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
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
Mystery find of microbial DNA elements called Borgs
C Rinke
Nature 610 (7933), 635-637
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
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
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