Data management and integrated analyses
The INF-project is established to support the demanding bioinformatic requirements of the CRC 1182. The project will develop data and metadata standards in order to facilitate data integration and future combined and comparative analyses. Besides developing a unified CRC 1182 data policy, INF will set up the necessary central storage server for the entire CRC 1182. Members of the CRC 1182 will be educated and supported in data preparation, management and analysis. While the main aim is on data standardization and storage, the requested bioinformatician will provide the CRC 1182 groups with basic analysis support. The INF-project will be embedded into recently established local networks of experts, such as the bioinformatics network and the clinical data management group. In the long-term we will evolve this into a central platform that – besides supervising the data management – generates and confirms novel hypotheses, employing the rich multivariate data collected during the first CRC 1182 funding period.
Following this overarching approach, general concepts and mechanisms for host-microbiota interactions can be tested. Future systems biology analyses can provide a unifying conceptual framework, which will ease the comparison of different models, including different organisms, but also different levels of organization. The “systems view” in biology states that the properties of a system at a given level of organization cannot be found in its components but rather emerge from their interactions. As a result, a particular biological system can only be fully understood – functionally and evolutionarily – by integrating distinct levels of organization. By formalizing the overall CRC 1182 research questions and results, the INF project will play an essential role in the emergence and testing of trans-model hypotheses.
The functional repertoire encoded within the native microbiome of the model nematode Caenorhabditis elegans
Zimmermann J, Obeng N, Yang W, Pees B, Petersen B, Waschina S, Kissoyan KAB, Aidley J, Hoeppner MP, Bunk B, Spröer C, Leippe M, Dierking K, Kaleta C*, Schulenburg H* (2019) BioRxiv 554345. * Shared senior authorship doi: 10.1101/554345
The inducible response of the nematode Caenorhabditis elegans to members of its natural microbiome across development and adult life
Yang W, Petersen C, Pees B, Zimmermann J, Waschina S, Dirksen P, Rosenstiel P, Tholey A, Leippe M, Dierking K, Kaleta C*, Schulenburg H*. BioRxiv 554758.* Shared senior authorship doi: 10.1101/554758
Functions of the Microbiota for the Physiology of Animal Metaorganisms
Esser D, · Lange J, · Marinos G, · Sieber M, Best L, Prasse D, Bathia J, Rühlemann MC, Boersch K, Jaspers C, Sommer F (2018) J Innate Immun DOI: 10.1159/000495115
Differential expression of immune receptors in two marine sponges upon exposure to microbial-associated molecular patterns.
Pita L, Hoeppner MP, Ribes M, Hentschel U (2018); Sci Rep. 8(1):16081.doi: 10.1038/s41598-018-34330-w
Gut dysbiosis with Bacilli dominance and accumulation of fermentation products precedes late-onset sepsis in preterm infants.
Graspeuntner S, Waschina S, Künzel S, Twisselmann N, Rausch TK, Cloppenborg-Schmidt K, Zimmermann J, Viemann D, Herting E, Göpel W, Baines JF, Kaleta C, Rupp J, Härtel C, Pagel J (2018) Clin Infect Dis. doi: 10.1093/cid/ciy882
Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development.
Pan WH, Sommer F, Falk-Paulsen M, Ulas T, Best P, Fazio A, Kachroo P, Luzius A, Jentzsch M, Rehman A, Müller F, Lengauer T, Walter J, Künzel S, Baines JF, Schreiber S, Franke A, Schultze JL, Bäckhed F, Rosenstiel P (2018); Genome Med. 10(1):27. doi: 10.1186/s13073-018-0534-5
The genomic rate of adaptation in the fungal wheat pathogen Zymoseptoria tritici
The sponge holobiont in a changing ocean: from microbes to ecosystems.
Pita L, Rix L, Slaby B M, Franke A, Hentschel U (2018); Microbiome, 6(46). doi: 10.1186/s40168-018-0428-1
The antibiotic resistome and microbiota landscape of refugees from Syria, Iraq and Afghanistan in Germany.
Häsler R, Kautz C, Rehman A, Podschun R, Gassling V, Brzoska P, Sherlock J, Gräsner J T, Hoppenstedt G, Schubert S, Ferlinz A, Lieb W, Laudes M, Heinsen F A, Scholz J, Harmsen D, Franke A, Eisend S, Kunze T, Fickenscher H, Ott S, Rosenstiel P, Schreiber S (2018); Microbiome., 6(1):37. doi: 10.1186/s40168-018-0414-7
FeaturedGenome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota.
Wang J, Thingholm L B, Skiecevičienė J, Rausch P, Kummen M, Hov J R, Degenhardt F, Heinsen F A, Rühlemann M C, Szymczak S, Holm K, Esko T, Sun J, Pricop-Jeckstadt M, Al-Dury S, Bohov P, Bethune J, Sommer F, Ellinghaus D, Berge R K, Hübenthal M, Koch M, Schwarz K, Rimbach G, Hübbe P, Pan W H, Sheibani-Tezerji R, Häsler R, Rosenstiel P, D’Amato M, Cloppenborg-Schmidt K, Künzel S, Laudes M, Marschall H U, Lieb W, Nöthlings U, Karlsen T H, Baines J F, Franke A (2016); Nat Genet., 48(11):1396-1406. doi: 10.1038/ng.3695