A2
Host-microbiota coevolution in the mammalian intestine
Understanding the forces that shape variation in host-associated bacterial communities within- and between host species is key to understanding the evolution and maintenance of metaorganisms.
While a multitude of studies have investigated the influence of genetic and environmental factors at the level of community profiling, little information on the underlying functional genomic basis exists. In this project, we will identify signatures of coevolution between hosts and their intestinal microbes, using a multi-tiered approach in the Western-Eastern house mouse and human-chimpanzee host species pairs. First, we will employ genetic mapping to identify host genes that vary within and/or between species and influence microbial traits. These efforts will be aided using a “systems genetics” approach by incorporating genome-wide expression data in the mouse system and molecular population genetic analysis of host genomic regions. Second, candidate bacterial group (trait) signals will be further investigated, using a combination of shotgun metagenomic sequencing and single-cell/isolate analysis to characterize them at the functional level and identify potential signatures of adaptation to their hosts.
Researchers
Prof. Dr. John Baines
Prof. Dr. Andre Franke
Shauni Doms
Alumni
Publications
2020
Differences in the microbiota of native and non-indigenous gelatinous zooplankton organisms in a low saline environment
Jaspers C, Weiland-Bräuer N, Rühlemann MC, Baines JF, Schmitz RA, Reusch TBH (2020) Science of the Total Environment, accepted
FeaturedA fungal pathogen induces systemic susceptibility and systemic shifts in wheat metabolome and microbiome composition
Seybold H, Demetrowitsch TJ, Hassani M A, Szymczak S, Reim E, Haueisen J, Lübbers L, Rühlemann M, Franke A, Schwarz k, H. Stukenbrock E (2020) Nature Communications. 11(1):1910. doi: 10.1038/s41467-020-15633-x
An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome
Lesker TR, Durairaj AC, Gálvez EJC, Lagkouvardos I, Baines JF, Clavel T, Sczyrba A, McHardy AC, Strowig T (2020) Cell Rep. 30(9): 2909–2922.e6. doi: 10.1016/j.celrep.2020.02.036
2019
FeaturedComparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms
Rausch P, Rühlemann M, Hermes BM, Doms S, Dagan T, Dierking K, Domin H, Fraune S, von Frieling J, Hentschel U, Heinsen F-A, Höppner M, Jahn MT, Jaspers C, Kissoyan KAB, Langfeldt D, Rehman A, Reusch TBH, Roeder T, Schmitz RA, Schulenburg H, Soluch R, Sommer F, Stukenbrock E, Weiland-Bräuer N, Rosenstiel P, Franke A, Bosch T, Baines JF (2019) Microbiome, doi: 10.1186/s40168-019-0743-1
Consistent alterations in faecal microbiomes of patients with primary sclerosing cholangitis independent of associated colitis
Rühlemann M, Liwinski T, Heinsen F-A, Bang C, Zenouzi R, Kummen M, Thingholm L, Tempel M, Lieb W, Karlsen T, Lohse A, Hov J, Denk G, Lammert F, Krawczyk M, Schramm C, Franke A (2019) Aliment Pharmacol Ther. 1-10. doi: 10.1111/apt.15375
FeaturedAlterations of the bile microbiome in primary sclerosing cholangitis
Liwinski T, Zenouzi R, John C, Ehlken H, Rühlemann MC, Bang C, Groth S, Lieb W, Kantowski M, Andersen N, Schachschal G, Karlsen TH, Hov JR, Rösch T, Lohse AW, Heeren J, Franke A, Schramm C (2019) Gut 0:1–8. doi:10.1136/gutjnl-2019-318416
FeaturedNeutrality in the metaorganism
Sieber M, Pita L, Weiland-Bräuer N, Dirksen P, Wang J, Mortzfeld B, Franzenburg S, Schmitz RA, Baines JF, Fraune S, Hentschel U, Schulenburg H, Bosch TCG, Traulsen A (2019) PLoS Biol., DOI: 10.1371/journal.pbio.3000298
FeaturedSequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family
Lagkouvardos I, Lesker TR, Hitch TCA, Gálvez EJC, Smit N, Neuhaus K, Wang J, Baines JF, Abt B, Stecher B, Overmann J, Strowig T, Clavel T. (2019) Microbiome 7(1):28. doi: 10.1186/s40168-019-0637-2
2018
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
Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development
Low-level mitochondrial heteroplasmy modulates DNA replication, glucose metabolism and lifespan in mice.
Hirose M, Schilf P, Gupta Y, Zarse K, Künstner A, Fähnrich A, Busch H, Yin J, Wright MN, Ziegler A, Vallier M, Belheouane M, Baines JF, Tautz D, Johann K, Oelkrug R, Mittag J, Lehnert H, Othman A, Jöhren O, Schwaninger M, Prehn C, Adamski J, Shima K, Rupp J, Häsler R, Fuellen G, Köhling R, Ristow M, Ibrahim SM (2018); Sci Rep. 8(1):5872. doi: 10.1038/s41598-018-24290-6
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 evolution of ecological facilitation within mixed-species biofilms in the mouse gastrointestinal tract.
Lin XB, Wang T, Stothard P, Corander J, Wang J, Baines JF, Knowles SCL, Baltrūnaitė L, Tasseva G, Schmaltz R, Tollenaar S, Cody LA, Grenier T, Wu W, Ramer-Tait AE, Walter J (2018); ISME J. doi: 10.1038/s41396-018-0211-0
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
Epidermal lipid composition, barrier integrity, and eczematous inflammation are associated with skin microbiome configuration
Baurecht H, Rühlemann M, Rodríguez E, Thielking F, Harder I, Erkens AS, Stölzl D, Ellinghaus E, Hotze M, Lieb W, Wang S, Heinsen FA, Franke A, Weidinger S (2018) J ALLERGY CLIN IMMUN . doi: 10.1016/j.jaci.2018.01.019
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
Metaorganisms in extreme environments: do microbes play a role in organismal adaptation?
Bang C, Dagan T, Deines P, Dubilier N, Duschl W J, Fraune S, Hentschel U, Hirt H, Hülter N, Lachnit T, Picazo D, Galan P L, Pogoreutz C, Rädecker N, Saad M M, Schmitz R A, Schulenburg H, Voolstra C R, Weiland-Bräuer N, Ziegler M, Bosch T C G (2018); Zoology, doi: 10.1016/j.zool.2018.02.004
2017
Application of the distance-based F test in an mGWAS investigating β diversity of intestinal microbiota identifies variants in SLC9A8 (NHE8) and 3 other loci.
Rühlemann M C, Degenhardt F, Thingholm L B, Wang J, Skiecevičienė J, Rausch P, Hov J R, Lieb W, Karlsen T H, Laudes M, Baines J F, Heinsen F A, Franke A (2017); Gut Microbes., 8:55. doi: 10.1080/19490976.2017.1356979
2016
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