Publications


Peer-reviewed publications and book chapters by the Rinke Lab research team

Protecting the invisible: Establishing guideline values for copper toxicity to marine microbiomes MC Thomas, G Waugh, I Vanwonterghem, NS Webster, C Rinke, R Fisher, ... Science of The Total Environment 904, 166658		2023
Genome Taxonomy Database and SeqCode: Microbial taxonomy and nomenclature in the age of big sequence data M Chuvochina, C Rinke, A Mussig, PA Chaumeil, D Parks, P Hugenholtz Biodiversity Information Science and Standards 7, e111135	1	2023
Proposal of names for 328 higher rank taxa defined in the Genome Taxonomy Database under two prokaryotic codes M Chuvochina, AJ Mussig, PA Chaumeil, A Skarshewski, C Rinke, ...	1	2023
Diversity, ecology and evolution of archaeal viruses L Fan, J Liu, C Rinke, BJ Baker, C Zhang Frontiers in Microbiology 14		2023
Mystery find of microbial DNA elements called Borgs C Rinke Nature 610 (7933), 635-637		2022
CorA gene rearrangement triggered the salinity-driven speciation of Poseidoniales L Fan, B Xu, S Chen, Y Liu, F Li, W Xie, A Prabhu, D Zou, R Wan, H Li, ... bioRxiv, 2022.09. 25.509439	1	2022
Three families of Asgard archaeal viruses identified in metagenome-assembled genomes S Medvedeva, J Sun, N Yutin, EV Koonin, T Nunoura, C Rinke, ... Nature Microbiology 7 (7), 962-973	15	2022
Chemotaxis shapes the microscale organization of the ocean’s microbiome JB Raina, BS Lambert, DH Parks, C Rinke, N Siboni, A Bramucci, ... Nature 605 (7908), 132-138	41	2022
ecology, metabolism and evolution of archaea-perspectives from Proceedings of the International Workshop on Geo-Omics of Archaea BP Hedlund, C Zhang, F Wang, C Rinke, WF Martin Frontiers in Microbiology 12, 827229	3	2022
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy DH Parks, M Chuvochina, C Rinke, AJ Mussig, PA Chaumeil, ... Nucleic acids research 50 (D1), D785-D794	561	2022
Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials J Sun, A Prabhu, STN Aroney, C Rinke Microbial genomics 8 (6)	26	2022
Microvolume DNA extraction methods for microscale amplicon and metagenomic studies AR Bramucci, A Focardi, C Rinke, P Hugenholtz, GW Tyson, JR Seymour, ... ISME Communications 1 (1), 79	10	2021
Viruses of Asgard archaea S Medvedeva, J Sun, N Yutin, EV Koonin, T Nunoura, C Rinke, ... bioRxiv, 2021.07. 29.453957	3	2021
A standardized archaeal taxonomy for the Genome Taxonomy Database C Rinke, M Chuvochina, AJ Mussig, PA Chaumeil, AA Davín, DW Waite, ... Nature Microbiology 6 (7), 946-959	207*	2021
Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages J Sun, PN Evans, EJ Gagen, BJ Woodcroft, BP Hedlund, T Woyke, ... ISME communications 1 (1), 30	25	2021
A genomic catalog of Earth’s microbiomes S Nayfach, S Roux, R Seshadri, D Udwary, N Varghese, F Schulz, D Wu, ... Nature biotechnology 39 (4), 499-509	484	2021
A complete domain-to-species taxonomy for Bacteria and Archaea DH Parks, M Chuvochina, PA Chaumeil, C Rinke, AJ Mussig, ... Nature biotechnology 38 (9), 1079-1086	904	2020
Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution N Dombrowski, TA Williams, J Sun, BJ Woodcroft, JH Lee, BQ Minh, ... Nature Communications 11 (1), 3939	68	2020
Defining the human gut host–phage network through single-cell viral tagging M Džunková, SJ Low, JN Daly, L Deng, C Rinke, P Hugenholtz Nature Microbiology 4 (12), 2192-2203	97	2019
A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.) C Rinke, F Rubino, LF Messer, N Youssef, DH Parks, M Chuvochina, ... The ISME journal 13 (3), 663-675	133	2019
The importance of designating type material for uncultured taxa M Chuvochina, C Rinke, DH Parks, MS Rappé, GW Tyson, P Yilmaz, ... Systematic and applied microbiology 42 (1), 15-21	89	2019
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life DH Parks, M Chuvochina, DW Waite, C Rinke, A Skarshewski, ... Nature biotechnology 36 (10), 996-1004	2438	2018
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (vol 35, pg 725, 2017) RM Bowers, NC Kyrpides, R Stepanauskas, M Harmon-Smith, D Doud, ... Nature Biotechnology 36 (7), 660-660		2018
Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. RM Bowers, NC Kyrpides, R Stepanauskas, M Harmon-Smith, D Doud, ... Nature biotechnology 36 (2), 196	23	2018
A proposal for a standardized bacterial taxonomy based on genome phylogeny DH Parks, M Chuvochina, DW Waite, C Rinke, A Skarshewski, ... BioRxiv, 256800	59	2018
Single-cell genomics of microbial dark matter C Rinke Microbiome Analysis: Methods and Protocols, 99-111	5	2018
Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients AK Hawley, MK Nobu, JJ Wright, WE Durno, C Morgan-Lang, B Sage, ... Nature communications 8 (1), 1507	113	2017
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life DH Parks, C Rinke, M Chuvochina, PA Chaumeil, BJ Woodcroft, ... Nature microbiology 2 (11), 1533-1542	1397	2017
A microfluidics-based in situ chemotaxis assay to study the behaviour of aquatic microbial communities BS Lambert, JB Raina, VI Fernandez, C Rinke, N Siboni, F Rubino, ... Nature microbiology 2 (10), 1344-1349	60	2017
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea RM Bowers, NC Kyrpides, R Stepanauskas, M Harmon-Smith, D Doud, ... Nature biotechnology 35 (8), 725-731	1310	2017
Comparative Genomic Analysis of the Class Epsilonproteobacteria and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.) DW Waite, I Vanwonterghem, C Rinke, DH Parks, Y Zhang, K Takai, ... Frontiers in microbiology 8, 682	359*	2017
Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota IV Kublanov, OM Sigalova, SN Gavrilov, AV Lebedinsky, C Rinke, ... Frontiers in microbiology 8, 195	40	2017
Recovery of nearly 8,000 metagenomeassembled genomes substantially expands the tree of life. Nat Microbiol 2: 1533–1542 DH Parks, C Rinke, M Chuvochina, PA Chaumeil, BJ Woodcroft, ...	157	2017
acdc–Automated Contamination Detection and Confidence estimation for single-cell genome data M Lux, J Krüger, C Rinke, I Maus, A Schlüter, T Woyke, A Sczyrba, ... BMC bioinformatics 17 (1), 1-11	26	2016
Validation of picogram-and femtogram-input DNA libraries for microscale metagenomics C Rinke, S Low, BJ Woodcroft, JB Raina, A Skarshewski, XH Le, ... PeerJ 4, e2486	73	2016
Phylogeny and physiology of candidate phylum ‘Atribacteria’(OP9/JS1) inferred from cultivation-independent genomics MK Nobu, JA Dodsworth, SK Murugapiran, C Rinke, EA Gies, G Webster, ... The ISME journal 10 (2), 273-286	166	2016
ProDeGe: a computational protocol for fully automated decontamination of genomes K Tennessen, E Andersen, S Clingenpeel, C Rinke, DS Lundberg, J Han, ... The ISME journal 10 (1), 269-272	72	2016
Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor MK Nobu, T Narihiro, C Rinke, Y Kamagata, SG Tringe, T Woyke, WT Liu The ISME journal 9 (8), 1710-1722	342	2015
In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3) NH Youssef, IF Farag, C Rinke, SJ Hallam, T Woyke, MS Elshahed PloS one 10 (6), e0127499	109	2015
Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum ‘Diapherotrites’ NH Youssef, C Rinke, R Stepanauskas, I Farag, T Woyke, MS Elshahed The ISME journal 9 (2), 447-460	84	2015
Reconstructing each cell's genome within complex microbial communities—dream or reality? S Clingenpeel, A Clum, P Schwientek, C Rinke, T Woyke Frontiers in microbiology 5, 771	67	2015
Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter” BP Hedlund, JA Dodsworth, SK Murugapiran, C Rinke, T Woyke Extremophiles 18, 865-875	137	2014
Stop codon reassignments in the wild NN Ivanova, P Schwientek, HJ Tripp, C Rinke, A Pati, M Huntemann, ... Science 344 (6186), 909-913	132	2014
Obtaining genomes from uncultivated environmental microorganisms using FACS–based single-cell genomics C Rinke, J Lee, N Nath, D Goudeau, B Thompson, N Poulton, E Dmitrieff, ... Nature protocols 9 (5), 1038-1048	281	2014
An environmental bacterial taxon with a large and distinct metabolic repertoire MC Wilson, T Mori, C Rückert, AR Uria, MJ Helf, K Takada, C Gernert, ... Nature 506 (7486), 58-62	599	2014
The candidate phylum Poribacteria by single-cell genomics: new insights into phylogeny, cell-compartmentation, eukaryote-like repeat proteins, and other genomic features J Kamke, C Rinke, P Schwientek, K Mavromatis, N Ivanova, A Sczyrba, ... PloS one 9 (1), e87353	81	2014
Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges J Kamke, A Sczyrba, N Ivanova, P Schwientek, C Rinke, K Mavromatis, ... The ISME journal 7 (12), 2287-2300	124	2013
Insights into the phylogeny and coding potential of microbial dark matter C Rinke, P Schwientek, A Sczyrba, NN Ivanova, IJ Anderson, JF Cheng, ... Nature 499 (7459), 431-437	2224	2013
Decontamination of MDA reagents for single cell whole genome amplification T Woyke, A Sczyrba, J Lee, C Rinke, D Tighe, S Clingenpeel, ... PloS one 6 (10), e26161	177	2011
Macro camera temperature logger array for deep‐sea hydrothermal vent and benthic studies C Rinke, RW Lee Limnology and Oceanography: Methods 7 (7), 527-534	7	2009
Pathways, activities and thermal stability of anaerobic and aerobic enzymes in thermophilic vent paralvinellid worms C Rinke, RW Lee Marine Ecology Progress Series 382, 99-112	11	2009
Molecular characterization of the symbionts associated with marine nematodes of the genus Robbea^‡ C Bayer, NR Heindl, C Rinke, S Lücker, JA Ott, S Bulgheresi Environmental Microbiology Reports 1 (2), 136-144	52	2009
Cell proliferation and growth inZoothamnium niveum (Oligohymenophora, Peritrichida) — Thiotrophic bacteria symbiosis U Kloiber, B Pflugfelder, C Rinke, M Bright Symbiosis 47, 43-50	6	2009
High genetic similarity between two geographically distinct strains of the sulfur-oxidizing symbiont ‘Candidatus Thiobios zoothamnicoli’ C Rinke, S Schmitz-Esser, A Loy, M Horn, M Wagner, M Bright FEMS microbiology ecology 67 (2), 229-241	24	2009
The effects of sulphide on growth and behaviour of the thiotrophic Zoothamnium niveum symbiosis C Rinke, R Lee, S Katz, M Bright Proceedings of the Royal Society B: Biological Sciences 274 (1623), 2259-2269	27	2007
“Candidatus Thiobios zoothamnicoli,” an Ectosymbiotic Bacterium Covering the Giant Marine Ciliate Zoothamnium niveum C Rinke, S Schmitz-Esser, K Stoecker, AD Nussbaumer, DA Molnár, ... Applied and environmental microbiology 72 (3), 2014-2021	82	2006
Carbonfixation,-incorporation and-transfer in the chemoautotrophic Zoothamnium niveum symbioses with 14 C bicarbonat autoradiography C Rinke na	6	2002
Protecting the Invisible Guardians: Establishing Guideline Values for Copper Toxicity to Marine Microbiomes MC Thomas, G Waugh, I Vanwonterghem, N Webster, C Rinke, R Fisher, ... Available at SSRN 4510814