Zhe Lyu

Also known as: Zhe Lu; Zhe Lü

https://orcid.org/0000-0003-0184-6609

Human microbiome, Anaerobe, Synthetic biology, Microbiology, Microbial ecology, Methanogen, Archaea

Current interests: 1. Microbiome and host health 2. Methanogenic archaea and methanogenesis 3. Archaea-bacterial interaction

Works (27)

Updated: March 2nd, 2024 06:39

2022 journal article

Editorial: The methane moment - Cross-boundary significance of methanogens: Preface

Frontiers in Microbiology, 13.

By: Z. Lyu*, A. Rotaru*, M. Pimentel, C. Zhang* & S. Rittmann*

co-author countries: Austria 🇦🇹 China 🇨🇳 Denmark 🇩🇰 United States of America 🇺🇸

Contributors: Z. Lyu*

Source: ORCID
Added: August 16, 2023

2021 journal article

Back to the Source: Molecular Identification of Methanogenic Archaea as Markers of Colonic Methane Production

Digestive Diseases and Sciences, 66(11), 3661–3664.

By: Z. Lyu*

co-author countries: United States of America 🇺🇸
MeSH headings : Archaea / genetics; Euryarchaeota; Humans; Methane
Source: ORCID
Added: August 16, 2023

2021 journal article

Tuning Gene Expression by Phosphate in the Methanogenic Archaeon Methanococcus maripaludis

ACS Synthetic Biology, 10(11), 3028–3039.

By: T. Akinyemi*, N. Shao*, Z. Lyu*, I. Drake*, Y. Liu* & W. Whitman*

co-author countries: United States of America 🇺🇸
MeSH headings : Formates / metabolism; Gene Expression / drug effects; Methane / metabolism; Methanococcus / drug effects; Methanococcus / genetics; Oxidoreductases / metabolism; Phosphates / pharmacology
Source: ORCID
Added: August 16, 2023

2020 journal article

Data-Driven Models Reveal Mutant Cell Behaviors Important for Myxobacterial Aggregation

MSystems, 5(4).

By: Z. Zhang*, C. Cotter*, Z. Lyu*, L. Shimkets* & O. Igoshin*

co-author countries: United States of America 🇺🇸

Ed(s): M. Rust

Source: ORCID
Added: August 16, 2023

2020 article

Data-driven models reveal mutant cell behaviors important for myxobacterial aggregation

Zhang, Z., Cotter, C. R., Lyu, Z., Shimkets, L. J., & Igoshin, O. A. (2020, February 10). [], Vol. 2.

By: Z. Zhang*, C. Cotter*, Z. Lyu*, L. Shimkets* & O. Igoshin*

co-author countries: United States of America 🇺🇸
Source: ORCID
Added: August 16, 2023

2020 journal article

Posttranslational Methylation of Arginine in Methyl Coenzyme M Reductase Has a Profound Impact on both Methanogenesis and Growth of Methanococcus maripaludis

Journal of Bacteriology, 202(3).

By: Z. Lyu*, N. Shao*, C. Chou*, H. Shi*, R. Patel*, E. Duin*, W. Whitman*

co-author countries: United States of America 🇺🇸

Ed(s): A. Becker

Source: ORCID
Added: August 16, 2023

2019 article

Diversity and Taxonomy of Methanogens

Lyu, Z., & Liu, Y. (2019, July). Biogenesis of Hydrocarbons, pp. 19–77.

By: Z. Lyu* & Y. Liu*

co-author countries: United States of America 🇺🇸
Source: ORCID
Added: August 16, 2023

2019 journal article

The Nbp35/ApbC homolog acts as a nonessential [4Fe‐4S] transfer protein in methanogenic archaea

FEBS Letters, 594(5), 924–932.

By: C. Zhao*, Z. Lyu*, F. Long*, T. Akinyemi*, K. Manakongtreecheep*, D. Söll*, W. Whitman*, D. Vinyard*, Y. Liu*

co-author countries: United States of America 🇺🇸
MeSH headings : Archaeal Proteins / genetics; Archaeal Proteins / metabolism; Cell Nucleus / metabolism; Cytosol / metabolism; Gene Deletion; Iron-Sulfur Proteins / genetics; Iron-Sulfur Proteins / metabolism; Methanococcus / genetics; Methanococcus / growth & development; Methanococcus / metabolism; Phylogeny
Source: ORCID
Added: August 16, 2023

2019 journal article

Transplanting the pathway engineering toolbox to methanogens

Current Opinion in Biotechnology, 59, 46–54.

By: Z. Lyu* & W. Whitman*

co-author countries: United States of America 🇺🇸
MeSH headings : Animals; Chemoautotrophic Growth; Ecosystem; Humans; Methane; Soil
Source: ORCID
Added: August 16, 2023

2018 journal article

Assembly of Methyl Coenzyme M Reductase in the Methanogenic Archaeon Methanococcus maripaludis

Journal of Bacteriology, 200(7).

By: Z. Lyu*, C. Chou*, H. Shi*, L. Wang*, R. Ghebreab*, D. Phillips*, Y. Yan*, E. Duin*, W. Whitman*

co-author countries: United States of America 🇺🇸

Ed(s): W. Metcalf

Source: ORCID
Added: August 16, 2023

2018 article

Diversity and Taxonomy of Methanogens

Biogenesis of Hydrocarbons, pp. 1–59.

By: Z. Lyu* & Y. Liu*

co-author countries: United States of America 🇺🇸
Source: ORCID
Added: August 16, 2023

2018 journal article

Metabolic shift at the class level sheds light on adaptation of methanogens to oxidative environments

The ISME Journal.

By: Z. Lyu* & Y. Lu*

co-author countries: China 🇨🇳 United States of America 🇺🇸
MeSH headings : Antioxidants / chemistry; Bayes Theorem; Cluster Analysis; DNA Repair; Euryarchaeota / genetics; Euryarchaeota / metabolism; Genome, Bacterial; Genomics; Methane / metabolism; Oxidative Stress; Phylogeny; RNA, Bacterial / genetics; RNA, Ribosomal, 16S / genetics; Reactive Oxygen Species / metabolism
Source: ORCID
Added: August 16, 2023

2018 journal article

Methanogenesis

Current Biology, 28(13), R727–R732.

By: Z. Lyu*, N. Shao*, T. Akinyemi* & W. Whitman*

co-author countries: United States of America 🇺🇸
Source: ORCID
Added: August 16, 2023

2017 journal article

An Important Role for Purifying Selection in Archaeal Genome Evolution

MSystems, 2(5), e00112–17.

By: Z. Lyu*, Z. Li*, F. He* & Z. Zhang*

co-author countries: China 🇨🇳 United States of America 🇺🇸

Ed(s): M. Rust

Source: ORCID
Added: August 16, 2023

2017 article

Mmp10 is required for post-translational methylation of arginine at the active site of methyl-coenzyme M reductase

Lyu, Z., Chou, C.-wen, Shi, H., Patel, R., Duin, E. C., & Whitman, W. B. (2017, October 30). (Vol. 10). Vol. 10.

By: Z. Lyu*, C. Chou*, H. Shi*, R. Patel*, E. Duin* & W. Whitman*

co-author countries: United States of America 🇺🇸
Source: ORCID
Added: August 16, 2023

2017 journal article

Sanguibacter gelidistatuariae sp. nov., a novel psychrotolerant anaerobe from an ice sculpture in Antarctica, and emendation of descriptions for the family Sanguibacteraceae, the genus Sanguibacter and species S. antarcticus, S. inulinus, S. kedieii, S. marinus, S.soli and S. suarezii.

International Journal of Systematic and Evolutionary Microbiology.

By: E. Pikuta*, Z. Lyu*, M. Williams*, N. Patel*, Y. Liu*, R. Hoover*, H. Busse*, P. Lawson*, W. Whitman*

co-author countries: Austria 🇦🇹 United States of America 🇺🇸
Source: ORCID
Added: August 16, 2023

2017 journal article

Williamwhitmania taraxaci gen. nov., sp. nov., a proteolytic anaerobe with a novel type of cytology from Lake Untersee in Antarctica, description of Williamwhitmaniaceae fam. nov., and emendation of the order Bacteroidales Krieg 2012.

International Journal of Systematic and Evolutionary Microbiology, 9.

Zhe Lyu

MeSH headings : Antarctic Regions; Bacterial Typing Techniques; Bacteroidetes / classification; Bacteroidetes / genetics; Bacteroidetes / isolation & purification; Base Composition; DNA, Bacterial / genetics; Fatty Acids / chemistry; Lakes / microbiology; Phylogeny; RNA, Ribosomal, 16S / genetics; Sequence Analysis, DNA; Vitamin K 2 / analogs & derivatives; Vitamin K 2 / chemistry
Source: ORCID
Added: August 16, 2023

2016 journal article

Engineering the Autotroph Methanococcus maripaludis for Geraniol Production.

ACS Synthetic Biology. http://europepmc.org/abstract/med/26886063

By: Z. Lyu, R. Jain, P. Smith, T. Fetchko, Y. Yan & W. Whitman

Source: ORCID
Added: August 16, 2023

2016 journal article

Evolution of the archaeal and mammalian information processing systems: towards an archaeal model for human disease.

http://europepmc.org/abstract/med/27261368

By: Z. Lyu & W. Whitman

Source: ORCID
Added: August 16, 2023

2016 journal article

Raineyella antarctica gen. nov., sp. nov., a psychrotolerant, d-amino-acid-utilizing anaerobe isolated from two geographic locations of the Southern Hemisphere.

International Journal of Systematic and Evolutionary Microbiology, 66(12), 5529–5536,

By: E. Pikuta*, R. Menes*, A. Bruce*, Z. Lyu*, N. Patel*, Y. Liu*, R. Hoover*, H. Busse*, P. Lawson*, W. Whitman*

co-author countries: Austria 🇦🇹 United States of America 🇺🇸 Uruguay 🇺🇾
Source: ORCID
Added: August 16, 2023

2015 journal article

Comparative genomics of three Methanocellales strains reveal novel taxonomic and metabolic features

Environmental Microbiology Reports, 2, n/a-n/a.

By: Z. Lyu* & Y. Lu*

co-author countries: China 🇨🇳
MeSH headings : Euryarchaeota / classification; Euryarchaeota / genetics; Euryarchaeota / metabolism; Genetic Variation; Genomics; Metabolic Networks and Pathways / genetics; Phylogeny
Source: ORCID
Added: August 16, 2023

2015 conference paper

Microbiological investigation of two chondrite meteorites: Murchison and Polonnaruwa

In R. B. Hoover, G. V. Levin, A. Y. Rozanov, & N. C. Wickramasinghe (Eds.), Instruments, Methods, and Missions for Astrobiology XVII.

By: E. Pikuta*, Z. Lyu*, W. Whitman*, G. LaBrake*, J. Wallis, K. Wickramarathne*, N. Wickramasinghe*, R. Hoover*

co-author countries: United Kingdom of Great Britain and Northern Ireland 🇬🇧 Sri Lanka 🇱🇰 United States of America 🇺🇸

Ed(s): R. Hoover*, G. Levin, A. Rozanov & N. Wickramasinghe*

Source: ORCID
Added: August 16, 2023

2015 conference paper

Molecular studies of anaerobic strains from Antarctica and their taxonomic identifications

In R. B. Hoover, G. V. Levin, A. Y. Rozanov, & N. C. Wickramasinghe (Eds.), Instruments, Methods, and Missions for Astrobiology XVII.

By: Z. Lyu*, E. Pikuta*, J. Hagel*, G. LaBrake*, R. Hoover* & W. Whitman

co-author countries: United States of America 🇺🇸

Ed(s): R. Hoover*, G. Levin, A. Rozanov & N. Wickramasinghe

Source: ORCID
Added: August 16, 2023

2014 journal article

Response of a paddy soil methanogen to syntrophic growth as revealed by transcriptional analyses

Applied and Environmental Microbiology, 5.

By: P. Liu*, Y. Yang*, Z. Lu* & Y. Lu*

co-author countries: China 🇨🇳
MeSH headings : Archaeal Proteins / genetics; Archaeal Proteins / metabolism; Euryarchaeota / enzymology; Euryarchaeota / genetics; Euryarchaeota / growth & development; Euryarchaeota / isolation & purification; Formate Dehydrogenases / genetics; Formate Dehydrogenases / metabolism; Hydrogenase / genetics; Hydrogenase / metabolism; Methane / metabolism; Oryza / growth & development; Oxidoreductases / genetics; Oxidoreductases / metabolism; Soil / chemistry; Soil Microbiology; Transcription, Genetic
Source: ORCID
Added: August 16, 2023

2012 journal article

Complete Genome Sequence of a Thermophilic Methanogen, Methanocella conradii HZ254, Isolated from Chinese Rice Field Soil

Journal of Bacteriology, 194(9), 2398–2399.

co-author countries: China 🇨🇳
Source: ORCID
Added: August 16, 2023

2012 journal article

Methanocella conradii sp. nov., a Thermophilic, Obligate Hydrogenotrophic Methanogen, Isolated from Chinese Rice Field Soil

Zhe Lyu

MeSH headings : Base Composition; DNA Restriction Enzymes / genetics; Methanomicrobiaceae / classification; Methanomicrobiaceae / genetics; Methanomicrobiaceae / growth & development; Methanomicrobiaceae / ultrastructure; Molecular Sequence Data; Phylogeny; RNA, Ribosomal, 16S; Soil Microbiology
Source: ORCID
Added: August 16, 2023

2008 journal article

Dynamics of the Methanogenic Archaeal Community during Plant Residue Decomposition in an Anoxic Rice Field Soil

Applied and Environmental Microbiology, 74(9), 2894–2901.

By: J. Peng*, Z. Lu*, J. Rui* & Y. Lu*

co-author countries: China 🇨🇳
Source: ORCID
Added: August 16, 2023

Employment

Updated: August 16th, 2023 17:26

2023 - present

North Carolina State University Raleigh, US
Assistant Professor of Microbial Physiology Plant and Microbial Biology

2022 - 2022

Baylor College of Medicine Houston, Texas, US
Assistant Professor of Translational Microbiome Molecular Virology and Microbiology

2022 - 2022

Baylor College of Medicine Houston, Texas, US
Director of CMMR Cultivation Labs Alkek Center for Metagenomics and Microbiome Research

2018 - 2022

Baylor College of Medicine Houston, TX, US
Assistant Lab Director Molecular Virology and Microbiology

2012 - 2018

University of Georgia Athens, GA, US
Postdoctoral Research Associate Microbiology

2006 - 2006

Shanghai Jiao Tong University Shanghai, CN
Research Internship School of Life Science & Biotechnology

Education

Updated: December 10th, 2019 13:40

2006 - 2012

China Agricultural University Beijing, CN
Ph.D College of Resources & Environmental Sciences

2002 - 2006

Shandong University Jinan, Shandong, CN
Bachelor of science Microbiology

Funding History

Funding history based on the linked ORCID record. Updated: December 19th, 2021 20:21

grant March 1, 2021 - February 28, 2026
Microbiome Discovery and Mechanisms to Combat Antibiotic Resistance at Mucosal Surfaces
National Institute of Allergy and Infectious Diseases

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