Publications
Selected Publications (See full list: GoogleScholar)
Hornstein, E. D., M. Charles, M. Franklin, B. Edwards, S. Vintila, M. Kleiner, H. Sederoff (2024). IPD3, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host Arabidopsis when restored long after its evolutionary loss. Plant Molecular Biology. doi: 10.1007/s11103-024-01422-3
Parnell, J. J., S. Vintila, C. Tang, M. R. Wagner, M. Kleiner (2023). Evaluation of ready-to-use freezer stocks of a synthetic microbial community for maize root colonization. Microbiology Spectrum. doi:10.1128/spectrum.02401-23
Kleiner, M., L. Polerecky, C. Lott, C. Bergin, S. Haeusler, M. Liebeke, C. Wentrup, N. Musat, M.M.M. Kuypers, N. Dubilier (2023). Mechanism of high energy efficiency of carbon fixation by sulfur-oxidizing symbionts revealed by single-cell analyses and metabolic modeling. BioRxiv. doi: 10.1101/2023.11.25.568684
Michellod, D., T. Bien, D. Birgel, M. Violette, M. Kleiner, S. Fearn, C. Zeidler, H. R. Gruber-Vodicka, N. Dubilier, M. Liebeke (2023). De novo phytosterol synthesis in animals. Science. doi: 10.1126/science.add7830
Kleiner, M., A. Kouris, M. Violette, G. D’Angelo, Y. Liu, A. Korenek, N. Tolic, T. Sachsenberg, J. McCalder, M.S. Lipton, M. Strous (2023). Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes. Microbiome. doi: 10.1186/s40168-022-01454-1
Sato, Y., J. Wippler, C. Wentrup, R. Ansorge, M. Sadowski, H. Gruber-Vodicka, N. Dubilier, M. Kleiner (2022). Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium. Microbiome. doi: 10.1186/s40168-022-01372-2
Salvato, F., S. Vintila, O. M. Finkel, J. Dangl, M. Kleiner (2022). Evaluation of protein extraction methods for metaproteomic analyses of root-associated microbes. Molecular Plant-Microbe Interactions. doi: 10.1094/MPMI-05-22-0116-TA
Beck, A.E, M. Kleiner, A.-K. Garrell (2022). Elucidating plant-microbe-environment interactions through omics-enabled metabolic modelling using synthetic communities. Frontiers in Plant Science. doi: 10.3389/fpls.2022.910377
Blakeley-Ruiz, J.A., M. Kleiner (2022). Considerations for constructing a protein sequence database for metaproteomics. Computational and Structural Biotechnology Journal doi: 10.1016/j.csbj.2022.01.018
Mordant, A., M. Kleiner (2021). Evaluation of Sample Preservation and Storage Methods for Metaproteomics Analysis of Intestinal Microbiomes. Microbiology Spectrum doi: 10.1128/Spectrum.01877-21
Jensen, M., J. Wippler, M. Kleiner (2021). Evaluation of RNAlater as a field-compatible preservation method for metaproteomic analyses of bacterium-animal symbioses. Microbiology Spectrum 9:e01429-21.
Wagner, M.R., C. Tang, F. Salvato, K. M. Clouse, A. Bartlett, S. Vintila, L. Phillips, S. Sermons, M. Hoffmann, P.J. Balint-Kurti, M. Kleiner (2021). Microbe-dependent heterosis in maize. Proceedings of the National Academy of Sciences
Kleiner, M., A. Kouris, M. Jensen, Y. Liu, J. McCalder, M. Strous (2021). Ultra-sensitive Protein-SIP to quantify activity and substrate uptake in microbiomes with stable isotopes. BioRxiv https://doi.org/10.1101/2021.03.29.437612
Van Den Bossche, T., B. J. Kunath, K. Schallert, S. S. Schäpe, P. E. Abraham, J. Armengaud, M. Ø. Arntzen, A. Bassignani, D. Benndorf, S. Fuchs, R. J. Giannone, T. J. Griffin, L. H. Hagen, R. Halder, C. Henry, R. L. Hettich, R. Heyer, P. Jagtap, N. Jehmlich, M. Jensen, C. Juste, M. Kleiner, O. Langella, T. Lehmann, E. Leith, P. May, B. Mesuere, G. Miotello, S. L. Peters, O. Pible, U. Reichl, B. Y. Renard, H. Schiebenhoefer, A. Scryba, A. Tanca, K. Trappe, J.-P. Trezzi, S. Uzzau, P. Verschaffelt, M. von Bergen, P. Wilmes, M. Wolf, L. Martens and T. Muth (2021). Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows. Nature Communications https://doi.org/10.1038/s41467-021-27542-8.
Salvato, F., R.L Hettich, M. Kleiner (2021). Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes. PLoS Pathogens 17(2): e1009245.
Wagner, M. R., C. Tang, F. Salvato, K. M. Clouse, A. Bartlett, S. Sermons, M. Hoffmann, P. J. Balint-Kurti and M. Kleiner (2020). Microbe-dependent heterosis in maize. BioRxiv https://doi.org/10.1101/2020.05.05.078766
Sato, Y., J. Wippler, C. Wentrup, N. Dubilier and M. Kleiner (2020). High-quality draft genome sequences of two deltaproteobacterial endosymbionts, Delta1a and Delta1b, from uncultured Sva0081 clade, assembled from metagenomes of the gutless marine worm Olavius algarvensis. Microbiology Resource Announcements 9:e00276-20.
Kleiner, M., B. Bushnell, K. E. Sanderson, L. V. Hooper and B. A. Duerkop (2020). Transductomics: sequencing based detection and analysis of transduced DNA in pure cultures and microbial communities. Microbiome 8:158.
Speare, L., S. Smith, F. Salvato, M. Kleiner and A. N. Septer (2020). Environmental viscosity modulates interbacterial killing during habitat transition. mBio 11(1): e03060-19.
Ponnudurai, R., S. E. Heiden, L. Sayavedra, T. Hinzke, M. Kleiner, C. Hentschker, H. Felbeck, S. M. Sievert, R. Schlueter, D. Becher, T. Schweder and S. Markert (2020). Comparative poteomics of related symbiotic mussel species reveals high variability of host-symbiont interactions. ISME Journal 14(2): 649-656.
Assié, A., N. Leisch, D. V. Meier, H. Gruber-Vodicka, H. E. Tegetmeyer, A. Meyerdirks, M. Kleiner, T. Hinzke, S. Joye, M. Saxton, N. Dubilier and J. M. Petersen (2020). Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria). ISME Journal 14(1): 104-122.
Hinzke, T., M. Kleiner, C. Breusing, H. Felbeck, R. Häsler, S. M. Sievert, R. Schlüter, P. Rosenstiel, T. B. H. Reusch, T. Schweder and S. Markert (2019). Host-microbe interactions in the chemosynthetic Riftia pachyptila symbiosis. mBio 10(6): e02243-19.
Zorz, J. K., C. Sharp, M. Kleiner, P. M. K. Gordon, R. T. Pon, X. Dong and M. Strous (2019). A shared core microbiome in soda lakes separated by large distances. Nature Communications 10:4230.
Seah, B. K. B., C. P. Antony, B. Huettel, J. Zarzycki, L. S. v. Borzyskowski, T. J. Erb, A. Kouris, M. Kleiner, M. Liebeke, N. Dubilier and H. R. Gruber-Vodicka (2019). Sulfur-oxidizing symbionts without canonical genes for autotrophic CO2 fixation. mBio 10(3): e01112-19.
Gruber-Vodicka, H. R., N. Leisch, M. Kleiner, T. Hinzke, M. Liebeke, M. McFall-Ngai, M. G. Hadfield and N. Dubilies (2019). Two intracellular and cell type-specific bacterial symbionts in the placozoan Trichoplax H2. Nature Microbiology. doi: 10.1038/s41564-019-0475-9
Kleiner, M. (2019). Metaproteomics: Much more than measuring gene expression in microbial communities. mSystems 4(3): e00115-19. doi: 10.1128/mSystems.00115-19
Hinzke, T., A. Kouris, R.-A. Hughes, M. Strous and M. Kleiner (2019). More is not always better: Evaluation of 1D and 2D-LC-MS/MS methods for metaproteomics. Frontiers in Microbiology 10(238). doi: 10.3389/fmicb.2019.00238
Rubin-Blum, M., N. Dubilier and M. Kleiner (2019). Genetic evidence for two carbon fixation pathways (the Calvin-Benson-Bassham Cycle and the Reverse Tricarboxylic Acid Cycle) in symbiotic and free-living bacteria. mSphere 4:e00394-18.
Duerkop, B. A., M. Kleiner, D. Paez-Espino, W. Zhu, B. Hassell, S. E. Winter, N. C. Kyrpides and L. V. Hooper (2018). Murine colitis reveals a disease-associated bacteriophage community. Nature Microbiology 3: 1023–1031. Free Full Text
Kleiner, M., X. Dong, T. Hinzke, J. Wippler, E. Thorson, B. Mayer and M. Strous (2018). Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities. Proceedings of the National Academy of Sciences 115(24): E5576-E5584. doi: 10.1073/pnas.1722325115
Zorz, J. K., J. A. Kozlowski, L. Y. Stein, M. Strous and M. Kleiner (2018). Comparative proteomics of three species of ammonia-oxidizing bacteria. Frontiers in Microbiology 9(938). doi: 10.3389/fmicb.2018.00938
Kleiner, M., E. Thorson, C. E. Sharp, X. Dong, C. Li and M. Strous (2017). Assessing species biomass contributions in microbial communities via metaproteomics. Nature Communications 1558. doi: 10.1038/s41467-017-01544-x
Dong, X., M. Kleiner, C. E. Sharp, E. Thorson, C. Li, D. Liu and M. Strous (2017). Fast and simple analysis of MiSeq amplicon sequencing data with MetaAmp. Frontiers in Microbiology 8(1461). doi: 10.3389/fmicb.2017.01461
Ponnudurai, R. P., M. Kleiner, L. Sayavedra, J. M. Petersen, M. Moche, A. Otto et al. (2017). Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis. The ISME Journal 11: 463-477. doi:10.1038/ismej.2016.124
Wippler, J., M. Kleiner, C. Lott, A. Gruhl, P. Abraham, R. Giannone et al. (2016). Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis. BMC Genomics 17(1): 942. doi.org/10.1186/s12864-016-3293-y
Yu, Y.-T. N., M. Kleiner and G. J. Velicer (2016). Spontaneous reversions of an evolutionary trait loss reveal regulators of a sRNA that controls multicellular development in the myxobacteria. Journal of Bacteriology 198(23): 3142-3151.
Petersen, J. M., A. Kemper, H. Gruber-Vodicka, U. Cardini, M. van der Geest, M. Kleiner et al. (2016). Chemosynthetic sulphur-oxidizing symbionts of marine invertebrate animals are capable of nitrogen fixation. Nature Microbiology 2:16195. doi:10.1038/nmicrobiol.2016.195
Hamann, E., H. Gruber-Vodicka, M. Kleiner, H. Tegetmeyer, D. Riedel, S. Littmann et al. (2016). Environmental Breviatea harbor mutualistic Arcobacter epibionts. Nature 534: 254-258. doi:10.1038/nature18297
Kleiner, M., C. Wentrup, T. Holler, G. Lavik, J. Harder, C. Lott, S. Littmann, M. M. M. Kuypers and N. Dubilier (2015). Use of carbon monoxide and hydrogen by a bacteria-animal symbiosis from seagrass sediments. Environmental Microbiology 17(12): 5023-5035. doi: 10.1111/1462-2920.12912
Sayavedra, L., M. Kleiner, R. Ponnudurai, S. Wetzel, E. Pelletier, V. Barbe et al. (2015). Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels. eLife 4:e07966. doi: 10.7554/eLife.07966
Kleiner, M., L. V. Hooper and B. A. Duerkop (2015). Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes. BMC Genomics 16(7). doi:10.1186/s12864-014-1207-4
Kleiner, M., J. C. Young, M. Shah, N. C. VerBerkmoes and N. Dubilier (2013). Metaproteomics reveals abundant transposase expression in mutualistic endosymbionts. mBio 4(3): e00223-13. doi: 10.1128/mBio.00223-13
Kleiner, M., C. Wentrup, C. Lott, H. Teeling, S. Wetzel, J. Young et al. (2012). Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use. Proceedings of the National Academy of Sciences 109(19): E1173-E1182. Original publication (open access)
Kleiner, M., J. M. Petersen and N. Dubilier (2012). Convergent and divergent evolution of metabolism in sulfur-oxidizing symbionts and the role of horizontal gene transfer. Current Opinion in Microbiology 15(5): 621-631. doi:10.1016/j.mib.2012.09.003