Manuel Kleiner

Considerations for constructing a protein sequence database for metaproteomics

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL.

De novo phytosterol synthesis in animals

Michellod, D., Bien, T., Birgel, D., Jensen, M., Kleiner, M., Fearn, S., … Liebeke, M. (2022, April 22). (Vol. 4). Vol. 4.

Activation of the Type VI Secretion System in the Squid Symbiont Vibrio fischeri Requires the Transcriptional Regulator TasR and the Structural Proteins TssM and TssA

JOURNAL OF BACTERIOLOGY, 11.

Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis

ELIFE, 10.

Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows

NATURE COMMUNICATIONS, 12.

Evaluation of RNAlater as a Field-Compatible Preservation Method for Metaproteomic Analyses of Bacterium-Animal Symbioses

MICROBIOLOGY SPECTRUM, 9(2).

Evaluation of RNAlater™ as a field-compatible preservation method for metaproteomic analyses of bacteria-animal symbioses

Jensen, M., Wippler, J., & Kleiner, M. (2021, June 17). (Vol. 6). Vol. 6.

Evaluation of Sample Preservation and Storage Methods for Metaproteomics Analysis of Intestinal Microbiomes

MICROBIOLOGY SPECTRUM, 9(3).

Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium

Sato, Y., Wippler, J., Wentrup, C., Ansorge, R., Sadowski, M., Gruber-Vodicka, H., … Kleiner, M. (2021, January 30). (Vol. 1). Vol. 1.

Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes

(D. A. Hogan, Ed.) [Review of ]. PLOS PATHOGENS, 17(2), e1009245.

Highly variable fidelity drives symbiont community composition in an obligate symbiosis

Mankowski, A., Kleiner, M., Erséus, C., Leisch, N., Sato, Y., Volland, J.-M., … Gruber-Vodicka, H. (2021, April 28). (Vol. 4). Vol. 4.

Life in the Dark: Phylogenetic and Physiological Diversity of Chemosynthetic Symbioses

ANNUAL REVIEW OF MICROBIOLOGY, VOL 75, 2021.

Microbe-dependent heterosis in maize

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 7.

Proteome and strain analysis of cyanobacterium Candidatus "Phormidium alkaliphilum" reveals traits for success in biotechnology

ISCIENCE, 24(12), 103405.

Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes

Kleiner, M., Kouris, A., Jensen, M., Grace, D. A., Liu, Y., Korenek, A., … Strous, M. (2021, March 30). (Vol. 3). Vol. 3.

Comparative proteomics of related symbiotic mussel species reveals high variability of host–symbiont interactions

The ISME Journal, 14(2), 649–656.

Environmental Viscosity Modulates Interbacterial Killing during Habitat Transition

MBIO, 11(1).

High-Quality Draft Genome Sequences of Two Deltaproteobacterial Endosymbionts, Delta1a and Delta1b, from the Uncultured Sva0081 Clade, Assembled from Metagenomes of the Gutless Marine Worm Olavius algarvensis

MICROBIOLOGY RESOURCE ANNOUNCEMENTS, 9(16).

High-Quality Draft Genome Sequences of the Uncultured Delta3 Endosymbiont (Deltaproteobacteria) Assembled from Metagenomes of the Gutless Marine Worm Olavius algarvensis

MICROBIOLOGY RESOURCE ANNOUNCEMENTS, 9(31).

High-Quality Draft Genome Sequences of the Uncultured Delta3 Endosymbiont (Deltaproteobacteria) Assembled from Metagenomes of the Gutless Marine Worm Olavius algarvensis

MICROBIOLOGY RESOURCE ANNOUNCEMENTS, 7(31).

Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria)

ISME JOURNAL, 14(1), 104–122.

Metabolic differences between symbiont subpopulations in the deep-sea tubeworm Riftia pachyptila

Hinzke, T., Kleiner, M., Meister, M., Schlüter, R., Hentschker, C., Pané-Farré, J., … Markert, S. (2020, April 9). (Vol. 4). Vol. 4.

Microbe-dependent heterosis in maize

Wagner, M. R., Tang, C., Salvato, F., Clouse, K. M., Bartlett, A., Sermons, S., … Kleiner, M. (2020, May 7). (Vol. 5). Vol. 5.

Microbial DNA on the move: sequencing based detection and analysis of transduced DNA in pure cultures and microbial communities

Kleiner, M., Bushnell, B., Sanderson, K. E., Hooper, L. V., & Duerkop, B. A. (2020, January 16). (Vol. 1). Vol. 1.

Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities

MICROBIOME, 8(1).

A shared core microbiome in soda lakes separated by large distances

NATURE COMMUNICATIONS, 10.

Chemosynthetic symbiont with a drastically reduced genome serves as primary energy storage in the marine flatworm Paracatenula

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 116(17), 8505–8514.

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(1), e00394–18.

Host-Microbe Interactions in the Chemosynthetic Riftia pachyptila Symbiosis.

MBio, 10(6).

Host-microbe interactions in the chemosyntheticRiftia pachyptilasymbiosis

Hinzke, T., Kleiner, M., Breusing, C., Felbeck, H., Häsler, R., Sievert, S. M., … Markert, S. (2019, May 27). (Vol. 5). Vol. 5.

Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities

MSYSTEMS, 4(3).

More Is Not Always Better: Evaluation of 1D and 2D-LC-MS/MS Methods for Metaproteomics

FRONTIERS IN MICROBIOLOGY, 10.

Sulfur-Oxidizing Symbionts without Canonical Genes for Autotrophic CO2 Fixation

MBIO, 10(3).

Sulfur-oxidizing symbionts without canonical genes for autotrophic CO2fixation

Seah, B. K. B., Antony, C. P., Huettel, B., Zarzycki, J., Borzyskowski, L. S., Erb, T. J., … Gruber-Vodicka, H. R. (2019, February 5). (Vol. 2). Vol. 2.

TheTrichoplaxmicrobiome: the simplest animal lives in an intimate symbiosis with two intracellular bacteria

Gruber-Vodicka, H. R., Leisch, N., Kleiner, M., Hinzke, T., Liebeke, M., McFall-Ngai, M., … Dubilier, N. (2019, March 5). (Vol. 3). Vol. 3.

Two intracellular and cell type-specific bacterial symbionts in the placozoan Trichoplax H2

NATURE MICROBIOLOGY, 4(9), 1465–1474.

A metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities

Kleiner, M., Dong, X., Hinzke, T., Wippler, J., Thorson, E., Mayer, B., & Strous, M. (2018, January 9). (Vol. 1). Vol. 1.

Author Correction: Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation

Nature Microbiology, 3(8), 961–961.

Centrifugation-based enrichment of bacterial cell populations for metaproteomic studies on bacteria-invertebrate symbioses

Springer, 1841, 319–334.

Comparative Proteomics of Three Species of Ammonia-Oxidizing Bacteria.

Frontiers in Microbiology.

Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria)

Assié, A., Leisch, N., Meier, D. V., Gruber-Vodicka, H., Tegetmeyer, H. E., Meyerdirks, A., … Petersen, J. M. (2018, October 8). (Vol. 10). Vol. 10.

Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities.

Proceedings of the National Academy of Sciences of the United States of America, 6(24), E5576–5584.

Murine colitis reveals a disease-associated bacteriophage community

NATURE MICROBIOLOGY, 3(9), 1023–1031.

Synergy of Sodium Nitroprusside and Nitrate in Inhibiting the Activity of Sulfate Reducing Bacteria in Oil-Containing Bioreactors.

Frontiers in Microbiology, 9.

Assessing species biomass contributions in microbial communities via metaproteomics

Nature Communications, 4(1).

Assessing species biomass contributions in microbial communities via metaproteomics

Kleiner, M., Thorson, E., Sharp, C. E., Dong, X., Liu, D., Li, C., & Strous, M. (2017, April). (Vol. 4). Vol. 4.

Fast and Simple Analysis of MiSeq Amplicon Sequencing Data with MetaAmp

Frontiers in Microbiology, 8.

Fast and simple analysis of MiSeq amplicon sequencing data with MetaAmp

Dong, X., Kleiner, M., Sharp, C. E., Thorson, E., Li, C., Liu, D., & Strous, M. (2017, April). (Vol. 4). Vol. 4.

Genome sequence of the sulfur-oxidizing Bathymodiolus thermophilus gill endosymbiont.

Standards in Genomic Sciences.

Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis

The ISME Journal, 11(2), 463–477.

Metaproteomics of phototrophic biomats from two soda lakes in the Canadian Rocky Mountains

http://www.ebi.ac.uk/pride/archive/projects/PXD006343

Normalization of metatranscriptomic and metaproteomic data for differential gene expression analyses: The importance of accounting for organism abundance

PeerJ Preprints, 5, e2846v1.

Normalization of metatranscriptomic and metaproteomic data for differential gene expression analyses: The importance of accounting for organism abundance

Kleiner, M. (2017, March 2). (Vol. 3). Vol. 3.

Quantification of mock microbial communities with metagenomes, 16S rRNA gene amplicons and metaproteomics

http://www.ebi.ac.uk/pride/archive/projects/PXD006118

Re-analysis of an ultra-deep and quantitative saliva proteome

http://www.ebi.ac.uk/pride/archive/projects/PXD006366

Short-chain alkanes fuel mussels and sponge Cycloclasticus symbionts from deep-sea gas and oil seeps

Nature Microbiology, 2(8), 17093.

Bathymodiolus azoricus host-symbiont proteomics

http://www.ebi.ac.uk/pride/archive/projects/PXD004061

Chemosynthetic sulphur-oxidizing symbionts of marine invertebrate animals are capable of nitrogen fixation

Nature Microbiology, 2(1), 16195.

Closely coupled evolutionary history of ecto- and endosymbionts from two distantly-related animal phyla

Molecular Ecology, 25(13), 3203–3223.

Differential proteomics of Lenisia limosa (Breviatea) and its epibiotic Arcobacter symbiont

http://www.ebi.ac.uk/pride/archive/projects/PXD003275

Environmental Breviatea harbor mutualistic Arcobacter epibionts

Nature, 534(7606), 254–258.

MiL-FISH: Multi-labelled oligonucleotides for fluorescence in situ hybridisation improve visualization of bacterial cells

Applied and Environmental Microbiology, 82(1), 62–70.

Proteomics of Candidatus Thiodiazotropha endoloripes, the chemosynthetic symbiont of the lucinid clam Loripes lucinalis from the Bay of Fetovaia

http://www.ebi.ac.uk/pride/archive/projects/PXD004536

Proteomics of Cycloclasticus endosymbiont of deep-sea mussel Bathymodiolus heckerae from Campeche Knolls, southern Gulf of Mexico

http://www.ebi.ac.uk/pride/archive/projects/PXD005351

Spontaneous Reversions of an Evolutionary Trait Loss Reveal Regulators of a Small RNA That Controls Multicellular Development in Myxobacteria

Journal of Bacteriology, 198(23), 3142–3151.

Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis

BMC Genomics, 17(1).

Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis

https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=77bbe652de0b4439b9a9e89016f99c93

Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels

ELife, 4, e07966.

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes

BMC Genomics, 16(7), 7.

Use of carbon monoxide and hydrogen by a bacteria-animal symbiosis from seagrass sediments

Environmental Microbiology, 17(12), 5023–5035.

Identification and activity of acetate-assimilating bacteria in diffuse fluids venting from deep-sea hydrothermal systems

FEMS Microbiology Ecology, 90(3), 731–746.

Metaproteomics Reveals Abundant Transposase Expression in Mutualistic Endosymbionts

Mbio, 4(3).

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.

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.

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 of the United States of America, 109(19), E1173–E1182.

Status quo in physiological proteomics of the uncultured Riftia pachyptila endosymbiont

Proteomics, 11(15), 3106–3117.

The Olavius algarvensis Metagenome Revisited: Lessons Learned from the Analysis of the Low-Diversity Microbial Consortium of a Gutless Marine Worm

Kleiner, M., Woyke, T., Ruehland, C., & Dubilier, N. (2011, November 10). Handbook of Molecular Microbial Ecology II, pp. 319–333.