Zhe Lyu

Also known as: Zhe Lu; Zhe Lü

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 (29)

Updated: November 27th, 2024 05:02

2024 article

Editorial: Cross-boundary significance of methanogens - the methane moment and beyond

Lyu, Z., Rotaru, A.-E., Pimentel, M., Zhang, C.-J., Rittmann, S. K.-M. R., & Ferry, J. G. (2024, June 24). FRONTIERS IN MICROBIOLOGY, Vol. 15.

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

author keywords: methanogenesis; microbiome; host; environment; agriculture; energy; health; biotechnology
Sources: Web Of Science, NC State University Libraries
Added: July 22, 2024

2024 article

Exploring the link between COVID-19 and gut microbiome at the community level

Li, B., Terwilliger, A., Maresso, A., Britton, R., Yousefipour, Z., Donnachie, E., & Lyu, Z. (2024, October 15). AMERICAN JOURNAL OF CLINICAL PATHOLOGY, Vol. 162, pp. S128–S129.

Sources: Web Of Science, NC State University Libraries
Added: November 25, 2024

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*

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*

MeSH headings : Archaea / genetics; Euryarchaeota; Humans; Methane
TL;DR: Diagnostic standards for overgrowth of methanogens are ambiguous, as the understanding of this phenomenon is still in its infancy, and the semi-quantitative hydrogen breath test has been proposed as an alternative to intestinal bacterial culture for SIBO diagnosis. (via Semantic Scholar)
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*

MeSH headings : Formates / metabolism; Gene Expression / drug effects; Methane / metabolism; Methanococcus / drug effects; Methanococcus / genetics; Oxidoreductases / metabolism; Phosphates / pharmacology
TL;DR: A library of differentially regulated promoters was designed and characterized based on the pst promoter, which responds to the inorganic phosphate concentration in the growth medium and resulted in significant improvements in the expression of a key methanogenic enzyme complex, methyl-coenzyme M reductase, and the potentially toxic arginine methyltransferase MmpX. (via Semantic Scholar)
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*

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*

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*

Ed(s): A. Becker

TL;DR: This work directly link the mmp10 gene to the arginine PTM of Mcr, demonstrate its association with methanogenesis activity, and offer insights on its substrate specificity and putative cofactor binding sites. (via Semantic Scholar)
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*

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.

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
TL;DR: The data indicate that Nbp35/ApbC is a nonessential [4Fe‐4S] cluster transfer protein in methanogenic archaea. (via Semantic Scholar)
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*

MeSH headings : Animals; Chemoautotrophic Growth; Ecosystem; Humans; Methane; Soil
TL;DR: This work states that modern methanogenesis is now a key process in virtually all anaerobic microbial communities, such as marine and lake sediments, wetland and rice soils, and human and cattle digestive tracts, and new opportunities for bioengineering methanogens are provided. (via Semantic Scholar)
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*

Ed(s): W. Metcalf

TL;DR: A working model for MCR assembly is formed and posttranslational modifications and F430 cofactors are embedded in the active sites and can be further tested by the heterologous expression system established here. (via Semantic Scholar)
Source: ORCID
Added: August 16, 2023

2018 article

Diversity and Taxonomy of Methanogens

Biogenesis of Hydrocarbons, pp. 1–59.

By: Z. Lyu* & Y. Liu*

UN Sustainable Development Goal Categories
2. Zero Hunger (OpenAlex)
Source: ORCID
Added: August 16, 2023

2018 journal article

Methanogenesis

Current Biology, 28(13), R727–R732.

TL;DR: Historically, methanogenesis has been viewed as a highly specialized metabolism restricted to a narrow group of prokaryotes, however, recent developments have revealed enormous diversity within the methanogens and suggest that this metabolism is one of the most ancient on earth. (via Semantic Scholar)
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*

Ed(s): M. Rust

TL;DR: This study suggests that purifying selection may play a more important role in archaeal genome evolution than previously hypothesized, indicating that there could be a major difference between the evolutionary regimes of Archaea and Bacteria. (via Semantic Scholar)
Source: ORCID
Added: August 16, 2023

2017 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*

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
TL;DR: This work systematically predicted and annotated antioxidant features from representative genomes across six well-established methanogen orders and suggested that the enrichment of antioxidant features in the Class II methanogens may have played a key role in the adaption of this group to oxidative environments today and historically. (via Semantic Scholar)
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*

TL;DR: This study demonstrates the importance of Mmp10 and the methyl-Arg PTM on Mcr activity and shows that the rates of methane formation of the complemented strains were not always restored to the wild type level. (via Semantic Scholar)
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*

TL;DR: A novel psychrotolerant bacterium, strain ISLP-3T, was isolated from a sample of naturally formed ice sculpture on the shore of Lake Podprudnoye in Antarctica, suggesting that this new isolate represents a novel species within the genus Sanguibacter. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
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
TL;DR: Based on average nucleotide identity, average amino acid identity and phylogenetic analyses, the novel isolate was placed within a unique phylogenetic cluster distant from all eight families in the order Bacteroidales and formed a novel family with the proposed name Williamwhitmaniaceae fam. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
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*

TL;DR: Phylogenetic analyses of the 16S rRNA gene sequences indicated that the strains were related to members of the family Propionibacteriaceae with formation of a separate branch within the radiation of the genera Granulicoccus and Luteococcus. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
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*

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*

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

TL;DR: The possibility that extremophilic bacteria from the lab collection might be able to metabolize organic matter in the studied meteorites was tested and the potential toxic or inhibitory growth effects were checked for different anaerobic cultures. (via Semantic Scholar)
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*

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

TL;DR: It is proposed that strain LZ-22 is a representative of a novel genus and species, with proposed names Raineyella antarctica gen. nov, Sanguibacter gelidistatuaria sp.nov, and A7p-90m may represent a novel family within the order Bacteroidales. (via Semantic Scholar)
UN Sustainable Development Goal Categories
14. Life Below Water (OpenAlex)
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.

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
TL;DR: It is proposed that Methanocella methanogens cope with low H2 and syntrophic growth by stabilizing the Mvh/Hdr/Fwd complex and activating formate-dependent methanogenesis. (via Semantic Scholar)
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.

By: Z. Lu* & Y. Lu

TL;DR: The complete genome sequence of a novel isolate in this group, Methanocella conradii strain HZ254, is reported, which indicates a key role in methane emissions in paddy fields. (via Semantic Scholar)
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
TL;DR: Strain HZ254T is proposed as a representative of a novel species, Methanocella conradii sp. (via Semantic Scholar)
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.

TL;DR: A highly dynamic structure of the methanogenic archaeal community was revealed during the decomposition of rice root and straw residues in anoxic rice field soil incubated at three temperatures, and the in situ concentration of acetate seems to be the key factor that regulates the shift of meethanogenic community. (via Semantic Scholar)
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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