A2
Evolution and Ecology

Host-microbiota coevolution in the mammalian intestine

This project aims to determine the genetic basis of evolutionary change among mammalian metaorganisms. Through the use of highly sophisticated and unique genetic resources in both the house mouse subspecies complex and humans, we identified highly interesting candidate host loci and microbial taxa that may be involved in adaptation by one or both partners. Common aspects that emerged from both model systems are host genes involved in circadian rhythms and bacterial taxa belonging to Bacteroides.

In the second funding period we will conduct a thorough functional characterization of the most influential candidate host genes and bacterial taxa. This includes the pinpointing of causative mutations, the use of knockout mouse models and the characterization of bacterial strain-level variation. Further, we will improve upon 16S rRNA gene-based mapping by extending mapping efforts to the level of functional elements of the gut microbiome, using shotgun metagenomic sequencing. Importantly, the shotgun metagenomic data will also enable us to extend mapping to non-bacterial elements of the gut microbiome, including novel archaeal taxa in mice.

The A2 project is comprised of a unique combination of evolutionary microbiome research, microbiology and state of the art genetic mapping analysis. The latter is made possible by one-of-a-kind mouse genetic resources and being lead participants in international consortia. Accordingly, our project is the first to clearly identify genetic variation in circadian processes as an aspect of ongoing evolutionary dynamics in mammalian metaorganisms, which will be explored in detail in this funding period.

The overall goal of our project is to identify and characterize the genetic basis of evolutionary change between mammalian metaorganisms. Using the house mouse species complex (A2.1, PI Baines) and Hominidae systems (A2.2, PI Franke), we hypothesize that mammals share themes and mechanisms of host-microbe interaction.

Accordingly, the main joint aims of the first funding period were to (i) identify host genomic regions influencing microbial traits by employing genetic mapping approaches, (ii) perform a fine-scale characterization of candidate bacterial taxa at the genomic level, (iii) identify signatures of coadaptation via population genetic and comparative genomic analyses. This work yielded many interesting results, which importantly include overlap in host genes and bacterial taxa between the two model systems.

A2
Researchers

Researchers

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A2.1: Characterizing the genetic basis of evolutionary change in the mouse metaorganism

A2.2: Characterizing genetic and evolutionary signals of host-microbe interactions in hominids

A2: Alumni

A2
Related Publications

Related Publications

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2020
A2
B2

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) Sci Total Environ. 734:139471. doi: 10.1016/j.scitotenv.2020.139471

2020
A2
A3

A 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

2020
A2

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
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INF
Z3

Comparative 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

2019
A2

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

2019
A2

Alterations 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

2019
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A4
B1
B2

Neutrality 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

2019
A2

Sequence 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
A2
B2
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INF
Z2

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

2018
A2
C2

Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development

Franke A, Schultze JL, Bäckhed F, Rosenstiel P (2018) Genome Med. 10(1):27. doi: 10.1186/s13073-018-0534-5.
2018
A2
Z3

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

2018
A2
C2
INF
Z3

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

2018
A2
Z3

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

2018
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B1
INF
Z2

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

2018
A2

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

2018
A2
C2
INF
Z3

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

2018
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A2
A3
A4
B1
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C1
Z1
Z2

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
A2
Z3

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
A2
C2
INF
Z3

Genome-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

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