Principal Investigator

Prof. Dr. John Baines

Institution

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

Contact

Vita

Education/Training

1994 – 1998
Bachelor of Science, Biochemistry, University of Maryland College Park, USA

1998 – 2000
Master of Science, Biology, University of Rochester, New York, USA

2000 – 2004
PhD work at the LMU Munich under supervision of Prof. Wolfgang Stephan:
“Empirical approaches to detecting the action of natural selection in Drosophila”


Research Experience/Academic Appointments

2004 – 2005
Postdoc, Institute of Genetics, University of Cologne in the group of Prof. Diethard Tautz

2005 – 2009
Group Leader, Department of Evolutionary Biology, LMU Munich

Since 2009
W2 Professor, Evolutionary Genomics, Institute for Experimental Medicine, CAU Kiel

Since 2009
Guest Group Leader, Max-Planck-Institute for Evolutionary Biology, Plön


Important Scientific Prizes/Functions

Since 2010
Faculty Member, International Max Planck Research School in Evolutionary Biology

Since 2011
Member of Steering Committee, Excellence Cluster “Inflammation at Interfaces”

Since 2012
Coordinator of study area “Evolutionary Medicine” within the Kiel Medical Faculty Master Program “Medical Life Sciences”

Research

Publications

2017

Improved detection of gene-microbe interactions in the mouse skin microbiota using high-resolution QTL mapping of 16S rRNA transcripts.

Belheouane M, Gupta Y, Künzel S, Ibrahim S, Baines J F (2017); Microbiome., 5(1):59. doi: 10.1186/s40168-017-0275-5

A distinct cutaneous microbiota pofile in autoimmune bullous disease patients.

Miodovnik M, Künstner A, Langan E A, Zillikens D, Gläser R, Sprecher E, Baines J F, Schmidt E, Ibrahim S M (2017); Exp Dermatol., doi: 10.1111/exd.13357

Meeting Report of the Pathogenesis of Pemphigus and Pemphigoid Meeting in Munich.

Schmidt E, Spindler V, Eming R, Amagai M, Antonicelli F, Baines J F, Belheouane M, Bernard P, Borradori L, Caproni M, Di Zenzo G, Grando S, Harman K, Jonkman M F, Koga H, Ludwig R J, Kowalczyk A P, Müller E J, Nishie W, Pas H, Payne A S, Sadik C D, Seppänen A, Setterfield J, Shimizu H, Sinha A A, Sprecher E, Sticherling M, Ujiie H, Zillikens D, Hertl M, Waschke J (2017); J Invest Dermatol., pii:S0022-202X(17)30173-2. doi: 10.1016/j.jid.2017.01.028

2016

Beneficial Effects of a Dietary Weight Loss Intervention on Human Gut Microbiome Diversity and Metabolism Are Not Sustained during Weight Maintenance.

Heinsen F A, Fangmann D, Müller N, Schulte D M, Rühlemann M C, Türk K, Settgast U, Lieb W, Baines J F, Schreiber S, Franke A, Laudes M (2016); Obes Facts., 9(6):379-391. doi: 10.1159/000449506

FeaturedFunctional variants in the sucrase-isomaltase gene associate with increased risk of irritable bowel syndrome.

Henström M, Diekmann L, Bonfiglio F, Hadizadeh F, Kuech E M, von Köckritz-Blickwede M, Thingholm L B, Zheng T, Assadi G, Dierks C, Heine M, Philipp U, Distl O, Money M E, Belheouane M, Heinsen F A, Rafter J, Nardone G9, Cuomo R, Usai-Satta P, Galeazzi F, Neri M, Walter S, Simrén M, Karling P, Ohlsson B, Schmidt P T, Lindberg G, Dlugosz A, Agreus L, Andreasson A, Mayer E, Baines J F, Engstrand L, Portincasa P, Bellini M, Stanghellini V, Barbara G, Chang L, Camilleri M, Franke A, Naim H Y, D’Amato M (2016); Gut., pii:gutjnl-2016-312456. doi: 10.1136/gutjnl-2016-312456

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota.

Lagkouvardos I, Pukall R, Abt B, Foesel B U, Meier-Kolthoff J P, Kumar N, Bresciani A, Martínez I, Just S, Ziegler C, Brugiroux S, Garzetti D, Wenning M, Bui T P N, Wang J, Hugenholtz F, Plugge C M, Peterson D A, Hornef M W, Baines J F, Smidt H, Walter J, Kristiansen K, Nielsen H B, Haller D, Overmann J, Stecher B, Clavel T (2016); Nat Microbiol., 1(11):16219. doi: 10.1038/nmicrobiol.2016.219

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); Nature Genetics. doi: 10.1038/ng.3695

FeaturedThe gut microbiota contributes to a mouse model of spontaneous bile duct inflammation.

Schrumpf E, Kummen M, Valestrand L, Greiner T U, Holm K, Arulampalam V, Reims H M, Baines J, Bäckhed F, Karlsen T H, Blumberg R S, Hov J R, Melum E (2016); J Hepatol., pii: S0168-8278(16)30559-1. doi: 10.1016/j.jhep.2016.09.020

FeaturedEpithelial calcineurin controls microbiota-dependent intestinal tumor development.

Peuker K, Muff S, Wang J, Künzel S, Bosse E, Zeissig Y, Luzzi G, Basic M, Strigli A, Ulbricht A, Kaser A, Arlt A, Chavakis T, van den Brink G R, Schafmayer C, Egberts J H, Becker T, Bianchi M E, Bleich A, Röcken C, Hampe J, Schreiber S, Baines J F, Blumberg R S, Zeissig S (2016); Nat Med., 22(5):506-15. doi: 10.1038/nm.4072

FeaturedStool frequency is associated with gut microbiota composition.

Hadizadeh F, Walter S, Belheouane M, Bonfiglio F, Heinsen F A, Andreasson A, Agreus L, Engstrand L, Baines J F, Rafter J, Franke A, D’Amato M (2016); Gut., pii:gutjnl-2016-311935. doi: 10.1136/gutjnl-2016-311935

Lipocalin 2 Protects from Inflammation and Tumorigenesis Associated with Gut Microbiota Alterations.

Moschen A R, Gerner R R, Wang J, Klepsch V, Adolph T E, Reider S J, Hackl H, Pfister A, Schilling J, Moser P L, Kempster S L, Swidsinski A, Orth Höller D, Weiss G, Baines J F, Kaser A, Tilg H (2016); Cell Host Microbe., 19(4):455-69. doi: 10.1016/j.chom.2016.03.007

Getting the Hologenome Concept Right: An Eco-Evolutionary Framework for Hosts and Their Microbiomes.

Theis K R, Dheilly N M, Klassen J L, Brucker R M, Baines J F, Bosch T C, Cryan J F, Gilbert S F, Goodnight C J, Lloyd E A, Sapp J, Vandenkoornhuyse P, Zilber-Rosenberg I, Rosenberg E, Bordenstein S R (2016); mSystems., 1(2).pii:e00028-16. doi: 10.1128/mSystems.00028-16

Analysis of factors contributing to variation in the C57BL/6J fecal microbiota across German animal facilities

Rausch P, Basic M, Batra A, Bischoff S C, Blaut M, Clavel T, Gläsner J, Gopalakrishnan S, Grassl G A, Günther C, Haller D, Hirose M, Ibrahim S, Loh G, Mattner J, Nagel S, Pabst O, Schmidt F, Siegmund B, Strowig T, Volynets V, Wirtz S, Zeissig S, Zeissig Y, Bleich A, Baines J F (2016); Int J Med Microbiol., 306(5):343-55. doi: 10.1016/j.ijmm.2016.03.004

The role of tissue-specific microbiota in initial establishment success of Pacific oysters.

Lokmer A, Kuenzel S, Baines, J F, Wegner K M (2016); Environmental Microbiology, 18(3):970-987. doi: 10.1111/1462-2920.13163

Dissecting genetics of cutaneous miRNA in a mouse model of an autoimmune blistering disease.

Gupta Y, Möller S, Witte M, Belheouane M, Sezin T, Hirose M, Vorobyev A, Niesar F, Bischof J, Ludwig R J, Zillikens D, Sadik C D, Restle T, Häsler R, Baines J F, Ibrahim S M (2016); BMC Genomics, 17:112. doi: 10.1186/s12864-016-2455-2.

2015

Composition of Bacterial Communities Associated with Aurelia aurita Changes with Compartment, Life Stage, and Population.

Weiland-Bräuer N, Neulinger S C, Pinnow N, Künzel S, Baines J F, Schmitz R A (2015); Appl Environ Microbiol., 81(17):6038-6052. doi: 10.1128/AEM.01601-15

Expression of the Blood-Group-Related Gene B4galnt2 Alters Susceptibility to Salmonella Infection.

Rausch P, Steck N, Suwandi A, Seidel J A, Künzel S, Bhullar K, Basic M, Bleich A, Johnsen J M, Vallance B A, Baines J F, Grassl G A (2015); PLoS Pathog, 11(7):e1005008. doi: 10.1371/journal.ppat.1005008

Analysis of intestinal microbiota in hybrid house mice reveals evolutionary divergence in a vertebrate hologenome.

Wang J, Kalyan S, Steck N, Turner L M, Harr B, Künzel S, Vallier M, Häsler R, Franke A, Oberg H-H, Ibrahim S M, Grassl G A, Kabelitz D, Baines J F (2015); Nature Commun., 6:6440. doi: 10.1038/ncomms7440

Geographical patterns of the standing and active human gut microbiome in health and IBD.

Rehman A, Rausch P, Wang J, Skieceviciene J, Kiudelis G, Bhagalia K, Amarapurkar D, Kupcinskas L, Schreiber S, Rosenstiel P, Baines J F, Ott S (2015); Gut, 65(2):238-248. doi: 10.1136/gutjnl-2014-308341

2014

Type I interferon signalling in the intestinal epithelium affects Paneth cells, microbial ecology and epithelial regeneration

Tschurtschenthaler M, Wang J, Fricke C, Fritz T M, Niederreiter L, Adolph T E, Sarcevic E, Künzel S, Offner F A, Kalinke U, Baines J F, Tilg H, Kaser A (2014); Gut., 63(12):1921-31. doi: 10.1136/gutjnl-2013-305863

Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice.

Wang J, Linnenbrink M, Künzel S, Fernandes R, Nadeau M J, Rosenstiel P, Baines J F (2014); Proc Natl Acad Sci U S A., 111(26):E2703-10. doi: 10.1073/pnas.1402342111

Composition of microbial supragingival biofilms in young healthy adults in correlation to experimentally induced gingivitis.

Langfeldt D, Neulinger S C, Heuer W, Staufenbiel I, Sven Künzel S, Baines J F, Eberhard J, Schmitz R A (2014); PLosOne, 9(2):e87449. doi: 10.1371/journal.pone.0087449

2013

Bacterial colonization of Hydra hatchlings follows a robust temporal pattern.

Franzenburg S, Fraune S, Altrock P M, Künzel S, Baines J F, Traulsen A, Bosch T C G (2013); ISME J., 7(4):781-90. doi: 10.1038/ismej.2012.156

Genome-wide mapping of gene-microbiota interactions in susceptibility to autoimmune skin blistering.

Srinivas G, Möller S, Wang J, Künzel S, Zillikens D, Baines J F, Ibrahim S M (2013); Nature Commun., 4:2462. doi: 10.1038/ncomms3462

Distinct antimicrobial peptide expression determines host species-specific bacterial associations

Franzenburg S, Walter J, Künzel S, Wang J, Baines J F, Bosch T C G, Fraune S (2013); Proc Natl Acad Sci USA, 110(39):E3730-8. doi: 10.1073/pnas.1304960110

Noninvasive analysis of microbiome dynamics in the fruit fly Drosophila melanogaster.

Fink C, Staubach F, Kuenzel S, Baines J F, Roeder T (2013); Appl Environ Microbiol., 79(22):6984-8. doi: 10.1128/AEM.01903-13

Non-invasive analysis of microbiome
 dynamics in the fruit fly Drosophila melanogaster.

Fink C, Staubach F, Kuenzel S, Baines J F, Roeder T (2013); Appl Environ Microbiol., 79(22):6984-6988. doi: 10.1128/AEM.01903-13

The role of biogeography in shaping diversity of the intestinal microbiota in house mice.

Linnenbrink M, Wang J, Hardouin E A, Künzel S, Metzler D, Baines J F (2013); Mol Ecol., 22(7):1904-16. doi: 10.1111/mec.12206

2012

MyD88-deficient Hydra reveal an ancient function of TLR signaling in sensing bacterial colonizers.

Franzenburg S, Fraune S, Künzel S, Baines J F, Domazet-Loso T, Bosch T C G (2012); Proc Natl Acad Sci USA, 109(47):19374-9. doi: 10.1073/pnas.1213110109

MyD88 deficient Hydra reveal an ancient function of TLR-signaling in sensing bacterial colonizers.

Franzenburg S, Fraune S, Künzel S, Baines J F, Domazet-Loso T, Bosch T C (2012); Proc Natl Acad Sci U S A., 109(47):19374-9. doi: 10.1073/pnas.1213110109

Expression of the blood-group-related glycosyltransferase B4galnt2 influences the intestinal microbiota in mice.

Staubach F, Künzel S, Baines A C, Yee A, McGee B M, Bäckhed F, Baines J F, Johnsen J M (2012); ISME J., 6(7):1345-55. doi: 10.1038/ismej.2011.204

Extended analysis of a genome-wide association study in primary sclerosing cholangitis detects multiple novel risk loci.

Folseraas T, Melum E, Rausch P, Juran B D, Ellinghaus E, Shiryaev A, Laerdahl J K, Ellinghaus D, Schramm C, Weismüller T J, Gotthardt D N, Hov J R, Clausen O P, Weersma R K, Janse M, Boberg K M, Björnsson E, Marschall H U, Cleynen I, Rosenstiel P, Holm K, Teufel A, Rust C, Gieger C, Wichmann H E, Bergquist A, Ryu E, Ponsioen C Y, Runz H, Sterneck M, Vermeire S, Beuers U, Wijmenga C, Schrumpf E, Manns M P, Lazaridis K N, Schreiber S, Baines J F, Franke A, Karlsen T H (2012); J Hepatol., 57(2):366-75. doi: 10.1016/j.jhep.2012.03.031

2011

Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 (Secretor) genotype

Rausch P, Rehman A, Künzel S, Häsler R, Ott S J, Schreiber S, Rosenstiel P, Franke A, Baines J F (2011); Proc Natl Acad Sci USA, 108 (47): 19030-5. doi: 10.1073/pnas.1106408108

Long-term balancing selection at the blood group-related gene B4galnt2 in the genus Mus (Rodentia; Muridae)

Linnenbrink M, Johnsen J M, Montero I, Brzezinski C R, Harr B, Baines J F (2011); Mol Biol Evol, 28 (11):2999-3003. doi: 10.1093/molbev/msr150

Nod2 is essential
 for temporal development of intestinal microbial communities.

Rehman A, Sina C, Gavrilova O, Häsler R, Ott S, Baines J F, Schreiber S, Rosenstiel P (2011); Gut, 60(10):1354-62. doi: 10.1136/gut.2010.216259