School of Chemistry and Molecular Biosciences

Honorary Professor Gene Tyson

BSc (Hons) (UQ) Microbiology, PhD (UQ) Microbiology
Honorary Professor & Honorary Professor
School of Chemistry and Molecular Biosciences

Google Scholar profile

Primary research interest

Molecular microbial ecology, diversity and evolution

About me

I am a microbial ecologist whose research applies culture-independent molecular approaches to understand the structure and function of microbial communities in the environment. During my dissertation research (University of California, Berkeley) I was the lead author on one of the first studies to use metagenomics. In this work I investigated the metabolic potential and population diversity of microbial communities involved in acid mine drainage (AMD) generation, and demonstrated, for the first time, that metagenomic data could be used to reconstruct near-complete genomes directly from environmental samples.

My group at The University of Queensland used the metagenomic and metatranscriptomic approaches I helped pioneer, to investigate microbial communities in a wide range of different communities in both engineered systems and natural environments. The group developed new ways to analyse genomic data by leading efforts in error correction for high-throughput sequencing platforms, single-cell sequencing and deep spatiotemporal metagenomics.

Research focus and collaborations

  • Molecular microbial ecology
  • Microbial diversity
  • Microbial evolution
  • The role of microorganisms in the biogeochemical cycles that underpin life on Earth
  • Phage – host interactions and co-evolution

International collaborators

  • Aalborg University, Denmark
  • Advanced Industrial Science & Technology (AIST), Japan
  • Cornell University
  • California Institute of Technology
  • University of Arizona
  • University of Colorado
  • Massachusetts Institute of Technology

Funded projects

  • ARC Linkage: From tailings to soil: in situ remediation in mine site rehabilitation
  • ARC Discovery:  Genome-level insight into the dynamics of a model coral microbiome
  • ARC Discovery: Intracellular manufacturing – high performance biomaterials from methane
  • ARC Linkage:  Iron cycling in wet tropical regimes: Bioleaching of chalcopyrite, goethite and hematite
  • U.S. Department of Energy – Biological and Environment Research: Pathways to carbon liberation: a systems approach to understanding carbon transformations and losses from thawing permafrost.
  • U.S. Department of Energy – Engineering Frontier Research Center Program:  Systems Level Dissection of Anaerobic Methane Cycling: Quantitative Measurements of Single Cell Ecophysiology, Genetic Mechanisms, and Microbial Interactions.
  • Gordon & Betty Moore Foundation:  Microscale experiments to understand a microscale world: combining microfluids and ecogenomics to investigate microbial processes in the ocean.
  • Great Barrier Reef Foundation: Sea-quence Bioinformatics Fellowships.
  • Queensland Government Department of Science, Information Technology, Innovation and the Arts (DSITIA) Accelerate Partnerships: Coral genomes along environmental gradients.
  • Queensland Government Smart Futures Research Partnerships Program:  Future gas through bioconversion of stranded and waste coal.

Teaching interests

  • Microbiology & Immunology
  • Genetics

Achievements and awards 

Invited lectures

I have presented invited talks at more than 30 international meetings since 2007, including “keynote” presentations at the International Symposium on Microbial Ecology (2016), University of Calgary-Microbiome Symposium (2015), Metagenomics@Melbourne Symposium (2013 & 2015), the Microbial Genomic Research: A Frontier in Future Green Biotechnology, Chung Ang University, Seoul (2011) and the New Zealand Microbial Ecology Consortium, University of Auckland, New Zealand (2010).

My “invited” presentations include the Joint Academic Microbiology Seminars, Australian Museum, Sydney (2016), 15th International Symposium on Microbial Ecology (ISME15) Seoul, Korea (2014); CBA Biodiversity Genomics Conference, Canberra, Australia (2013), the 14th International Symposium on Microbial Ecology (ISME14) “The Power of the Small” in Copenhagen (2012), American Society for Microbiology (ASM), San Diego, USA (2010).

Synergistic activities

  • Editorial board member for the International Society for Microbial Ecology Journal, Environmental Microbiologyand Frontiers in Evolutionary and Genomic Microbiology.
  • Assessor for the following research funding authorities: Australian Research Council (ARC), National Science Foundation (NSF) – Systematic Biology & Biodiversity Program and National Science Foundation (NSF) – Biological Oceanography Program.
  • Reviewer for the following international journals: Nature, Science, Applied and Environmental Microbiology, PLoS Biology, PLoS ONE, ISME Journal, Nature Review Microbiology, Proceedings of the National Academy of Sciences.

Outreach and media exposure

  • Outreach - 2016: presentation about careers in Bioinformatics & ACE tour to 1st year UQ Bioinformatics students (18th & 19th May). Guest lecturer to undergraduate course "Genes, genomes and development" students at James Cook University (4th April).
  • Media exposure: my research has been published in more than 30 articles in the mainstream science media, including: ABC Science Feb 2014 (Methane microbe may speed up warming), Sydney Morning Herald Nov 2013 (Secrets from the Deep), F1000 Prime Aug 2013, Altmetric Jul 2013; Phys Org Jul 2013, Phys Org Sep 2008, Webwire Mar 2008, Phys Org Mar 2007, Scientist July 2006, Chicago Tribune 2006, Science Daily Feb 2004, Eureka Alert Feb 2004, Science Scoop Feb 2004, New York Times Feb 2004.

Publications

Book Chapters (6)
Journal Articles (162)
Conference Papers (20)
Research Report (1)
Data Collections (2)

Book Chapters

Hugenholtz, Philip, Tyson, Gene W. and Blackall, Linda L. (2018). Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization. Gene probes: principles and protocols. (pp. 029-042) edited by Marilena Aquino de Muro and Ralph Rapley. New Jersey, United States: Humana Press. doi: 10.1385/1-59259-238-4:029
Bragg,Lauren and Tyson, Gene W. (2014). Metagenomics using next-generation sequencing. Environmental Microbiology: Methods and Protocols. (pp. 183-201) edited by Ian T. Paulsen and Andrew J. Holmes. New York, NY United States: Humana Press Inc.. doi: 10.1007/978-1-62703-712-9_15
Carvalhais, Lilia C., Dennis, Paul G., Tyson, Gene W. and Schenk, Peer M. (2013). Rhizosphere Metatranscriptomics: Challenges and Opportunities. Molecular Microbial Ecology of the Rhizosphere. (pp. 1137-1144) edited by Frans J. de Bruijn. Hoboken, NJ United States: Wiley-Blackwell. doi: 10.1002/9781118297674.ch109
Tyson, Gene W. and Hugenholtz, Philip (2005). Environmental shotgun sequencing. Encyclopedia of genetics, genomics, proteomics, and bioinformatics. (pp. 1386-1391) edited by Lynn B. Jorde. West Sussex, U.K.: John Wiley & Sons. doi: 10.1002/047001153X.g205313
Banfield, Jillian, F., Tyson, Gene W., Allen, E. E. and Whitaker, B. J. (2005). The search for a molecular-level understanding of the processes that underpin the Earth's biogeochemical cycles. Molecular geomicrobiology. (pp. 1-7) edited by Banfield, Jillian F., Cervini-Silva, Javiera and Nealson, Kenneth M.. Chantilly, U.S.: Mineralogical Society of America, Geochemical Society.
Hugenholtz, P., Tyson, G. and Blackall, L. L. (2002). Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridisation (FISH). Gene Probes - Principles and Protocols. (pp. 1-17) edited by Aquino de Muro. M and Rapley. R. London: Humana Press.

Journal Articles

Messer, Lauren F., Bourne, David G., Robbins, Steven J., Clay, Megan, Bell, Sara C., McIlroy, Simon J. and Tyson, Gene W. (2024). A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience. Nature Communications, 15 (1) 2902, 2902. doi: 10.1038/s41467-024-46905-5
Chklovski, Alex, Parks, Donovan H., Woodcroft, Ben J. and Tyson, Gene W. (2024). Author Correction: CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nature Methods, 21 (4), 735-735. doi: 10.1038/s41592-024-02248-z
Wilson, Liam A., Melville, Jamie N., Pedroso, Marcelo M., Krco, Stefan, Hoelzl, Robert, Zaugg, Julian, Southam, Gordon, Virdis, Bernardino, Evans, Paul, Supper, Jenna, Harmer, Jeffrey R., Tyson, Gene, Clark, Alice, Schenk, Gerhard and Bernhardt, Paul V. (2024). Kinetic, electrochemical and spectral characterization of bacterial and archaeal rusticyanins; unexpected stability issues and consequences for applications in biotechnology. Journal of Inorganic Biochemistry, 256 112539, 1-10. doi: 10.1016/j.jinorgbio.2024.112539
Yap, Chloe X., Henders, Anjali K., Alvares, Gail A., Wood, David L.A., Krause, Lutz, Tyson, Gene W., Restuadi, Restuadi, Wallace, Leanne, McLaren, Tiana, Hansell, Narelle K., Cleary, Dominique, Grove, Rachel, Hafekost, Claire, Harun, Alexis, Holdsworth, Helen, Jellett, Rachel, Khan, Feroza, Lawson, Lauren P., Leslie, Jodie, Frenk, Mira Levis, Masi, Anne, Mathew, Nisha E., Muniandy, Melanie, Nothard, Michaela, Miller, Jessica L., Nunn, Lorelle, Holtmann, Gerald, Strike, Lachlan T., de Zubicaray, Greig I. ... Gratten, Jacob (2024). Erratum: Autism-related dietary preferences mediate autism-gut microbiome associations (Cell (2021) 184(24) (5916–5931.e17), (S0092867421012319), (10.1016/j.cell.2021.10.015)). Cell, 187 (2), 495-510. doi: 10.1016/j.cell.2023.12.001
Wu, Mengxiong, Li, Jie, Lai, Chun-Yu, Leu, Andy O, Sun, Shengjie, Gu, Rui, Erler, Dirk V, Liu, Lian, Li, Lin, Tyson, Gene W, Yuan, Zhiguo, McIlroy, Simon J and Guo, Jianhua (2024). Nitrate-driven anaerobic oxidation of ethane and butane by bacteria. The ISME Journal, 18 (1) ARTN wrad011. doi: 10.1093/ismejo/wrad011
Ellenbogen, Jared B., Borton, Mikayla A., McGivern, Bridget B., Cronin, Dylan R., Hoyt, David W., Freire-Zapata, Viviana, McCalley, Carmody K., Varner, Ruth K., Crill, Patrick M., Wehr, Richard A., Chanton, Jeffrey P., Woodcroft, Ben J., Tfaily, Malak M., Tyson, Gene W., Rich, Virginia I. and Wrighton, Kelly C. (2023). Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost. Msystems, 9 (1), e0069823. doi: 10.1128/msystems.00698-23
Zhang, Xueqin, Xie, Mengying, Cai, Chen, Rabiee, Hesamoddin, Wang, Zhiyao, Virdis, Bernardino, Tyson, Gene W., McIlroy, Simon J., Yuan, Zhiguo and Hu, Shihu (2023). Pyrogenic carbon promotes anaerobic oxidation of methane coupled with iron reduction via the redox-cycling mechanism. Environmental Science and Technology, 57 (48), 19793-19804. doi: 10.1021/acs.est.3c05907
Zhang, Xueqin, Joyce, Georgina H., Leu, Andy O., Zhao, Jing, Rabiee, Hesamoddin, Virdis, Bernardino, Tyson, Gene W., Yuan, Zhiguo, McIlroy, Simon J. and Hu, Shihu (2023). Multi-heme cytochrome-mediated extracellular electron transfer by the anaerobic methanotroph ‘Candidatus Methanoperedens nitroreducens’. Nature Communications, 14 (1) 6118, 1-14. doi: 10.1038/s41467-023-41847-w
Zhou, Joyce, Boyd, Joel A., Nyeverecz, Bozica, Vivian, Charlotte, Angel, Nicola, Wood, David L. A., Hugenholtz, Philip, Tyson, Gene W., Krause, Lutz and Ó Cuív, Páraic (2023). Draft genome sequence of two “Candidatus Intestinicoccus colisanans” strains isolated from faeces of healthy humans. BMC Research Notes, 16 (1) 174, 1-4. doi: 10.1186/s13104-023-06447-3
Chklovski, Alex, Parks, Donovan H., Woodcroft, Ben J. and Tyson, Gene W. (2023). CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nature Methods, 20 (8), 1203-1212. doi: 10.1038/s41592-023-01940-w
Li, Jie, Liu, Tao, McIlroy, Simon J., Tyson, Gene W. and Guo, Jianhua (2023). Phylogenetic and metabolic diversity of microbial communities performing anaerobic ammonium and methane oxidations under different nitrogen loadings. ISME Communications, 3 (1) 39, 1-10. doi: 10.1038/s43705-023-00246-4
Volmer, James G., Soo, Rochelle M., Evans, Paul N., Hoedt, Emily C., Astorga Alsina, Ana L., Woodcroft, Benjamin J., Tyson, Gene W., Hugenholtz, Philip and Morrison, Mark (2023). Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated. BMC Biology, 21 (1) 59, 1-17. doi: 10.1186/s12915-023-01524-2
McIlroy, Simon J., Leu, Andy O., Zhang, Xueqin, Newell, Rhys, Woodcroft, Ben J., Yuan, Zhiguo, Hu, Shihu and Tyson, Gene W. (2023). Anaerobic methanotroph ‘Candidatus Methanoperedens nitroreducens’ has a pleomorphic life cycle. Nature Microbiology, 8 (2), 321-331. doi: 10.1038/s41564-022-01292-9
Chklovski, Alex and Tyson, Gene W. (2023). Machine learning improves genome quality prediction across the microbial tree of life. Nature Methods. doi: 10.1038/s41592-023-01941-9
Wu, Mengxiong, Li, Jie, Leu, Andy O., Erler, Dirk V., Stark, Terra, Tyson, Gene W., Yuan, Zhiguo, McIlroy, Simon J. and Guo, Jianhua (2022). Anaerobic oxidation of propane coupled to nitrate reduction by a lineage within the class Symbiobacteriia. Nature Communications, 13 (1) 6115, 1-12. doi: 10.1038/s41467-022-33872-y
Hallstrøm, Søren, Raina, Jean-Baptiste, Ostrowski, Martin, Parks, Donovan H., Tyson, Gene W., Hugenholtz, Philip, Stocker, Roman, Seymour, Justin R. and Riemann, Lasse (2022). Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean. The ISME Journal, 16 (11), 2525-2534. doi: 10.1038/s41396-022-01299-4
Ou, Ya-Fei, Dong, Hong-Po, McIlroy, Simon J., Crowe, Sean A., Hallam, Steven J., Han, Ping, Kallmeyer, Jens, Simister, Rachel L., Vuillemin, Aurele, Leu, Andy O., Liu, Zhanfei, Zheng, Yan-Ling, Sun, Qian-Li, Liu, Min, Tyson, Gene W. and Hou, Li-Jun (2022). Expanding the phylogenetic distribution of cytochrome b-containing methanogenic archaea sheds light on the evolution of methanogenesis. The ISME Journal, 16 (10), 1-15. doi: 10.1038/s41396-022-01281-0
Zhang, Xueqin, McIlroy, Simon J., Vassilev, Igor, Rabiee, Hesamoddin, Plan, Manuel, Cai, Chen, Virdis, Bernardino, Tyson, Gene W., Yuan, Zhiguo and Hu, Shihu (2022). Polyhydroxyalkanoate-driven current generation via acetate by an anaerobic methanotrophic consortium. Water Research, 221 118743, 1-9. doi: 10.1016/j.watres.2022.118743
Wilson, Rachel M., Hough, Moira A., Verbeke, Brittany A., Hodgkins, Suzanne B., Tyson, Gene, Sullivan, Matthew B., Brodie, Eoin, Riley, William J., Woodcroft, Ben, McCalley, Carmody, Dominguez, Sky C., Crill, Patrick M., Varner, Ruth K., Frolking, Steve, Cooper, William T., Chanton, Jeff P., Saleska, Scott D., Rich, Virginia I. and Tfaily, Malak M. (2022). Plant organic matter inputs exert a strong control on soil organic matter decomposition in a thawing permafrost peatland. Science of the Total Environment, 820 152757, 152757. doi: 10.1016/j.scitotenv.2021.152757
Raina, Jean-Baptiste, Lambert, Bennett S., Parks, Donovan H., Rinke, Christian, Siboni, Nachshon, Bramucci, Anna, Ostrowski, Martin, Signal, Brandon, Lutz, Adrian, Mendis, Himasha, Rubino, Francesco, Fernandez, Vicente I., Stocker, Roman, Hugenholtz, Philip, Tyson, Gene W. and Seymour, Justin R. (2022). Chemotaxis shapes the microscale organization of the ocean’s microbiome. Nature, 605 (7908), 132-138. doi: 10.1038/s41586-022-04614-3
Hough, Moira, McCabe, Samantha, Vining, S. Rose, Pickering Pedersen, Emily, Wilson, Rachel M., Lawrence, Ryan, Chang, Kuang-Yu, Bohrer, Gil, Riley, William J., Crill, Patrick M., Varner, Ruth K., Blazewicz, Steven J., Dorrepaal, Ellen, Tfaily, Malak M., Saleska, Scott R., Rich, Virginia I., Frolking, Steve, Hodgkins, Suzanne B., McCalley, Carmody K., Cooper, William T., Chanton, Jeffrey P., Sullivan, Matthew B., Tyson, Gene W., Brodie, Eoin L., Woodcroft, Ben J. and Dominguez, Sky (2022). Coupling plant litter quantity to a novel metric for litter quality explains C storage changes in a thawing permafrost peatland. Global Change Biology, 28 (3), 950-968. doi: 10.1111/gcb.15970
Chadwick, Grayson L., Skennerton, Connor T., Laso-Pérez, Rafael, Leu, Andy O., Speth, Daan R., Yu, Hang, Morgan-Lang, Connor, Hatzenpichler, Roland, Goudeau, Danielle, Malmstrom, Rex, Brazelton, William J., Woyke, Tanja, Hallam, Steven J., Tyson, Gene W., Wegener, Gunter, Boetius, Antje and Orphan, Victoria J. (2022). Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea. PLoS Biology, 20 (1) e3001508, e3001508. doi: 10.1371/journal.pbio.3001508
Bramucci, Anna R., Focardi, Amaranta, Rinke, Christian, Hugenholtz, Philip, Tyson, Gene W., Seymour, Justin R. and Raina, Jean-Baptiste (2021). Microvolume DNA extraction methods for microscale amplicon and metagenomic studies. ISME Communications, 1 (1) 79. doi: 10.1038/s43705-021-00079-z
Wang, Yulin, Ye, Jun, Ju, Feng, Liu, Lei, Boyd, Joel A., Deng, Yu, Parks, Donovan H., Jiang, Xiaotao, Yin, Xiaole, Woodcroft, Ben J., Tyson, Gene W., Hugenholtz, Philip, Polz, Martin F. and Zhang, Tong (2021). Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years. Microbiome, 9 (1) 199, 199. doi: 10.1186/s40168-021-01151-5
Yap, Chloe X., Henders, Anjali K., Alvares, Gail A., Wood, David L.A., Krause, Lutz, Tyson, Gene W., Restuadi, Restuadi, Wallace, Leanne, McLaren, Tiana, Hansell, Narelle K., Cleary, Dominique, Grove, Rachel, Hafekost, Claire, Harun, Alexis, Holdsworth, Helen, Jellett, Rachel, Khan, Feroza, Lawson, Lauren P., Leslie, Jodie, Frenk, Mira Levis, Masi, Anne, Mathew, Nisha E., Muniandy, Melanie, Nothard, Michaela, Miller, Jessica L., Nunn, Lorelle, Holtmann, Gerald, Strike, Lachlan T., de Zubicaray, Greig I. ... Gratten, Jacob (2021). Autism-related dietary preferences mediate autism-gut microbiome associations. Cell, 184 (24), 5916-5931.e17. doi: 10.1016/j.cell.2021.10.015
Emerson, Joanne B., Varner, Ruth K., Wik, Martin, Parks, Donovan H., Neumann, Rebecca B., Johnson, Joel E., Singleton, Caitlin M., Woodcroft, Ben J., Tollerson, Rodney, Owusu-Dommey, Akosua, Binder, Morgan, Freitas, Nancy L., Crill, Patrick M., Saleska, Scott R., Tyson, Gene W. and Rich, Virginia I. (2021). Diverse sediment microbiota shape methane emission temperature sensitivity in Arctic lakes. Nature Communications, 12 (1) 5815. doi: 10.1038/s41467-021-25983-9
Yu, Hang, Skennerton, Connor T., Chadwick, Grayson L., Leu, Andy O., Aoki, Masataka, Tyson, Gene W. and Orphan, Victoria J. (2021). Sulfate differentially stimulates but is not respired by diverse anaerobic methanotrophic archaea. The ISME Journal, 16 (1), 168-177. doi: 10.1038/s41396-021-01047-0
Shi, Ling-Dong, Lv, Pan-Long, McIlroy, Simon J., Wang, Zhen, Dong, Xiao-Li, Kouris, Angela, Lai, Chun-Yu, Tyson, Gene W., Strous, Marc and Zhao, He-Ping (2021). Methane-dependent selenate reduction by a bacterial consortium. ISME Journal, 15 (12), 3683-3692. doi: 10.1038/s41396-021-01044-3
Pribyl, Alena L., Parks, Donovan H., Angel, Nicola Z., Boyd, Joel A., Hasson, Alexander G., Fang, Liang, MacDonald, Samantha L., Wills, Blake A., Wood, David L. A., Krause, Lutz, Tyson, Gene W. and Hugenholtz, Philip (2021). Critical evaluation of faecal microbiome preservation using metagenomic analysis. ISME Communications, 1 (1) 14, 14. doi: 10.1038/s43705-021-00014-2
Parks, Donovan H., Rigato, Fabio, Vera-Wolf, Patricia, Krause, Lutz, Hugenholtz, Philip, Tyson, Gene W. and Wood, David L. A. (2021). Evaluation of the microba community profiler for taxonomic profiling of metagenomic datasets from the human gut microbiome. Frontiers in Microbiology, 12 643682, 1-15. doi: 10.3389/fmicb.2021.643682
Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I-Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric ... Eloe-Fadrosh, Emiley A. (2021). Author Correction: A genomic catalog of Earth’s microbiomes (Nature Biotechnology, (2021), 39, 4, (499-509), 10.1038/s41587-020-0718-6). Nature Biotechnology, 39 (4), 521-521. doi: 10.1038/s41587-021-00898-4
Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I-Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric ... Eloe-Fadrosh, Emiley A. (2021). A genomic catalog of Earth’s microbiomes. Nature Biotechnology, 39 (4), 499-509. doi: 10.1038/s41587-020-0718-6
Nayfach, Stephen, Roux, Simon, Seshadri, Rekha, Udwary, Daniel, Varghese, Neha, Schulz, Frederik, Wu, Dongying, Paez-Espino, David, Chen, I-Min, Huntemann, Marcel, Palaniappan, Krishna, Ladau, Joshua, Mukherjee, Supratim, Reddy, T. B.K., Nielsen, Torben, Kirton, Edward, Faria, José P., Edirisinghe, Janaka N., Henry, Christopher S., Jungbluth, Sean P., Chivian, Dylan, Dehal, Paramvir, Wood-Charlson, Elisha M., Arkin, Adam P., Tringe, Susannah G., Visel, Axel, Abreu, Helena, Acinas, Silvia G., Allen, Eric ... Eloe-Fadrosh, Emiley A. (2021). Publisher Correction: A genomic catalog of Earth’s microbiomes (Nature Biotechnology, (2021), 39, 4, (499-509), 10.1038/s41587-020-0718-6). Nature Biotechnology, 39 (4), 520-520. doi: 10.1038/s41587-020-00769-4
Altemani, Faisal, Barrett, Helen L., Gomez-Arango, Luisa, Josh, Peter, McIntyre, H. David, Callaway, Leonie K., Morrison, Mark, Tyson, Gene W. and Dekker Nitert, Marloes (2021). Pregnant women who develop preeclampsia have lower abundance of the butyrate-producer Coprococcus in their gut microbiota. Pregnancy Hypertension, 23, 211-219. doi: 10.1016/j.preghy.2021.01.002
Wilson, R. M., Zayed, A. A., Crossen, K. B., Woodcroft, B., Tfaily, M. M., Emerson, J., Raab, N., Hodgkins, S. B., Verbeke, B., Tyson, G., Crill, P., Saleska, S., Chanton, J. P., Rich, V. I., IsoGenie Project Coordinators and IsoGenie Project Field Team (2021). Functional capacities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation. PLoS One, 16 (2) e0245857, 1-33. doi: 10.1371/journal.pone.0245857
Donner, Erica, Zamyadi, Arash, Jex, Aaron, Short, Michael, Drigo, Barbara, McCarthy, David, Crosbie, Nicholas, Ahmed, Warish, Mueller, Jochen, Thomas, Kevin, Monis, Paul, Keegan, Alex, Ginige, Maneesha, Hugenholtz, Philip, Tyson, Gene, Hill, Kelly and Blackall, Linda (2021). Wastewater monitoring for SARS-CoV-2. Microbiology Australia, 42 (1), 18-22. doi: 10.1071/ma21006
Zinke, Laura A., Evans, Paul N., Santos-Medellín, Christian, Schroeder, Alena L., Parks, Donovan H., Varner, Ruth K., Rich, Virginia I., Tyson, Gene W. and Emerson, Joanne B. (2021). Evidence for non-methanogenic metabolisms in globally distributed archaeal clades basal to the Methanomassiliicoccales. Environmental Microbiology, 23 (1), 340-357. doi: 10.1111/1462-2920.15316
Gagen, Emma J., Levett, Alan, Paz, Anat, Bostelmann, Heike, Valadares, Rafael Borges da Silva, Bitencourt, José Augusto Pires, Gastauer, Markus, Nunes, Gisele Lopes, Oliveira, Guilherme, Vasconcelos, Paulo M., Tyson, Gene W. and Southam, Gordon (2020). Accelerating microbial iron cycling promotes re‐cementation of surface crusts in iron ore regions. Microbial Biotechnology, 13 (6) 1751-7915.13646, 1960-1971. doi: 10.1111/1751-7915.13646
Bolduc, Benjamin, Hodgkins, Suzanne B., Varner, Ruth K., Crill, Patrick M., McCalley, Carmody K., Chanton, Jeffrey P., Tyson, Gene W., Riley, William J., Palace, Michael, Duhaime, Melissa B., Hough, Moira A., Saleska, Scott R., Sullivan, Matthew B., Rich, Virginia I., IsoGenie Project Coordinators, IsoGenie Project Team, A2A Project Team, Hoelzle, Robert and Evans, Paul (2020). The IsoGenie database: an interdisciplinary data management solution for ecosystems biology and environmental research. PeerJ, 8 e9467, e9467. doi: 10.7717/peerj.9467
Leu, Andy O., McIlroy, Simon J., Ye, Jun, Parks, Donovan H., Orphan, Victoria J. and Tyson, Gene W. (2020). Lateral gene transfer drives metabolic flexibility in the anaerobic methane-oxidizing archaeal family methanoperedenaceae. mBio, 11 (3) e01325-20, 1-16. doi: 10.1128/mBio.01325-20
Rinke, Christian, Rubino, Francesco, Messer, Lauren F., Youssef, Noha, Parks, Donovan H., Chuvochina, Maria, Brown, Mark, Jeffries, Thomas, Tyson, Gene W., Seymour, Justin R. and Hugenholtz, Philip (2020). Correction: A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.). The ISME Journal, 14 (3), 878-878. doi: 10.1038/s41396-019-0556-z
Leu, Andy O., Cai, Chen, McIlroy, Simon J., Southam, Gordon, Orphan, Victoria J., Yuan, Zhiguo, Hu, Shihu and Tyson, Gene W. (2020). Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae. The ISME Journal, 14 (4), 1030-1041. doi: 10.1038/s41396-020-0590-x
Gagen, Emma J., Zaugg, Julian, Tyson, Gene W. and Southam, Gordon (2019). Goethite Reduction by a Neutrophilic Member of the Alphaproteobacterial Genus Telmatospirillum. Frontiers in Microbiology, 10 2938, 2938. doi: 10.3389/fmicb.2019.02938
Luangthongkam, Pawarisa, Strong, Peter James, Syed Mahamud, Syarifah Nuraqmar, Evans, Paul, Jensen, Paul, Tyson, Gene, Laycock, Bronwyn, Lant, Paul Andrew and Pratt, Steven (2019). The effect of methane and odd-chain fatty acids on 3-hydroxybutyrate (3HB) and 3-hydroxyvalerate (3HV) synthesis by a Methylosinus-dominated mixed culture. Bioresources and Bioprocessing, 6 (1) 50. doi: 10.1186/s40643-019-0285-1
Robbins, Steven J., Singleton, Caitlin M., Chan, Cheong Xin, Messer, Lauren F., Geers, Aileen U., Ying, Hua, Baker, Alexander, Bell, Sara C., Morrow, Kathleen M., Ragan, Mark A., Miller, David J., Forêt, Sylvain, Voolstra, Christian R., Tyson, Gene W. and Bourne, David G. (2019). A genomic view of the reef-building coral Porites lutea and its microbial symbionts. Nature Microbiology, 4 (12), 2090-2100. doi: 10.1038/s41564-019-0532-4
Hua, Zheng-Shuang, Wang, Yu-Lin, Evans, Paul N., Qu, Yan-Ni, Goh, Kian Mau, Rao, Yang-Zhi, Qi, Yan-Ling, Li, Yu-Xian, Huang, Min-Jun, Jiao, Jian-Yu, Chen, Ya-Ting, Mao, Yan-Ping, Shu, Wen-Sheng, Hozzein, Wael, Hedlund, Brian P., Tyson, Gene W., Zhang, Tong and Li, Wen-Jun (2019). Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea. Nature Communications, 10 (1) 4574, 4574. doi: 10.1038/s41467-019-12574-y
Cai, Chen, Shi, Ying, Guo, Jianhua, Tyson, Gene W., Hu, Shihu and Yuan, Zhiguo (2019). Acetate production from anaerobic oxidation of methane via intracellular storage compounds. Environmental Science & Technology, 53 (13) acs.est.9b00077, 7371-7379. doi: 10.1021/acs.est.9b00077
Zhang, Xueqin, Xia, Jun, Pu, Jiaoyang, Cai, Chen, Tyson, Gene W., Yuan, Zhiguo and Hu, Shihu (2019). Biochar-mediated anaerobic oxidation of methane. Environmental Science and Technology, 53 (12) acs.est.9b01345, 6660-6668. doi: 10.1021/acs.est.9b01345
Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S. G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P. A., Jansson, Janet K., Kim, Jihyun F., Klenk, Hans-Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., McHardy, Alice C., Meyer, Folker, Ouzounis, Christos A. ... Xenarios, Ioannis (2019). Consent insufficient for data release Response. Science, 364 (6439), 446-446. doi: 10.1126/science.aax7509
Wilson, Rachel M., Neumann, Rebecca B., Crossen, Kelsey B., Raab, Nicole M., Hodgkins, Suzanne B., Saleska, Scott R., Bolduc, Ben, Woodcroft, Ben J., Tyson, Gene W., Chanton, Jeffrey P. and Rich, Virginia (2019). Microbial community analyses inform geochemical reaction network models for predicting pathways of greenhouse gas production. Frontiers in Earth Science, 7 59. doi: 10.3389/feart.2019.00059
Nguyen, Marcus, Long, S. Wesley, McDermott, Patrick F., Olsen, Randall J., Olson, Robert, Stevens, Rick L., Tyson, Gregory H., Zhao, Shaohua and Davis, James J. (2019). Using machine learning to predict antimicrobial MICs and associated genomic features for nontyphoidal Salmonella. Journal of Clinical Microbiology, 57 (2). doi: 10.1128/JCM.01260-18
Amann, Rudolf I., Baichoo, Shakuntala, Blencowe, Benjamin J., Bork, Peer, Borodovsky, Mark, Brooksbank, Cath, Chain, Patrick S. G., Colwell, Rita R., Daffonchio, Daniele G., Danchin, Antoine, de Lorenzo, Victor, Dorrestein, Pieter C., Finn, Robert D., Fraser, Claire M., Gilbert, Jack A., Hallam, Steven J., Hugenholtz, Philip, Ioannidis, John P. A., Jansson, Janet K., Kim, Jihyun F., Klenk, Hans-Peter, Klotz, Martin G., Knight, Rob, Konstantinidis, Konstantinos T., Kyrpides, Nikos C., Mason, Christopher E., McHardy, Alice C., Meyer, Folker, Ouzounis, Christos A. ... Xenarios, Ioannis (2019). Toward unrestricted use of public genomic data. Science, 363 (6425), 350-352. doi: 10.1126/science.aaw1280
Evans, Paul N., Boyd, Joel A., Leu, Andy O., Woodcroft, Ben J., Parks, Donovan H., Hugenholtz, Philip and Tyson, Gene W. (2019). An evolving view of methane metabolism in the Archaea. Nature Reviews Microbiology, 17 (4), 219-232. doi: 10.1038/s41579-018-0136-7
Boyd, Joel A., Jungbluth, Sean P., Leu, Andy O., Evans, Paul N., Woodcroft, Ben J., Chadwick, Grayson L., Orphan, Victoria J., Amend, Jan P., Rappé, Michael S. and Tyson, Gene W. (2019). Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi. The ISME Journal, 13 (5), 1269-1279. doi: 10.1038/s41396-018-0343-2
Martinez, Miguel A., Woodcroft, Ben J., Ignacio Espinoza, Julio C., Zayed, Ahmed A., Singleton, Caitlin M., Boyd, Joel A., Li, Yueh-Fen, Purvine, Samuel, Maughan, Heather, Hodgkins, Suzanne B., Anderson, Darya, Sederholm, Maya, Temperton, Ben, Bolduc, Benjamin, Saleska, Scott R., Tyson, Gene W. and Rich, Virginia I. (2019). Discovery and ecogenomic context of a global Caldiserica-related phylum active in thawing permafrost, Candidatus Cryosericota phylum nov., Ca. Cryosericia class nov., Ca. Cryosericales ord. nov., Ca. Cryosericaceae fam. nov., comprising the four species Cryosericum septentrionale gen. nov. sp. nov., Ca. C. hinesii sp. nov., Ca. C. odellii sp. nov., Ca. C. terrychapinii sp. nov. Systematic and Applied Microbiology, 42 (1), 54-66. doi: 10.1016/j.syapm.2018.12.003
Chuvochina, Maria, Rinke, Christian, Parks, Donovan H., Rappé, Michael S., Tyson, Gene W., Yilmaz, Pelin, Whitman, William B. and Hugenholtz, Philip (2019). The importance of designating type material for uncultured taxa. Systematic and Applied Microbiology, 42 (1), 15-21. doi: 10.1016/j.syapm.2018.07.003
Rinke, Christian, Rubino, Francesco, Messer, Lauren F., Youssef, Noha, Parks, Donovan H., Chuvochina, Maria, Brown, Mark, Jeffries, Thomas, Tyson, Gene W., Seymour, Justin R. and Hugenholtz, Philip (2018). A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.). The ISME Journal, 13 (3), 663-675. doi: 10.1038/s41396-018-0282-y
Trubl, Gareth, Jang, Ho Bin, Roux, Simon, Emerson, Joanne B., Solonenko, Natalie, Vik, Dean R., Solden, Lindsey, Ellenbogen, Jared, Runyon, Alexander T., Bolduc, Benjamin, Woodcroft, Ben J., Saleska, Scott R., Tyson, Gene W., Wrighton, Kelly C., Sullivan, Matthew B. and Rich, Virginia I. (2018). Soil viruses are underexplored players in ecosystem carbon processing. mSystems, 3 (5) e0007618. doi: 10.1128/mSystems.00076-18
Hoedt, Emily C., Parks, Donovan H., Volmer, James G., Rosewarne, Carly P., Denman, Stuart E., McSweeney, Christopher S., Muir, Jane G., Gibson, Peter R., Cuív, Páraic Ó, Hugenholtz, Philip, Tyson, Gene W. and Morrison, Mark (2018). Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size. ISME Journal, 12 (12), 2942-2953. doi: 10.1038/s41396-018-0225-7
Emerson, Joanne B., Roux, Simon, Brum, Jennifer R., Bolduc, Benjamin, Woodcroft, Ben J., Jang, Ho Bin, Singleton, Caitlin M., Solden, Lindsey M., Naas, Adrian E., Boyd, Joel A., Hodgkins, Suzanne B., Wilson, Rachel M., Trubl, Gareth, Li, Changsheng, Frolking, Steve, Pope, Phillip B., Wrighton, Kelly C., Crill, Patrick M., Chanton, Jeffrey P., Saleska, Scott R., Tyson, Gene W., Rich, Virginia I. and Sullivan, Matthew B. (2018). Host-linked soil viral ecology along a permafrost thaw gradient. Nature Microbiology, 3 (8), 870-880. doi: 10.1038/s41564-018-0190-y
Woodcroft, Ben J., Singleton, Caitlin M., Boyd, Joel A., Evans, Paul N., Emerson, Joanne B., Zayed, Ahmed A. F., Hoelzle, Robert D., Lamberton, Timothy O., McCalley, Carmody K., Hodgkins, Suzanne B., Wilson, Rachel M., Purvine, Samuel O., Nicora, Carrie D., Li, Changsheng, Frolking, Steve, Chanton, Jeffrey P., Crill, Patrick M., Saleska, Scott R., Rich, Virginia I. and Tyson, Gene W. (2018). Genome-centric view of carbon processing in thawing permafrost. Nature, 560 (7716), 49-54. doi: 10.1038/s41586-018-0338-1
Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B.K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R, Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Glöckner, Frank O., Gilbert, Jack A, Nelson, William C., Hallam, Steven J., Jungbluth, Sean P. ... Woyke, Tanja (2018). Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (Nature Biotechnology (2017) 35 (725-731) DOI: 10.1038/nbt.3893). Nature Biotechnology, 36 (7), 660-660. doi: 10.1038/nbt0718-660a
Raudsepp, Maija J., Fluggen, Markus, Shypanski, Adam H., Tyson, Gene W., Golding, Suzanne D. and Southam, Gordon (2018). Biogenic methane cycling in a laboratory model of an abandoned bituminous coal mine. Geomicrobiology Journal, 35 (6), 491-502. doi: 10.1080/01490451.2017.1392652
Singleton, Caitlin M., McCalley, Carmody K., Woodcroft, Ben J., Boyd, Joel A., Evans, Paul N., Hodgkins, Suzanne B., Chanton, Jeffrey P., Frolking, Steve, Crill, Patrick M., Saleska, Scott R., Rich, Virginia I. and Tyson, Gene W. (2018). Methanotrophy across a natural permafrost thaw environment. The ISME journal, 12 (10), 2544-2558. doi: 10.1038/s41396-018-0065-5
Cai, Chen, Leu, Andy O., Xie, Guo-Jun, Guo, Jianhua, Feng, Yuexing, Zhao, Jian-Xin, Tyson, Gene W., Yuan, Zhiguo and Hu, Shihu (2018). A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction. The ISME Journal, 12 (8), 1929-1939. doi: 10.1038/s41396-018-0109-x
Boyd, Joel A., Woodcroft, Ben J. and Tyson, Gene W. (2018). GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes. Nucleic Acids Research, 46 (10), e59-e59. doi: 10.1093/nar/gky174
Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Glockner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P. ... Woyke, Tanja (2018). Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (vol 35, pg 725, 2017). Nature Biotechnology, 36 (2), 196-196. doi: 10.1038/nbt0218-196a
Parks, Donovan H., Rinke, Christian, Chuvochina, Maria, Chaumeil, Pierre-Alain, Woodcroft, Ben J., Evans, Paul N., Hugenholtz, Philip and Tyson, Gene W. (2017). Author correction: recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nature Microbiology, 3 (2), 253-253. doi: 10.1038/s41564-017-0083-5
Tout, Jessica, Astudillo-García, Carmen, Taylor, Michael W., Tyson, Gene W., Stocker, Roman, Ralph, Peter J., Seymour, Justin R. and Webster, Nicole S. (2017). Redefining the sponge-symbiont acquisition paradigm: sponge microbes exhibit chemotaxis towards host-derived compounds. Environmental Microbiology Reports, 9 (6), 750-755. doi: 10.1111/1758-2229.12591
Shiffman, Miriam E, Soo, Rochelle M, Dennis, Paul G, Morrison, Mark, Tyson, Gene W and Hugenholtz, Philip (2017). Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion. PeerJ, 5, 1-32. doi: 10.7717/peerj.4075
Skennerton, Connor T., Chourey, Karuna, Iyer, Ramsunder, Hettich, Robert L., Tyson, Gene W. and Orphan, Victoria J. (2017). Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea (vol 8, e00530-17, 2017). Mbio, 8 (5), 1-2. doi: 10.1128/mBio.01561-17
Raudsepp, Maija J., Gagen, Emma J., Golding, Suzanne D., Tyson, Gene W. and Southam, Gordon (2017). The effect of bituminous coal on methanogenic mixed cultures and pure cultures of Methanococcus and Methanosarcina. Fuel, 205, 60-70. doi: 10.1016/j.fuel.2017.05.059
Cayford, Barry I., Jiang, Guangming, Keller, Jurg, Tyson, Gene and Bond, Philip L. (2017). Comparison of microbial communities across sections of a corroding sewer pipe and the effects of wastewater flooding. Biofouling, 33 (9), 780-792. doi: 10.1080/08927014.2017.1369050
Parks, Donovan H., Rinke, Christian, Chuvochina, Maria, Chaumeil, Pierre-Alain, Woodcroft, Ben J., Evans, Paul N., Hugenholtz, Philip and Tyson, Gene W. (2017). Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nature Microbiology, 2 (11), 1533-1542. doi: 10.1038/s41564-017-0012-7
Lambert, Bennett S., Raina, Jean-Baptiste, Fernandez, Vicente I., Rinke, Christian, Siboni, Nachshon, Rubino, Francesco, Hugenholtz, Philip, Tyson, Gene W., Seymour, Justin R. and Stocker, Roman (2017). A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities. Nature Microbiology, 2 (10), 1344-1349. doi: 10.1038/s41564-017-0010-9
Bowers, Robert M., Kyrpides, Nikos C., Stepanauskas, Ramunas, Harmon-Smith, Miranda, Doud, Devin, Reddy, T. B. K., Schulz, Frederik, Jarett, Jessica, Rivers, Adam R., Eloe-Fadrosh, Emiley A., Tringe, Susannah G., Ivanova, Natalia N., Copeland, Alex, Clum, Alicia, Becraft, Eric D., Malmstrom, Rex R., Birren, Bruce, Podar, Mircea, Bork, Peer, Weinstock, George M., Garrity, George M., Dodsworth, Jeremy A., Yooseph, Shibu, Sutton, Granger, Gloeckner, Frank O., Gilbert, Jack A., Nelson, William C., Hallam, Steven J., Jungbluth, Sean P. ... Woyke, Tanja (2017). Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology, 35 (8), 725-731. doi: 10.1038/nbt.3893
Bohorquez, H., Seal, J.B., Cohen, A.J., Kressel, A., Bugeaud, E., Bruce, D.S., Carmody, I.C., Reichman, T.W., Battula, N., Alsaggaf, M., Therapondos, G., Bzowej, N., Tyson, G., Joshi, S., Nicolau-Raducu, R., Girgrah, N. and Loss, G.E. (2017). Safety and outcomes in 100 consecutive donation after circulatory death liver transplants using a protocol that includes thrombolytic therapy. American Journal of Transplantation, 17 (8), 2155-2164. doi: 10.1111/ajt.14261
Pedroso, Marcelo Monteiro, Selleck, Christopher, Enculescu, Charmaine, Harmer, Jeffrey R., Mitic, Natasa, Craig, Whitney R., Helweh, Waleed, Hugenholtz, Philip, Tyson, Gene W., Tierney, David L., Larrabee, James A. and Schenk, Gerhard (2017). Characterization of a highly efficient antibiotic-degrading metallo-β-lactamase obtained from an uncultured member of a permafrost community. Metallomics, 9 (8), 1157-1168. doi: 10.1039/c7mt00195a
Skennerton, Connor T., Chourey, Karuna, Iyer, Ramsunder, Hettich, Robert L., Tyson, Gene W. and Orphan, Victoria J. (2017). Methane-fueled syntrophy through extracellular electron transfer: uncovering the genomic traits conserved within diverse bacterial partners of anaerobic methanotrophic archaea. MBio, 8 (4) e00530-17, e00530-17. doi: 10.1128/mBio.00530-17
Deng, Jia, McCalley, Carmody K., Frolking, Steve, Chanton, Jeff, Crill, Patrick, Varner, Ruth, Tyson, Gene, Rich, Virginia, Hines, Mark, Saleska, Scott R. and Li, Changsheng (2017). Adding stable carbon isotopes improves model representation of the role of microbial communities in peatland methane cycling. Journal of Advances in Modeling Earth Systems, 9 (2), 1412-1430. doi: 10.1002/2016MS000817
Dennis, Paul G., Virdis, Bernardino, Vanwonterghem, Inka, Hassan, Alif, Hugenholtz, Phil, Tyson, Gene W. and Rabaey, Korneel (2016). Anode potential influences the structure and function of anodic electrode and electrolyte-associated microbiomes. Scientific Reports, 6 (1) 39114, 39114. doi: 10.1038/srep39114
Santini, Talitha C., Malcolm, Laura I., Tyson, Gene W. and Warren, Lesley A. (2016). PH and organic carbon dose rates control microbially driven bioremediation efficacy in alkaline bauxite residue. Environmental Science and Technology, 50 (20), 11164-11173. doi: 10.1021/acs.est.6b01973
Vanwonterghem, Inka, Evans, Paul N., Parks, Donovan H., Jensen, Paul D., Woodcroft, Ben J., Hugenholtz, Philip and Tyson, Gene W. (2016). Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nature Microbiology, 1 (16170) 16170, 16170. doi: 10.1038/nmicrobiol.2016.170
Rinke, Christian, Low, Serene, Woodcroft, Ben J., Raina, Jean-Baptista, Skarshewski, Adam, Le, Xuyen H., Butler, Margaret K., Stocker, Roman, Seymour, Justin, Tyson, Gene W. and Hugenholtz, Philip (2016). Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics. PeerJ, 4 (9) e2486, 1-28. doi: 10.7717/peerj.2486
Vanwonterghem, Inka, Jensen, Paul D., Rabaey, Korneel and Tyson, Gene W. (2016). Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion. Environmental Microbiology, 18 (9), 3144-3158. doi: 10.1111/1462-2920.13382
Robbins, Steven J., Evans, Paul N., Parks, Donovan H., Golding, Suzanne D. and Tyson, Gene W. (2016). Genome-centric analysis of microbial populations enriched by hydraulic fracture fluid additives in a coal bed methane production well. Frontiers in Microbiology, 7 (731) 731, 1-15. doi: 10.3389/fmicb.2016.00731
Skennerton, Connor T., Haroon, Mohamed F., Briegel, Ariane, Shi, Jian, Jensen, Grant J., Tyson, Gene W. and Orphan, Victoria J. (2016). Phylogenomic analysis of Candidatus 'Izimaplasma' species: free-living representatives from a Tenericutes clade found in methane seeps. ISME Journal, 10 (11), 2679-2692. doi: 10.1038/ismej.2016.55
Angly, Florent E., Pantos, Olga, Morgan, Thomas C., Rich, Virginia, Tonin, Hemerson, Bourne, David G., Mercurio, Philip, Negri, Andrew P. and Tyson, Gene W. (2016). Diuron tolerance and potential degradation by pelagic microbiomes in the Great Barrier Reef lagoon. PeerJ, 4 (3) 1758, e1758. doi: 10.7717/peerj.1758
Raudsepp, M. J., Gagen, E. J., Evans, P., Tyson, G. W., Golding, S. D. and Southam, G. (2016). The influence of hydrogeological disturbance and mining on coal seam microbial communities. Geobiology, 14 (2), 163-175. doi: 10.1111/gbi.12166
Strong, Peter James, Laycock, Bronwyn, Syed Mahamud, Syarifah, Jensen, Paul, Lant, Paul A., Gene Tyson and Pratt, Steven (2016). The opportunity for high-performance biomaterials from methane. Microorganisms, 4 (1) 11, 11. doi: 10.3390/microorganisms4010011
Robbins, Steven J., Evans, Paul N., Esterle, Joan S., Golding, Suzanne D. and Tyson, Gene W. (2016). The effect of coal rank on biogenic methane potential and microbial composition. International Journal of Coal Geology, 154, 205-212. doi: 10.1016/j.coal.2016.01.001
Abdul Rahman, Nurdyana, Parks, Donovan H., Vanwonterghem, Inka, Morrison, Mark, Tyson, Gene W. and Hugenholtz, Philip (2016). A phylogenomic analysis of the bacterial phylum fibrobacteres. Frontiers in Microbiology, 6 (JAN) 1469, 1469.1-1469.15. doi: 10.3389/fmicb.2015.01469
Angly, Florent E., Heath, Candice, Morgan, Thomas C., Tonin, Hemerson, Rich, Virginia, Schaffelke, Britta, Bourne, David G. and Tyson, Gene W. (2016). Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events. PeerJ, 4 (1) e1511, 1-24. doi: 10.7717/peerj.1511
Barr, Jeremy J., Dutilh, Bas E., Skennerton, Connor T., Fukushima, Toshikazu, Hastie, Marcus L., Gorman, Jeffrey J., Tyson, Gene W. and Bond, Philip L. (2016). Metagenomic and metaproteomic analyses of Accumulibacter phosphatis enriched floccular and granular biofilm. Environmental Microbiology, 18 (1), 273-287. doi: 10.1111/1462-2920.13019
Kao-Kniffin, J., Woodcroft, B.J., Carver, S.M., Bockheim J.G., Handelsman, J., Tyson, G.W., Hinkel, K.M. and Mueller, C.W. (2015). Archaeal and bacterial communities across a chronosequence of drained lake basins in arctic Alaska. Scientific Reports, 5 (1) 18165. doi: 10.1038/srep18165
Evans, Paul N., Parks, Donovan H., Chadwick, Grayson L., Robbins, Steven J., Orphan, Victoria J., Golding, Suzanne D. and Tyson, Gene W. (2015). Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics. Science, 350 (6259), 434-438. doi: 10.1126/science.aac7745
ReFuGe 2020 Consortium, Voolstra, Christian R, Miller, David J., Ragan, Mark A., Hoffmann, Ary A., Hoegh-Guldberg, Ove, Bourne, David G., Ball, Eldon E., Ying, Hua, Forêt, Sylvain, Takahashi, Shunichi, Weynberg, Karen D., van Oppen, Madeleine J. H., Morrow, Kathleen, Chan, Cheong Xin, Rosic, Nedeljka, Leggat, William, Sprungala, Susanne, Imelfort, Michael, Tyson, Gene W., Kassahn, Karin S., Lundgren, Petra B., Beeden, Roger J., Ravasi, Timothy, Berumen, Michael L., Abal, Eva and Fyffe, Theresa (2015). The ReFuGe 2020 Consortium—using “omics” approaches to explore the adaptability and resilience of coral holobionts to environmental change. Frontiers in Marine Science, 2 (Art No.: 68) 68. doi: 10.3389/fmars.2015.00068
Patil, Sunil A., Arends, Jan B. A., Vanwonterghem, Inka, Van Meerbergen, Jarne, Guo, Kun, Tyson, Gene W. and Rabaey, Korneel (2015). Selective enrichment establishes a stable performing community for microbial electrosynthesis of acetate from CO2. Environmental Science and Technology, 49 (14), 8833-8843. doi: 10.1021/es506149d
Parks, Donovan H., Imelfort, Michael, Skennerton, Connor T., Hugenholtz, Philip and Tyson, Gene W. (2015). CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, 25 (7), 1043-1055. doi: 10.1101/gr.186072.114
Wang, Jack T.H., Daly, Joshua N., Willner, Dana L., Patil, Jayee, Hall, Roy A., Schembri, Mark A., Tyson, Gene W. and Hugenholtz, Philip (2015). Do You Kiss Your Mother with That Mouth? An Authentic Large-Scale Undergraduate Research Experience in Mapping the Human Oral Microbiome. Journal of Microbiology and Biology Education, 16 (1), 50-60. doi: 10.1128/jmbe.v16i1.816
Liu, Yiwen, Sharma, Keshab R., Ni, Bing-Jie, Fan, Lu, Murthy, Sudhir, Tyson, Gene Q. and Yuan, Zhiguo (2015). Effects of nitrate dosing on sulfidogenic and methanogenic activities in sewer sediment. Water Research, 74, 155-165. doi: 10.1016/j.watres.2015.02.017
Soo, Rochelle M., Woodcroft, Ben J., Parks, Donovan H., Tyson, Gene W. and Hugenholtz, Philip (2015). Back from the dead; the curious tale of the predatory cyanobacterium Vampirovibrio chlorellavorus.. PeerJ, 2015 (5) e968, Art. No.: e968-Art. No.: e968. doi: 10.7717/peerj.968
Hu, Shihu, Zeng, Raymond J., Haroon, Mohamed F., Keller, Jurg, Lant, Paul A., Tyson, Gene W. and Yuan, Zhiguo (2015). A laboratory investigation of interactions between denitrifying anaerobic methane oxidation (DAMO) and anammox processes in anoxic environments. Scientific Reports, 5 (8706) 8706, 1-9. doi: 10.1038/srep08706
Vanwonterghem, Inka, Jensen, Paul D., Rabaey, Korneel and Tyson, Gene W. (2015). Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters.. Scientific Reports, 5 (1) 8496, 8496. doi: 10.1038/srep08496
Pantos, Olga, Bongaerts, Pim, Dennis, Paul G., Tyson, Gene W. and Hoegh-Guldberg, OVe (2015). Habitat-specific environmental conditions primarily control the microbiomes of the coral Seriatopora hystrix. The ISME Journal, 9 (9), 1916-1927. doi: 10.1038/ismej.2015.3
Sekiguchi, Yuji, Ohashi, Akiko, Parks, Donovan H., Yamauchi, Toshihiro, Tyson, Gene W. and Hugenholtz, Philip (2015). First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking. PeerJ, 3 (e740) e740, 1-24. doi: 10.7717/peerj.740
Waldor, Matthew K., Tyson, Gene, Borenstein, Elhanan, Ochman, Howard, Moeller, Andrew, Finlay, Brett B., Kong, Hedi H., Gordon, Jeffrey I., Nelson, Karen E., Dabbagh, Karim and Smith, Hamilton (2015). Where next for microbiome research?. PLoS Biology, 13 (1), 1-9. doi: 10.1371/journal.pbio.1002050
Susilawati, Rita, Evans, Paul N., Esterle, Joan S., Robbins, Steven J., Tyson, Gene W., Golding, Suzanne D. and Mares, Tennille E. (2015). Temporal changes in microbial community composition during culture enrichment experiments with Indonesian coals. International Journal of Coal Geology, 137, 66-76. doi: 10.1016/j.coal.2014.10.015
Tout, Jessica, Jeffries, Thomas C., Petrou, Katherina, Tyson, Gene W., Webster, Nicole S., Garren, Melissa, Stocker, Roman, Ralph, Peter J. and Seymour, Justin R. (2015). Chemotaxis by natural populations of coral reef bacteria.. ISME Journal, 9 (8), 1764-1777. doi: 10.1038/ismej.2014.261
McCalley, Carmody K., Woodcroft, Ben J., Hodgkins, Suzanne B., Wehr, Richard A., Kim, Eun-Hae, Mondav, Rhiannon, Crill, Patrick M., Chanton, Jeffrey P., Rich, Virginia I., Tyson, Gene W. and Saleska, Scott R. (2014). Methane dynamics regulated by microbial community response to permafrost thaw. Nature, 514 (7523), 478-481. doi: 10.1038/nature13798
Imelfort, Michael, Parks, Donovan, Woodcroft, Ben J., Dennis, Paul, Hugenholtz, Philip and Tyson, Gene W. (2014). GroopM: an automated tool for the recovery of population genomes from related metagenomes. PeerJ, 2014 (1) e603, 1-16. doi: 10.7717/peerj.603
Skennerton, Connor T., Barr, Jeremy J., Slater, Frances R., Bond, Philip L. and Tyson, Gene W. (2014). Expanding our view of genomic diversity in Candidatus Accumulibacter clades. Environmental Microbiology, 17 (5), 1574-1585. doi: 10.1111/1462-2920.12582
Parks, Donovan H., Tyson, Gene W., Hugenholtz, Philip and Beiko, Robert G. (2014). STAMP: Statistical analysis of taxonomic and functional profiles.. Bioinformatics., 30 (21), 3123-3124. doi: 10.1093/bioinformatics/btu494
Angly, Florent E., Fields, Christopher J. and Tyson, Gene W. (2014). The Bio-Community Perl toolkit for microbial ecology. Bioinformatics, 30 (13), 1926-1927. doi: 10.1093/bioinformatics/btu130
Vanwonterghem, Inka, Jensen, Paul D., Ho, Dang P., Batstone Damien J. and Tyson, Gene W. (2014). Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques. Current Opinion in Biotechnology, 27, 55-64. doi: 10.1016/j.copbio.2013.11.004
De Vrieze, Jo, Gildemyn, Sylvia, Arends, Jan B. A., Vanwonterghem, Inka, Verbeken, Kim, Boon, Nico, Verstraete, Willy, Tyson, Gene W., Hennebel, Tom and Rabaey, Korneel (2014). Biomass retention on electrodes rather than electrical current enhances stability in anaerobic digestion. Water Research, 54, 211-221. doi: 10.1016/j.watres.2014.01.044
Vanwonterghem, Inka, Jensen, Paul D., Dennis, Paul G., Hugenholtz, Philip, Rabaey, Korneel and Tyson, Gene W. (2014). Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters. ISME Journal, Advance Online (10), 1-14. doi: 10.1038/ismej.2014.50
Angly, Florent E., Dennis, Paul G., Skarshewski, Adam, Vanwonterghem, Inka, Hugenholtz, Philip and Tyson, Gene W. (2014). CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction. Microbiome, 2 (11) 11, 11. doi: 10.1186/2049-2618-2-11
Soo, Rochelle M., Skennerton, Connor T., Sekiguchi, Yuji, Imelfort, Michael, Paech, Samuel J., Dennis, Paul G., Steen, Jason A., Parks, Donovan H., Tyson, Gene W. and Hugenholtz, Philip (2014). An expanded genomic representation of the phylum Cyanobacteria. Genome Biology and Evolution, Advance Access (5), 1-42. doi: 10.1093/gbe/evu073
Mondav, Rhiannon, Woodcroft, Ben J., Kim, Eun-Hae, McCalley, Carmody K., Hodgkins, Suzanne B., Crill, Patrick M., Chanton, Jeffrey, Hurst, Gregory B., VerBerkmoes, Nathan C., Saleska, Scott R., Hugenholtz, Philip, Rich, Virginia I. and Tyson, Gene W. (2014). Discovery of a novel methanogen prevalent in thawing permafrost. Nature Communications, 5 (1) 3212, 3212.1-3212.7. doi: 10.1038/ncomms4212
Pervin, Hasina M., Dennis, Paul G., Lim, Hui J., Tyson, Gene W., Batstone, Damien J. and Bond, Philip L. (2013). Drivers of microbial community composition in mesophilic and thermophilic temperature-phased anaerobic digestion pre-treatment reactors. Water Research, 47 (19), 7098-7108. doi: 10.1016/j.watres.2013.07.053
Haroon, Mohamed F., Hu, Shihu, Shi, Ying, Imelfort, Michael, Keller, Jurg, Hugenholtz, Philip, Yuan, Zhiguo and Tyson, Gene W. (2013). Erratum: Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature, 501 (7468), 578-578. doi: 10.1038/nature12619
Dove, Sophie G., Kline, David I., Pantos, Olga, Angly, Florent E., Tyson, Gene W. and Hoegh-Guldberg, Ove (2013). Future reef decalcification under a business-as-usual CO2 emission scenario. Proceedings of the National Academy of Sciences of the United States of America, 110 (38), 15342-15347. doi: 10.1073/pnas.1302701110
Bourne, David G, Dennis, Paul G., Uthicke, Sven, Soo, Rochelle M., Tyson, Gene W. and Webster, Nicole (2013). Coral reef invertebrate microbiomes correlate with the presence of photosymbionts. Isme Journal, 7 (7), 1459-1459. doi: 10.1038/ismej.2013.71
Bourne, David G., Dennis, Paul G., Uthicke, Sven, Soo, Rochelle M., Tyson, Gene W. and Webster, Nicole (2013). Coral reef invertebrate microbiomes correlate with the presence of photosymbionts. Isme Journal, 7 (7), 1452-1458. doi: 10.1038/ismej.2012.172
Dennis, Paul G., Harnisch, Falk, Yeoh, Yun Kit, Tyson, Gene W. and Rabaey, Korneel (2013). Dynamics of cathode-associated microbial communities and metabolite profiles in a glycerol-fed bioelectrochemical system. Applied and Environmental Microbiology, 79 (13), 4008-4014. doi: 10.1128/AEM.00569-13
Albertsen, Mads, Hugenholtz, Philip, Skarshewski, Adam, Nielsen, Kare L., Tyson, Gene W. and Nielsen, Per H. (2013). Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nature Biotechnology, 31 (6), 533-538+. doi: 10.1038/nbt.2579
Solonenko, Sergei A., Ignacio-Espinoza, J. Cesar, Alberti, Adriana, Cruaud, Corinne, Hallam, Steven, Konstantinidis, Kostas, Tyson, Gene, Wincker, Patrick and Sullivan, Matthew B. (2013). Sequencing platform and library preparation choices impact viral metagenomes. Bmc Genomics, 14 (1) 320, 320.1-320.12. doi: 10.1186/1471-2164-14-320
Bragg, Lauren M., Stone, Glenn, Butler, Margaret K., Hugenholtz, Philip and Tyson, Gene W. (2013). Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data. Plos Computational Biology, 9 (4) e1003031, e1003031.1-e1003031.18. doi: 10.1371/journal.pcbi.1003031
Dennis, Paul G., Seymour, Justin, Kumbun, Kimber and Tyson, Gene W. (2013). Diverse populations of lake water bacteria exhibit chemotaxis towards inorganic nutrients. ISME Journal, 7 (8), 1661-1664. doi: 10.1038/ismej.2013.47
Skennerton, Connor T., Imelfort, Michael and Tyson, Gene W. (2013). Crass: identification and reconstruction of CRISPR from unassembled metagenomic data. Nucleic Acids Research, 41 (10), e105.1-e105.10. doi: 10.1093/nar/gkt183
Carvalhais, Lilia C., Dennis, Paul G., Badri, Dayakar V., Tyson, Gene W., Vivanco, Jorge M. and Schenk, Peer M. (2013). Activation of the jasmonic acid plant defence pathway alters the composition of rhizosphere bacterial communities. PLoS ONE, 8 (2) e56457, e56457. doi: 10.1371/journal.pone.0056457
Haroon, Mohamed F., Hu, Shihu, Shi, Ying, Imelfort, Michael, Keller, Jurg, Hugenholtz, Philip, Yuan, Zhiguo and Tyson, Gene W. (2013). Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature, 500 (7464), 567-570. doi: 10.1038/nature12375
Haroon, Mohamed F., Skennerton, Connor T., Steen, Jason A., Lachner, Nancy, Hugenholtz, Philip and Tyson, Gene W. (2013). In-solution fluorescence in situ hybridization and fluorescence-activated cell sorting for single cell and population genome recovery. Methods in Enzymology, 531, 3-19. doi: 10.1016/B978-0-12-407863-5.00001-0
Dennis, Paul G., Guo, Kun, Imelfort, Michael, Jensen, Paul, Tyson, Gene W. and Rabaey, Korneel (2012). Spatial uniformity of microbial diversity in a continuous bioelectrochemical system. Bioresource Technology, 129 (10), 599-605. doi: 10.1016/j.biortech.2012.11.098
Carvalhais, Lilia C., Dennis, Paul G., Tyson, Gene W. and Schenk, Peer M. (2012). Application of metatranscriptomics to soil environments. Journal of Microbiological Methods, 91 (2), 246-251. doi: 10.1016/j.mimet.2012.08.011
Cayford, Barry I., Dennis, Paul G., Keller, Jurg, Tyson, Gene W. and Bond, Philip L. (2012). High-throughput amplicon sequencing reveals distinct communities within a corroding concrete sewer system. Applied and Environmental Microbiology, 78 (19), 7160-7162. doi: 10.1128/AEM.01582-12
Angly, Florent E., Willner, Dana, Rohwer, Forest, Hugenholtz, Philip and Tyson, Gene W. (2012). Grinder: a versatile amplicon and shotgun sequence simulator. Nucleic Acids Research, 40 (12), e94.1-e94.8. doi: 10.1093/nar/gks251
Bragg, Lauren, Stone, Glenn, Imelfort, Michael, Hugenholtz, Philip and Tyson, Gene W. (2012). Fast, accurate error-correction of amplicon pyrosequences using Acacia. Nature Methods, 9 (5), 245-246. doi: 10.1038/nmeth.1990
Shi, Yanmei, Tyson, Gene, Eppley, John M. and DeLong, Edward F. (2011). Integrated metatranscriptomic and metagenomic analyses of stratified microbial assemblages in the open ocean. The ISME Journal, 5 (6), 999-1013. doi: 10.1038/ismej.2010.189
Skennerton, Connor T., Angly, Florent E., Breitbart, Mya, Bragg, Lauren, He, Shaomei, McMahon, Katherine D., Hugenholtz, Philip and Tyson, Gene W. (2011). Phage encoded H-NS: A potential Achilles heel in the bacterial defence system. Plos One, 6 (5) e20095, e20095-1-e20095-7. doi: 10.1371/journal.pone.0020095
Angly, Florent and Tyson, Gene (2011). Are divergent viral communities controlling individual gut microbiota?. Medecine Sciences, 27 (3), 229-231. doi: 10.1051/medsci/2011273229
Yilmaz, S, Haroon, MF, Rabkin, BA, Tyson, GW and Hugenholtz, P (2010). Fixation-free fluorescence in situ hybridization for targeted enrichment of microbial populations. The ISME Journal, 4 (10), 1352-1356. doi: 10.1038/ismej.2010.73
Shi, Yanmei, Tyson, Gene W. and DeLong, Edward F. (2009). Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. Nature, 459 (7244), 266-269. doi: 10.1038/nature08055
Baker, Brett J., Tyson, Gene W., Goosherst, Lindsey and Banfield, Jillian F. (2009). Insights into the Diversity of Eukaryotes in Acid Mine Drainage Biofilm Communities. Applied and Environmental Microbiology, 75 (7), 2192-2199. doi: 10.1128/AEM.02500-08
Martinex, Asuncion, Tyson, Gene W. and DeLong, Edward F. (2009). Widespread known and novel phosphonate utilization pathways in marine bacteria revealed by functional screening and metagenomic analyses. Environmental Microbiology, 12 (1), 222-238. doi: 10.1111/j.1462-2920.2009.02062.x
Hugenhotz, Philip and Tyson, Gene W. (2008). Microbiology: Metagenomics. Nature, 455 (7212), 481-483. doi: 10.1038/455481a
Frias-Lopez, Jorge, Shi,Yanmei, Tyson, Gene, Coleman, Maureen, Schuster, Stephan, Chisholm, Sallie and DeLong, Edward (2008). Microbial community gene expression in ocean surface waters. Proceedings of the National Academy of Sciences of the United States of America, 105 (10), 3805-3810. doi: 10.1073/pnas.0708897105
Tyson, Gene W. and Banfield, Jillian F. (2008). Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environmental Microbiology, 10 (1), 200-207. doi: 10.1111/j.1462-2920.2007.01444.x
Eppley John M., Tyson Gene W., Getz Wayne M. and Banfield Jillian F. (2007). Strainer: Software for analysis of population variation in community genomic datasets. BMC Bioinformatics, 8 (398) 398, 1-11. doi: 10.1186/1471-2105-8-398
Eppley, John M., Tyson, Gene W., Getz, Wayne M. and Banfield, Jillian F. (2007). Genetic exchange across a species boundary in the Archaeal genus Ferroplasma. Genetics, 177 (1), 407-416. doi: 10.1534/genetics.107.072892
Lo, Ian, Denef, Vincent J., VerBerkmoes, Nathan C., Shah, Manesh B., Goltsman, Daniela, DiBartolo, Genevieve, Tyson, Gene W., Allen, Eric E., Ram, Rachna J., Detter, J. Chris, Richardson, Paul, Thelen, Michael P., Hettich, Robert L. and Banfield, Jillian F. (2007). Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria. Nature, 446 (7135), 537-541. doi: 10.1038/nature05624
Allen, Eric E., Tyson, Gene W., Whitaker, Rachel J., Detter, John C., Richardson, Paul M. and Banfield, Jillian F. (2007). Genome dynamics in a natural archaeal population. Proceedings of the National Academy of Sciences of the United States of America, 104 (6), 1883-1888. doi: 10.1073/pnas.0604851104
Baker, Brett J., Tyson, Gene W., Webb, Richard I., Flanagan, Judith, Hugenholtz, Philip, Allen, Eric E. and Banfield, Jillian F. (2006). Lineages of acidophilic archaea revealed by community genomic analysis. Science, 314 (5807), 1933-1935. doi: 10.1126/science.1132690
Tyson, Gene W., Lo, Ian, Baker, Brett J., Allen, Eric E., Hugenholtz, Philip and Banfield, Jillian F. (2005). Genome-Directed Isolation of the Key Nitrogen Fixer Leptospirillum ferrodiazotrophum sp. nov. from an Acidophilic Microbial Community. Applied and Environmental Microbiology, 71 (10), 6319-6324. doi: 10.1128/AEM.71.10.6319-6324.2005
Tyson, Gene W. and Banfield, Jillian F. (2005). Cultivating the uncultivated: A community genomics perspective. Trends in Microbiology, 13 (9), 411-415. doi: 10.1016/j.tim.2005.07.003
Ram, Rachna J., VerBerkmoes, Nathan C., Thelen, Michael P., Tyson, Gene W., Baker, Brett J., Blake, Robert C., Shah, Manesh, Hettich, Robert L. and Banfield, Jillian F. (2005). Community proteomics of a natural microbial biofilm. Science, 308 (5730), 1915-1920. doi: 10.1126/science.1109070
Banfield, , Tyson, GW, Allen, EE and Whitaker, RJ (2005). The search for a molecular-level understanding of the processes that underpin the earth's biogeochemical cycles. Molecular Geomicrobiology, 59 (1), 1-7. doi: 10.2138/rmg.2005.59.1
Tyson, Gene W., Chapman, Jarrod, Hugenholtz, Philip, Allen, Eric E., Ram, Rachna J., Richardson, Paul M., Solovyev, Victor V., Rubin, Edward M., Rokhsar, Daniel S. and Banfield, Jillian F. (2004). Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature, 428 (6978), 37-43. doi: 10.1038/nature02340
Bjornsson, Lovisa, Hugenholtz, Philip, Tyson, Gene W. and Blackall, Linda L. (2002). Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Microbiology, 148 (8), 2309-2318. doi: 10.1099/00221287-148-8-2309
Hugenholtz, P., Tyson, G. W. and Blackall, L. L. (2002). Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization. Methods in molecular biology (Clifton, N.J.), 179, 29-42.
Hugenholtz, Philip, Tyson, Gene W., Webb, Richard I., Wagner, Ankia M. and Blackall, Linda L. (2001). Investigation of candidate division TM7, a recently recognized major lineage of the domain bacteria with no known pure-culture representatives. Applied And Environmental Microbiology, 67 (1), 411-419. doi: 10.1128/AEM.67.1.411-419.2001

Conference Papers

Shah, Ayesha, Sternes, Peter R., Kang, Seungha, Pintos, Camila Ayala, Fairlie, Thomas, Tyson, Gene W., Morrison, Mark and Holtmann, Gerald J. (2023). DENSITY OF THE MUCOSAL BACTERIAL COLONIZATION ALONG THE GASTROINTESTINAL TRACT IN HEALTH AND DISEASE. Digestive Disease Week (DDW), Chicago Il, May 06-09, 2023. PHILADELPHIA: W B SAUNDERS CO-ELSEVIER INC.
Shah, Ayesha, Sternes, Peter R., Pintos, Camila Ayala, Kang, Seungha, Jones, Michael P., Tyson, Gene, Morrison, Mark and Holtmann, Gerald J. (2022). Influence of proton pump inhibitors on the mucosa associated microbiome in the small intestine and colon. American Gastroenterological Association Conference 2022, Chicago, IL United States, 6-9 May 2022. Philadelphia, PA United States: Elsevier. doi: 10.1016/s0016-5085(22)62401-6
Cuiv, Paraic O., Krause, Lutz, Wood, David, Hugenholtz, Phil and Tyson, Gene (2020). Fast forward bioprospecting of the gut microbiota for novel live biotherapeutics and anti-inflammatory bioactives. FNM 2020 ‐ 4th Meeting of the Federation of Neurogastroenterology and Motility, Adelaide, SA Australia, 25 - 28 March 2020. Chichester, West Sussex United Kingdom: Wiley-Blackwell.
Shah, Ayesha, Kang, Seungha, Tyson, Gene, Zaugg, Julian, Hugenholtz, Phil, Morrison, Mark and Holtmann, Gerald J. (2020). Variations of the mucosa associated microbiota along the human gastrointestinal tract in health and inflammatory bowel disease. Crohn's and Colitis Congress, Austin, TX, United States, 23-25 January 2020. Philadelphia, PA, United States: Elsevier . doi: 10.1016/s0016-5085(20)32052-7
Santini, T. C., Warren, K., Raudsepp, M., Carter, N., Hamley, D., McCosker, C., Couperthwaite, S., Southam, G., Tyson, G. W. and Warren, L. A. (2019). Accelerating bauxite residue remediation with microbial biotechnology. Light Metals Symposium held at the TMS Annual Meeting and Exhibition, 2019, San Antonio, TX United States, 10-14 March 2019. Cham, Switzerland: Springer. doi: 10.1007/978-3-030-05864-7_10
Woodcroft, Ben J., Boyd, Joel A. and Tyson, Gene W. (2016). OrfM: a fast open reading frame predictor for metagenomic data. Oxford, United Kingdom: Oxford University Press. doi: 10.1093/bioinformatics/btw241
Wang, Jack T.H., Daly, Joshua N., Willner, Dana L., Patil, Jayee, Hall, Roy, Tyson, Gene W., Hugenholtz, Philip and Schembri, Mark A. (2014). Embedding Undergraduate Research throughout Microbiology Majors. ASM Conference for Undergraduate Educators, Danvers, MA United States, 15-18 May 2014.
Golding, S. D., Hamilton, S. K., Baublys, K. A., Esterle, J. S., Tyson, G., Robbins, S., Rudolph, V., Zheng, H., Gilcrease, P. C. and Papendick, S. L. (2013). Future gas through bioconversion of waster coal. Goldschmidt Conference 2013, Florence, Italy, 25-30 August 2013. Twickenham, Middlesex, United Kingdom: Mineralogical Society. doi: 10.1180/minmag.2013.077.5.7
Pervin, H.P., Hastie, M., Dennis, P.G., Jensen, P., Gorman, J., Tyson, G.W., Batstone, D. and Bond, P.L. (2013). Microbial community composition and function associated with enhanced anaerobic digestion of organic biosolids.. 2nd Water Research Conference, Singapore EXPO, Singapore, 20-23 January, 2013.
Pervin, H.P., Dennis, P.G., Lim, H.J., Tyson, G.W., Batstone, D. and Bond, P.L. (2013). Microbial community dynamics correlate to reactor parameters and performance in a pre-treatment stage of temperature–phased anaerobic digestion.. 2nd Water Research Conference, Singapore International Convention and Exhibition Centre, 20-23 January 2013.
Cayford, Barry I., Dennis, Paul G., Tyson, Gene W. and Bond, Philip L. (2012). Microbial communities involved in the corrosion of concrete sewer infrastructure. 14th International Symposium on Microbial Ecology (ISME14), Copenhagan, Denmark, 19-24 August 2012.
Cayford, B. I., Tyson, G. W., Dennis, P. G., Keller, J. and Bond, P .L. (2012). Microbial corrosion of concrete sewer pipes. Australian Society for Microbiology Annual Scientific Meeting (ASM2012), Brisbane, Australia, 1-4 July 2012.
Pervin, H. P., Hastie, M., Dennis, P. G., Gorman, J., Tyson, G. W., Batstone, D. and Bond, P. L. (2012). Determining ecosystem community and function important for enhanced anaerobic digestion of organic biosolids. Australian Society for Microbiology Annual Scientific Meeting (ASM2012), Brisbane, Australia, 1-4 July 2012.
Barr, Jeremy, Dutilh, Bas, Cook, Andrew, Fukushima, Toshikazu, Hastie, Marcus, Gorman, Jeffery, Pan, Chongle, Hettich, Rorbert, Tyson, Gene and Bond, Philip (2012). Metaproteomic and metagenomic characterisation of floccular and granular phosphorus removal biofilms. 14th International Symposium on Microbial Ecology (ISME14), Copenhagan, Denmark, 19-24 August 2012.
Cayford, B. I., Tyson, G. W., Keller, J and Bond, P. L. (2011). Microbial community composition associated with sewer corrosion. Engineers Australia Queensland Water Panel's Post-Graduate Presentation Evening, Engineers Australia Queensland Branch, 18 May 2011.
Papendick, Samuel, Tyson, Gene, Esterle, Joan, Golding, Suzanne D., Rudolph, Victor and Gilcrease, Patrick C. (2011). Coal-to-biomethane potential of microbial consortia native to coal seam formation waters. Sustainable Engineering Forum: Core Programming Topic at the 2011 AIChE Annual Meeting, Minneapolis, MN, October 16, 2011-October 21, 2011. New York NY United States: AIChE.
Papendick, Samuel, Tyson, Gene, Esterle, Joan, Golding, Suzanne D., Rudolph, Victor and Gilcrease, Patrick C. (2011). Coal-to-biomethane potential of microbial consortia native to coal seam formation waters. Catalysis and Reaction Engineering Division - Core Programming Topic at the 2011 AIChE Annual Meeting, Minneapolis, MN, October 16, 2011-October 21, 2011. New York NY United States: AIChE.
Bender, Robert A., Downs, Diana, Kiley, Patricia, LaRossa, Robert A., Sonenshein, Abraham L., Storz, Gisela, Bender, Robert, Roth, John, Schilling, Christoff, Rine's, Jasper, Merrick, Mike, Tyson, Gene, Skovran, Elizabeth, Liao, J., Stephanopolous', Greg, Anesiades, Nikolas, San, Kai-Yu, Durot, Maxim, Reich, Claudia, De Crecy-Legard, Valerie, Dean's, Dennis, Barras, Frederic, Dwyer, Daniel, De Reuse, Hilde, Massé, Eric, Hwa, Terrance, Vanderpool, Carin, Henkin's, Tina, Warner, Digby ... Straight, Paul (2008). Bridges cnd Chasms: Summary of the IMAGE 2 meeting in Montreal, Canada, 30 April to 3 May 2007. American Society for Microbiology. doi: 10.1128/JB.01097-07
Whitaker, R, Allen, E, Tyson, G and Banfield, J (2005). Population dynamics in acid mine drainage biofilms from the Richmond Mine at Iron Mountain, California. 15th Annual V M Goldschmidt Conference, Moscow Id, May, 2005. OXFORD: PERGAMON-ELSEVIER SCIENCE LTD.
Ram, RJ, VerBerkmoes, N, Tyson, GW, Baker, BJ, Thelen, MP, Hettich, RL and Banfield, JF (2005). Challenges of life in an extremely acidic environment. 229th National Meeting of the American-Chemical-Society, San Diego Ca, Mar 13-17, 2005. WASHINGTON: AMER CHEMICAL SOC.

Research Report

Orphan, Victoria J., Tyson, Gene, Meile, Christof, McGlynn, Shawn, Yu, Hang, Chadwick, Grayson, Marlow, Jeffrey, Trembath-Reichert, Elizabeth, Dekas, Anne, Hettich, Robert, Pan, Chongle, Ellisman, Mark, Hatzenpichler, Roland, Skennerton, Connor and Scheller, Silvan (2017). Systems level dissection of anaerobic methane cycling: quantitative measurements of single cell ecophysiology, genetic mechanisms, and microbial interactions. Oak Ridge, TN, United States: Office of Scientific and Technical Information (OSTI). doi: 10.2172/1414771

Data Collections

Tyson, Gene and Rinke, Christian (2015). Microscale Experiments to Understand a Microscale World. The University of Queensland. (Dataset) doi: 10.48610/b5ed324
Parks, Donovan H., Imelfort, Michael, Skennerton, Connor T., Hugenholtz, Philip and Tyson, Gene W. (2015). CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes: supplemental material. Cold Spring Harbor Laboratory Press. (Dataset) doi: 10.14264/uql.2016.841

Areas of research

Molecular genetics and genomics theme