Z3

Next generation sequencing applications for studying metaorganisms

The main purpose of the Z3-project is to provide a standardized central hub for next generation sequencing(NGS)-based applications among CRC 1182 projects. This includes the metagenomic analysis of host-associated microbial communities, bacterial genome sequencing and the individual transcriptomic analysis of both hosts and microbes.

The metagenomic sequencing will be provided on two levels:
(i) bacterial community profiling based on 16S rRNA gene amplicon sequencing and
(ii) functional (shotgun) metagenomics.

Transcriptomic analyses will be provided using standardized RNAseq protocols using different RNA purification methods. The technical sequence assessment will be performed using the NGS infrastructure at the Institute of Clinical Molecular Biology.

The main goal of the project is to maintain a high level of standardization to ensure comparability between the diverse data sets generated by the CRC 1182. Further, the Z3 project will closely monitor the most current technical advances in the field and provide these to the CRC 1182, when possible.

Researchers

Jan Schubert

Technician
Kiel University Institute for Experimental Medicine

Prof. Dr. John Baines

Principal Investigator
Kiel University Institute for Experimental Medicine Max-Planck-Institute for Evolutionary Biology

Publications

2017

FeaturedCRC1182 PublicationThe resilience of the intestinal microbiota influences health and disease.

Sommer F, Anderson J M, Bharti R, Raes J, Rosenstiel P (2017); Nat Rev Microbiol., doi: 10.1038/nrmicro.2017.58

FeaturedCRC1182 PublicationEfficacy of Sterile Fecal Filtrate Transfer for Treating Patients With Clostridium difficile Infection. Gastroenterology.

Ott S J, Waetzig G H, Rehman A, Moltzau-Anderson J, Bharti R, Grasis J A, Cassidy L, Tholey A, Fickenscher H, Seegert D, Rosenstiel P, Schreiber S (2017); Gastroenterology, 152(4):799-811.e7. doi: 10.1053/j.gastro.2016.11.010

2016

CRC1182 PublicationEpithelial IL-23R Signaling Licenses Protective IL-22 Responses in Intestinal Inflammation.

Aden K, Rehman A, Falk-Paulsen M, Secher T, Kuiper J, Tran F, Pfeuffer S, Sheibani-Tezerji R, Breuer A, Luzius A, Jentzsch M, Häsler R, Billmann-Born S, Will O, Lipinski S, Bharti R, Adolph T, Iovanna J L, Kempster S L, Blumberg R S, Schreiber S, Becher B, Chamaillard M, Kaser A, Rosenstiel P (2016); Cell Rep., 16(8):2208-18. doi: 10.1016/j.celrep.2016.07.054

CRC1182 PublicationThe native microbiome of the nematode Caenorhabditis elegans: Gateway to a new host-microbiome model.

Dirksen P, Marsh SA, Braker I, Heitland N, Wagner S, Nakad R, Mader S, Petersen C, Kowallik V, Rosenstiel P C, Felix M A, Schulenburg H (2016); BMC Biology, 14:38. doi:10.1186/s12915-016-0258-1