607
U6  - https://doi.org/https://doi.org/10.3390/microorganisms8121887
DO  - https://doi.org/https://doi.org/10.3390/microorganisms8121887
VL  - 8
IS  - 12
SP  - 20
S1  - 20
PB  - MDPI
CY  - Basel
ER  -