Metaproteomics, Microbiome, Symbiosis, Metagenomics, Microbial Physiology, Carbon Fixation Pathways
2025 journal article
A pilot study of metaproteomics and DNA metabarcoding as tools to assess dietary intake in humans
Food & Function.
2024 journal article
<i>IPD3</i>, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host <i>Arabidopsis</i> when restored long after its evolutionary loss
PLANT MOLECULAR BIOLOGY, 114(2).
2024 article
Adaptations in gut Bacteroidales facilitate stable co-existence with their lytic bacteriophages
Cortés-Martín, A., Buttimer, C., Maier, J. L., Tobin, C. A., Draper, L. A., Ross, R. P., … Shkoporov, A. N. (2024, November 17).
2024 journal article
An intranuclear bacterial parasite of deep-sea mussels expresses apoptosis inhibitors acquired from its host
NATURE MICROBIOLOGY, 9(11).
2024 review
Community standards and future opportunities for synthetic communities in plant-microbiota research
[Review of ]. NATURE MICROBIOLOGY, 9(11), 2774–2784.
2024 article
Data-Independent Acquisition Mass Spectrometry as a Tool for Metaproteomics: Interlaboratory Comparison Using a Model Microbiome
Rajczewski, A. T., Blakeley-Ruiz, J. A., Meyer, A., Vintila, S., McIlvin, M. R., Bossche, T. V. D., … Jagtap, P. D. (2024, September 22).
2024 article
Dietary protein from different sources escapes host digestion and is differentially modified by the microbiota
Awan, A., Bartlett, A., Blakeley-Ruiz, J. A., Richie, T., Theriot, C. M., & Kleiner, M. (2024, June 27).
2024 article
Drought stress homogenizes maize growth responses to diverse natural soil microbiomes
Swift, J. F., Kolp, M. R., Carmichael, A., Ford, N. E., Hansen, P. M., Sikes, B. A., … Wagner, M. R. (2024, July 18). PLANT AND SOIL, Vol. 7.
2024 article
Effective Seed Sterilization Methods Require Optimization Across Maize Genotypes
Parnell, J. J., Pal, G., Awan, A., Vintila, S., Houdinet, G., Hawkes, C. V., … Kleiner, M. (2024, July 17). PHYTOBIOMES JOURNAL, Vol. 7.
2024 journal article
Enterococcal quorum-controlled protease alters phage infection
FEMS MICROBES, 5.
2024 article
Genomic and proteomic characterization of sulfate-reducing symbionts of gutless marine annelids
D'Angelo, G., Kleiner, M., Mankowski, A., Cifuentes-Anticevic, J., Kroeber, E., Violette, M., … Liebeke, M. (2024, December 9).
2024 article
Meta-omics reveals role of photosynthesis in Microbially Induced Carbonate Precipitation at a CO2-rich Geyser
Violette, M., Hyland, E., Burgener, L., Ghosh, A., Montoya, B., & Kleiner, M. (2024, July 20).
2024 journal article
Metabolically-versatile Ca. Thiodiazotropha symbionts of the deep-sea lucinid clam Lucinoma kazani have the genetic potential to fix nitrogen
ISME COMMUNICATIONS, 4(1).
2024 article
Metabolically-versatileCa.Thiodiazotropha symbionts of the deep-sea lucinid clamLucinoma kazanihave the genetic potential to fix nitrogen
Ratinskaia, L., Malavin, S., Zvi-Kedem, T., Vintila, S., Kleiner, M., & Rubin-Blum, M. (2024, April 5).
2024 article
Metaproteomics and DNA metabarcoding as tools to assess dietary intake in humans
Petrone, B. L., Bartlett, A., Jiang, S., Korenek, A., Vintila, S., Tenekjian, C., … Kleiner, M. (2024, April 10).
2024 journal article
Pseudo-pac site sequences used by phage P22 in generalized transduction of <i>Salmonella</i>
PLOS PATHOGENS, 20(6).
Ed(s): P. Secor
2024 article
Stable isotope fingerprinting can directly link intestinal microorganisms with their carbon source and captures diet-induced substrate switching in vivo
Mordant, A., Blakeley-Ruiz, J. A., & Kleiner, M. (2024, December 11).
2023 journal article
De novo phytosterol synthesis in animals
SCIENCE, 380(6644), 520–526.
2023 article
Effective seed sterilization methods require optimization across maize genotypes
Parnell, J. J., Pal, G., Awan, A., Vintila, S., Houdinet, G., Hawkes, C. V., … Kleiner, M. (2023, December 15).
2023 article
Environmental legacy effects impact maize growth and microbiome assembly under drought stress
Swift, J. F., Kolp, M. R., Carmichael, A., Ford, N. E., Hansen, P. M., Sikes, B. A., … Wagner, M. R. (2023, April 12).
2023 article
Evaluation of ready-to-use freezer stocks of a synthetic microbial community for maize root colonization
Parnell, J. J., Vintila, S., Tang, C., Wagner, M. R., & Kleiner, M. (2023, December 12). (K. L. Hockett, Ed.). MICROBIOLOGY SPECTRUM, Vol. 12.
Ed(s): K. Hockett
2023 article
Evaluation of ready-to-use freezer stocks of a synthetic microbial community for maize root colonization
Parnell, J. J., Vintila, S., Tang, C., Wagner, M. R., & Kleiner, M. (2023, May 10).
2023 article
Large Quantities of Bacterial DNA and Protein in Common Dietary Protein Source Used in Microbiome Studies
Bartlett, A., Blakeley-Ruiz, J. A., Richie, T., Theriot, C. M., & Kleiner, M. (2023, December 7).
2023 article
Mechanism of high energy efficiency of carbon fixation by sulfur-oxidizing symbionts revealed by single-cell analyses and metabolic modeling
Kleiner, M., Polerecky, L., Lott, C., Bergin, C., Häusler, S., Liebeke, M., … Dubilier, N. (2023, November 26).
2023 article
Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels
Zvi-Kedem, T., Vintila, S., Kleiner, M., Tchernov, D., & Rubin-Blum, M. (2023, February 10).
2023 journal article
Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels
ISME COMMUNICATIONS, 3(1).
2023 article
Re-engineering a lost trait: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
Hornstein, E. D., Charles, M., Franklin, M., Edwards, B., Vintila, S., Kleiner, M., & Sederoff, H. (2023, March 7).
2023 journal article
Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes
MICROBIOME, 11(1).
2022 journal article
Considerations for constructing a protein sequence database for metaproteomics
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 20, 937–952.
Contributors: J. Blakeley-Ruiz n
2022 article
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.
2022 review
Dietary protein and the intestinal microbiota: An understudied relationship
[Review of ]. ISCIENCE, 25(11).
2022 journal article
Elucidating Plant-Microbe-Environment Interactions Through Omics-Enabled Metabolic Modelling Using Synthetic Communities
FRONTIERS IN PLANT SCIENCE, 13.
2022 journal article
Evaluation of Protein Extraction Methods for Metaproteomic Analyses of Root-Associated Microbes
MOLECULAR PLANT-MICROBE INTERACTIONS, 35(11), 977–988.
2022 journal article
Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium
MICROBIOME, 10(1).
2021 journal article
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, 203(21).
2021 journal article
Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis
ELIFE, 10.
2021 journal article
Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows
NATURE COMMUNICATIONS, 12(1).
2021 journal article
Evaluation of RNAlater as a Field-Compatible Preservation Method for Metaproteomic Analyses of Bacterium-Animal Symbioses
MICROBIOLOGY SPECTRUM, 9(2).
Ed(s): J. Gralnick
2021 article
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.
2021 journal article
Evaluation of Sample Preservation and Storage Methods for Metaproteomics Analysis of Intestinal Microbiomes
MICROBIOLOGY SPECTRUM, 9(3).
Ed(s): C. Khursigara
2021 article
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).
2021 review
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).
Ed(s): D. Hogan
2021 article
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).
2021 article
Life in the Dark: Phylogenetic and Physiological Diversity of Chemosynthetic Symbioses
ANNUAL REVIEW OF MICROBIOLOGY, VOL 75, 2021, Vol. 75, pp. 695–718.
2021 journal article
Microbe-dependent heterosis in maize
Proceedings of the National Academy of Sciences, 118(30).
2021 journal article
Proteome and strain analysis of cyanobacterium Candidatus "Phormidium alkaliphilum" reveals traits for success in biotechnology
ISCIENCE, 24(12).
2021 article
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.
2020 journal article
Environmental Viscosity Modulates Interbacterial Killing during Habitat Transition
MBIO, 11(1).
2020 journal article
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).
2020 journal article
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).
2020 journal article
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).
Ed(s): F. Stewart
2020 article
Metabolic differences between symbiont subpopulations in the deep-sea tubewormRiftia pachyptila
Hinzke, T., Kleiner, M., Meister, M., Schlüter, R., Hentschker, C., Pané-Farré, J., … Markert, S. (2020, April 9).
2020 article
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.
2020 article
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).
2020 journal article
Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities
MICROBIOME, 8(1).
2019 journal article
A shared core microbiome in soda lakes separated by large distances
NATURE COMMUNICATIONS, 10.
2019 journal article
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.
2019 journal article
Comparative proteomics of related symbiotic mussel species reveals high variability of host–symbiont interactions
The ISME Journal.
2019 journal article
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.
Ed(s): S. Hallam
2019 journal article
Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria)
ISME JOURNAL, 14(1), 104–122.
2019 journal article
Host-Microbe Interactions in the Chemosynthetic Riftia pachyptila Symbiosis.
MBio, 10(6).
Ed(s): D. Distel & E. Ruby
2019 article
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.
2019 journal article
Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities
MSYSTEMS, 4(3).
2019 journal article
More Is Not Always Better: Evaluation of 1D and 2D-LC-MS/MS Methods for Metaproteomics
FRONTIERS IN MICROBIOLOGY, 10.
2019 journal article
Sulfur-Oxidizing Symbionts without Canonical Genes for Autotrophic CO2 Fixation
MBIO, 10(3).
Ed(s): S. Giovannoni
2019 article
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.
2019 article
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.
2019 journal article
Two intracellular and cell type-specific bacterial symbionts in the placozoan Trichoplax H2
NATURE MICROBIOLOGY, 4(9), 1465–1474.
2018 article
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.
2018 journal article
Author Correction: Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation
Nature Microbiology, 3(8), 961–961.
2018 journal article
Centrifugation-based enrichment of bacterial cell populations for metaproteomic studies on bacteria-invertebrate symbioses
Springer, 1841, 319–334.
Ed(s): D. Becher
2018 journal article
Comparative Proteomics of Three Species of Ammonia-Oxidizing Bacteria.
Frontiers in Microbiology.
2018 article
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.
2018 journal article
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, 115(24), E5576–E5584.
2018 journal article
Murine colitis reveals a disease-associated bacteriophage community
NATURE MICROBIOLOGY, 3(9), 1023–1031.
2018 journal article
Synergy of Sodium Nitroprusside and Nitrate in Inhibiting the Activity of Sulfate Reducing Bacteria in Oil-Containing Bioreactors
FRONTIERS IN MICROBIOLOGY, 9.
2017 journal article
Assessing species biomass contributions in microbial communities via metaproteomics
NATURE COMMUNICATIONS, 8.
2017 article
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.
2017 journal article
Fast and Simple Analysis of MiSeq Amplicon Sequencing Data with MetaAmp
Frontiers in Microbiology, 8.
2017 article
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.
2017 journal article
Genome sequence of the sulfur-oxidizing Bathymodiolus thermophilus gill endosymbiont.
Standards in Genomic Sciences.
2017 dataset
Metaproteomics of phototrophic biomats from two soda lakes in the Canadian Rocky Mountains
http://www.ebi.ac.uk/pride/archive/projects/PXD006343
2017 journal article
Normalization of metatranscriptomic and metaproteomic data for differential gene expression analyses: The importance of accounting for organism abundance
PeerJ Preprints, 5, e2846v1.
2017 article
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.
2017 dataset
Quantification of mock microbial communities with metagenomes, 16S rRNA gene amplicons and metaproteomics
http://www.ebi.ac.uk/pride/archive/projects/PXD006118
2017 dataset
Re-analysis of an ultra-deep and quantitative saliva proteome
http://www.ebi.ac.uk/pride/archive/projects/PXD006366
2017 journal article
Short-chain alkanes fuel mussels and sponge Cycloclasticus symbionts from deep-sea gas and oil seeps
Nature Microbiology, 2, 17093.
2016 dataset
Bathymodiolus azoricus host-symbiont proteomics
http://www.ebi.ac.uk/pride/archive/projects/PXD004061
2016 journal article
Chemosynthetic sulphur-oxidizing symbionts of marine invertebrate animals are capable of nitrogen fixation
Nature Microbiology, 2, 16195.
2016 journal article
Closely coupled evolutionary history of ecto- and endosymbionts from two distantly-related animal phyla
Molecular Ecology, 25(13), 3203–3223.
2016 dataset
Differential proteomics of Lenisia limosa (Breviatea) and its epibiotic Arcobacter symbiont
http://www.ebi.ac.uk/pride/archive/projects/PXD003275
2016 journal article
Environmental Breviatea harbor mutualistic Arcobacter epibionts
Nature, 534(7606), 254–258.
2016 journal article
Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis
The ISME Journal, 11(2), 463–477.
2016 dataset
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
2016 dataset
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
2016 journal article
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.
Ed(s): C. Mullineaux
2016 journal article
Transcriptomic and proteomic insights into innate immunity and adaptations to a symbiotic lifestyle in the gutless marine worm Olavius algarvensis
BMC Genomics, 17(1).
2016 dataset
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
2015 journal article
Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels
ELife, 4, e07966.
2015 journal article
Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes
BMC Genomics, 16(7), 7.
2015 journal article
MiL-FISH: Multi-labelled oligonucleotides for fluorescence in situ hybridisation improve visualization of bacterial cells
Applied and Environmental Microbiology, 82(1), 62–70.
2015 journal article
Use of carbon monoxide and hydrogen by a bacteria-animal symbiosis from seagrass sediments
Environmental Microbiology, 17(12), 5023–5035.
2014 journal article
Identification and activity of acetate-assimilating bacteria in diffuse fluids venting from deep-sea hydrothermal systems
FEMS Microbiology Ecology, 90(3), 731–746.
2013 journal article
Metaproteomics Reveals Abundant Transposase Expression in Mutualistic Endosymbionts
Mbio, 4(3).
Contributors: , J. Young*, M. Shah *, N. VerBerkmoes* & N. Dubilier * *
2012 journal article
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.
2012 journal article
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.
2012 journal article
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.
Contributors: , C. Wentrup*, C. Lott *, H. Teeling *, S. Wetzel*, J. Young*, Y. Chang *, M. Shah * *
2011 journal article
Status quo in physiological proteomics of the uncultured Riftia pachyptila endosymbiont
Proteomics, 11(15), 3106–3117.
Contributors: S. Markert *, A. Gardebrecht*, H. Felbeck*, S. Sievert *, J. Klose*, D. Becher *, D. Albrecht *, A. Thurmer
2011 article
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.
Updated: September 24th, 2023 12:41
2017 - present
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