Microbial Dark Matter

Peer-reviewed publications and book chapters

Microbial Dark Matter (MDM) research team (Rinke lab)

An updated list including citations can be found on Google Scholar

	TITLE	YEAR
	Resolving widespread incomplete and uneven archaeal classifications based on a rank-normalized genome-based taxonomy C Rinke, M Chuvochina, AJ Mussig, PA Chaumeil, AA Davin, DW Waite, ... bioRxiv, 2020.03. 01.972265	2021
	Recoding enhances the metabolic capabilities of two novel methylotrophic Asgardarchaeota lineages J Sun, PN Evans, EJ Gagen, BJ Woodcroft, BP Hedlund, T Woyke, ... bioRxiv	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	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), 1-15	2020
	A rank-normalized archaeal taxonomy based on genome phylogeny resolves widespread incomplete and uneven classifications C Rinke, M Chuvochina, AJ Mussig, PA Chaumeil, DW Waite, ... bioRxiv	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	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	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	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	2018
	Single-cell genomics of microbial dark matter C Rinke Microbiome Analysis, 99-111	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), 1-10	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	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	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	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	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	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	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	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	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	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	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	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	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	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 (5), 865-875	2014
	Stop codon reassignments in the wild NN Ivanova, P Schwientek, HJ Tripp, C Rinke, A Pati, M Huntemann, ... Science 344 (6186), 909-913	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	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	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	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	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	2013
	S. Malfa i, BK Swan, EA Gies, JA Dodsworth, BP Hedlund, G. Tsiamis, SM Sievert, W C Rinke, P Schwientek, A Sczyrba, NN Ivanova, IJ Anderson, JF Cheng, ... T. Liu, JA Eisen, SJ Hallam, NC Kyrpides, R. Stepanauskas, EM Rubin, P …	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	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	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	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	2009
	Cell proliferation and growth in Zoothamnium niveum (Oligohymenophora, Peritrichida)—Thiotrophic bacteria symbiosis U Kloiber, B Pflugfelder, C Rinke, M Bright Symbiosis 47 (1), 43-50	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	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	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

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