Dr Chris Rinke

Featured projects	Duration
Bacterial CRISPRi Genome Innovation Hub Collaborative Project (UQ infrastructure)	2023

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

Fan, Lu, Xu, Bu, Chen, Songze, Liu, Yang, Li, Fuyan, Xie, Wei, Prabhu, Apoorva, Zou, Dayu, Wan, Ru, Li, Hongliang, Liu, Haodong, Liu, Yuhang, Kao, Shuh-Ji, Chen, Jianfang, Zhu, Yuanqing, Rinke, Christian, Li, Meng, Zhu, Maoyan and Zhang, Chuanlun (2024). Gene inversion led to the emergence of brackish archaeal heterotrophs in the aftermath of the Cryogenian snowball earth. PNAS Nexus, 3 (2) pgae057. doi: 10.1093/pnasnexus/pgae057

Thomas, Marie C., Waugh, Gretel, Vanwonterghem, Inka, Webster, Nicole S., Rinke, Christian, Fisher, Rebecca, Luter, Heidi M. and Negri, Andrew P. (2023). Protecting the invisible: establishing guideline values for copper toxicity to marine microbiomes. Science of The Total Environment, 904 166658, 1-17. doi: 10.1016/j.scitotenv.2023.166658

Fan, Lu, Liu, Junfeng, Rinke, Christian, Baker, Brett J. and Zhang, Changyi (2023). Editorial: Diversity, ecology and evolution of archaeal viruses. Frontiers in Microbiology, 14 1333790, 1-2. doi: 10.3389/fmicb.2023.1333790

Chuvochina, Maria, Mussig, Aaron J., Chaumeil, Pierre-Alain, Skarshewski, Adam, Rinke, Christian, Parks, Donovan H. and Hugenholtz, Philip (2023). Proposal of names for 329 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes. FEMS Microbiology Letters, 370 fnad071, 1-33. doi: 10.1093/femsle/fnad071

Peng, Yi, Prabhu, Apoorva and Rinke, Chris (2023). Facing our plastic waste crisis: biorecycling as a promising solution. Microbiology Australia, 44 (1), 52-56. doi: 10.1071/ma23013

Rinke, Christian (2022). Mystery find of microbial DNA elements called Borgs. Nature, 610 (7933), 635-637. doi: 10.1038/d41586-022-02975-3

Medvedeva, Sofia, Sun, Jiarui, Yutin, Natalya, Koonin, Eugene V., Nunoura, Takuro, Rinke, Christian and Krupovic, Mart (2022). Three families of Asgard archaeal viruses identified in metagenome-assembled genomes. Nature Microbiology, 7 (7), 962-973. doi: 10.1038/s41564-022-01144-6

Sun, Jiarui, Prabhu, Apoorva, Aroney, Samuel T. N. and Rinke, Christian (2022). Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials. Microbial Genomics, 8 (6) 000842. doi: 10.1099/mgen.0.000842

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

Sun, Jiarui, Evans, Paul N., Gagen, Emma J., Woodcroft, Ben J., Hedlund, Brian P., Woyke, Tanja, Hugenholtz, Philip and Rinke, Christian (2022). Correction: Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota. ISME Communications, 2 (1) 6, 6. doi: 10.1038/s43705-021-00048-6

Hedlund, Brian P., Zhang, Chuanlun, Wang, Fengping, Rinke, Christian and Martin, William F. (2022). Editorial: ecology, metabolism and evolution of Archaea-perspectives from Proceedings of the International Workshop on Geo-Omics of Archaea. Frontiers in Microbiology, 12 827229, 827229. doi: 10.3389/fmicb.2021.827229

Parks, Donovan H., Chuvochina, Maria, Rinke, Christian, Mussig, Aaron J., Chaumeil, Pierre-Alain and Hugenholtz, Philip (2022). GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Research, 50 (D1), D785-D794. doi: 10.1093/nar/gkab776

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

Sun, Jiarui, Evans, Paul N., Gagen, Emma J., Woodcroft, Ben J., Hedlund, Brian P., Woyke, Tanja, Hugenholtz, Philip and Rinke, Christian (2021). Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages. ISME Communications, 1 (1) 30, 1-14. doi: 10.1038/s43705-021-00032-0

Rinke, Christian, Chuvochina, Maria, Mussig, Aaron J., Chaumeil, Pierre-Alain, Davín, Adrián A., Waite, David W., Whitman, William B., Parks, Donovan H. and Hugenholtz, Philip (2021). A standardized archaeal taxonomy for the Genome Taxonomy Database. Nature Microbiology, 6 (7), 946-959. doi: 10.1038/s41564-021-00918-8

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

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

Dombrowski, Nina, Williams, Tom A., Sun, Jiarui, Woodcroft, Benjamin J., Lee, Jun-Hoe, Minh, Bui Quang, Rinke, Christian and Spang, Anja (2020). Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution. Nature Communications, 11 (1) 3939, 3939. doi: 10.1038/s41467-020-17408-w

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

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

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

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

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

Tennessen, Kristin, Andersen, Evan, Clingenpeel, Scott, Rinke, Christian, Lundberg, Derek S, Han, James, Dangl, Jeff L, Ivanova, Natalia, Woyke, Tanja, Kyrpides, Nikos and Pati, Amrita (2015). ProDeGe: a computational protocol for fully automated decontamination of genomes. The ISME Journal, 10 (1), 269-272. doi: 10.1038/ismej.2015.100

Youssef, Noha H., Farag, Ibrahim F., Rinke, Christian, Hallam, Steven J., Woyke, Tanja and Elshahed, Mostafa S. (2015). In silico analysis of the metabolic potential and niche specialization of candidate phylum "Latescibacteria" (WS3). PLoS One, 10 (6) e0127499, 1-21. doi: 10.1371/journal.pone.0127499

Nobu, Masaru K., Narihiro, Takashi, Rinke, Christian, Kamagata, Yoichi, Tringe, Susannah G., Woyke, Tanja and Liu, Wen-Tso (2015). Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor. The ISME Journal, 9 (8), 1710-1722. doi: 10.1038/ismej.2014.256

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

Hedlund, Brian P., Dodsworth, Jeremy A., Murugapiran, Senthil K., Rinke, Christian and Woyke, Tanja (2014). Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter”. Extremophiles, 18 (5), 865-875. doi: 10.1007/s00792-014-0664-7

Youssef, Noha H., Rinke, Christian, Stepanauskas, Ramunas, Farag, Ibrahim, Woyke, Tanja and Elshahed, Mostafa S. (2014). Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum ‘Diapherotrites’. The ISME Journal, 9 (2), 447-460. doi: 10.1038/ismej.2014.141

Ivanova, N. N., Schwientek, P., Tripp, H. J., Rinke, C., Pati, A., Huntemann, M., Visel, A., Woyke, T., Kyrpides, N. C. and Rubin, E. M. (2014). Stop codon reassignments in the wild. Science, 344 (6186), 909-913. doi: 10.1126/science.1250691

Rinke, Christian, Lee, Janey, Nath, Nandita, Goudeau, Danielle, Thompson, Brian, Poulton, Nicole, Dmitrieff, Elizabeth, Malmstrom, Rex, Stepanauskas, Ramunas and Woyke, Tanja (2014). Obtaining genomes from uncultivated environmental microorganisms using FACS–based single-cell genomics. Nature Protocols, 9 (5), 1038-1048. doi: 10.1038/nprot.2014.067

Kamke, Janine, Rinke, Christian, Schwientek, Patrick, Mavromatis, Kostas, Ivanova, Natalia, Sczyrba, Alexander, Woyke, Tanja and Hentschel, Ute (2014). The candidate phylum Poribacteria by single-cell genomics: new insights into phylogeny, cell-compartmentation, eukaryote-like repeat proteins, and other genomic features. PLoS One, 9 (1) e87353, 1-10. doi: 10.1371/journal.pone.0087353

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

Kamke, Janine, Sczyrba, Alexander, Ivanova, Natalia, Schwientek, Patrick, Rinke, Christian, Mavromatis, Kostas, Woyke, Tanja and Hentschel, Ute (2013). Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges. The ISME Journal, 7 (12), 2287-2300. doi: 10.1038/ismej.2013.111

Woyke, Tanja, Sczyrba, Alexander, Lee, Janey, Rinke, Christian, Tighe, Damon, Clingenpeel, Scott, Malmstrom, Rex, Stepanauskas, Ramunas and Cheng, Jan-Fang (2011). Decontamination of MDA reagents for single cell whole genome amplification. PLoS One, 6 (10) e26161, 1-5. doi: 10.1371/journal.pone.0026161

Rinke, Christian and Lee, Raymond W. (2009). Macro camera temperature logger array for deep-sea hydrothermal vent and benthic studies: Macro camera temperature logger array. Limnology and Oceanography: Methods, 7 (7), 527-534. doi: 10.4319/lom.2009.7.527

Rinke, C. and Lee, R.W. (2009). Pathways, activities and thermal stability of anaerobic and aerobic enzymes in thermophilic vent paralvinellid worms. Marine Ecology Progress Series, 382, 99-112. doi: 10.3354/meps07980

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

Kloiber, Ulrike, Pflugfelder, Bettina, Rinke, Christian and Bright, Monika (2009). Cell proliferation and growth in Zoothamnium niveum (Oligohymenophora, Peritrichida) — thiotrophic bacteria symbiosis. Symbiosis, 47 (1), 43-50. doi: 10.1007/bf03179969

Rinke, Christian, Schmitz-Esser, Stephan, Loy, Alexander, Horn, Matthias, Wagner, Michael and Bright, Monika (2009). High genetic similarity between two geographically distinct strains of the sulfur-oxidizing symbiont 'Candidatus Thiobios zoothamnicoli'. FEMS Microbiology Ecology, 67 (2), 229-241. doi: 10.1111/j.1574-6941.2008.00628.x

Rinke, Christian, Lee, Raymond, Katz, Sigrid and Bright, Monika (2007). The effects of sulphide on growth and behaviour of the thiotrophic Zoothamnium niveum symbiosis. Proceedings. Biological sciences, 274 (1623), 2259-2269. doi: 10.1098/rspb.2007.0631

Rinke, Christian, Schmitz-Esser, Stephan, Stoecker, Kilian, Nussbaumer, Andrea D., Molnár, Dávid A., Vanura, Katrina, Wagner, Michael, Horn, Matthias, Ott, Jörg A. and Bright, Monika (2006). “Candidatus Thiobios zoothamnicoli,” an Ectosymbiotic Bacterium Covering the Giant Marine Ciliate Zoothamnium niveum. Applied and Environmental Microbiology, 72 (3), 2014-2021. doi: 10.1128/aem.72.3.2014-2021.2006

Tyson, Gene and Rinke, Christian (2015). Microscale Experiments to Understand a Microscale World. The University of Queensland. (Dataset) doi: 10.48610/b5ed324

Dr Chris Rinke

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Book Chapter

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Data Collection

Areas of research