Dr Christian Rinke
ARC Future Fellow
School of Chemistry and Molecular Biosciences
+61 7 336 54957
Researcher biography
Christian Rinke is an ARC Future Fellow at the Australian Centre for Ecogenomics (ACE), University of Queensland, Australia. He received his PhD in Zoology from the Marine Biology Department at the University of Vienna, Austria and has since shifted his focus to the microbial world.
His research interests include genomics and the phylogeny and ecology of symbiotic and free living microbes. He focuses on the uncultured majority of microbes which elude current culturing efforts. This so called "Microbial Dark Matter" can only be explored with culture-independent approaches. Chris pioneered methods in high throughput single-cell genomics, the separation and sequencing of single bacterial and archaeal cells, and metagenomics, the direct sequencing of environmental samples. His lab uses both methods as well as other "omics" techniques to learn more about the phylogenetic and metabolic diversity encoded in microbial dark matter.
Book Chapter
Rinke, Christian (2018). Single-cell genomics of microbial dark matter. Microbiome analysis. (pp. 99-111) New York, United States: Humana Press. doi: 10.1007/978-1-4939-8728-3_7
Journal Articles
Parks, Donovan H., Chuvochina, Maria, Chaumeil, Pierre-Alain, Rinke, Christian, Mussig, Aaron J. and Hugenholtz, Philip (2020). Author Correction: A complete domain-to-species taxonomy for Bacteria and Archaea (Nature Biotechnology, (2020), 38, 9, (1079-1086), 10.1038/s41587-020-0501-8). Nature Biotechnology, 38 (9), 1098-1098. doi: 10.1038/s41587-020-0539-7
Parks, Donovan H., Chuvochina, Maria, Chaumeil, Pierre-Alain, Rinke, Christian, Mussig, Aaron J. and Hugenholtz, Philip (2020). A complete domain-to-species taxonomy for bacteria and archaea. Nature Biotechnology, 38 (9), 1098-1098. doi: 10.1038/s41587-020-0501-8
Džunková, Mária, Low, Soo Jen, Daly, Joshua N., Deng, Li, Rinke, Christian and Hugenholtz, Philip (2019). Defining the human gut host–phage network through single-cell viral tagging. Nature Microbiology, 4 (12), 2192-2203. doi: 10.1038/s41564-019-0526-2
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
Parks, Donovan H, Chuvochina, Maria, Waite, David W, Rinke, Christian, Skarshewski, Adam, Chaumeil, Pierre-Alain and Hugenholtz, Philip (2018). A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nature Biotechnology, 36 (10), 996-1004. doi: 10.1038/nbt.4229
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
Waite, David W., Vanwonterghem, Inka, Rinke, Christian, Parks, Donovan H., Zhang, Ying, Takai, Ken, Sievert, Stefan M., Simon, Jorg, Campbell, Barbara J., Hanson, Thomas E., Woyke, Tanja, Klotz, Martin G. and Hugenholtz, Philip (2018). Addendum: Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.) (vol 8, 682, 2017). Frontiers in Microbiology, 9 (APR) 772, 772. doi: 10.3389/fmicb.2018.00772
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
Hawley, Alyse K., Nobu, Masaru K., Wright, Jody J., Durno, W. Evan, Morgan-Lang, Connor, Sage, Brent, Schwientek, Patrick, Swan, Brandon K., Rinke, Christian, Torres-Beltran, Monica, Mewis, Keith, Liu, Wen-Tso, Stepanauskas, Ramunas, Woyke, Tanja and Hallam, Steven J. (2017). Diverse marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients. Nature Communications, 8 (1) 1507, 1507. doi: 10.1038/s41467-017-01376-9
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
Waite, David W., Vanwonterghem, Inka, Rinke, Christian, Parks, Donovan H. , Zhang, Ying, Takai, Ken, Sievert, Stefan M. , Simon, Joerg, Campbell, Barbara J. , Hanson, Thomas E. , Woyke, Tanja, Klotz, Martin G. and Hugenholtz, Philip (2017). Comparative genomic analysis of the class Epsilonproteobacteria and proposed reclassification to Epsilonbacteraeota (phyl. nov.). Frontiers in Microbiology, 8 (APR) 682 doi: 10.3389/fmicb.2017.00682.
Kublanov, Ilya V., Sigalova, Olga M., Gavrilov, Sergey N., Lebedinsky, Alexander V., Rinke, Christian, Kovaleva, Olga, Chernyh, Nikolai A., Ivanova, Natalia, Daum, Chris, Reddy, T. B. K., Klenk, Hans-Peter, Spring, Stefan, Göker, Markus, Reva, Oleg N., Miroshnichenko, Margarita L., Kyrpides, Nikos C., Woyke, Tanja, Gelfand, Mikhail S. and Bonch-Osmolovskaya, Elizaveta A. (2017). Genomic analysis of Caldithrix abyssi, the thermophilic anaerobic bacterium of the novel bacterial phylum Calditrichaeota. Frontiers in Microbiology, 8 (195) 195, 195. doi: 10.3389/fmicb.2017.00195
Lux, Markus, Kruger, Jan, Rinke, Christian, Maus, Irena, Schluter, Andreas, Woyke, Tanja, Sczyrba, Alexander and Hammer, Barbara (2016). Acdc - automated contamination detection and confidence estimation for single-cell genome data. BMC Bioinformatics, 17 (1) 543, 543. doi: 10.1186/s12859-016-1397-7
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
Nobu, Masaru K., Dodsworth, Jeremy A., Murugapiran, Senthil K., Rinke, Christian, Gies, Esther A., Webster, Gordon, Schwientek, Patrick, Kille, Peter, Parkes, R. John, Sass, Henrik, Jorgensen, Bo B., Weightman, Andrew J., Liu, Wen-Tso, Hallam, Steven J., Tsiamis, George, Woyke, Tanja and Hedlund, Brian P. (2016). Phylogeny and physiology of candidate phylum 'Atribacteria' (OP9/JS1) inferred from cultivation-independent genomics. The ISME Journal, 10 (2), 273-286. doi: 10.1038/ismej.2015.97
Clingenpeel, Scott, Clum, Alicia, Schwientek, Patrick, Rinke, Christian and Woyke, Tanja (2015). Reconstructing each cell's genome within complex microbial communities-dream or reality?. Frontiers in Microbiology, 5, 771. doi: 10.3389/fmicb.2014.00771
Rinke, Christian, Schwientek, Patrick, Sczyrba, Alexander, Ivanova, Natalia N., Anderson, Iain J., Cheng, Jan-Fang, Darling, Aaron, Malfatti, Stephanie, Swan, Brandon K., Gies, Esther A., Dodsworth, Jeremy A., Hedlund, Brian P., Tsiamis, George, Sievert, Stefan M., Liu, Wen-Tso, Eisen, Jonathan A., Hallam, Steven J., Kyrpides, Nikos C., Stepanauskas, Ramunas, Rubin, Edward M., Hugenholtz, Philip and Woyke, Tanja (2013). Insights into the phylogeny and coding potential of microbial dark matter. Nature, 499 (7459), 431-437. doi: 10.1038/nature12352
Bayer, Christoph, Heindl, Niels R, Rinke, Christian, Lücker, Sebastian, Ott, Joerg A and Bulgheresi, Silvia (2009). Molecular characterization of the symbionts associated with marine nematodes of the genus Robbea. Environmental microbiology reports, 1 (2), 136-144. doi: 10.1111/j.1758-2229.2009.00019.x
Dataset Collection
Tyson, Gene and Rinke, Christian (2015). Microscale Experiments to Understand a Microscale World. The University of Queensland. (Collection) doi: 10.14264/uql.2017.105