2023
Rühlemann M.C., Bang C., Gogarten J.F., Hermes B.M., Groussin M., Waschina S., Poyet M., Ulrich M., Akoua-Koffi C., Deschner T., Muyembe-Tamfum J.J., Robbins M.M., Surbeck M., Wittig R.M., Zuberbühler K., Baines J.F., Leendertz F.H., Franke A. Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids. BioRxiv. Doi: https://10.1101/2023.03.01.530589v1
Fokt H., Doms S., Rühlemann M.C., Godfroid M., Schmitz R.A., Hermes B.M., Baines J.F. 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
Chung C.J., Hermes B.M., Gupta Y., Ibrahim S., Belheouane M., Baines JF. Genome-wide mapping of gene-microbe interactions in the murine lung microbiota based on quantitative microbial profiling. Animal Microbiome. In press.
Ma Y., He J., Sieber M., von Frieling J., Bruchhaus I., Baines J.F., Bickmeyer U., Roeder T. The microbiome of the marine flatworm Macrostomum lignano provides fitness advantages and exhibits circadian rhythmicity. Communications Biology, 6(1):289. https://doi.org/10.1038/s42003-023-04671-y
Borges A.S.G., Basu M., Brinks E., Bang C., Cho G.S., Baines J.F., Franke A., Franz C.M.A.P. Fast Identification Method for Screening Bacteria from Faecal Samples Using Oxford Nanopore Technologies MinION Sequencing. Current Microbiology, 80(3):101. https://doi.org/10.1007/s00284-023-03201-7
Matute J.D., Duan J., Flak M.B., Griebel P., Tascon-Arcila J.A., Doms S., Hanley T., Antanaviciute A., Gundrum J., Mark Welch J.L., Sit B., Abtahi S., Fuhler G.M., Grootjans J., Tran F., Stengel S.T., White J.R., Krupka N., Haller D., Clare S., Lawley T.D., Kaser A., Simmons A., Glickman J.N., Bry L., Rosenstiel P., Borisy G., Waldor M.K., Baines J.F., Turner J.R., Blumberg R.S. Intelectin-1 binds and alters the localization of the mucus barrier-modifying bacterium Akkermansia muciniphila. Journal Experimental Medicine. 220(1):e20211938. https://doi.org10.1084/jem.20211938
Vallier M., Suwandi A., Ehrhardt K., Belheouane M., Berry D., Čepić A., Galeev A., Johnsen J.M., Grassl G.A., Baines J.F. Pathometagenomics reveals susceptibility to intestinal infection by Morganella to be mediated by the blood group-related B4galnt2 gene in wild mice. Gut Microbes. 15(1):2164448. https://doi.org10.1080/19490976.2022.2164448
Belheouane, M., Hermes, B. M., Van Beek, N., Benoit, S., Bernard, P., Drenovska, K., Gerdes, S., Gläser, R., Goebeler, M., Günther, C., von Georg, A., Hammers, C. M., Holtsche, M. M., Homey, B., Horváth, O. N., Hübner, F., Linnemann, B., Joly, P., Márton, D., … Baines, J. F. (2022). Characterization of the skin microbiota in bullous pemphigoid patients and controls reveals novel microbial indicators of disease. Journal of Advanced Research, 44:71-79. https://doi.org/10.1016/j.jare.2022.03.019
Fokt H., Doms S., Rühlemann M.C., Godfroid M., Schmitz R.A., Hermes B.M., Baines J.F. 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
Chung C.J., Hermes B.M., Gupta Y., Ibrahim S., Belheouane M., Baines JF. Genome-wide mapping of gene-microbe interactions in the murine lung microbiota based on quantitative microbial profiling. Animal Microbiome. In press.
Ma Y., He J., Sieber M., von Frieling J., Bruchhaus I., Baines J.F., Bickmeyer U., Roeder T. The microbiome of the marine flatworm Macrostomum lignano provides fitness advantages and exhibits circadian rhythmicity. Communications Biology, 6(1):289. https://doi.org/10.1038/s42003-023-04671-y
Borges A.S.G., Basu M., Brinks E., Bang C., Cho G.S., Baines J.F., Franke A., Franz C.M.A.P. Fast Identification Method for Screening Bacteria from Faecal Samples Using Oxford Nanopore Technologies MinION Sequencing. Current Microbiology, 80(3):101. https://doi.org/10.1007/s00284-023-03201-7
Matute J.D., Duan J., Flak M.B., Griebel P., Tascon-Arcila J.A., Doms S., Hanley T., Antanaviciute A., Gundrum J., Mark Welch J.L., Sit B., Abtahi S., Fuhler G.M., Grootjans J., Tran F., Stengel S.T., White J.R., Krupka N., Haller D., Clare S., Lawley T.D., Kaser A., Simmons A., Glickman J.N., Bry L., Rosenstiel P., Borisy G., Waldor M.K., Baines J.F., Turner J.R., Blumberg R.S. Intelectin-1 binds and alters the localization of the mucus barrier-modifying bacterium Akkermansia muciniphila. Journal Experimental Medicine. 220(1):e20211938. https://doi.org10.1084/jem.20211938
Vallier M., Suwandi A., Ehrhardt K., Belheouane M., Berry D., Čepić A., Galeev A., Johnsen J.M., Grassl G.A., Baines J.F. Pathometagenomics reveals susceptibility to intestinal infection by Morganella to be mediated by the blood group-related B4galnt2 gene in wild mice. Gut Microbes. 15(1):2164448. https://doi.org10.1080/19490976.2022.2164448
Belheouane, M., Hermes, B. M., Van Beek, N., Benoit, S., Bernard, P., Drenovska, K., Gerdes, S., Gläser, R., Goebeler, M., Günther, C., von Georg, A., Hammers, C. M., Holtsche, M. M., Homey, B., Horváth, O. N., Hübner, F., Linnemann, B., Joly, P., Márton, D., … Baines, J. F. (2022). Characterization of the skin microbiota in bullous pemphigoid patients and controls reveals novel microbial indicators of disease. Journal of Advanced Research, 44:71-79. https://doi.org/10.1016/j.jare.2022.03.019
2022
Doms S., Fokt H., Rühlemann M.C., Chung C.J., Kuenstner A., Ibrahim S.M., Franke A., Turner L.M., Baines J.F. 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. Elife, 11:e75419. https://doi.org/10.7554/eLife.75419
Specht H.E., Mannig N., Belheouane M., Andreani N.A., Tenbrock K., Biemann R., Borucki K., Dahmen B., Dempfle A., Baines J.F., Herpertz-Dahlmann B., Seitz J.. Lower serum levels of IL-1β and IL-6 cytokines in adolescents with anorexia nervosa and their association with gut microbiota in a longitudinal study. Frontiers Psychiatry, 13:920665. https://doi.org/10.3389/fpsyt.2022.920665
Suwandi A, Alvarez KG, Galeev A, Steck N, Riedel CU, Puente JL, Baines JF, Grassl GA. B4galnt2-mediated host glycosylation influences the susceptibility to Citrobacter rodentium infection. Frontiers Microbiology, 13:980495. https://doi.org/10.3389/fmicb.2022.980495
Fokt H., Unni R., Repnik U., Schmitz R.A., Bramkamp M., Baines J.F., Unterweger D. Bacteroides muris sp. nov. isolated from the cecum of wild-derived house mice. Archives of Microbiology, 204(9):546. https://doi.org/10.1007/s00203-022-03148-6
Gröbner, E.-M., Zeiler, M., Fischmeister, F. P. S., Kollndorfer, K., Schmelz, S., Schneider, A., Haid-Stecher, N., Sevecke, K., Wagner, G., Keller, L., Adan, R., Danner, U., van Elburg, A., van der Vijgh, B., Kooij, K. L., Fetissov, S., Andreani, N. A., Baines, J. F., Dempfle, A., … Karwautz, A. (2022). The effects of probiotics administration on the gut microbiome in adolescents with anorexia nervosa-A study protocol for a longitudinal, double-blind, randomized, placebo-controlled trial. European Eating Disorders Review: The Journal of the Eating Disorders Association, 30(1), 61–74. https://doi.org/10.1002/erv.2876
Henneke, L., Schlicht, K., Andreani, N. A., Hollstein, T., Demetrowitsch, T., Knappe, C., Hartmann, K., Jensen-Kroll, J., Rohmann, N., Pohlschneider, D., Geisler, C., Schulte, D. M., Settgast, U., Türk, K., Zimmermann, J., Kaleta, C., Baines, J. F., Shearer, J., Shah, S., … Laudes, M. (2022). A dietary carbohydrate—Gut Parasutterella—Human fatty acid biosynthesis metabolic axis in obesity and type 2 diabetes. Gut Microbes, 14(1), 2057778. https://doi.org/10.1080/19490976.2022.2057778
Rausch, P., Hartmann, M., Baines, J. F., & von Bismarck, P. (2022). Analysis of the fecal and oral microbiota in chronic recurrent multifocal osteomyelitis. Arthritis Research & Therapy, 24(1), 54. https://doi.org/10.1186/s13075-021-02711-8
Specht H.E., Mannig N., Belheouane M., Andreani N.A., Tenbrock K., Biemann R., Borucki K., Dahmen B., Dempfle A., Baines J.F., Herpertz-Dahlmann B., Seitz J.. Lower serum levels of IL-1β and IL-6 cytokines in adolescents with anorexia nervosa and their association with gut microbiota in a longitudinal study. Frontiers Psychiatry, 13:920665. https://doi.org/10.3389/fpsyt.2022.920665
Suwandi A, Alvarez KG, Galeev A, Steck N, Riedel CU, Puente JL, Baines JF, Grassl GA. B4galnt2-mediated host glycosylation influences the susceptibility to Citrobacter rodentium infection. Frontiers Microbiology, 13:980495. https://doi.org/10.3389/fmicb.2022.980495
Fokt H., Unni R., Repnik U., Schmitz R.A., Bramkamp M., Baines J.F., Unterweger D. Bacteroides muris sp. nov. isolated from the cecum of wild-derived house mice. Archives of Microbiology, 204(9):546. https://doi.org/10.1007/s00203-022-03148-6
Gröbner, E.-M., Zeiler, M., Fischmeister, F. P. S., Kollndorfer, K., Schmelz, S., Schneider, A., Haid-Stecher, N., Sevecke, K., Wagner, G., Keller, L., Adan, R., Danner, U., van Elburg, A., van der Vijgh, B., Kooij, K. L., Fetissov, S., Andreani, N. A., Baines, J. F., Dempfle, A., … Karwautz, A. (2022). The effects of probiotics administration on the gut microbiome in adolescents with anorexia nervosa-A study protocol for a longitudinal, double-blind, randomized, placebo-controlled trial. European Eating Disorders Review: The Journal of the Eating Disorders Association, 30(1), 61–74. https://doi.org/10.1002/erv.2876
Henneke, L., Schlicht, K., Andreani, N. A., Hollstein, T., Demetrowitsch, T., Knappe, C., Hartmann, K., Jensen-Kroll, J., Rohmann, N., Pohlschneider, D., Geisler, C., Schulte, D. M., Settgast, U., Türk, K., Zimmermann, J., Kaleta, C., Baines, J. F., Shearer, J., Shah, S., … Laudes, M. (2022). A dietary carbohydrate—Gut Parasutterella—Human fatty acid biosynthesis metabolic axis in obesity and type 2 diabetes. Gut Microbes, 14(1), 2057778. https://doi.org/10.1080/19490976.2022.2057778
Rausch, P., Hartmann, M., Baines, J. F., & von Bismarck, P. (2022). Analysis of the fecal and oral microbiota in chronic recurrent multifocal osteomyelitis. Arthritis Research & Therapy, 24(1), 54. https://doi.org/10.1186/s13075-021-02711-8
2021
Basu, M., Philipp, L.-M., Baines, J., & Sebens, S. (2021). The Microbiome Tumor Axis: How the Microbiome Could Contribute to Clonal Heterogeneity and Disease Outcome in Pancreatic Cancer. Frontiers in Oncology, 11. https://doi.org/10.3389/fonc.2021.740606
Galeev, A., Suwandi, A., Cepic, A., Basu, M., Baines, J. F., & Grassl, G. A. (2021). The role of the blood group-related glycosyltransferases FUT2 and B4GALNT2 in susceptibility to infectious disease. International Journal of Medical Microbiology: IJMM, 311(3), 151487. https://doi.org/10.1016/j.ijmm.2021.151487
Gogarten, J. F., Rühlemann, M., Archie, E., Tung, J., Akoua-Koffi, C., Bang, C., Deschner, T., Muyembe-Tamfun, J.-J., Robbins, M. M., Schubert, G., Surbeck, M., Wittig, R. M., Zuberbühler, K., Baines, J. F., Franke, A., Leendertz, F. H., & Calvignac-Spencer, S. (2021). Primate phageomes are structured by superhost phylogeny and environment. Proceedings of the National Academy of Sciences of the United States of America, 118(15), e2013535118. https://doi.org/10.1073/pnas.2013535118
Rühlemann, M. C., Hermes, B. M., Bang, C., Doms, S., Moitinho-Silva, L., Thingholm, L. B., Frost, F., Degenhardt, F., Wittig, M., Kässens, J., Weiss, F. U., Peters, A., Neuhaus, K., Völker, U., Völzke, H., Homuth, G., Weiss, S., Grallert, H., Laudes, M., … Franke, A. (2021). Genome-wide association study in 8,956 German individuals identifies influence of ABO histo-blood groups on gut microbiome. Nature Genetics, 53(2), 147–155. https://doi.org/10.1038/s41588-020-00747-1
Schulz, N., Belheouane, M., Dahmen, R., Ruan, V. A., Specht, H. E., Dempfle, A., Herpertz-Dahlmann, B., Baines, J., & Seitz, J. (2021). Gut microbiota alteration in adolescent anorexia nervosa does not normalize with short-term weight restoration. The International Journal of Eating Disorders, 54(6). https://doi.org/10.1002/eat.23435
Strigli, A., Gopalakrishnan, S., Zeissig, Y., Basic, M., Wang, J., Schwerd, T., Doms, S., Peuker, K., Hartwig, J., Harder, J., Hönscheid, P., Arnold, P., Kurth, T., Rost, F., Petersen, B.-S., Forster, M., Franke, A., Kelsen, J. R., Rohlfs, M., … Zeissig, S. (2021). Deficiency in X-linked inhibitor of apoptosis protein promotes susceptibility to microbial triggers of intestinal inflammation. Science Immunology, 6(65), eabf7473. https://doi.org/10.1126/sciimmunol.abf7473
Galeev, A., Suwandi, A., Cepic, A., Basu, M., Baines, J. F., & Grassl, G. A. (2021). The role of the blood group-related glycosyltransferases FUT2 and B4GALNT2 in susceptibility to infectious disease. International Journal of Medical Microbiology: IJMM, 311(3), 151487. https://doi.org/10.1016/j.ijmm.2021.151487
Gogarten, J. F., Rühlemann, M., Archie, E., Tung, J., Akoua-Koffi, C., Bang, C., Deschner, T., Muyembe-Tamfun, J.-J., Robbins, M. M., Schubert, G., Surbeck, M., Wittig, R. M., Zuberbühler, K., Baines, J. F., Franke, A., Leendertz, F. H., & Calvignac-Spencer, S. (2021). Primate phageomes are structured by superhost phylogeny and environment. Proceedings of the National Academy of Sciences of the United States of America, 118(15), e2013535118. https://doi.org/10.1073/pnas.2013535118
Rühlemann, M. C., Hermes, B. M., Bang, C., Doms, S., Moitinho-Silva, L., Thingholm, L. B., Frost, F., Degenhardt, F., Wittig, M., Kässens, J., Weiss, F. U., Peters, A., Neuhaus, K., Völker, U., Völzke, H., Homuth, G., Weiss, S., Grallert, H., Laudes, M., … Franke, A. (2021). Genome-wide association study in 8,956 German individuals identifies influence of ABO histo-blood groups on gut microbiome. Nature Genetics, 53(2), 147–155. https://doi.org/10.1038/s41588-020-00747-1
Schulz, N., Belheouane, M., Dahmen, R., Ruan, V. A., Specht, H. E., Dempfle, A., Herpertz-Dahlmann, B., Baines, J., & Seitz, J. (2021). Gut microbiota alteration in adolescent anorexia nervosa does not normalize with short-term weight restoration. The International Journal of Eating Disorders, 54(6). https://doi.org/10.1002/eat.23435
Strigli, A., Gopalakrishnan, S., Zeissig, Y., Basic, M., Wang, J., Schwerd, T., Doms, S., Peuker, K., Hartwig, J., Harder, J., Hönscheid, P., Arnold, P., Kurth, T., Rost, F., Petersen, B.-S., Forster, M., Franke, A., Kelsen, J. R., Rohlfs, M., … Zeissig, S. (2021). Deficiency in X-linked inhibitor of apoptosis protein promotes susceptibility to microbial triggers of intestinal inflammation. Science Immunology, 6(65), eabf7473. https://doi.org/10.1126/sciimmunol.abf7473
2020
Belheouane, M., Vallier, M., Čepić, A., Chung, C. J., Ibrahim, S., & Baines, J. F. (2020). Assessing similarities and disparities in the skin microbiota between wild and laboratory populations of house mice. The ISME Journal. 14, pp 2367–2380 https://doi.org/10.1038/s41396-020-0690-7
Willers, M., Ulas, T., Völlger, L., Vogl, T., Heinemann, A. S., 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., … Viemann, D. (2020). S100A8 and S100A9 Are Important for Postnatal Development of Gut Microbiota and Immune System in Mice and Infants. Gastroenterology, 159(6), 2130-2145.e5. https://doi.org/10.1053/j.gastro.2020.08.019
Stolzer I., Kaden-Volynets V., Ruder B., Letizia M., Bittel M., Rausch P., Basic M., Bleich A., Baines J. F., Neurath, M. F., Wirtz S., Weidinger C., Bischoff S. C., Christoph Becker C., & Günther C. (2020). Environmental microbial factors determine the pattern of inflammatory lesions in a murine model of Crohn’s Disease–Like inflammation. Inflammatory Bowel Diseases, 26 (1), pp 66–79. https://doi.org/10.1093/ibd/izz142
Lesker, T. R., Durairaj, A. C., Gálvez, E. J. C., Lagkouvardos, I., Baines, J. F., Clavel, T., Sczyrba, A., McHardy, A. C., & Strowig, T. (2020). An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome. Cell Reports, 30(9), 2909-2922.e6. https://doi.org/10.1016/j.celrep.2020.02.036
Merker, M., Tueffers, L., Vallier, M., Groth, E. E., Sonnenkalb, L., Unterweger, D., Baines, J. F., Niemann, S., & Schulenburg, H. (2020). Evolutionary Approaches to Combat Antibiotic Resistance: Opportunities and Challenges for Precision Medicine. Frontiers in Immunology, 11, 1938. https://doi.org/10.3389/fimmu.2020.01938
Moltzau Anderson, J., Lipinski, S., Sommer, F., Pan, W.-H., Boulard, O., Rehman, A., Falk-Paulsen, M., Stengel, S. T., Aden, K., Häsler, R., Bharti, R., Künzel, S., Baines, J. F., Chamaillard, M., & Rosenstiel, P. (2020). NOD2 Influences Trajectories of Intestinal Microbiota Recovery After Antibiotic Perturbation. Cellular and Molecular Gastroenterology and Hepatology, 10(2), 365–389. https://doi.org/10.1016/j.jcmgh.2020.03.008
Willers, M., Ulas, T., Völlger, L., Vogl, T., Heinemann, A. S., 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., … Viemann, D. (2020). S100A8 and S100A9 Are Important for Postnatal Development of Gut Microbiota and Immune System in Mice and Infants. Gastroenterology, 159(6), 2130-2145.e5. https://doi.org/10.1053/j.gastro.2020.08.019
Stolzer I., Kaden-Volynets V., Ruder B., Letizia M., Bittel M., Rausch P., Basic M., Bleich A., Baines J. F., Neurath, M. F., Wirtz S., Weidinger C., Bischoff S. C., Christoph Becker C., & Günther C. (2020). Environmental microbial factors determine the pattern of inflammatory lesions in a murine model of Crohn’s Disease–Like inflammation. Inflammatory Bowel Diseases, 26 (1), pp 66–79. https://doi.org/10.1093/ibd/izz142
Lesker, T. R., Durairaj, A. C., Gálvez, E. J. C., Lagkouvardos, I., Baines, J. F., Clavel, T., Sczyrba, A., McHardy, A. C., & Strowig, T. (2020). An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome. Cell Reports, 30(9), 2909-2922.e6. https://doi.org/10.1016/j.celrep.2020.02.036
Merker, M., Tueffers, L., Vallier, M., Groth, E. E., Sonnenkalb, L., Unterweger, D., Baines, J. F., Niemann, S., & Schulenburg, H. (2020). Evolutionary Approaches to Combat Antibiotic Resistance: Opportunities and Challenges for Precision Medicine. Frontiers in Immunology, 11, 1938. https://doi.org/10.3389/fimmu.2020.01938
Moltzau Anderson, J., Lipinski, S., Sommer, F., Pan, W.-H., Boulard, O., Rehman, A., Falk-Paulsen, M., Stengel, S. T., Aden, K., Häsler, R., Bharti, R., Künzel, S., Baines, J. F., Chamaillard, M., & Rosenstiel, P. (2020). NOD2 Influences Trajectories of Intestinal Microbiota Recovery After Antibiotic Perturbation. Cellular and Molecular Gastroenterology and Hepatology, 10(2), 365–389. https://doi.org/10.1016/j.jcmgh.2020.03.008
2019
Graspeuntner, S., Waschina, S., Künzel, S., Twisselmann, N., Rausch, T. K., Cloppenborg-Schmidt, K., Zimmermann, J., Viemann, D., Herting, E., Göpel, W., Baines, J. F., Kaleta, C., Rupp, J., Härtel, C., & Pagel, J. (2019). Gut Dysbiosis With Bacilli Dominance and Accumulation of Fermentation Products Precedes Late-onset Sepsis in Preterm Infants. Clinical Infectious Diseases, 69(2), 268–277. https://doi.org/10.1093/cid/ciy882
Guedj, A., Volman, Y., Geiger-Maor, A., Bolik, J., Schumacher, N., Kunzel, S., Baines, J. F., Nevo, Y., Elgavish, S., Galun, E., Amsalem, H., Schmidt-Arras, D., & Rachmilewitz, J. (2019). Gut microbiota shape “inflamm-ageing” cytokines and account for age-dependent decline in DNA damage repair. Gut. https://doi.org/10.1136/gutjnl-2019-318491
Herp, S., Brugiroux, S., Garzetti, D., Ring, D., Jochum, L. M., Beutler, M., Eberl, C., Hussain, S., Walter, S., Gerlach, R. G., Ruscheweyh, H. J., Huson, D., Sellin, M. E., Slack, E., Hanson, B., Loy, A., Baines, J. F., Rausch, P., Basic, M., … Stecher, B. (2019). Mucispirillum schaedleri Antagonizes Salmonella Virulence to Protect Mice against Colitis. Cell Host & Microbe, 25(5), 681-694.e8. https://doi.org/10.1016/j.chom.2019.03.004
Lagkouvardos, I., Lesker, T. R., Hitch, T. C. A., Gálvez, E. J. C., Smit, N., Neuhaus, K., Wang, J., Baines, J. F., Abt, B., Stecher, B., Overmann, J., Strowig, T., & Clavel, T. (2019). Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family. Microbiome, 7(1), 28. https://doi.org/10.1186/s40168-019-0637-2
Langan, E. a., Künstner, A., Miodovnik, M., Zillikens, D., Thaçi, D., Baines, J. f., Ibrahim, S. m., Solbach, W., & Knobloch, J. k. (2019). Combined culture and metagenomic analyses reveal significant shifts in the composition of the cutaneous microbiome in psoriasis. British Journal of Dermatology, 181(6), 1254–1264. https://doi.org/10.1111/bjd.17989
Rausch, P., Rühlemann, M., Hermes, B. M., Doms, S., Dagan, T., Dierking, K., Domin, H., Fraune, S., von Frieling, J., Hentschel, U., Heinsen, F.-A., Höppner, M., Jahn, M. T., Jaspers, C., Kissoyan, K. A. B., Langfeldt, D., Rehman, A., Reusch, T. B. H., Roeder, T., … Baines, J. F. (2019). Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms. Microbiome, 7(1), 133. https://doi.org/10.1186/s40168-019-0743-1
Seitz, J., Belheouane, M., Schulz, N., Dempfle, A., Baines, J. F., & Herpertz-Dahlmann, B. (2019). The Impact of Starvation on the Microbiome and Gut-Brain Interaction in Anorexia Nervosa. Frontiers in Endocrinology, 10, 41. https://doi.org/10.3389/fendo.2019.00041
Sieber, M., Pita, L., Weiland-Bräuer, N., Dirksen, P., Wang, J., Mortzfeld, B., Franzenburg, S., Schmitz, R. A., Baines, J. F., Fraune, S., Hentschel, U., Schulenburg, H., Bosch, T. C. G., & Traulsen, A. (2019). Neutrality in the Metaorganism. PLoS Biology, 17(6), e3000298. https://doi.org/10.1371/journal.pbio.3000298
Stolzer, I., Kaden-Volynets, V., Ruder, B., Letizia, M., Bittel, M., Rausch, P., Basic, M., Bleich, A., Baines, J. F., Neurath, M. F., Wirtz, S., Weidinger, C., Bischoff, S. C., Becker, C., & Günther, C. (2019). Environmental Microbial Factors Determine the Pattern of Inflammatory Lesions in a Murine Model of Crohn’s Disease–Like Inflammation. Inflammatory Bowel Diseases. https://doi.org/10.1093/ibd/izz142
Suwandi, A., Galeev, A., Riedel, R., Sharma, S., Seeger, K., Sterzenbach, T., García Pastor, L., Boyle, E. C., Gal-Mor, O., Hensel, M., Casadesús, J., Baines, J. F., & Grassl, G. A. (2019). Std fimbriae-fucose interaction increases Salmonella-induced intestinal inflammation and prolongs colonization. PLoS Pathogens, 15(7), e1007915. https://doi.org/10.1371/journal.ppat.1007915
Vorobyev, A., Gupta, Y., Sezin, T., Koga, H., Bartsch, Y. C., Belheouane, M., Künzel, S., Sina, C., Schilf, P., Körber-Ahrens, H., Beltsiou, F., Ernst, A. L., Khil’chenko, S., Al-Aasam, H., Manz, R. A., Diehl, S., Steinhaus, M., Jascholt, J., Kouki, P., … Ludwig, R. J. (2019). Gene-diet interactions associated with complex trait variation in an advanced intercross outbred mouse line. Nature Communications, 10(1), 1–15. https://doi.org/10.1038/s41467-019-11952-w
Guedj, A., Volman, Y., Geiger-Maor, A., Bolik, J., Schumacher, N., Kunzel, S., Baines, J. F., Nevo, Y., Elgavish, S., Galun, E., Amsalem, H., Schmidt-Arras, D., & Rachmilewitz, J. (2019). Gut microbiota shape “inflamm-ageing” cytokines and account for age-dependent decline in DNA damage repair. Gut. https://doi.org/10.1136/gutjnl-2019-318491
Herp, S., Brugiroux, S., Garzetti, D., Ring, D., Jochum, L. M., Beutler, M., Eberl, C., Hussain, S., Walter, S., Gerlach, R. G., Ruscheweyh, H. J., Huson, D., Sellin, M. E., Slack, E., Hanson, B., Loy, A., Baines, J. F., Rausch, P., Basic, M., … Stecher, B. (2019). Mucispirillum schaedleri Antagonizes Salmonella Virulence to Protect Mice against Colitis. Cell Host & Microbe, 25(5), 681-694.e8. https://doi.org/10.1016/j.chom.2019.03.004
Lagkouvardos, I., Lesker, T. R., Hitch, T. C. A., Gálvez, E. J. C., Smit, N., Neuhaus, K., Wang, J., Baines, J. F., Abt, B., Stecher, B., Overmann, J., Strowig, T., & Clavel, T. (2019). Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family. Microbiome, 7(1), 28. https://doi.org/10.1186/s40168-019-0637-2
Langan, E. a., Künstner, A., Miodovnik, M., Zillikens, D., Thaçi, D., Baines, J. f., Ibrahim, S. m., Solbach, W., & Knobloch, J. k. (2019). Combined culture and metagenomic analyses reveal significant shifts in the composition of the cutaneous microbiome in psoriasis. British Journal of Dermatology, 181(6), 1254–1264. https://doi.org/10.1111/bjd.17989
Rausch, P., Rühlemann, M., Hermes, B. M., Doms, S., Dagan, T., Dierking, K., Domin, H., Fraune, S., von Frieling, J., Hentschel, U., Heinsen, F.-A., Höppner, M., Jahn, M. T., Jaspers, C., Kissoyan, K. A. B., Langfeldt, D., Rehman, A., Reusch, T. B. H., Roeder, T., … Baines, J. F. (2019). Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms. Microbiome, 7(1), 133. https://doi.org/10.1186/s40168-019-0743-1
Seitz, J., Belheouane, M., Schulz, N., Dempfle, A., Baines, J. F., & Herpertz-Dahlmann, B. (2019). The Impact of Starvation on the Microbiome and Gut-Brain Interaction in Anorexia Nervosa. Frontiers in Endocrinology, 10, 41. https://doi.org/10.3389/fendo.2019.00041
Sieber, M., Pita, L., Weiland-Bräuer, N., Dirksen, P., Wang, J., Mortzfeld, B., Franzenburg, S., Schmitz, R. A., Baines, J. F., Fraune, S., Hentschel, U., Schulenburg, H., Bosch, T. C. G., & Traulsen, A. (2019). Neutrality in the Metaorganism. PLoS Biology, 17(6), e3000298. https://doi.org/10.1371/journal.pbio.3000298
Stolzer, I., Kaden-Volynets, V., Ruder, B., Letizia, M., Bittel, M., Rausch, P., Basic, M., Bleich, A., Baines, J. F., Neurath, M. F., Wirtz, S., Weidinger, C., Bischoff, S. C., Becker, C., & Günther, C. (2019). Environmental Microbial Factors Determine the Pattern of Inflammatory Lesions in a Murine Model of Crohn’s Disease–Like Inflammation. Inflammatory Bowel Diseases. https://doi.org/10.1093/ibd/izz142
Suwandi, A., Galeev, A., Riedel, R., Sharma, S., Seeger, K., Sterzenbach, T., García Pastor, L., Boyle, E. C., Gal-Mor, O., Hensel, M., Casadesús, J., Baines, J. F., & Grassl, G. A. (2019). Std fimbriae-fucose interaction increases Salmonella-induced intestinal inflammation and prolongs colonization. PLoS Pathogens, 15(7), e1007915. https://doi.org/10.1371/journal.ppat.1007915
Vorobyev, A., Gupta, Y., Sezin, T., Koga, H., Bartsch, Y. C., Belheouane, M., Künzel, S., Sina, C., Schilf, P., Körber-Ahrens, H., Beltsiou, F., Ernst, A. L., Khil’chenko, S., Al-Aasam, H., Manz, R. A., Diehl, S., Steinhaus, M., Jascholt, J., Kouki, P., … Ludwig, R. J. (2019). Gene-diet interactions associated with complex trait variation in an advanced intercross outbred mouse line. Nature Communications, 10(1), 1–15. https://doi.org/10.1038/s41467-019-11952-w
2018
Doms, S., Hermes, B.-M., & Baines, J. F. (2018). Evolutionary Perspectives on the Human Gut Microbiome. In D. Haller (Ed.), The Gut Microbiome in Health and Disease (pp. 67–78). Springer International Publishing. https://doi.org/10.1007/978-3-319-90545-7_5
Graspeuntner, S., Bohlmann, M. K., Gillmann, K., Speer, R., Kuenzel, S., Mark, H., Hoellen, F., Lettau, R., Griesinger, G., König, I. R., Baines, J. F., & Rupp, J. (2018). Microbiota-based analysis reveals specific bacterial traits and a novel strategy for the diagnosis of infectious infertility. PloS One, 13(1), e0191047. https://doi.org/10.1371/journal.pone.0191047
Graspeuntner, S., Loeper, N., Künzel, S., Baines, J. F., & Rupp, J. (2018). Selection of validated hypervariable regions is crucial in 16S-based microbiota studies of the female genital tract. Scientific Reports, 8(1), 1–7. https://doi.org/10.1038/s41598-018-27757-8
Hirose, M., Schilf, P., Gupta, Y., Zarse, K., Künstner, A., Fähnrich, A., Busch, H., Yin, J., Wright, M. N., Ziegler, A., Vallier, M., Belheouane, M., Baines, J. F., Tautz, D., Johann, K., Oelkrug, R., Mittag, J., Lehnert, H., Othman, A., … Ibrahim, S. M. (2018). Low-level mitochondrial heteroplasmy modulates DNA replication, glucose metabolism and lifespan in mice. Scientific Reports, 8(1), 5872. https://doi.org/10.1038/s41598-018-24290-6
Lin, X. B., Wang, T., Stothard, P., Corander, J., Wang, J., Baines, J. F., Knowles, S. C. L., Baltrūnaitė, L., Tasseva, G., Schmaltz, R., Tollenaar, S., Cody, L. A., Grenier, T., Wu, W., Ramer-Tait, A. E., & Walter, J. (2018). The evolution of ecological facilitation within mixed-species biofilms in the mouse gastrointestinal tract. The ISME Journal, 12(11), 2770–2784. https://doi.org/10.1038/s41396-018-0211-0
Maixner, F., Turaev, D., Cazenave-Gassiot, A., Janko, M., Krause-Kyora, B., Hoopmann, M. R., Kusebauch, U., Sartain, M., Guerriero, G., O’Sullivan, N., Teasdale, M., Cipollini, G., Paladin, A., Mattiangeli, V., Samadelli, M., Tecchiati, U., Putzer, A., Palazoglu, M., Meissen, J., … Zink, A. (2018). The Iceman’s Last Meal Consisted of Fat, Wild Meat, and Cereals. Current Biology, 28(14), 2348-2355.e9. https://doi.org/10.1016/j.cub.2018.05.067
Pan, W.-H., 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, J. F., Schreiber, S., Franke, A., Schultze, J. L., Bäckhed, F., & Rosenstiel, P. (2018). Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development. Genome Medicine, 10(1), 27. https://doi.org/10.1186/s13073-018-0534-5
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. (2018). 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. Gut Microbes, 9(1), 68–75. https://doi.org/10.1080/19490976.2017.1356979
Graspeuntner, S., Bohlmann, M. K., Gillmann, K., Speer, R., Kuenzel, S., Mark, H., Hoellen, F., Lettau, R., Griesinger, G., König, I. R., Baines, J. F., & Rupp, J. (2018). Microbiota-based analysis reveals specific bacterial traits and a novel strategy for the diagnosis of infectious infertility. PloS One, 13(1), e0191047. https://doi.org/10.1371/journal.pone.0191047
Graspeuntner, S., Loeper, N., Künzel, S., Baines, J. F., & Rupp, J. (2018). Selection of validated hypervariable regions is crucial in 16S-based microbiota studies of the female genital tract. Scientific Reports, 8(1), 1–7. https://doi.org/10.1038/s41598-018-27757-8
Hirose, M., Schilf, P., Gupta, Y., Zarse, K., Künstner, A., Fähnrich, A., Busch, H., Yin, J., Wright, M. N., Ziegler, A., Vallier, M., Belheouane, M., Baines, J. F., Tautz, D., Johann, K., Oelkrug, R., Mittag, J., Lehnert, H., Othman, A., … Ibrahim, S. M. (2018). Low-level mitochondrial heteroplasmy modulates DNA replication, glucose metabolism and lifespan in mice. Scientific Reports, 8(1), 5872. https://doi.org/10.1038/s41598-018-24290-6
Lin, X. B., Wang, T., Stothard, P., Corander, J., Wang, J., Baines, J. F., Knowles, S. C. L., Baltrūnaitė, L., Tasseva, G., Schmaltz, R., Tollenaar, S., Cody, L. A., Grenier, T., Wu, W., Ramer-Tait, A. E., & Walter, J. (2018). The evolution of ecological facilitation within mixed-species biofilms in the mouse gastrointestinal tract. The ISME Journal, 12(11), 2770–2784. https://doi.org/10.1038/s41396-018-0211-0
Maixner, F., Turaev, D., Cazenave-Gassiot, A., Janko, M., Krause-Kyora, B., Hoopmann, M. R., Kusebauch, U., Sartain, M., Guerriero, G., O’Sullivan, N., Teasdale, M., Cipollini, G., Paladin, A., Mattiangeli, V., Samadelli, M., Tecchiati, U., Putzer, A., Palazoglu, M., Meissen, J., … Zink, A. (2018). The Iceman’s Last Meal Consisted of Fat, Wild Meat, and Cereals. Current Biology, 28(14), 2348-2355.e9. https://doi.org/10.1016/j.cub.2018.05.067
Pan, W.-H., 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, J. F., Schreiber, S., Franke, A., Schultze, J. L., Bäckhed, F., & Rosenstiel, P. (2018). Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development. Genome Medicine, 10(1), 27. https://doi.org/10.1186/s13073-018-0534-5
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. (2018). 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. Gut Microbes, 9(1), 68–75. https://doi.org/10.1080/19490976.2017.1356979
2017
Belheouane, M., Gupta, Y., Künzel, S., Ibrahim, S., & Baines, J. F. (2017). Improved detection of gene-microbe interactions in the mouse skin microbiota using high-resolution QTL mapping of 16S rRNA transcripts. Microbiome, 5(1), 59. https://doi.org/10.1186/s40168-017-0275-5
Claussen, J. C., Skiecevičienė, J., Wang, J., Rausch, P., Karlsen, T. H., Lieb, W., Baines, J. F., Franke, A., & Hütt, M.-T. (2017). Boolean analysis reveals systematic interactions among low-abundance species in the human gut microbiome. PLOS Computational Biology, 13(6), e1005361. https://doi.org/10.1371/journal.pcbi.1005361
Hadizadeh, F., Bonfiglio, F., Belheouane, M., Vallier, M., Sauer, S., Bang, C., Bujanda, L., Andreasson, A., Agreus, L., Engstrand, L., Talley, N. J., Rafter, J., Baines, J. F., Walter, S., Franke, A., & D’Amato, M. (2017). Faecal microbiota composition associates with abdominal pain in the general population. Gut. https://doi.org/10.1136/gutjnl-2017-314792
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. (2017). Stool frequency is associated with gut microbiota composition. Gut, 66(3), 559–560. https://doi.org/10.1136/gutjnl-2016-311935
Herpertz-Dahlmann, B., Seitz, J., & Baines, J. (2017). Food matters: How the microbiome and gut–brain interaction might impact the development and course of anorexia nervosa. European Child & Adolescent Psychiatry, 26(9), 1031–1041. https://doi.org/10.1007/s00787-017-0945-7
Hirose, M., Künstner, A., Schilf, P., Sünderhauf, A., Rupp, J., Jöhren, O., Schwaninger, M., Sina, C., Baines, J. F., & Ibrahim, S. M. (2017). Mitochondrial gene polymorphism is associated with gut microbial communities in mice. Scientific Reports, 7(1), 1–9. https://doi.org/10.1038/s41598-017-15377-7
Hopfner, F., Künstner, A., Müller, S. H., Künzel, S., Zeuner, K. E., Margraf, N. G., Deuschl, G., Baines, J. F., & Kuhlenbäumer, G. (2017). Gut microbiota in Parkinson disease in a northern German cohort. Brain Research, 1667, 41–45. https://doi.org/10.1016/j.brainres.2017.04.019
Jäckel, S., Kiouptsi, K., Lillich, M., Hendrikx, T., Khandagale, A., Kollar, B., Hörmann, N., Reiss, C., Subramaniam, S., Wilms, E., Ebner, K., Brühl, M.-L. von, Rausch, P., Baines, J. F., Haberichter, S., Lämmle, B., Binder, C. J., Jurk, K., Ruggeri, Z. M., … Reinhardt, C. (2017). Gut microbiota regulate hepatic von Willebrand factor synthesis and arterial thrombus formation via Toll-like receptor-2. Blood, 130(4), 542–553. https://doi.org/10.1182/blood-2016-11-754416
Miodovnik, M., Künstner, A., Langan, E. A., Zillikens, D., Gläser, R., Sprecher, E., Baines, J. F., Schmidt, E., & Ibrahim, S. M. (2017). A distinct cutaneous microbiota profile in autoimmune bullous disease patients. Experimental Dermatology. https://doi.org/10.1111/exd.13357
Rausch, P., Künzel, S., Suwandi, A., Grassl, G. A., Rosenstiel, P., & Baines, J. F. (2017). Multigenerational Influences of the Fut2 Gene on the Dynamics of the Gut Microbiota in Mice. Frontiers in Microbiology, 8. https://doi.org/10.3389/fmicb.2017.00991
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). 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. Gut Microbes, 1–8. https://doi.org/10.1080/19490976.2017.1356979
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., … Waschke, J. (2017). Meeting Report of the Pathogenesis of Pemphigus and Pemphigoid Meeting in Munich, September 2016. The Journal of Investigative Dermatology. https://doi.org/10.1016/j.jid.2017.01.028
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. (2017). The gut microbiota contributes to a mouse model of spontaneous bile duct inflammation. Journal of Hepatology, 66(2), 382–389. https://doi.org/10.1016/j.jhep.2016.09.020
Sommer, F., Rühlemann, M. C., Bang, C., Höppner, M., Rehman, A., Kaleta, C., Schmitt-Kopplin, P., Dempfle, A., Weidinger, S., Ellinghaus, E., Krauss-Etschmann, S., Schmidt-Arras, D., Aden, K., Schulte, D., Ellinghaus, D., Schreiber, S., Tholey, A., Rupp, J., Laudes, M., … Franke, A. (2017). Microbiomarkers in inflammatory bowel diseases: Caveats come with caviar. Gut, 66(10), 1734–1738. https://doi.org/10.1136/gutjnl-2016-313678
Tronstad, R. R., Kummen, M., Holm, K., von Volkmann, H. L., Anmarkrud, J. A., Høivik, M. L., Moum, B., Gilja, O. H., Hausken, T., Baines, J., Karlsen, T. H., Fiskerstrand, T., & Hov, J. R. (2017). Guanylate Cyclase C Activation Shapes the Intestinal Microbiota in Patients with Familial Diarrhea and Increased Susceptibility for Crohn’s Disease. Inflammatory Bowel Diseases, 23(10), 1752–1761. https://doi.org/10.1097/MIB.0000000000001264
Vallier, M., Abou Chakra, M., Hindersin, L., Linnenbrink, M., Traulsen, A., & Baines, J. F. (2017). Evaluating the maintenance of disease-associated variation at the blood group-related gene B4galnt2 in house mice. BMC Evolutionary Biology, 17(1), 187. https://doi.org/10.1186/s12862-017-1035-7
Claussen, J. C., Skiecevičienė, J., Wang, J., Rausch, P., Karlsen, T. H., Lieb, W., Baines, J. F., Franke, A., & Hütt, M.-T. (2017). Boolean analysis reveals systematic interactions among low-abundance species in the human gut microbiome. PLOS Computational Biology, 13(6), e1005361. https://doi.org/10.1371/journal.pcbi.1005361
Hadizadeh, F., Bonfiglio, F., Belheouane, M., Vallier, M., Sauer, S., Bang, C., Bujanda, L., Andreasson, A., Agreus, L., Engstrand, L., Talley, N. J., Rafter, J., Baines, J. F., Walter, S., Franke, A., & D’Amato, M. (2017). Faecal microbiota composition associates with abdominal pain in the general population. Gut. https://doi.org/10.1136/gutjnl-2017-314792
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. (2017). Stool frequency is associated with gut microbiota composition. Gut, 66(3), 559–560. https://doi.org/10.1136/gutjnl-2016-311935
Herpertz-Dahlmann, B., Seitz, J., & Baines, J. (2017). Food matters: How the microbiome and gut–brain interaction might impact the development and course of anorexia nervosa. European Child & Adolescent Psychiatry, 26(9), 1031–1041. https://doi.org/10.1007/s00787-017-0945-7
Hirose, M., Künstner, A., Schilf, P., Sünderhauf, A., Rupp, J., Jöhren, O., Schwaninger, M., Sina, C., Baines, J. F., & Ibrahim, S. M. (2017). Mitochondrial gene polymorphism is associated with gut microbial communities in mice. Scientific Reports, 7(1), 1–9. https://doi.org/10.1038/s41598-017-15377-7
Hopfner, F., Künstner, A., Müller, S. H., Künzel, S., Zeuner, K. E., Margraf, N. G., Deuschl, G., Baines, J. F., & Kuhlenbäumer, G. (2017). Gut microbiota in Parkinson disease in a northern German cohort. Brain Research, 1667, 41–45. https://doi.org/10.1016/j.brainres.2017.04.019
Jäckel, S., Kiouptsi, K., Lillich, M., Hendrikx, T., Khandagale, A., Kollar, B., Hörmann, N., Reiss, C., Subramaniam, S., Wilms, E., Ebner, K., Brühl, M.-L. von, Rausch, P., Baines, J. F., Haberichter, S., Lämmle, B., Binder, C. J., Jurk, K., Ruggeri, Z. M., … Reinhardt, C. (2017). Gut microbiota regulate hepatic von Willebrand factor synthesis and arterial thrombus formation via Toll-like receptor-2. Blood, 130(4), 542–553. https://doi.org/10.1182/blood-2016-11-754416
Miodovnik, M., Künstner, A., Langan, E. A., Zillikens, D., Gläser, R., Sprecher, E., Baines, J. F., Schmidt, E., & Ibrahim, S. M. (2017). A distinct cutaneous microbiota profile in autoimmune bullous disease patients. Experimental Dermatology. https://doi.org/10.1111/exd.13357
Rausch, P., Künzel, S., Suwandi, A., Grassl, G. A., Rosenstiel, P., & Baines, J. F. (2017). Multigenerational Influences of the Fut2 Gene on the Dynamics of the Gut Microbiota in Mice. Frontiers in Microbiology, 8. https://doi.org/10.3389/fmicb.2017.00991
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). 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. Gut Microbes, 1–8. https://doi.org/10.1080/19490976.2017.1356979
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., … Waschke, J. (2017). Meeting Report of the Pathogenesis of Pemphigus and Pemphigoid Meeting in Munich, September 2016. The Journal of Investigative Dermatology. https://doi.org/10.1016/j.jid.2017.01.028
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. (2017). The gut microbiota contributes to a mouse model of spontaneous bile duct inflammation. Journal of Hepatology, 66(2), 382–389. https://doi.org/10.1016/j.jhep.2016.09.020
Sommer, F., Rühlemann, M. C., Bang, C., Höppner, M., Rehman, A., Kaleta, C., Schmitt-Kopplin, P., Dempfle, A., Weidinger, S., Ellinghaus, E., Krauss-Etschmann, S., Schmidt-Arras, D., Aden, K., Schulte, D., Ellinghaus, D., Schreiber, S., Tholey, A., Rupp, J., Laudes, M., … Franke, A. (2017). Microbiomarkers in inflammatory bowel diseases: Caveats come with caviar. Gut, 66(10), 1734–1738. https://doi.org/10.1136/gutjnl-2016-313678
Tronstad, R. R., Kummen, M., Holm, K., von Volkmann, H. L., Anmarkrud, J. A., Høivik, M. L., Moum, B., Gilja, O. H., Hausken, T., Baines, J., Karlsen, T. H., Fiskerstrand, T., & Hov, J. R. (2017). Guanylate Cyclase C Activation Shapes the Intestinal Microbiota in Patients with Familial Diarrhea and Increased Susceptibility for Crohn’s Disease. Inflammatory Bowel Diseases, 23(10), 1752–1761. https://doi.org/10.1097/MIB.0000000000001264
Vallier, M., Abou Chakra, M., Hindersin, L., Linnenbrink, M., Traulsen, A., & Baines, J. F. (2017). Evaluating the maintenance of disease-associated variation at the blood group-related gene B4galnt2 in house mice. BMC Evolutionary Biology, 17(1), 187. https://doi.org/10.1186/s12862-017-1035-7
2016
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). Dissecting genetics of cutaneous miRNA in a mouse model of an autoimmune blistering disease. BMC Genomics, 17. https://doi.org/10.1186/s12864-016-2455-2
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). Beneficial Effects of a Dietary Weight Loss Intervention on Human Gut Microbiome Diversity and Metabolism Are Not Sustained during Weight Maintenance. Obesity Facts, 9(6), 379–391. https://doi.org/10.1159/000449506
Henström, M., Diekmann, L., Bonfiglio, F., Hadizadeh, F., Kuech, E. M., Köckritz-Blickwede, M. von, 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, G., Cuomo, R., … D’Amato, M. (2016). Functional variants in the sucrase–isomaltase gene associate with increased risk of irritable bowel syndrome. Gut, 67, 263-270. https://doi.org/10.1136/gutjnl-2016-312456
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., … Clavel, T. (2016). The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nature Microbiology, 1(10), 16131. https://doi.org/10.1038/nmicrobiol.2016.131
Lokmer, A., Goedknegt, M. A., Thieltges, D. W., Fiorentino, D., Kuenzel, S., Baines, J. F., & Wegner, K. M. (2016). Spatial and Temporal Dynamics of Pacific Oyster Hemolymph Microbiota across Multiple Scales. Frontiers in Microbiology, 7, 1367. https://doi.org/10.3389/fmicb.2016.01367
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., … Zeissig, S. (2016). Epithelial calcineurin controls microbiota-dependent intestinal tumor development. Nature Medicine. https://doi.org/10.1038/nm.4072
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., … Baines, J. F. (2016). Analysis of factors contributing to variation in the C57BL/6J fecal microbiota across German animal facilities. International Journal of Medical Microbiology, 306(5), 343–355. https://doi.org/10.1016/j.ijmm.2016.03.004
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. (2016). Geographical patterns of the standing and active human gut microbiome in health and IBD. Gut, 65(2), 238–248. https://doi.org/10.1136/gutjnl-2014-308341
Theis, K. R., Dheilly, N. M., Klassen, J. L., Brucker, R. M., Baines, J. F., Bosch, T. C. G., 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). Getting the Hologenome Concept Right: An Eco-Evolutionary Framework for Hosts and Their Microbiomes, mSystems, 1(2), e00028-16. https://doi.org/10.1128/mSystems.00028-16
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., … Franke, A. (2016). Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota. Nature Genetics, 48(11), 1396–1406. https://doi.org/10.1038/ng.3695
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). Beneficial Effects of a Dietary Weight Loss Intervention on Human Gut Microbiome Diversity and Metabolism Are Not Sustained during Weight Maintenance. Obesity Facts, 9(6), 379–391. https://doi.org/10.1159/000449506
Henström, M., Diekmann, L., Bonfiglio, F., Hadizadeh, F., Kuech, E. M., Köckritz-Blickwede, M. von, 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, G., Cuomo, R., … D’Amato, M. (2016). Functional variants in the sucrase–isomaltase gene associate with increased risk of irritable bowel syndrome. Gut, 67, 263-270. https://doi.org/10.1136/gutjnl-2016-312456
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., … Clavel, T. (2016). The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nature Microbiology, 1(10), 16131. https://doi.org/10.1038/nmicrobiol.2016.131
Lokmer, A., Goedknegt, M. A., Thieltges, D. W., Fiorentino, D., Kuenzel, S., Baines, J. F., & Wegner, K. M. (2016). Spatial and Temporal Dynamics of Pacific Oyster Hemolymph Microbiota across Multiple Scales. Frontiers in Microbiology, 7, 1367. https://doi.org/10.3389/fmicb.2016.01367
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., … Zeissig, S. (2016). Epithelial calcineurin controls microbiota-dependent intestinal tumor development. Nature Medicine. https://doi.org/10.1038/nm.4072
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., … Baines, J. F. (2016). Analysis of factors contributing to variation in the C57BL/6J fecal microbiota across German animal facilities. International Journal of Medical Microbiology, 306(5), 343–355. https://doi.org/10.1016/j.ijmm.2016.03.004
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. (2016). Geographical patterns of the standing and active human gut microbiome in health and IBD. Gut, 65(2), 238–248. https://doi.org/10.1136/gutjnl-2014-308341
Theis, K. R., Dheilly, N. M., Klassen, J. L., Brucker, R. M., Baines, J. F., Bosch, T. C. G., 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). Getting the Hologenome Concept Right: An Eco-Evolutionary Framework for Hosts and Their Microbiomes, mSystems, 1(2), e00028-16. https://doi.org/10.1128/mSystems.00028-16
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., … Franke, A. (2016). Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota. Nature Genetics, 48(11), 1396–1406. https://doi.org/10.1038/ng.3695
2015
Huebbe, P., Dose, J., Schloesser, A., Campbell, G., Glüer, C.-C., Gupta, Y., Ibrahim, S., Minihane, A.-M., Baines, J. F., Nebel, A., & Rimbach, G. (2015). Apolipoprotein E (APOE) genotype regulates body weight and fatty acid utilization-Studies in gene-targeted replacement mice. Molecular Nutrition & Food Research, 59(2), 334–343. https://doi.org/10.1002/mnfr.201400636
Kalyan, S., Wang, J., Quabius, E. S., Huck, J., Wiltfang, J., Baines, J. F., & Kabelitz, D. (2015). Systemic immunity shapes the oral microbiome and susceptibility to bisphosphonate-associated osteonecrosis of the jaw. Journal of Translational Medicine, 13(1). https://doi.org/10.1186/s12967-015-0568-z
Ellebrecht, C. T., Srinivas, G., Bieber, K., Banczyk, D., Kalies, K., Künzel, S., Hammers, C. M., Baines, J. F., Zillikens, D., Ludwig, R. J., & Westermann, J. (2015). Skin microbiota-associated inflammation precedes autoantibody induced tissue damage in experimental epidermolysis bullosa acquisita. Journal of Autoimmunity. https://doi.org/10.1016/j.jaut.2015.08.007
Lokmer, A., Kuenzel, S., Baines, J., & Wegner, K. M. (2015). The Role of Tissue-specific Microbiota in Initial Establishment Success of Pacific oysters. Environmental Microbiology. https://doi.org/10.1111/1462-2920.13163
Vences, M., Granzow, S., Künzel, S., Tebbe, C. C., Baines, J. F., & Dohrmann, A. B. (2015). Composition and variation of the skin microbiota in sympatric species of European newts (Salamandridae). Amphibia-Reptilia, 36(1), 5–12. https://doi.org/10.1163/15685381-00002970
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). Analysis of intestinal microbiota in hybrid house mice reveals evolutionary divergence in a vertebrate hologenome. Nature Communications, 6(1), 1–10. https://doi.org/10.1038/ncomms7440
Weiland-Bräuer, N., Neulinger, S. C., Pinnow, N., Künzel, S., Baines, J. F., & Schmitz, R. A. (2015). Composition of Bacterial Communities Associated with Aurelia aurita Changes with Compartment, Life Stage, and Population. Applied and Environmental Microbiology, 81(17), 6038–6052. https://doi.org/10.1128/AEM.01601-15
Kalyan, S., Wang, J., Quabius, E. S., Huck, J., Wiltfang, J., Baines, J. F., & Kabelitz, D. (2015). Systemic immunity shapes the oral microbiome and susceptibility to bisphosphonate-associated osteonecrosis of the jaw. Journal of Translational Medicine, 13(1). https://doi.org/10.1186/s12967-015-0568-z
Ellebrecht, C. T., Srinivas, G., Bieber, K., Banczyk, D., Kalies, K., Künzel, S., Hammers, C. M., Baines, J. F., Zillikens, D., Ludwig, R. J., & Westermann, J. (2015). Skin microbiota-associated inflammation precedes autoantibody induced tissue damage in experimental epidermolysis bullosa acquisita. Journal of Autoimmunity. https://doi.org/10.1016/j.jaut.2015.08.007
Lokmer, A., Kuenzel, S., Baines, J., & Wegner, K. M. (2015). The Role of Tissue-specific Microbiota in Initial Establishment Success of Pacific oysters. Environmental Microbiology. https://doi.org/10.1111/1462-2920.13163
Vences, M., Granzow, S., Künzel, S., Tebbe, C. C., Baines, J. F., & Dohrmann, A. B. (2015). Composition and variation of the skin microbiota in sympatric species of European newts (Salamandridae). Amphibia-Reptilia, 36(1), 5–12. https://doi.org/10.1163/15685381-00002970
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). Analysis of intestinal microbiota in hybrid house mice reveals evolutionary divergence in a vertebrate hologenome. Nature Communications, 6(1), 1–10. https://doi.org/10.1038/ncomms7440
Weiland-Bräuer, N., Neulinger, S. C., Pinnow, N., Künzel, S., Baines, J. F., & Schmitz, R. A. (2015). Composition of Bacterial Communities Associated with Aurelia aurita Changes with Compartment, Life Stage, and Population. Applied and Environmental Microbiology, 81(17), 6038–6052. https://doi.org/10.1128/AEM.01601-15
2014
Langfeldt, D., Neulinger, S. C., Heuer, W., Staufenbiel, I., Künzel, S., Baines, J. F., Eberhard, J., & Schmitz, R. A. (2014). Composition of microbial oral biofilms during maturation in young healthy adults. PloS One, 9(2), e87449. https://doi.org/10.1371/journal.pone.0087449
Tschurtschenthaler, M., Wang, J., Fricke, C., Fritz, T. M. J., Niederreiter, L., Adolph, T. E., Sarcevic, E., Künzel, S., Offner, F. A., Kalinke, U., Baines, J. F., Tilg, H., & Kaser, A. (2014). Type I interferon signalling in the intestinal epithelium affects Paneth cells, microbial ecology and epithelial regeneration. Gut, 63(12), 1921–1931. https://doi.org/10.1136/gutjnl-2013-305863
Wang, J., Kuenzel, S., & Baines, J. F. (2014). Draft Genome Sequences of 11 Staphylococcus epidermidis Strains Isolated from Wild Mouse Species. Genome Announcements, 2(1). https://doi.org/10.1128/genomeA.01148-13
Yun, Y., Srinivas, G., Kuenzel, S., Linnenbrink, M., Alnahas, S., Bruce, K. D., Steinhoff, U., Baines, J. F., & Schaible, U. E. (2014). Environmentally Determined Differences in the Murine Lung Microbiota and Their Relation to Alveolar Architecture. PloS One, 9(12), e113466. https://doi.org/10.1371/journal.pone.0113466
Wang, J., Linnenbrink, M., Künzel, S., Fernandes, R., Nadeau, M.-J., Rosenstiel, P., & Baines, J. F. (2014). Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice. Proceedings of the National Academy of Sciences of the United States of America, 111(26), E2703-2710. https://doi.org/10.1073/pnas.1402342111
Tschurtschenthaler, M., Wang, J., Fricke, C., Fritz, T. M. J., Niederreiter, L., Adolph, T. E., Sarcevic, E., Künzel, S., Offner, F. A., Kalinke, U., Baines, J. F., Tilg, H., & Kaser, A. (2014). Type I interferon signalling in the intestinal epithelium affects Paneth cells, microbial ecology and epithelial regeneration. Gut, 63(12), 1921–1931. https://doi.org/10.1136/gutjnl-2013-305863
Wang, J., Kuenzel, S., & Baines, J. F. (2014). Draft Genome Sequences of 11 Staphylococcus epidermidis Strains Isolated from Wild Mouse Species. Genome Announcements, 2(1). https://doi.org/10.1128/genomeA.01148-13
Yun, Y., Srinivas, G., Kuenzel, S., Linnenbrink, M., Alnahas, S., Bruce, K. D., Steinhoff, U., Baines, J. F., & Schaible, U. E. (2014). Environmentally Determined Differences in the Murine Lung Microbiota and Their Relation to Alveolar Architecture. PloS One, 9(12), e113466. https://doi.org/10.1371/journal.pone.0113466
Wang, J., Linnenbrink, M., Künzel, S., Fernandes, R., Nadeau, M.-J., Rosenstiel, P., & Baines, J. F. (2014). Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice. Proceedings of the National Academy of Sciences of the United States of America, 111(26), E2703-2710. https://doi.org/10.1073/pnas.1402342111
2013
Fink, C., Staubach, F., Kuenzel, S., Baines, J. F., & Roeder, T. (2013). Noninvasive analysis of microbiome dynamics in the fruit fly Drosophila melanogaster. Applied and Environmental Microbiology, 79(22), 6984–6988. https://doi.org/10.1128/AEM.01903-13
Franzenburg, S., Fraune, S., Altrock, P. M., Künzel, S., Baines, J. F., Traulsen, A., & Bosch, T. C. G. (2013). Bacterial colonization of Hydra hatchlings follows a robust temporal pattern. The ISME Journal, 7(4), 781–790. https://doi.org/10.1038/ismej.2012.156
Franzenburg, S., Walter, J., Künzel, S., Wang, J., Baines, J. F., Bosch, T. C. G., & Fraune, S. (2013). Distinct antimicrobial peptide expression determines host species-specific bacterial associations. Proceedings of the National Academy of Sciences of the United States of America, 110(39), E3730-3738. https://doi.org/10.1073/pnas.1304960110
Lachnit, T., Fischer, M., Künzel, S., Baines, J. F., & Harder, T. (2013). Compounds associated with algal surfaces mediate epiphytic colonization of the marine macroalga Fucus vesiculosus. FEMS Microbiology Ecology, 84(2), 411–420. https://doi.org/10.1111/1574-6941.12071
Linnenbrink, M., Wang, J., Hardouin, E. A., Künzel, S., Metzler, D., & Baines, J. F. (2013). The role of biogeography in shaping diversity of the intestinal microbiota in house mice. Molecular Ecology, 22(7), 1904–1916. https://doi.org/10.1111/mec.12206
Srinivas, G., Möller, S., Wang, J., Künzel, S., Zillikens, D., Baines, J. F., & Ibrahim, S. M. (2013). Genome-wide mapping of gene–microbiota interactions in susceptibility to autoimmune skin blistering. Nature Communications, 4(1), 1–7. https://doi.org/10.1038/ncomms3462
Staubach, F., Baines, J. F., Künzel, S., Bik, E. M., & Petrov, D. A. (2013). Host Species and Environmental Effects on Bacterial Communities Associated with Drosophila in the Laboratory and in the Natural Environment. PLoS One, 8(8), e70749. https://doi.org/10.1371/journal.pone.0070749
Franzenburg, S., Fraune, S., Altrock, P. M., Künzel, S., Baines, J. F., Traulsen, A., & Bosch, T. C. G. (2013). Bacterial colonization of Hydra hatchlings follows a robust temporal pattern. The ISME Journal, 7(4), 781–790. https://doi.org/10.1038/ismej.2012.156
Franzenburg, S., Walter, J., Künzel, S., Wang, J., Baines, J. F., Bosch, T. C. G., & Fraune, S. (2013). Distinct antimicrobial peptide expression determines host species-specific bacterial associations. Proceedings of the National Academy of Sciences of the United States of America, 110(39), E3730-3738. https://doi.org/10.1073/pnas.1304960110
Lachnit, T., Fischer, M., Künzel, S., Baines, J. F., & Harder, T. (2013). Compounds associated with algal surfaces mediate epiphytic colonization of the marine macroalga Fucus vesiculosus. FEMS Microbiology Ecology, 84(2), 411–420. https://doi.org/10.1111/1574-6941.12071
Linnenbrink, M., Wang, J., Hardouin, E. A., Künzel, S., Metzler, D., & Baines, J. F. (2013). The role of biogeography in shaping diversity of the intestinal microbiota in house mice. Molecular Ecology, 22(7), 1904–1916. https://doi.org/10.1111/mec.12206
Srinivas, G., Möller, S., Wang, J., Künzel, S., Zillikens, D., Baines, J. F., & Ibrahim, S. M. (2013). Genome-wide mapping of gene–microbiota interactions in susceptibility to autoimmune skin blistering. Nature Communications, 4(1), 1–7. https://doi.org/10.1038/ncomms3462
Staubach, F., Baines, J. F., Künzel, S., Bik, E. M., & Petrov, D. A. (2013). Host Species and Environmental Effects on Bacterial Communities Associated with Drosophila in the Laboratory and in the Natural Environment. PLoS One, 8(8), e70749. https://doi.org/10.1371/journal.pone.0070749
2012
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., … Karlsen, T. H. (2012). Extended Analysis of a Genome-Wide Association Study in Primary Sclerosing Cholangitis Detects Multiple Novel Risk Loci. Journal of Hepatology, 57(2), 366–375. https://doi.org/10.1016/j.jhep.2012.03.031
Franzenburg, S., Fraune, S., Künzel, S., Baines, J. F., Domazet-Loso, T., & Bosch, T. C. G. (2012). MyD88-deficient Hydra reveal an ancient function of TLR signaling in sensing bacterial colonizers. Proceedings of the National Academy of Sciences of the United States of America, 109(47), 19374–19379. https://doi.org/10.1073/pnas.1213110109
Staubach, F., Künzel, S., Baines, A. C., Yee, A., McGee, B. M., Bäckhed, F., Baines, J. F., & Johnsen, J. M. (2012). Expression of the blood-group-related glycosyltransferase B4galnt2 influences the intestinal microbiota in mice. The ISME Journal, 6(7), 1345–1355. https://doi.org/10.1038/ismej.2011.204
Franzenburg, S., Fraune, S., Künzel, S., Baines, J. F., Domazet-Loso, T., & Bosch, T. C. G. (2012). MyD88-deficient Hydra reveal an ancient function of TLR signaling in sensing bacterial colonizers. Proceedings of the National Academy of Sciences of the United States of America, 109(47), 19374–19379. https://doi.org/10.1073/pnas.1213110109
Staubach, F., Künzel, S., Baines, A. C., Yee, A., McGee, B. M., Bäckhed, F., Baines, J. F., & Johnsen, J. M. (2012). Expression of the blood-group-related glycosyltransferase B4galnt2 influences the intestinal microbiota in mice. The ISME Journal, 6(7), 1345–1355. https://doi.org/10.1038/ismej.2011.204
2011
Linnenbrink, M., Johnsen, J. M., Montero, I., Brzezinski, C. R., Harr, B., & Baines, J. F. (2011). Long-term balancing selection at the blood group-related gene B4galnt2 in the genus Mus (Rodentia; Muridae). Molecular Biology and Evolution, 28(11), 2999–3003. https://doi.org/10.1093/molbev/msr150
Rehman, A., Sina, C., Gavrilova, O., Häsler, R., Ott, S., Baines, J. F., Schreiber, S., & Rosenstiel, P. (2011). Nod2 is essential for temporal development of intestinal microbial communities. Gut, 60(10), 1354–1362. https://doi.org/10.1136/gut.2010.216259
Rausch, P., Rehman, A., Kunzel, S., Hasler, R., Ott, S. J., Schreiber, S., Rosenstiel, P., Franke, A., & Baines, J. F. (2011). Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 (Secretor) genotype. Proceedings of the National Academy of Sciences, 108(47), 19030–19035. https://doi.org/10.1073/pnas.1106408108
Rehman, A., Sina, C., Gavrilova, O., Häsler, R., Ott, S., Baines, J. F., Schreiber, S., & Rosenstiel, P. (2011). Nod2 is essential for temporal development of intestinal microbial communities. Gut, 60(10), 1354–1362. https://doi.org/10.1136/gut.2010.216259
Rausch, P., Rehman, A., Kunzel, S., Hasler, R., Ott, S. J., Schreiber, S., Rosenstiel, P., Franke, A., & Baines, J. F. (2011). Colonic mucosa-associated microbiota is influenced by an interaction of Crohn disease and FUT2 (Secretor) genotype. Proceedings of the National Academy of Sciences, 108(47), 19030–19035. https://doi.org/10.1073/pnas.1106408108
2009 and earlier
Parsch, J., Zhang, Z. & Baines, J.F. (2009). The influence of demography and weak selection on the McDonald-Kreitman test: an empirical study in Drosophila. Molecular Biology and Evolution, 26(3), 691–698. doi:10.1093/molbev/msn297.
Johnsen, J. M., Teschke, M., Pavlidis, P., McGee, B.M., Tautz, D., Ginsburg, D. & Baines, J. F. (2009). Selection on cis-regulatory variation at B4galnt2 and its influence on von Willebrand factor in house mice. Molecular Biology and Evolution, 26(3), 567–578. doi:10.1093/molbev/msn284.
Grath, S., Baines, J. F. & Parsch, J. (2009). Molecular evolution of sex-biased genes in the Drosophila ananassae subgroup. BMC Evolutionary Biology, 9, 291. doi:0.1186/1471-2148-9-291.
Carpenter, J., Hutter, S., Baines, J. F., Roller, J., Saminadin-Peter, S. S., Parsch, J. & Jiggins, F .M. (2009). The transcriptional response of Drosophila melanogaster to infection with the sigma virus (Rhabdoviridae). PloS One, 4(8), e6838. doi:10.1371/journal.pone.0006838.
Baines, J.F., Sawyer, S.A., Hartl, D.L. and Parsch, J. (2008). Effects of X-linkage and sex-biased gene expression on the rate of adaptive protein evolution in Drosophila. Molecular Biology and Evolution, 25(8), 1639–1650. doi:10.1534/genetics.106.069419.
Schug, M.D., Baines, J. F., Killon-Atwood, A., Mohanty, S., Das, A., Grath, S., Smith, S. G., Zargham, S., McEvey, S. F. & Stephan, W. (2008). Evolution of mating isolation between populations of Drosophila ananassae. Molecular Ecology, 17(11), 2706–2721. doi:10.1111/j.1365-294X.2008.03770.x.
Hense, W., Baines, J. F. & Parsch, J. (2007). X chromosome inactivation during Drosophila spermatogenesis. PLoS Biology, 5(10), e273. doi:10.1371/journal.pbio.0050273.
Baines, J. F. & Harr, B. (2007). Reduced X-linked diversity in derived populations of house mice. Genetics, 175(4). 1911–1921. doi: 10.1534/genetics.106.069419.
Beye, M., Gattermeier, I., Hasselmann, M., Gempe, T., Schioett, M., Baines, J. F., Schlipalius, D., Mougel, F., Emore, C., Rueppell, O., Sirviö, A., Guzmán-Novoa, E., Hunt, G., Solignac, M. & Page, R. E. (2006). Exceptionally high levels of recombination across the honey bee genome. Genome Research, 16(11), 1339–1344. doi:10.1101/gr.5680406.
Harr, B., Voolstra, C., Heinen, T. J, Baines, J. F., Rottscheidt, R., Ihle, S., Müller, W., Bonhomme, F. & Tautz, D. (2006). A change of expression in the conserved signaling gene MKK7 is associated with a selective sweep in the western house mouse Mus musculus domesticus. Journal of Evolutionary Biology, 19(5), 1486–1496. doi:10.1111/j.1420-9101.2006.01130.x.
Baines, J. F., Das, A., Mousset, S. & Stephan, W. (2004). The role of natural selection in genetic differentiation of worldwide populations of Drosophila ananassae. Genetics, 168(4), 1987–1998. doi:10.1534/genetics.104.027482.
Baines, J. F., Parsch, J. & Stephan, W. (2004). Pleiotropic effect of disrupting a conserved sequence involved in a long-range compensatory interaction in the Drosophila Adh gene. Genetics, 166(1), 237-242. https://doi.org/10.1534/genetics.166.1.237
Baines, J. F., Chen, Y., Das, A. & Stephan, W. (2002). DNA sequence variation at a duplicated gene: excess of replacement polymorphism and extensive haplotype structure in the Drosophila melanogaster bicoid region. Molecular Biology and Evolution, 19(7), 989–998. https://doi.org/10.1534/genetics.166.1.237
Chen, Y., Carlini, D.B., Baines, J. F., Parsch, J., Braverman, J. M., Tanda, S. & Stephan, W. (1999). RNA secondary structure and compensatory evolution. Genes & Genetic Systems, 74(6), 271–286. https://doi.org/10.1266/ggs.74.271
Johnsen, J. M., Teschke, M., Pavlidis, P., McGee, B.M., Tautz, D., Ginsburg, D. & Baines, J. F. (2009). Selection on cis-regulatory variation at B4galnt2 and its influence on von Willebrand factor in house mice. Molecular Biology and Evolution, 26(3), 567–578. doi:10.1093/molbev/msn284.
Grath, S., Baines, J. F. & Parsch, J. (2009). Molecular evolution of sex-biased genes in the Drosophila ananassae subgroup. BMC Evolutionary Biology, 9, 291. doi:0.1186/1471-2148-9-291.
Carpenter, J., Hutter, S., Baines, J. F., Roller, J., Saminadin-Peter, S. S., Parsch, J. & Jiggins, F .M. (2009). The transcriptional response of Drosophila melanogaster to infection with the sigma virus (Rhabdoviridae). PloS One, 4(8), e6838. doi:10.1371/journal.pone.0006838.
Baines, J.F., Sawyer, S.A., Hartl, D.L. and Parsch, J. (2008). Effects of X-linkage and sex-biased gene expression on the rate of adaptive protein evolution in Drosophila. Molecular Biology and Evolution, 25(8), 1639–1650. doi:10.1534/genetics.106.069419.
Schug, M.D., Baines, J. F., Killon-Atwood, A., Mohanty, S., Das, A., Grath, S., Smith, S. G., Zargham, S., McEvey, S. F. & Stephan, W. (2008). Evolution of mating isolation between populations of Drosophila ananassae. Molecular Ecology, 17(11), 2706–2721. doi:10.1111/j.1365-294X.2008.03770.x.
Hense, W., Baines, J. F. & Parsch, J. (2007). X chromosome inactivation during Drosophila spermatogenesis. PLoS Biology, 5(10), e273. doi:10.1371/journal.pbio.0050273.
Baines, J. F. & Harr, B. (2007). Reduced X-linked diversity in derived populations of house mice. Genetics, 175(4). 1911–1921. doi: 10.1534/genetics.106.069419.
Beye, M., Gattermeier, I., Hasselmann, M., Gempe, T., Schioett, M., Baines, J. F., Schlipalius, D., Mougel, F., Emore, C., Rueppell, O., Sirviö, A., Guzmán-Novoa, E., Hunt, G., Solignac, M. & Page, R. E. (2006). Exceptionally high levels of recombination across the honey bee genome. Genome Research, 16(11), 1339–1344. doi:10.1101/gr.5680406.
Harr, B., Voolstra, C., Heinen, T. J, Baines, J. F., Rottscheidt, R., Ihle, S., Müller, W., Bonhomme, F. & Tautz, D. (2006). A change of expression in the conserved signaling gene MKK7 is associated with a selective sweep in the western house mouse Mus musculus domesticus. Journal of Evolutionary Biology, 19(5), 1486–1496. doi:10.1111/j.1420-9101.2006.01130.x.
Baines, J. F., Das, A., Mousset, S. & Stephan, W. (2004). The role of natural selection in genetic differentiation of worldwide populations of Drosophila ananassae. Genetics, 168(4), 1987–1998. doi:10.1534/genetics.104.027482.
Baines, J. F., Parsch, J. & Stephan, W. (2004). Pleiotropic effect of disrupting a conserved sequence involved in a long-range compensatory interaction in the Drosophila Adh gene. Genetics, 166(1), 237-242. https://doi.org/10.1534/genetics.166.1.237
Baines, J. F., Chen, Y., Das, A. & Stephan, W. (2002). DNA sequence variation at a duplicated gene: excess of replacement polymorphism and extensive haplotype structure in the Drosophila melanogaster bicoid region. Molecular Biology and Evolution, 19(7), 989–998. https://doi.org/10.1534/genetics.166.1.237
Chen, Y., Carlini, D.B., Baines, J. F., Parsch, J., Braverman, J. M., Tanda, S. & Stephan, W. (1999). RNA secondary structure and compensatory evolution. Genes & Genetic Systems, 74(6), 271–286. https://doi.org/10.1266/ggs.74.271
Last updated May 2023