skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota

Abstract

The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H 2 during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is determined by a nitrate reductase of the Nap family, while nitrite reduction to ammonia is presumably catalyzed by an octaheme cytochrome c nitrite reductase εHao. The genome contained genes of respiratory polysulfide/thiosulfate reductase, however, elemental sulfur and thiosulfate were not used as the electron acceptors for anaerobic respiration with acetate or H 2, probably due to the lack of the gene of the maturation protein. Nevertheless, elemental sulfur and thiosulfate stimulated growth on fermentable substrates (peptides), being reduced to sulfide, most probably through the action of the cytoplasmic sulfide dehydrogenase and/or NAD(P)-dependent [NiFe]-hydrogenase (sulfhydrogenase) encoded by the genome. Surprisingly, the genome of this anaerobic microorganism encoded all genes formore » cytochrome c oxidase, however, its maturation machinery seems to be non-operational due to genomic rearrangements of supplementary genes. Despite the fact that sugars were not among the substrates reported when C. abyssi was first described, our genomic analysis revealed multiple genes of glycoside hydrolases, and some of them were predicted to be secreted. This finding aided in bringing out four carbohydrates that supported the growth of C. abyssi: starch, cellobiose, glucomannan and xyloglucan. The genomic analysis demonstrated the ability of C. abyssi to synthesize nucleotides and most amino acids and vitamins. Finally, the genomic sequence allowed us to perform a phylogenomic analysis, based on 38 protein sequences, which confirmed the deep branching of this lineage and justified the proposal of a novel phylum Calditrichaeota.« less

Authors:
 [1];  [1];  [1];  [1];  [2];  [1];  [1];  [3];  [3];  [3];  [4];  [5];  [5];  [6];  [1];  [3];  [7];  [8];  [1]
  1. Russian Academy of Sciences, Moscow (Russia)
  2. Univ. of Queensland, St. Lucia, QLD (Australia)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Newcastle Univ., Newcastle upon Tyne (United Kingdom)
  5. Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
  6. Univ. of Pretoria, Pretoria (South Africa)
  7. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  8. Russian Academy of Sciences, Moscow (Russia); M.V. Lomonosov Moscow State Univ., Moscow (Russia); Skolkovo Institute of Science and Technology, Moscow (Russia); National Research Univ. - Higher School of Economics, Moscow (Russia)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1379740
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 8; Journal Issue: FEB; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; bacterial evolution; phylogenomics; taxonomy; phylum; Caldithrix; genomic analysis; sequencing

Citation Formats

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, Goker, Markus, Reva, Oleg N., Miroshnichenko, Margarita L., Kyrpides, Nikos C., Woyke, Tanja, Gelfand, Mikhail S., and Bonch-Osmolovskaya, Elizaveta A. Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota. United States: N. p., 2017. Web. doi:10.3389/fmicb.2017.00195.
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, Goker, Markus, Reva, Oleg N., Miroshnichenko, Margarita L., Kyrpides, Nikos C., Woyke, Tanja, Gelfand, Mikhail S., & Bonch-Osmolovskaya, Elizaveta A. Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota. United States. doi:10.3389/fmicb.2017.00195.
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, Goker, Markus, Reva, Oleg N., Miroshnichenko, Margarita L., Kyrpides, Nikos C., Woyke, Tanja, Gelfand, Mikhail S., and Bonch-Osmolovskaya, Elizaveta A. Mon . "Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota". United States. doi:10.3389/fmicb.2017.00195. https://www.osti.gov/servlets/purl/1379740.
@article{osti_1379740,
title = {Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota},
author = {Kublanov, Ilya V. and Sigalova, Olga M. and Gavrilov, Sergey N. and Lebedinsky, Alexander V. and Rinke, Christian and Kovaleva, Olga and Chernyh, Nikolai A. and Ivanova, Natalia and Daum, Chris and Reddy, T. B. K. and Klenk, Hans -Peter and Spring, Stefan and Goker, Markus and Reva, Oleg N. and Miroshnichenko, Margarita L. and Kyrpides, Nikos C. and Woyke, Tanja and Gelfand, Mikhail S. and Bonch-Osmolovskaya, Elizaveta A.},
abstractNote = {The genome of Caldithrix abyssi, the first cultivated representative of a phylum-level bacterial lineage, was sequenced within the framework of Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. The genomic analysis revealed mechanisms allowing this anaerobic bacterium to ferment peptides or to implement nitrate reduction with acetate or molecular hydrogen as electron donors. The genome encoded five different [NiFe]- and [FeFe]-hydrogenases, one of which, group 1 [NiFe]-hydrogenase, is presumably involved in lithoheterotrophic growth, three other produce H2 during fermentation, and one is apparently bidirectional. The ability to reduce nitrate is determined by a nitrate reductase of the Nap family, while nitrite reduction to ammonia is presumably catalyzed by an octaheme cytochrome c nitrite reductase εHao. The genome contained genes of respiratory polysulfide/thiosulfate reductase, however, elemental sulfur and thiosulfate were not used as the electron acceptors for anaerobic respiration with acetate or H2, probably due to the lack of the gene of the maturation protein. Nevertheless, elemental sulfur and thiosulfate stimulated growth on fermentable substrates (peptides), being reduced to sulfide, most probably through the action of the cytoplasmic sulfide dehydrogenase and/or NAD(P)-dependent [NiFe]-hydrogenase (sulfhydrogenase) encoded by the genome. Surprisingly, the genome of this anaerobic microorganism encoded all genes for cytochrome c oxidase, however, its maturation machinery seems to be non-operational due to genomic rearrangements of supplementary genes. Despite the fact that sugars were not among the substrates reported when C. abyssi was first described, our genomic analysis revealed multiple genes of glycoside hydrolases, and some of them were predicted to be secreted. This finding aided in bringing out four carbohydrates that supported the growth of C. abyssi: starch, cellobiose, glucomannan and xyloglucan. The genomic analysis demonstrated the ability of C. abyssi to synthesize nucleotides and most amino acids and vitamins. Finally, the genomic sequence allowed us to perform a phylogenomic analysis, based on 38 protein sequences, which confirmed the deep branching of this lineage and justified the proposal of a novel phylum Calditrichaeota.},
doi = {10.3389/fmicb.2017.00195},
journal = {Frontiers in Microbiology},
number = FEB,
volume = 8,
place = {United States},
year = {2017},
month = {2}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 7 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Structural composition of alternative complex III: Variations on the same theme
journal, November 2013

  • Refojo, Patrícia N.; Ribeiro, Miguel A.; Calisto, Filipa
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1827, Issue 11-12
  • DOI: 10.1016/j.bbabio.2013.01.001

Biochemistry, evolution and physiological function of the Rnf complex, a novel ion-motive electron transport complex in prokaryotes
journal, November 2010

  • Biegel, Eva; Schmidt, Silke; González, José M.
  • Cellular and Molecular Life Sciences, Vol. 68, Issue 4
  • DOI: 10.1007/s00018-010-0555-8

Metalloproteins Containing Cytochrome, Iron–Sulfur, or Copper Redox Centers
journal, March 2014

  • Liu, Jing; Chakraborty, Saumen; Hosseinzadeh, Parisa
  • Chemical Reviews, Vol. 114, Issue 8
  • DOI: 10.1021/cr400479b

Physiological function and catalytic versatility of bacterial multihaem cytochromes c involved in nitrogen and sulfur cycling
journal, November 2011

  • Simon, Jörg; Kern, Melanie; Hermann, Bianca
  • Biochemical Society Transactions, Vol. 39, Issue 6
  • DOI: 10.1042/BST20110713

Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline
journal, July 2007

  • Weinberg, Zasha; Barrick, Jeffrey E.; Yao, Zizhen
  • Nucleic Acids Research, Vol. 35, Issue 14
  • DOI: 10.1093/nar/gkm487

GOHTAM: a website for 'Genomic Origin of Horizontal Transfers, Alignment and Metagenomics'
journal, March 2012


A Reversible Electron-Bifurcating Ferredoxin- and NAD-Dependent [FeFe]-Hydrogenase (HydABC) in Moorella thermoacetica
journal, January 2013

  • Wang, S.; Huang, H.; Kahnt, J.
  • Journal of Bacteriology, Vol. 195, Issue 6
  • DOI: 10.1128/JB.02158-12

Software for analysis of bacterial genomes
journal, March 2000

  • Mironov, A. A.; Vinokurova, N. P.; Gelfand, M. S.
  • Molecular Biology, Vol. 34, Issue 2
  • DOI: 10.1007/BF02759643

FolM, A New Chromosomally Encoded Dihydrofolate Reductase in Escherichia coli
journal, November 2003


An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
journal, December 2011

  • McDonald, Daniel; Price, Morgan N.; Goodrich, Julia
  • The ISME Journal, Vol. 6, Issue 3
  • DOI: 10.1038/ismej.2011.139

[FeFe]- and [NiFe]-hydrogenase diversity, mechanism, and maturation
journal, June 2015

  • Peters, John W.; Schut, Gerrit J.; Boyd, Eric S.
  • Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Vol. 1853, Issue 6
  • DOI: 10.1016/j.bbamcr.2014.11.021

Base-Calling of Automated Sequencer Traces Using Phred.  I. Accuracy Assessment
journal, March 1998

  • Ewing, Brent; Hillier, LaDeana; Wendl, Michael C.
  • Genome Research, Vol. 8, Issue 3
  • DOI: 10.1101/gr.8.3.175

Caldicellulosiruptor kronotskyensis sp. nov. and Caldicellulosiruptor hydrothermalis sp. nov., two extremely thermophilic, cellulolytic, anaerobic bacteria from Kamchatka thermal springs
journal, June 2008

  • Miroshnichenko, M. L.; Kublanov, I. V.; Kostrikina, N. A.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 6
  • DOI: 10.1099/ijs.0.65236-0

Solexa Ltd
journal, June 2004


Comparative Genomics of Thiamin Biosynthesis in Procaryotes: NEW GENES AND REGULATORY MECHANISMS
journal, October 2002

  • Rodionov, Dmitry A.; Vitreschak, Alexey G.; Mironov, Andrey A.
  • Journal of Biological Chemistry, Vol. 277, Issue 50
  • DOI: 10.1074/jbc.M208965200

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997

  • Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A.
  • Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402
  • DOI: 10.1093/nar/25.17.3389

Microbial nitrate respiration – Genes, enzymes and environmental distribution
journal, August 2011


In vivo interaction of the Excherichia coli integration host factor with its specific binding sites
journal, January 1995

  • Engelhorn, Manuel; Boccard, Freédeéric; Murtin, Christine
  • Nucleic Acids Research, Vol. 23, Issue 15
  • DOI: 10.1093/nar/23.15.2959

Hydrogenase of the hyperthermophile Pyrococcus furiosus is an elemental sulfur reductase or sulfhydrogenase: evidence for a sulfur-reducing hydrogenase ancestor.
journal, June 1993

  • Ma, K.; Schicho, R. N.; Kelly, R. M.
  • Proceedings of the National Academy of Sciences, Vol. 90, Issue 11
  • DOI: 10.1073/pnas.90.11.5341

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
journal, March 2010


Microbial life in Bourlyashchy, the hottest thermal pool of Uzon Caldera, Kamchatka
journal, September 2015


Investigation of the catabolism of acetate and peptides in the new anaerobic thermophilic bacterium Caldithrix abyssi
journal, March 2006


InterPro: the integrative protein signature database
journal, January 2009

  • Hunter, S.; Apweiler, R.; Attwood, T. K.
  • Nucleic Acids Research, Vol. 37, Issue Database
  • DOI: 10.1093/nar/gkn785

The Transporter Classification Database: recent advances
journal, January 2009

  • Saier, M. H.; Yen, M. R.; Noto, K.
  • Nucleic Acids Research, Vol. 37, Issue Database
  • DOI: 10.1093/nar/gkn862

An Anaerobic-Type α-Ketoglutarate Ferredoxin Oxidoreductase Completes the Oxidative Tricarboxylic Acid Cycle of Mycobacterium tuberculosis
journal, November 2009


Uncultivated thermophiles: current status and spotlight on ‘Aigarchaeota’
journal, June 2015

  • Hedlund, Brian P.; Murugapiran, Senthil K.; Alba, Timothy W.
  • Current Opinion in Microbiology, Vol. 25
  • DOI: 10.1016/j.mib.2015.06.008

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
journal, January 2009

  • Cantarel, B. L.; Coutinho, P. M.; Rancurel, C.
  • Nucleic Acids Research, Vol. 37, Issue Database
  • DOI: 10.1093/nar/gkn663

Ori-Finder: A web-based system for finding oriC s in unannotated bacterial genomes
journal, February 2008


Taxonomic use of DNA G+C content and DNA–DNA hybridization in the genomic age
journal, February 2014

  • Klenk, Hans-Peter; Meier-Kolthoff, Jan P.; Göker, Markus
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 64, Issue 2
  • DOI: 10.1099/ijs.0.056994-0

Transcriptional Regulation of Central Carbon and Energy Metabolism in Bacteria by Redox-Responsive Repressor Rex
journal, December 2011

  • Ravcheev, D. A.; Li, X.; Latif, H.
  • Journal of Bacteriology, Vol. 194, Issue 5
  • DOI: 10.1128/JB.06412-11

IMG 4 version of the integrated microbial genomes comparative analysis system
journal, October 2013

  • Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt963

The Alternative complex III: Properties and possible mechanisms for electron transfer and energy conservation
journal, October 2012

  • Refojo, Patrícia N.; Teixeira, Miguel; Pereira, Manuela M.
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1817, Issue 10
  • DOI: 10.1016/j.bbabio.2012.05.003

Characterization of the Menaquinone Reduction Site in the Diheme Cytochrome b Membrane Anchor of Wolinella succinogenes NiFe-hydrogenase
journal, October 2003

  • Gross, Roland; Pisa, René; Sänger, Monica
  • Journal of Biological Chemistry, Vol. 279, Issue 1
  • DOI: 10.1074/jbc.M310610200

Octaheme tetrathionate reductase is a respiratory enzyme with novel heme ligation
journal, September 2004

  • Mowat, Christopher G.; Rothery, Emma; Miles, Caroline S.
  • Nature Structural & Molecular Biology, Vol. 11, Issue 10
  • DOI: 10.1038/nsmb827

Identification of 16S Ribosomal DNA-Defined Bacterial Populations at a Shallow Submarine Hydrothermal Vent near Milos Island (Greece)
journal, July 2000


Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
journal, March 1998


RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria
journal, January 2013

  • Novichkov, Pavel S.; Kazakov, Alexey E.; Ravcheev, Dmitry A.
  • BMC Genomics, Vol. 14, Issue 1
  • DOI: 10.1186/1471-2164-14-745

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
journal, February 2008


The RAST Server: Rapid Annotations using Subsystems Technology
journal, January 2008

  • Aziz, Ramy K.; Bartels, Daniela; Best, Aaron A.
  • BMC Genomics, Vol. 9, Issue 1, Article No. 75
  • DOI: 10.1186/1471-2164-9-75

KEGG as a reference resource for gene and protein annotation
journal, October 2015

  • Kanehisa, Minoru; Sato, Yoko; Kawashima, Masayuki
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1070

Mutational analysis of the dimethylsulfoxide respiratory (dor) operon of Rhodobacter capsulatus
journal, June 1999


Structure of chi hotspots of generalized recombination
journal, May 1981


Deletion Strains Reveal Metabolic Roles for Key Elemental Sulfur-Responsive Proteins in Pyrococcus furiosus
journal, September 2011

  • Bridger, S. L.; Clarkson, S. M.; Stirrett, K.
  • Journal of Bacteriology, Vol. 193, Issue 23
  • DOI: 10.1128/JB.05445-11

Rfam 12.0: updates to the RNA families database
journal, November 2014

  • Nawrocki, Eric P.; Burge, Sarah W.; Bateman, Alex
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1063

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
journal, November 2012

  • Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin
  • Nucleic Acids Research, Vol. 41, Issue D1
  • DOI: 10.1093/nar/gks1219

Occurrence, Classification, and Biological Function of Hydrogenases:  An Overview
journal, October 2007

  • Vignais, Paulette M.; Billoud, Bernard
  • Chemical Reviews, Vol. 107, Issue 10, p. 4206-4272
  • DOI: 10.1021/cr050196r

Caldithrix palaeochoryensis sp. nov., a thermophilic, anaerobic, chemo-organotrophic bacterium from a geothermally heated sediment, and emended description of the genus Caldithrix
journal, October 2009

  • Miroshnichenko, M. L.; Kolganova, T. V.; Spring, S.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 60, Issue 9
  • DOI: 10.1099/ijs.0.016667-0

ARB: a software environment for sequence data
journal, February 2004


Involvement of a Mate Chaperone (TorD) in the Maturation Pathway of Molybdoenzyme TorA
journal, May 2003

  • Ilbert, Marianne; Méjean, Vincent; Giudici-Orticoni, Marie-Thérèse
  • Journal of Biological Chemistry, Vol. 278, Issue 31
  • DOI: 10.1074/jbc.M302730200

Ecology and habitats of extremophiles
journal, January 1995

  • Kristj�nsson, J. K.; Hreggvidsson, G. O.
  • World Journal of Microbiology & Biotechnology, Vol. 11, Issue 1
  • DOI: 10.1007/BF00339134

The Pfam protein families database: towards a more sustainable future
journal, December 2015

  • Finn, Robert D.; Coggill, Penelope; Eberhardt, Ruth Y.
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1344

MEME SUITE: tools for motif discovery and searching
journal, May 2009

  • Bailey, T. L.; Boden, M.; Buske, F. A.
  • Nucleic Acids Research, Vol. 37, Issue Web Server
  • DOI: 10.1093/nar/gkp335

Accelerated Profile HMM Searches
journal, October 2011


The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage
journal, January 2008

  • Ganesan, Hamilton; Rakitianskaia, Anna S.; Davenport, Colin F.
  • BMC Bioinformatics, Vol. 9, Issue 1
  • DOI: 10.1186/1471-2105-9-333

Enzyme phylogenies as markers for the oxidation state of the environment: The case of respiratory arsenate reductase and related enzymes
journal, January 2008

  • Duval, Simon; Ducluzeau, Anne-Lise; Nitschke, Wolfgang
  • BMC Evolutionary Biology, Vol. 8, Issue 1
  • DOI: 10.1186/1471-2148-8-206

Repetitive extragenic palindromic sequences: A major component of the bacterial genome
journal, July 1984


Phylogeny-driven target selection for large-scale genome-sequencing (and other) projects
journal, May 2013

  • Göker, Markus; Klenk, Hans-Peter
  • Standards in Genomic Sciences, Vol. 8, Issue 2
  • DOI: 10.4056/sigs.3446951

Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation
journal, February 2013

  • Buckel, Wolfgang; Thauer, Rudolf K.
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1827, Issue 2
  • DOI: 10.1016/j.bbabio.2012.07.002

Stabilization of translationally active mRNA by prokaryotic REP sequences
journal, January 1987


Diversity and evolution of bioenergetic systems involved in microbial nitrogen compound transformations
journal, February 2013


The Acetate Switch
journal, March 2005


Evolution of cytochrome bc complexes: From membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates
journal, November 2013

  • Dibrova, Daria V.; Cherepanov, Dmitry A.; Galperin, Michael Y.
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1827, Issue 11-12
  • DOI: 10.1016/j.bbabio.2013.07.006

Consed: A Graphical Tool for Sequence Finishing
journal, March 1998

  • Gordon, David; Abajian, Chris; Green, Phil
  • Genome Research, Vol. 8, Issue 3
  • DOI: 10.1101/gr.8.3.195

Multiple Rieske proteins in prokaryotes: Where and why?
journal, November 2005

  • Schneider, Dirk; Schmidt, Christian L.
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1710, Issue 1
  • DOI: 10.1016/j.bbabio.2005.09.003

Genome sequencing in microfabricated high-density picolitre reactors
journal, July 2005

  • Margulies, Marcel; Egholm, Michael; Altman, William E.
  • Nature, Vol. 437, Issue 7057, p. 376-380
  • DOI: 10.1038/nature03959

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
journal, November 2013

  • Overbeek, Ross; Olson, Robert; Pusch, Gordon D.
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1226

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
journal, November 2013

  • Caspi, Ron; Altman, Tomer; Billington, Richard
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt1103

Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy
journal, April 2011

  • Letunic, I.; Bork, P.
  • Nucleic Acids Research, Vol. 39, Issue suppl
  • DOI: 10.1093/nar/gkr201

Insights into the phylogeny and coding potential of microbial dark matter
journal, July 2013

  • Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander
  • Nature, Vol. 499, Issue 7459
  • DOI: 10.1038/nature12352

Infernal 1.1: 100-fold faster RNA homology searches
journal, September 2013


The Phylogeny and Signature Sequences Characteristics of Fibrobacteres , Chlorobi , and Bacteroidetes
journal, January 2004


IslandViewer: an integrated interface for computational identification and visualization of genomic islands
journal, January 2009


Caldithrix abyssi gen. nov., sp. nov., a nitrate-reducing, thermophilic, anaerobic bacterium isolated from a Mid-Atlantic Ridge hydrothermal vent, represents a novel bacterial lineage
journal, January 2003

  • Miroshnichenko, M. L.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 53, Issue 1
  • DOI: 10.1099/ijs.0.02390-0

En route to a genome-based classification of Archaea and Bacteria?
journal, June 2010


Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes
journal, November 2015

  • Oren, Aharon; da Costa, Milton S.; Garrity, George M.
  • International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue 11
  • DOI: 10.1099/ijsem.0.000664

Genome-wide Analysis of Substrate Specificities of the Escherichia coli Haloacid Dehalogenase-like Phosphatase Family
journal, September 2006

  • Kuznetsova, Ekaterina; Proudfoot, Michael; Gonzalez, Claudio F.
  • Journal of Biological Chemistry, Vol. 281, Issue 47
  • DOI: 10.1074/jbc.M605449200

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea
journal, December 2009

  • Wu, Dongying; Hugenholtz, Philip; Mavromatis, Konstantinos
  • Nature, Vol. 462, Issue 7276
  • DOI: 10.1038/nature08656

Pre_GI: a global map of ontological links between horizontally transferred genomic islands in bacterial and archaeal genomes
journal, January 2015