Manuel Kleiner
Metaproteomics, Microbiome, Symbiosis, Metagenomics, Microbial Physiology, Carbon Fixation Pathways
Works (103)
Updated: October 2nd, 2024 05:06
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).
author keywords: Mycorrhizae; Symbiosis; Non-mycorrhizal; Genetic engineering; Systems biology; Plant transcriptomics
TL;DR:
Interestingly, the effect of expressing IPD3 in Arabidopsis and knocking it out in Lotus was strongest in plants not exposed to AMF, which is revealed to be due to changes in IPD3 genotype causing a transcriptional state, which partially mimics AMF exposure in non-inoculated plants.
(via Semantic Scholar)
open access via link.springer.com (publisher PDF)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science; OpenAlex)
15. Life on Land
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 22, 2024
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).
Source: ORCID
Added: October 1, 2024
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).
Source: ORCID
Added: July 1, 2024
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.
author keywords: Root microbiome; Soil microbiome; Maize; Drought; Precipitation gradient
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: July 30, 2024
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.
author keywords: germination; gnotobiotic; microbiome; microbiota; plant-microbe interactions; root-associated microbiota; seed microbiome; seed sterilization; seedling contamination; SynCom; synthetic community
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: July 22, 2024
2024 journal article
Enterococcal quorum-controlled protease alters phage infection
FEMS MICROBES, 5.
author keywords: Enterococcus; bacteriophage; quorum sensing; protease; proteomics; phage-host interactions
Sources: Web Of Science, NC State University Libraries
Added: September 16, 2024
2024 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
author keywords: Synthetic communities; maize; root colonization; plant-microbe interactions; plant microbiome; SynCom
TL;DR:
Comparing the reproducibility, stability, and colonization ability of freshly prepared versus frozen SynCom inocula shows that ready-to-use SynCom stocks provide comparable results to those of freshly constructed SynCom and thus allow for significant time savings when working with SynComs.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: December 13, 2023
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).
Source: ORCID
Added: August 1, 2024
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).
author keywords: symbiosis; chemosynthesis; lucinid; deep sea; nitrogen fixation; ONT sequencing; omics
UN Sustainable Development Goal Categories
14. Life Below Water
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: June 24, 2024
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).
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: April 8, 2024
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).
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Source: ORCID
Added: April 15, 2024
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
Sources: ORCID, Web Of Science, NC State University Libraries
Added: July 1, 2024
2023 journal article
De novo phytosterol synthesis in animals
SCIENCE, 380(6644), 520–526.
MeSH headings : Animals; Cholesterol / metabolism; Phylogeny; Plants / metabolism; Sitosterols / metabolism; Annelida / metabolism
TL;DR:
It is demonstrated that the marine annelids Olavius and Inanidrilus synthesize the phytosterol sitosterol de novo, indicating that the evolution of sterols in animals is more complex than previously assumed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
14. Life Below Water
(OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: May 5, 2023
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).
Source: ORCID
Added: December 16, 2023
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).
Source: ORCID
Added: April 18, 2023
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).
Source: ORCID
Added: May 11, 2023
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).
TL;DR:
Large quantities of microbial DNA and protein are found in casein-based diets, which highlight the necessity of evaluating diet samples in diet-microbiota studies to ensure that potential microbial content of the diet can be accounted for in microbiome measurements.
(via Semantic Scholar)
Source: ORCID
Added: December 8, 2023
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).
TL;DR:
This study combined single-cell analyses of CO2 fixation, CO2 release and bulk uptake, with measurements of O2 respiration, sulfur content, and polyhydroxyalkanoate content, as well as mathematical modelling to investigate how energy derived from sulfur oxidation drives carbon fluxes within the symbiosis and between the holobiont and its habitat found that under aerobic conditions without external energy sources only the primary symbiont relied on internal sulfur storage.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Source: ORCID
Added: November 27, 2023
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).
TL;DR:
This work curated metagenome-assembled genomes of Idas modiolaeformis symbionts and used genomecentered metatranscriptomics and metaproteomics to assess key symbiont functions, indicating that these flexible associations allow for expanding the range of substrates and environmental niches, via new metabolic functions and handoffs.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: February 11, 2023
2023 journal article
Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels
ISME COMMUNICATIONS, 3(1).
UN Sustainable Development Goal Categories
14. Life Below Water
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: September 5, 2023
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).
TL;DR:
Despite the long interval since loss of AM and IPD3 in Arabidopsis, molecular connections to symbiosis machinery remain in place in this nonAM species, with implications for both basic science and the prospect of engineering this trait for agriculture.
(via Semantic Scholar)
Source: ORCID
Added: March 8, 2023
2023 journal article
Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes
MICROBIOME, 11(1).
MeSH headings : Humans; Carbon Isotopes / analysis; Carbon Isotopes / metabolism; Chromatography, Liquid; Tandem Mass Spectrometry / methods; Microbiota; DNA Probes
TL;DR:
An ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by 50–99% as compared to other SIP and Protein-Sip approaches and thus enables isotope labeling experiments on much larger scales and with higher replication.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: March 13, 2023
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
author keywords: Metaproteome; Metagenomics; Microbiome; Microbial community; Multi-omics; Microbiota; Microbial ecology
TL;DR:
An overview of existing strategies for database construction and the relevant studies that have sought to test and validate these strategies is provided, and a decision tree and best practices for choosing and implementing database construction strategies are provided.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: April 25, 2022
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.
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: May 19, 2022
2022 review
Dietary protein and the intestinal microbiota: An understudied relationship
[Review of ]. ISCIENCE, 25(11).
TL;DR:
This review focuses on recent studies investigating the impact of dietary protein quantity and source on the intestinal microbiota and resulting host health consequences and highlights major open questions critical to understanding health outcomes mediated by interactions between dietary protein and the microbiota.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: December 5, 2022
2022 journal article
Elucidating Plant-Microbe-Environment Interactions Through Omics-Enabled Metabolic Modelling Using Synthetic Communities
FRONTIERS IN PLANT SCIENCE, 13.
author keywords: synthetic communities; plant microbiome; plant microbial interactions; metabolic modelling; flux balance analysis; elementary flux mode analysis
TL;DR:
The utility of metabolic models as applied to a community setting is highlighted, different applications for both flux balance and elementary flux mode simulation approaches are identified, and the importance of ecological theory in guiding data interpretation is emphasized.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: December 5, 2022
2022 journal article
Evaluation of Protein Extraction Methods for Metaproteomic Analyses of Root-Associated Microbes
MOLECULAR PLANT-MICROBE INTERACTIONS, 35(11), 977–988.
author keywords: endosphere; metaproteomics; microbiome; microbiota; phytobiome; plant-microbe interactions; rhizoplane
MeSH headings : Arabidopsis; Microbiota; Chromatography, Liquid; Proteome; Mass Spectrometry; Plants
TL;DR:
This work optimized and evaluated different protein extraction methods for metaproteomics of plant-associated microbiota in two different plant species (Arabidopsis and maize) and found that the optimal extraction method differed between the two species.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: November 1, 2022
2022 journal article
Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium
MICROBIOME, 10(1).
author keywords: Microbiome; Animal-bacterial symbiosis; Symbiont transmission; Phylosymbiosis; Intraspecific genetic variation
MeSH headings : Animals; Bacteria / genetics; Microbial Consortia; Phylogeny; Sulfates; Sulfur; Symbiosis; Annelida / microbiology
TL;DR:
Fidelity was highest for the two chemoautotrophic, sulphur-oxidizing symbionts that dominated the microbial consortium of all O. algarvensis individuals and was only intermediate to absent in the sulphate-reducing and spirochaetal Symbionts with lower abundance, suggesting differences in fidelity are likely driven by both selective and stochastic forces.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
14. Life Below Water
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: November 7, 2022
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).
author keywords: type VI secretion systems; Aliivibrio fischeri; microbial interactions; genomic island; symbiosis
MeSH headings : Aliivibrio fischeri / genetics; Aliivibrio fischeri / metabolism; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Gene Expression Regulation, Bacterial / physiology; Genotype; Mutation; Promoter Regions, Genetic; Type VI Secretion Systems / genetics; Type VI Secretion Systems / metabolism
TL;DR:
A model whereby T6SS expression requires conserved structural proteins, in addition to the essential regulator TasR, and this ability to self-regulate may be a strategy to activate T 6SS expression upon transfer of T6 SS-encoding elements into a new bacterial host is proposed.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
14. Life Below Water
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: November 1, 2021
2021 journal article
Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis
ELIFE, 10.
MeSH headings : Animals; Bacteria / isolation & purification; Bacterial Physiological Phenomena; Hydrothermal Vents / microbiology; Polychaeta / microbiology; Symbiosis
TL;DR:
Metaproteomic analysis, microscopy, and flow cytometry strongly suggest that Riftia symbiont cells of different sizes represent metabolically dissimilar stages of a physiological differentiation process; it is proposed that this division of labor between smaller and larger symbionts benefits the productivity of the symbiosis as a whole.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(Web of Science; OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: January 18, 2021
2021 journal article
Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows
NATURE COMMUNICATIONS, 12(1).
MeSH headings : Adult; Bacteria / classification; Bacteria / genetics; Bacteria / isolation & purification; Bacterial Proteins / chemistry; Bacterial Proteins / genetics; Feces / microbiology; Female; Gastrointestinal Microbiome; Humans; Intestines / microbiology; Laboratories; Mass Spectrometry; Peptides / chemistry; Proteomics / methods; Workflow
TL;DR:
A community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of meetaproteome investigation study (CAMPI), which provides insights into the robustness of current methods, suggests further improvements to the field, and may pave the way for future community- driven metaproteinomics projects.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: January 3, 2022
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
author keywords: mass spectrometry; 1D-LC-MS/MS; microbial communities; preservation methods; microbiome; field sampling; environmental microbiology
MeSH headings : Animals; Annelida / microbiology; Annelida / physiology; Bacteria / classification; Bacteria / genetics; Bacteria / isolation & purification; Bacterial Physiological Phenomena; Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Phylogeny; Preservation, Biological / methods; Proteomics; Symbiosis
TL;DR:
This study shows that RNAlater can serve as a low-hazard, easy-to-transport alternative to flash freezing for field preservation of samples for metaproteomic analyses, and recommendsRNAlater for protein preservation of field-collected samples targeted for meetaproteomics analyses.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(Web of Science; OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: October 28, 2021
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.
TL;DR:
RNAlater™ can serve as a low hazard, easy to transport alternative to flash freezing for field preservation of samples for metaproteomics and is recommended for protein preservation of field-collected samples when targeted for metAProteomcis.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: August 9, 2021
2021 journal article
Evaluation of Sample Preservation and Storage Methods for Metaproteomics Analysis of Intestinal Microbiomes
MICROBIOLOGY SPECTRUM, 9(3).
Ed(s): C. Khursigara
author keywords: gut microbes; intestinal microbiome; LC-MS/MS; metaproteomics; microbiota; sample preservation; storage
MeSH headings : Animals; Bacteria / chemistry; Bacteria / genetics; Bacteria / isolation & purification; Bacterial Proteins / chemistry; Chromatography, Liquid; Feces / chemistry; Feces / microbiology; Female; Gastrointestinal Microbiome; Male; Mice; Mice, Inbred C57BL; Peptides / chemistry; Preservation, Biological / methods; Proteomics / methods; Tandem Mass Spectrometry
TL;DR:
This study evaluated methods to preserve fecal microbiome samples for metaproteomics analyses when flash-freezing is not possible and suggests that preservation at room temperature in RNAlater or an RN alater-like solution performs as well as freezing for the preservation of intestinal microbiome samples before metaproteinomics analyses.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: December 16, 2021
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).
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: August 9, 2021
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
MeSH headings : Bacteria / classification; Bacteria / isolation & purification; Bacteria / metabolism; Computational Biology; Host Microbial Interactions; Humans; Microbiota; Proteome / analysis; Proteome / metabolism; Proteomics / methods
TL;DR:
The objective in this Pearl is to highlight what the authors feel are 5 essential elements to be considered for a metaproteomics research campaign and to introduce nonexpert readers to the topic without going into too much technical detail.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: February 26, 2021
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).
TL;DR:
It is hypothesized that in gutless oligochaetes, selection within host species for locally adapted and temporally stable symbiont communities leads to varying levels of Symbiont fidelity and shuffles the composition of symbionts assemblages across geographic and evolutionary scales.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: August 9, 2021
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.
author keywords: chemosymbiosis; host-microbe associations; nutritional interactions; adaptations to symbiosis; metabolism; thiotroph; methanotroph
MeSH headings : Animals; Bacteria / genetics; Bacteria / metabolism; Ecosystem; Hydrothermal Vents; Phylogeny; Symbiosis / physiology
TL;DR:
A review of the phylogenetic and metabolic diversity of these symbioses and selected research directions that could advance the understanding of the processes that shaped the evolutionary and ecological success of these associations are highlighted.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: November 15, 2021
2021 journal article
Microbe-dependent heterosis in maize
Proceedings of the National Academy of Sciences, 118(30).
author keywords: hybrid vigor; microbiome; maize; endophytes; rhizosphere
MeSH headings : Bacteria / metabolism; Fungi / physiology; Hybrid Vigor; Seedlings / growth & development; Seedlings / microbiology; Soil Microbiology; Zea mays / growth & development; Zea mays / microbiology
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries, ORCID, Crossref
Added: July 21, 2021
2021 journal article
Proteome and strain analysis of cyanobacterium Candidatus "Phormidium alkaliphilum" reveals traits for success in biotechnology
ISCIENCE, 24(12).
TL;DR:
Diverse photosystem antennae proteins, and high-affinity terminal oxidase, compared with other soda lake cyanobacteria, appear to contribute to the success of Ca.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: November 7, 2021
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.
TL;DR:
This work presents an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by ∼90% as compared to other SIP and Protein-Sip approaches and thus enables isotope labeling experiments on much larger scales and with higher replication.
(via Semantic Scholar)
Source: ORCID
Added: August 9, 2021
2020 journal article
Environmental Viscosity Modulates Interbacterial Killing during Habitat Transition
MBIO, 11(1).
author keywords: Aliivibrio fischeri; aggregation; competition; proteomics; type VI secretion
MeSH headings : Aliivibrio fischeri / genetics; Aliivibrio fischeri / physiology; Animals; Decapodiformes / microbiology; Ecosystem; Gene Expression Regulation, Bacterial; Genotype; Proteomics; Seawater; Symbiosis; Type VI Secretion Systems / genetics; Type VI Secretion Systems / metabolism; Viscosity
TL;DR:
How environmental viscosity impacts T6SS-mediated competition by using a liquid hydrogel medium that mimics the viscous host environment is investigated and shows that competitor cells form aggregates under host-like conditions, thereby facilitating the contact required for killing, and reveals how V. fischeri regulates a key competitive mechanism in response to the physical environment.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: April 6, 2020
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).
TL;DR:
High-quality metagenome-assembled genome sequences from the gutless marine worm Olavius algarvensis (Annelida) are presented, including an improved draft genome sequence of the previously described sulfate-reducing symbiont Delta1.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: May 8, 2020
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).
Sources: Web Of Science, NC State University Libraries
Added: October 5, 2020
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
TL;DR:
Two high-quality, draft metagenome-assembled genomes of deltaproteobacterial OalgDelta3 endosymbionts from the gutless marine worm Olavius algarvensis are presented.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: June 14, 2021
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).
TL;DR:
Metaproteomic analysis and statistical evaluation strongly suggest that Riftia symbiont cells of different sizes represent metabolically dissimilar stages of a physiological differentiation process, and proposes that this division of labor between smaller and larger symbionts benefits the productivity of the symbiosis as a whole.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: August 9, 2021
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.
TL;DR:
It is shown that heterosis of root biomass and other traits in maize is strongly dependent on the belowground microbial environment, an ecological phenomenon whereby soil microbes differentially impact the early growth of inbred and hybrid maize.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: May 8, 2020
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).
TL;DR:
The transductomics approach allows for the detection and characterization of genes that are potentially transferred between microbes in complex microbial communities at the time of measurement and thus provides insights into real-time ongoing horizontal gene transfer.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: August 9, 2021
2020 journal article
Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities
MICROBIOME, 8(1).
MeSH headings : Animals; DNA, Bacterial / analysis; DNA, Bacterial / genetics; Gastrointestinal Microbiome / genetics; Gene Transfer, Horizontal / genetics; Genomics; Male; Mice; Mice, Inbred C57BL; Microbiota / genetics; Reproducibility of Results; Transduction, Genetic
TL;DR:
A DNA sequencing-based “transductomics” approach that detects and characterizes microbial DNA transferred via transduction and provides insights into real-time ongoing horizontal gene transfer is developed and could be used to understand how phenotypes spread within microbiomes.
(via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: December 21, 2020
2019 journal article
A shared core microbiome in soda lakes separated by large distances
NATURE COMMUNICATIONS, 10.
TL;DR:
The authors report amplicon, metagenome, and proteome sequencing from microbial mat communities of four alkaline lakes in Canada, and compare these lakes to central Asian soda lakes, revealing a shared core microbiome despite the geographical distance.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: October 7, 2019
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.
author keywords: endosymbiont; chemoautotrophic; ecophysiology; energy storage; host nutrition
MeSH headings : Animals; Chemoautotrophic Growth / genetics; Chemoautotrophic Growth / physiology; Genome, Bacterial / genetics; Metabolic Networks and Pathways; Platyhelminths / metabolism; Platyhelminths / microbiology; Platyhelminths / physiology; Rhodospirillaceae / genetics; Rhodospirillaceae / physiology; Symbiosis / genetics; Symbiosis / physiology
TL;DR:
Study of a species of Paracatenula from Sant’Andrea, Elba, Italy, using genomics, gene expression, imaging analyses, as well as targeted and untargeted MS, shows that its symbiont, Ca.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: May 6, 2019
2019 journal article
Comparative proteomics of related symbiotic mussel species reveals high variability of host–symbiont interactions
The ISME Journal.
MeSH headings : Amino Acids / genetics; Amino Acids / metabolism; Animals; Bacteria / genetics; Bacteria / metabolism; Carbonic Anhydrases / metabolism; Chemoautotrophic Growth; Genome, Bacterial / genetics; Gills / metabolism; Host Microbial Interactions; Mytilidae / metabolism; Mytilidae / microbiology; Proteomics; Symbiosis / genetics; Symbiosis / physiology
TL;DR:
Common strategies of metabolic support between hosts and symbionts, such as the oxidation of sulfide by the host, which provides a thiosulfate reservoir for the thiotrophic symbionte, and a cycling mechanism that could supply the host with symbiont-derived amino acids are identified.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(Web of Science; OpenAlex)
Source: ORCID
Added: January 30, 2020
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
author keywords: carbon dioxide assimilation; carbon metabolism; electron transport; lithoautotrophic metabolism; symbiosis
MeSH headings : Animals; Bacterial Proteins / metabolism; Carbon Cycle; Carbon Dioxide / metabolism; Chromatiaceae / physiology; Citric Acid Cycle; DNA, Bacterial; Photosynthesis; Phylogeny; Polychaeta / microbiology; Symbiosis
TL;DR:
Comparative genomics shows that Thioflavicoccus mobilis, a cultured, free-living gammaproteobacterial sulfur oxidizer, possesses the genes for both carbon fixation pathways, and genomic and transcriptomic data suggest a potential electron flow toward the rTCA cycle carboxylase 2-oxoglutarate:ferredoxin oxidoreductase, via a rare variant of NADH dehydrogenase/heterodisulfide reductase in the E.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: February 7, 2019
2019 journal article
Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria)
ISME JOURNAL, 14(1), 104–122.
MeSH headings : Animals; Bivalvia / microbiology; Carbon Cycle; Citric Acid Cycle; Epsilonproteobacteria / classification; Epsilonproteobacteria / genetics; Epsilonproteobacteria / metabolism; Gammaproteobacteria / genetics; Photosynthesis; Phylogeny; Symbiosis
TL;DR:
This work discovered campylobacterotal epibionts (“Candidatus Thiobarba”) of deep-sea mussels that have acquired a complete CBB cycle and may have lost most key genes of the rTCA cycle, calling into question current assumptions about the distribution of carbon fixation pathways in microbial lineages, and the interpretation of stable isotope measurements in the environment.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
15. Life on Land
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: January 6, 2020
2019 journal article
Host-Microbe Interactions in the Chemosynthetic Riftia pachyptila Symbiosis.
MBio, 10(6).
Ed(s): D. Distel & E. Ruby
author keywords: host-microbe interactions; symbiosis; holobiont; chemosynthesis; hydrothermal vents; metaproteomics
MeSH headings : Adaptation, Biological; Animal Nutritional Physiological Phenomena; Animals; Aquatic Organisms; Energy Metabolism; Metabolic Networks and Pathways; Metabolome; Microbiota; Oxidation-Reduction; Polychaeta / metabolism; Polychaeta / microbiology; Polychaeta / ultrastructure; Proteome; Proteomics / methods; Seawater; Symbiosis
TL;DR:
This study studied the deep-sea Riftia pachyptila symbiosis, a model association in which the tubeworm host is associated with only one phylotype of endosymbiotic bacteria and completely depends on this sulfur-oxidizing symbiont for nutrition, and identified both metabolic interaction processes and interactions that serve to maintain the symbiotic balance.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(Web of Science; OpenAlex)
Source: ORCID
Added: January 30, 2020
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.
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: August 9, 2021
2019 journal article
Metaproteomics: Much More than Measuring Gene Expression in Microbial Communities
MSYSTEMS, 4(3).
author keywords: LC-MS; metagenomics; metaproteomics; metatranscriptomics; microbiome; microbiota; proteomics; symbiosis
TL;DR:
A brief overview of the questions that can be addressed, as well as new metaproteomics-based approaches that are developing to address even more questions in the study of microbial communities and plant and animal microbiota are provided.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: September 9, 2019
2019 journal article
More Is Not Always Better: Evaluation of 1D and 2D-LC-MS/MS Methods for Metaproteomics
FRONTIERS IN MICROBIOLOGY, 10.
author keywords: microbiota; microbiome; mock community; method evaluation; microbial ecology; Q Exactive; liquid chromatography; GeLC
TL;DR:
It is shown here that, while 1D-LC approaches are faster and easier to set up and lead to more identifications per minute of runtime, 2D- LC approaches allow for a higher overall number of identifications with up to >10,000 protein groups identified.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: March 4, 2019
2019 journal article
Sulfur-Oxidizing Symbionts without Canonical Genes for Autotrophic CO2 Fixation
MBIO, 10(3).
Ed(s): S. Giovannoni
author keywords: gammaproteobacteria; chemosynthesis; ectosymbiont; lithoheterotrophy; meiofauna; protist
MeSH headings : Aquatic Organisms / microbiology; Autotrophic Processes; Bacteria / genetics; Bacteria / metabolism; Carbon Cycle / genetics; Carbon Dioxide / metabolism; Ciliophora / microbiology; Gene Expression Profiling; Genomics; Italy; Oxidation-Reduction; RNA, Ribosomal, 16S / genetics; Sulfur / metabolism; Symbiosis
TL;DR:
It is shown that Kentron bacteria are the only thiotrophic symbionts that appear to be entirely heterotrophic, unlike all other thiotroph symbiont studied to date, which possess either the Calvin-Benson-Bassham or the reverse tricarboxylic acid cycle for autotrophy.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: July 22, 2019
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.
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: August 9, 2021
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.
TL;DR:
This study shows that even the simplest animals known have evolved highly specific and intimate associations with symbiotic, intracellular bacteria, and highlights that symbioses with microorganisms are a basal trait of animal life.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: August 9, 2021
2019 journal article
Two intracellular and cell type-specific bacterial symbionts in the placozoan Trichoplax H2
NATURE MICROBIOLOGY, 4(9), 1465–1474.
MeSH headings : Animals; Bacteria / classification; Bacteria / genetics; Bacteria / metabolism; Biosynthetic Pathways; Endoplasmic Reticulum, Rough / microbiology; Genome, Bacterial / genetics; Microbiota / genetics; Phylogeny; Placozoa / cytology; Placozoa / microbiology; Species Specificity; Symbiosis; Vacuoles / microbiology; Water Microbiology
TL;DR:
This study shows that one of the simplest animals has evolved highly specific and intimate associations with symbiotic, intracellular bacteria and highlights that symbioses can provide access to otherwise elusive microbial dark matter.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
14. Life Below Water
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: September 9, 2019
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.
TL;DR:
The direct Protein-SIF method that is developed allows linking microbial species in communities to the environmental carbon sources they consume by determining their stable carbon isotope signature and allows assessing which carbon fixation pathway is used by autotrophic microorganisms that directly assimilate CO2.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: August 9, 2021
2018 journal article
Author Correction: Chemosynthetic symbionts of marine invertebrate animals are capable of nitrogen fixation
Nature Microbiology, 3(8), 961–961.
TL;DR:
In this Article, the completeness and number of contigs for draft genomes from two individuals of Laxus oneistus are incorrect in the main text, although the correct information is included in Table 1.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Sources: Crossref, NC State University Libraries
Added: January 25, 2020
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
author keywords: Bacteria-invertebrate symbiosis; Metaproteome; Differential pelleting; Rate-zonal density gradient centrifugation; Isopycnic density gradient centrifugation; Percoll (R); HistoDenz (TM)
MeSH headings : Animals; Bacteria / metabolism; Centrifugation / methods; Centrifugation, Density Gradient; Invertebrates / microbiology; Proteome; Proteomics / methods; Symbiosis
UN Sustainable Development Goal Categories
14. Life Below Water
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: February 7, 2019
2018 journal article
Comparative Proteomics of Three Species of Ammonia-Oxidizing Bacteria.
Frontiers in Microbiology.
author keywords: nitrification; Nitrosomonas europaea; Nitrosomonas ureae; Nitrosospira multiformis; Calvin-Benson-Bassham cycle; Q Exactive Plus; proteomics; ammonia-oxidizing bacteria (AOB)
TL;DR:
The first published proteomes of N. ureae and N. multiformis are presented, and the first comparative proteomics study of ammonia-oxidizing bacteria is presented, which gives new insights into consistent metabolic features and differences between members of this environmentally and industrially important group.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation
(Web of Science)
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: February 3, 2019
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.
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: August 9, 2021
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.
author keywords: Protein-SIP; metaproteome; microbial ecology; microbiome; Q Exactive
MeSH headings : Animals; Carbon / metabolism; Carbon Isotopes / metabolism; Environmental Microbiology; Isotope Labeling / methods; Metabolic Networks and Pathways / physiology; Microbiota / physiology; Proteome / metabolism; Proteomics / methods; Software; Symbiosis / physiology
TL;DR:
The direct protein stable isotope fingerprint (SIF) method developed allows linking microbial species in communities to the environmental carbon sources they consume by determining their stable carbon isotope signature and confirms previous physiological hypotheses and can provide unexpected insights into the symbionts’ metabolism.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(Web of Science; OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2018 journal article
Murine colitis reveals a disease-associated bacteriophage community
NATURE MICROBIOLOGY, 3(9), 1023–1031.
MeSH headings : Animals; Bacteriophages / genetics; Bacteriophages / isolation & purification; Cells, Cultured; Colitis / pathology; Colitis / virology; Disease Models, Animal; Dysbiosis / virology; Gastrointestinal Microbiome / physiology; Genome, Viral / genetics; Humans; Intestinal Mucosa / virology; Male; Mice; Mice, Inbred C57BL; Mice, Knockout
TL;DR:
It is discovered that during colitis the intestinal phage population is altered and transitions from an ordered state to a stochastic dysbiosis, providing a tool for interrogating phage dynamics in IBD.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: October 19, 2018
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.
author keywords: souring control; biocide; sulfate reduction; hydrogen sulfide; sodium nitroprusside
TL;DR:
Interestingly, nitrate and SNP were found to be highly synergistic with 0.003 mM (1 ppm) of SNP and 1 mM of sodium nitrate being sufficient in inhibiting souring, and using SNP as an additive may greatly increase the efficacy of nitrate injection in oil reservoirs.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
6. Clean Water and Sanitation
(OpenAlex)
15. Life on Land
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2017 journal article
Assessing species biomass contributions in microbial communities via metaproteomics
NATURE COMMUNICATIONS, 8.
MeSH headings : Archaea / classification; Archaea / genetics; Archaea / metabolism; Bacteria / classification; Bacteria / genetics; Bacteria / metabolism; Bacteriophages / classification; Bacteriophages / genetics; Bacteriophages / metabolism; Biomass; Genomics / methods; Humans; Lakes / microbiology; Microbiota / genetics; Microbiota / physiology; Proteome / metabolism; Proteomics / methods; RNA, Ribosomal, 16S / genetics; Saliva / microbiology
TL;DR:
The method is applied to communities from two different environments, microbial mats from two alkaline soda lakes, and saliva from multiple individuals and it is shown that assessment of species biomass contributions adds an important dimension to the analysis of microbial community structure.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
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.
Source: ORCID
Added: February 3, 2019
2017 journal article
Fast and Simple Analysis of MiSeq Amplicon Sequencing Data with MetaAmp
Frontiers in Microbiology, 8.
author keywords: metagenomics; amplicon sequencing; bioinformatics; microbial ecology; microbiome
TL;DR:
The MetaAmp pipeline for processing of SSU rRNA gene and other non-coding or protein-c coding amplicon sequencing data by investigators that are inexperienced with bioinformatics procedures is presented.
(via Semantic Scholar)
Source: ORCID
Added: February 3, 2019
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.
Source: ORCID
Added: February 3, 2019
2017 journal article
Genome sequence of the sulfur-oxidizing Bathymodiolus thermophilus gill endosymbiont.
Standards in Genomic Sciences.
author keywords: Uncultured endosymbiont; Hydrothermal vents; Marine invertebrate symbiosis; Thiotrophy; Autotrophy
TL;DR:
The first draft genome sequence of the sulfur-oxidizing symbiont of B. thermophilus is reported, which revealed pathways for the use of sulfide and thiosulfate as energy sources and encodes the Calvin-Benson-Bassham cycle for CO2 fixation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: February 3, 2019
2017 dataset
Metaproteomics of phototrophic biomats from two soda lakes in the Canadian Rocky Mountains
http://www.ebi.ac.uk/pride/archive/projects/PXD006343
Source: ORCID
Added: February 3, 2019
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.
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Sources: NC State University Libraries, NC State University Libraries, ORCID
Added: February 7, 2019
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.
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: August 9, 2021
2017 dataset
Quantification of mock microbial communities with metagenomes, 16S rRNA gene amplicons and metaproteomics
http://www.ebi.ac.uk/pride/archive/projects/PXD006118
Source: ORCID
Added: February 3, 2019
2017 dataset
Re-analysis of an ultra-deep and quantitative saliva proteome
http://www.ebi.ac.uk/pride/archive/projects/PXD006366
Source: ORCID
Added: February 3, 2019
2017 journal article
Short-chain alkanes fuel mussels and sponge Cycloclasticus symbionts from deep-sea gas and oil seeps
Nature Microbiology, 2, 17093.
MeSH headings : Alkanes / metabolism; Animals; Bivalvia / microbiology; Carbon / metabolism; Energy Metabolism; Gene Expression Profiling; Genomics; Gulf of Mexico; Piscirickettsiaceae / genetics; Piscirickettsiaceae / metabolism; Piscirickettsiaceae / physiology; Porifera / microbiology; Symbiosis
TL;DR:
The results indicate that the metabolic versatility of bacteria within the Cycloclasticus clade is higher than previously assumed, and highlight the expanded role of these keystone species in the degradation of marine hydrocarbons.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 3, 2019
2016 dataset
Bathymodiolus azoricus host-symbiont proteomics
http://www.ebi.ac.uk/pride/archive/projects/PXD004061
Source: ORCID
Added: February 3, 2019
2016 journal article
Chemosynthetic sulphur-oxidizing symbionts of marine invertebrate animals are capable of nitrogen fixation
Nature Microbiology, 2, 16195.
MeSH headings : Animals; Aquatic Organisms / microbiology; Bacteria / enzymology; Bacteria / genetics; Bivalvia / microbiology; Chromadorea / microbiology; Gene Expression Profiling; Nitrogen Fixation; Nitrogenase / genetics; Proteome / analysis; Sequence Analysis, DNA; Symbiosis
TL;DR:
The genomes of the chemosynthetic symbionts from the lucinid bivalve Loripes lucinalis and the stilbonematid nematode Laxus oneistus are sequenced and nitrogen fixation genes of both host species are encoded.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 3, 2019
2016 journal article
Closely coupled evolutionary history of ecto- and endosymbionts from two distantly-related animal phyla
Molecular Ecology, 25(13), 3203–3223.
author keywords: cospeciation; gutless oligochaetes; nematodes; Phallodrilinae; Stilbonematinae; Thiosymbion
MeSH headings : Animals; Annelida / microbiology; Biological Evolution; DNA, Bacterial / genetics; Gammaproteobacteria / genetics; Genetic Markers; Nematoda / microbiology; Oceans and Seas; Phylogeny; RNA, Ribosomal, 16S / genetics; Sequence Analysis, DNA; Symbiosis
TL;DR:
This closely coupled evolutionary history of marine symbioses in a group of closely related sulphur‐oxidizing bacteria suggests that switches between symbiotic lifestyles and between the two host phyla occurred multiple times during the evolution of the Cand.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 3, 2019
2016 dataset
Differential proteomics of Lenisia limosa (Breviatea) and its epibiotic Arcobacter symbiont
http://www.ebi.ac.uk/pride/archive/projects/PXD003275
Source: ORCID
Added: February 3, 2019
2016 journal article
Environmental Breviatea harbor mutualistic Arcobacter epibionts
Nature, 534(7606), 254–258.
MeSH headings : Arcobacter / genetics; Arcobacter / physiology; Eukaryota / enzymology; Eukaryota / genetics; Eukaryota / physiology; Genetic Fitness; Hydrogen / metabolism; Hydrogenase / genetics; Hydrogenase / metabolism; NADP / metabolism; Proteomics; Symbiosis / genetics; Transcriptome; Virulence / genetics; Virulence Factors / genetics; Virulence Factors / metabolism
TL;DR:
The cultivation of Lenisia limosa, a newly discovered breviate protist, symbiotically colonized by relatives of the animal-associated bacterium Arcobacter, supports the notion that molecular mechanisms involved in virulence can also support mutualism.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 3, 2019
2016 journal article
Metabolic and physiological interdependencies in the Bathymodiolus azoricus symbiosis
The ISME Journal, 11(2), 463–477.
MeSH headings : Animals; Biosynthetic Pathways; Gammaproteobacteria / physiology; Gills / microbiology; Hydrothermal Vents; Methane / metabolism; Mytilidae / genetics; Mytilidae / microbiology; Oxidation-Reduction; Proteome; Species Specificity; Sulfur / metabolism; Symbiosis
TL;DR:
This study used a combination of proteomics and genomics to investigate the physiology and metabolism of the individual symbiotic partners of the hydrothermal vent mussel B. azoricus and its symbionts and identified numerous ‘symbiosis-specific’ host proteins that are likely involved in symbiont digestion and carbon transfer from the symbionte to the host.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: February 3, 2019
2016 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.
MeSH headings : Bacteria / cytology; Bacteria / genetics; Flow Cytometry; In Situ Hybridization, Fluorescence / methods; Oligonucleotide Probes / chemistry; Oligonucleotide Probes / genetics; Staining and Labeling
TL;DR:
It is shown here that MiL-FISH is a multifaceted alternative to standard monolabeled FISH that can be used for a wide range of biological and medical applications.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 3, 2019
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
Source: ORCID
Added: February 3, 2019
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
Source: ORCID
Added: February 3, 2019
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
MeSH headings : Bacterial Proteins / genetics; Bacterial Proteins / metabolism; Biological Evolution; Gene Expression Regulation, Bacterial; Gene Expression Regulation, Developmental; Histidine Kinase / genetics; Histidine Kinase / metabolism; Mutation; Myxococcus xanthus / genetics; Myxococcus xanthus / growth & development; Myxococcus xanthus / metabolism; RNA, Bacterial / genetics; RNA, Bacterial / metabolism
TL;DR:
A two-component system operon (encoding a histidine kinase and a σ54 response regulator) associated with the production and processing of Pxr sRNA is revealed that represents an evolutionary integration of two- component signaling and sRNA gene regulation to control a bacterial social trait.
(via Semantic Scholar)
Source: ORCID
Added: February 3, 2019
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).
author keywords: RNA-Seq; Annelida; Oligochaeta; Phallodrilinae; PGRP; FREP; SRCR; Respiratory pigment; Carbon monoxide; Immunology; Chemosynthetic symbiosis
MeSH headings : Adaptation, Biological / genetics; Adaptation, Biological / immunology; Amino Acid Sequence; Animals; Biomarkers; Computational Biology / methods; Gene Expression Profiling / methods; High-Throughput Nucleotide Sequencing; Immunity, Innate / genetics; Microbiota; Models, Biological; Oligochaeta / genetics; Oligochaeta / immunology; Oligochaeta / metabolism; Proteome; Proteomics / methods; Receptors, Pattern Recognition / metabolism; Symbiosis / genetics; Symbiosis / immunology; Transcriptome
TL;DR:
It is shown how this worm, over the course of evolutionary time, has modified widely-used proteins and changed their expression patterns in adaptation to its symbiotic lifestyle and described expressed components of the innate immune system in a marine oligochaete.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: February 3, 2019
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
Source: ORCID
Added: February 3, 2019
2015 journal article
Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels
ELife, 4, e07966.
MeSH headings : Animals; Aquatic Organisms / microbiology; Bacteria / genetics; Bacteria / growth & development; Bacterial Toxins / biosynthesis; Bacterial Toxins / genetics; Bivalvia / microbiology; DNA, Bacterial / chemistry; DNA, Bacterial / genetics; Gene Expression Profiling; Genome, Bacterial; Hydrothermal Vents; Molecular Sequence Data; Proteome / analysis; Seawater; Sequence Analysis, DNA; Symbiosis
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 3, 2019
2015 journal article
Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes
BMC Genomics, 16(7), 7.
author keywords: Virus metagenomics; Viral metagenomes; Virus-like particles; Microbiome; Bacteriophage; CsCl density gradient
MeSH headings : Animals; Bacteriophages / genetics; Bacteriophages / isolation & purification; Contig Mapping; DNA, Viral / analysis; DNA, Viral / isolation & purification; Feces / virology; Genetic Techniques / standards; Intestines / virology; Metagenome; Metagenomics / methods; Mice; Mice, Inbred C57BL; Reproducibility of Results; Sequence Analysis, DNA
TL;DR:
The CsCl density gradient centrifugation method, which is frequently used for VLP purification, was most efficient in removing host derived DNA, but also showed strong discrimination against specific phages and showed a lower reproducibility of quantitative results.
(via Semantic Scholar)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 3, 2019
2015 journal article
Use of carbon monoxide and hydrogen by a bacteria-animal symbiosis from seagrass sediments
Environmental Microbiology, 17(12), 5023–5035.
MeSH headings : Animals; Bacteria / metabolism; Carbon Dioxide / metabolism; Carbon Monoxide / metabolism; Energy Metabolism; Geologic Sediments / microbiology; Hydrogen / metabolism; Mediterranean Region; Oligochaeta / microbiology; Oxidation-Reduction; Seawater / microbiology; Spectrometry, Mass, Secondary Ion; Sulfur Compounds / metabolism; Symbiosis
TL;DR:
Direct evidence is provided that the O .
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 3, 2019
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.
author keywords: Epsilonproteobacteria; Gammaproteobacteria; heterotrophy; 16S rRNA gene; nanoSIMS; stable isotopes
MeSH headings : Acetates / metabolism; Aquatic Organisms / genetics; Base Sequence; Epsilonproteobacteria / classification; Epsilonproteobacteria / genetics; Epsilonproteobacteria / metabolism; Gammaproteobacteria / classification; Gammaproteobacteria / genetics; Gammaproteobacteria / metabolism; Heterotrophic Processes; Hydrothermal Vents / microbiology; In Situ Hybridization, Fluorescence; Microbial Consortia / genetics; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S / genetics; Seawater / microbiology; Sequence Analysis, DNA
TL;DR:
The rapid growth of microorganisms upon acetate addition suggests that acetate consumers in diffuse fluids are copiotrophic opportunists, which quickly exploit their energy sources, whenever available under the spatially and temporally highly fluctuating conditions.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 3, 2019
2013 journal article
Metaproteomics Reveals Abundant Transposase Expression in Mutualistic Endosymbionts
Mbio, 4(3).
Contributors: * , J. Young*, M. Shah *, N. VerBerkmoes* & N. Dubilier *
MeSH headings : Animals; Bacteria / enzymology; Bacterial Physiological Phenomena; Bacterial Proteins / biosynthesis; Gene Expression; Metagenomics / methods; Oligochaeta / microbiology; Proteome / analysis; Proteomics / methods; Symbiosis; Transposases / biosynthesis
TL;DR:
It is hypothesized that increased transposase expression, which has not previously been described, may play a role in TE expansion, and could be one explanation for the sometimes very rapid emergence and evolution of new obligate symbionts and pathogens from facultative ones.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: February 3, 2019
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.
Source: ORCID
Added: February 3, 2019
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.
MeSH headings : Animals; Aquatic Organisms / microbiology; Aquatic Organisms / physiology; Bacteria / genetics; Bacteria / metabolism; Bacterial Physiological Phenomena; Evolution, Molecular; Gene Transfer, Horizontal; Genetic Variation; Genomics / methods; Invertebrates / microbiology; Invertebrates / physiology; Metabolic Networks and Pathways / genetics; Oxidation-Reduction; Phylogeny; RNA, Ribosomal, 16S / genetics; Sulfur Compounds / metabolism; Symbiosis
TL;DR:
It is hypothesize that horizontal gene transfer (HGT) would explain many of these incongruencies, and conclude that HGT may have played a significant role in shaping the metabolic evolution of GammaSOX symbionts.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Sources: Crossref, NC State University Libraries
Added: September 12, 2020
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 *
author keywords: 3-hydroxypropionate bi-cycle; Calvin cycle; proton-translocating pyrophosphatase; pyrophosphate dependent phosphofructokinase; metagenomics
MeSH headings : Animals; Bacteria / growth & development; Bacteria / metabolism; Carbon / metabolism; Carbon Cycle; Chromatography, High Pressure Liquid; Ecosystem; Electrophoresis, Polyacrylamide Gel; Energy Metabolism; Host-Pathogen Interactions; Hydrogen / metabolism; Mass Spectrometry; Metabolic Networks and Pathways; Metabolomics / methods; Oligochaeta / metabolism; Oligochaeta / microbiology; Proteomics / methods; Seawater; Symbiosis
TL;DR:
The high expression of proteins involved in pathways for energy and carbon uptake and conservation in the O. algarvensis symbiosis indicates that the oligotrophic nature of its environment exerted a strong selective pressure in shaping these associations.
(via Semantic Scholar)
Source: ORCID
Added: February 3, 2019
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
author keywords: Carbon fixation; Endosymbionts; Metaproteome; Microbiology; Riftia pachyptila; Sulfide oxidation
MeSH headings : Animals; Bacteria / chemistry; Bacteria / metabolism; Bacterial Physiological Phenomena; Bacterial Proteins / analysis; Bacterial Proteins / chemistry; Bacterial Proteins / metabolism; Carbon / metabolism; Carbon Cycle / physiology; Electrophoresis, Gel, Two-Dimensional; Membrane Proteins / analysis; Membrane Proteins / chemistry; Membrane Proteins / metabolism; Membrane Transport Proteins / analysis; Membrane Transport Proteins / chemistry; Membrane Transport Proteins / metabolism; Metabolic Networks and Pathways; Nitrogen / metabolism; Polychaeta / microbiology; Polychaeta / physiology; Proteomics; Sulfur / metabolism; Symbiosis / physiology
TL;DR:
The proteomic view supports the hypothesis that the Riftia symbiont uses nitrate as an alternative electron acceptor, and a comprehensive survey of the symbiotic physiology was established.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: February 3, 2019
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.
UN Sustainable Development Goal Categories
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: February 3, 2019
Employment
Updated: September 24th, 2023 12:41
2017 - present
NC State University Raleigh, NC, US
Associate Professor, Microbiomes and Complex Microbial Communities
Plant and Microbial Biology
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