Principal Investigator, Steering Committee

Prof. Dr. John Baines

Institution

Kiel University
University Hospital Schleswig Holstein
Institute for Experimental Medicine
Evolutionary Medicine Lab
Max-Planck-Institute for Evolutionary Biology
Guest Group Evolutionary Genomics
Vita

Education/Training

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”

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

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

Research Experience/Academic Appointments

Since 2016
W3 Professor and Leader of Section of Evolutionary Medicine, Institute for Experimental Medicine, CAU Kiel

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

2009 – 2016
W2 Professor, Evolutionary Genomics, Institute for Experimental Medicine, CAU Kiel

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

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

Important Scientific Prizes/Functions

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

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

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

2016
Awarded Schleswig-Holstein Excellence Chair

Contact

+49 431 500 30310 / +49 4522 763 367
+49 431 500 30308 / +49 4522 763 351
j.baines@iem.uni-kiel.de
https://www.evolbio.mpg.de/16329/group_evolgenomics http://web.evolbio.mpg.de/evolgenomics/ https://gepris.dfg.de/gepris/person/1856938?context=person&task=showDetail&id=1856938&

Associated Research Groups

Prof. Dr. John Baines
Publications

Publications

Filter by

Year All
2024
B1

Shaping tiny worlds: Paternal microbiota manipulation influences offspring microbial colonization and development in a sex role-reversed pipefish

Wagner, K. S., Salasc, F., Marten, S. M., & Roth, O. (2024). bioRxiv, 2024-10. doi: https://doi.org/10.1101/2024.10.09.617486

2024
C4

The archaeome in metaorganism research, with a focus on marine models and their bacteria–archaea interactions

von Hoyningen-Huene, A. J., Bang, C., Rausch, P., Rühlemann, M., Fokt, H., He, J., Jensen, N., Knop, M., Petersen, C., Schmittmann, L., Zimmer, T., Baines, J. F., Bosch, T. C. G., Hentschel, U., Reusch, T. B. H., Roeder, T., Franke, A., Schulenburg, H., Stukenbrock, E., & Schmitz, R. A. (2024). Frontiers in Microbiology, 15, 1347422. doi: https://doi.org/10.3389/fmicb.2024.1347422

2023
A2
C2
Z3

A mitochondrial sirtuin shapes the intestinal microbiota by controlling lysozyme expression

Knop M, Treitz C, Bettendorf S, Bossen J, von Frieling J, Doms S, Bruchhaus I, Kuehnlein RP, Baines JF, Tholey A, Roeder T (2023) A mitochondrial sirtuin shapes the intestinal microbiota by controlling lysozyme expression. bioRxiv, doi: https://doi.org/10.1101/2023.06.02.543385

2023
A2
B2
B4

Comparative genomics of novel Bacteroides acidifaciens isolates reveals candidates for adaptation to host subspecies in house mice

Hanna Fokt, Shauni Doms, Malte C. Rühlemann, Maxime Godfroid, Ruth A. Schmitz, Britt M. Hermes, John F. Baines (2023) Comparative genomics of novel Bacteroides acidifaciens isolates reveals candidates for adaptation to host subspecies in house mice BioRxiv doi: https://doi.org/10.1101/2023.01.31.526425

 

2023
A2
A4
C1
C2

The microbiome of the marine flatworm Macrostomum lignano provides fitness advantages and exhibits circadian rhythmicity

Ma Y, He J, Sieber M, von Frieling J, Bruchhaus I, Baines JF, Bickmeyer U, Roeder T (2023) The microbiome of the marine flatworm Macrostomum lignano provides fitness advantages and exhibits circadian rhythmicity. Communications Biology 6: 289. https://doi.org/10.1038/s42003-023-04671-y.

2023
A1
A2
B2
B4
Z2
Z3

Closely related Bacteroides of the murine intestinal microbiota affect each other’s growth positively or negatively

Hanna Fokt, Gabija Sakalyte, Rahul Unni, Mohammad Abukhalaf, Liam Cassidy, Georgios Marinos, Maxime Godfroid, Birhanu M Kinfu, Ruth A Schmitz, Christoph Kaleta, Andreas Tholey, John F Baines, Tal Dagan, Daniel Unterweger (2023) BioRxiv doi: https://doi.org/10.1101/2023.03.05.530569
2023
A2
C2
Z3

A mitochondrial sirtuin shapes the intestinal microbiota by controlling lysozyme expression

Knop M, Treitz C, Bettendorf S, Bossen J, von Frieling J, Doms S, Bruchhaus I, Kuehnlein RP, Baines JF, Tholey A, Roeder T (2023) A mitochondrial sirtuin shapes the intestinal microbiota by controlling lysozyme expression. bioRxiv, doi: https://doi.org/10.1101/2023.06.02.543385

2023
A2
Z3

Pathometagenomics reveals susceptibility to intestinal infection by Morganella to be mediated by the blood group-related B4galnt2 gene in wild mice

Marie Vallier, Abdulhadi Suwandi, Katrin Ehrhardt, Meriem Belheouane, David Berry, Aleksa Čepić, Alibek Galeev, Jill M. Johnsen, Guntram A. Grassl, and John F. Baines (2023): GUT MICROBES , VOL. 15, NO. 1, 2164448
https://doi.org/10.1080/19490976.2022.2164448

 

2022
A2
B4
Z2

Bacteroides muris sp. nov. isolated from the cecum of wild-derived house mice.

Hanna Fokt, Rahul Unni, Urska Repnik, Ruth A. Schmitz, Marc Bramkamp, John F. Baines, Daniel Unterweger. Archives of Microbiology 204:546.
doi: 10.1007/s00203-022-03148-6

2022
A2
Z3

Key features of the genetic architecture and evolution of host-microbe interactions revealed by high-resolution genetic mapping of the mucosa-associated gut microbiome in hybrid mice

Doms S, Fokt H, Ruehlemann MC, Chung CJ, Kuenstner A, Ibrahim S, Franke A, Turner LM, Baines JF (2022):  eLife; 11:e75419. doi: 10.7554/eLife.75419

2021
A2
Featured

Primate phageomes are structured by superhost phylogeny and environment.

Gogarten, JF, Rühlemann M, Archie E, Tung J, Akoua-Koffi C, Bang C, Deschner T, Muyembe-Tamfun J-J, Robbins MM, Schubert G, Surbeck M, Wittig RM, Zuberbühler K, Baines JF, Franke A, Leendertz FH, Calvignac-Spencer S, PNAS. 118 (15) e2013535118. doi: 10.1073/pnas.2013535118

2021
A2
INF
Featured

Genome-wide association study in 8,956 German individuals identifies influence of ABO histo-blood groups on gut microbiome.

Rühlemann MC, Hermes BM, Bang C, Doms S, Moitinho-Silva L, Thingholm LB, Frost F, Degenhardt F, Wittig M, Kässens J, Weiss FU, Peters A, Neuhaus K, Völker U, Völzke H, Homuth G, Weiss S, Laudes M, Lieb W, Haller D, Lerch MM, Baines JF, Franke A (2021) Nat Genet. 53, 147–155. doi: 10.1038/s41588-020-00747-1

2020
A2
Featured

S100A8 and S100A9 Are Important for Postnatal Development of Gut Microbiota and Immune System in Mice and Infants.

Willers M, Ulas T, Völlger L, Vogl T, Heinemann AS, Pirr S, Pagel J, Fehlhaber B, Halle O, Schöning J, Schreek S, Löber U, Essex M, Hombach P, Graspeuntner S, Basic M, Bleich A, Cloppenborg-Schmidt K, Künzel S, Jonigk D, Rupp J, Hansen G, Förster R, Baines JF, Härtel C, Schultze JL, Forslund SK, Roth J, Viemann D (2020)  Gastroenterology. 159(6):2130-2145.e5. doi: 1053/j.gastro.2020.08.019.

2020
A2
Featured

Assessing similarities and disparities in the skin microbiota between wild and laboratory populations of house mice

Belheouane M, Vallier M, Čepić A, Chung CJ, Ibrahim S, Baines FJ (2020) ISME J. 14, 2367–2380 doi: 10.1038/s41396-020-0690-7

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
C2
Z3

NOD2 influences trajectories of intestinal microbiota recovery after antibiotic perturbation

Moltzau Anderson J, Lipinski S, Sommer F, Pan W-H, Boulard O, Rehman A, Falk-Paulsen M, Stengel ST, Aden K, Häsler R, Bharti R, Künzel S, Baines JF, Chamaillard M, Rosenstiel P (2020) Cell Mol Gastroenterol Hepatol. 10(2): 365-389. doi: 10.1016/j.jcmgh.2020.03.008

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
A1
A2
A3
B1
B2
C1
C2
INF
Z3
Featured

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
A4
B1
B2
Featured

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
Featured

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
INF

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

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

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
Featured

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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