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 (27)
Updated: April 3rd, 2024 20:53
2022 journal article
Editorial: The methane moment - Cross-boundary significance of methanogens: Preface
Frontiers in Microbiology, 13.
www.frontiersin.org (publisher PDF)
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.
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.
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).
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.
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).
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.
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.
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).
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.
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
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.
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
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.
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 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.
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.
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.
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
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
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,
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.
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.
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.
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.
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
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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