Literature DB >> 18245282

"Candidatus Cloacamonas acidaminovorans": genome sequence reconstruction provides a first glimpse of a new bacterial division.

Eric Pelletier1, Annett Kreimeyer, Stéphanie Bocs, Zoé Rouy, Gábor Gyapay, Rakia Chouari, Delphine Rivière, Akila Ganesan, Patrick Daegelen, Abdelghani Sghir, Georges N Cohen, Claudine Médigue, Jean Weissenbach, Denis Le Paslier.   

Abstract

Many microorganisms live in anaerobic environments. Most of these microorganisms have not yet been cultivated. Here, we present, from a metagenomic analysis of an anaerobic digester of a municipal wastewater treatment plant, a reconstruction of the complete genome of a bacterium belonging to the WWE1 candidate division. In silico proteome analysis indicated that this bacterium might derive most of its carbon and energy from the fermentation of amino acids, and hence, it was provisionally classified as "Candidatus Cloacamonas acidaminovorans." "Candidatus Cloacamonas acidaminovorans" is probably a syntrophic bacterium that is present in many anaerobic digesters. This report highlights how environmental sequence data might provide genomic and functional information about a new bacterial clade whose members are involved in anaerobic digestion.

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Year:  2008        PMID: 18245282      PMCID: PMC2293186          DOI: 10.1128/JB.01248-07

Source DB:  PubMed          Journal:  J Bacteriol        ISSN: 0021-9193            Impact factor:   3.490


  31 in total

1.  Identification of genes that are associated with DNA repeats in prokaryotes.

Authors:  Ruud Jansen; Jan D A van Embden; Wim Gaastra; Leo M Schouls
Journal:  Mol Microbiol       Date:  2002-03       Impact factor: 3.501

2.  Molecular evidence for novel planctomycete diversity in a municipal wastewater treatment plant.

Authors:  Rakia Chouari; Denis Le Paslier; Patrick Daegelen; Philippe Ginestet; Jean Weissenbach; Abdelghani Sghir
Journal:  Appl Environ Microbiol       Date:  2003-12       Impact factor: 4.792

3.  AMIGene: Annotation of MIcrobial Genes.

Authors:  Stéphanie Bocs; Stéphane Cruveiller; David Vallenet; Grégory Nuel; Claudine Médigue
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

4.  Diversity of the archaeal community in 44 anaerobic digesters as determined by single strand conformation polymorphism analysis and 16S rDNA sequencing.

Authors:  Marion Leclerc; Jean-Philippe Delgènes; Jean-Jacques Godon
Journal:  Environ Microbiol       Date:  2004-08       Impact factor: 5.491

5.  Novel major bacterial candidate division within a municipal anaerobic sludge digester.

Authors:  Rakia Chouari; Denis Le Paslier; Catherine Dauga; Patrick Daegelen; Jean Weissenbach; Abdelghani Sghir
Journal:  Appl Environ Microbiol       Date:  2005-04       Impact factor: 4.792

6.  Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.

Authors:  T Z DeSantis; P Hugenholtz; N Larsen; M Rojas; E L Brodie; K Keller; T Huber; D Dalevi; P Hu; G L Andersen
Journal:  Appl Environ Microbiol       Date:  2006-07       Impact factor: 4.792

7.  Phylogenetic and functional diversity of propionate-oxidizing bacteria in an anaerobic digester sludge.

Authors:  Herto Dwi Ariesyady; Tsukasa Ito; Kazumi Yoshiguchi; Satoshi Okabe
Journal:  Appl Microbiol Biotechnol       Date:  2007-01-30       Impact factor: 4.813

8.  Cyclohexa-1,5-diene-1-carbonyl-coenzyme A (CoA) hydratases of Geobacter metallireducens and Syntrophus aciditrophicus: Evidence for a common benzoyl-CoA degradation pathway in facultative and strict anaerobes.

Authors:  Franziska Peters; Yoshifumi Shinoda; Michael J McInerney; Matthias Boll
Journal:  J Bacteriol       Date:  2006-11-22       Impact factor: 3.490

9.  Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin.

Authors:  Alexander Bolotin; Benoit Quinquis; Alexei Sorokin; S Dusko Ehrlich
Journal:  Microbiology       Date:  2005-08       Impact factor: 2.777

10.  A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action.

Authors:  Kira S Makarova; Nick V Grishin; Svetlana A Shabalina; Yuri I Wolf; Eugene V Koonin
Journal:  Biol Direct       Date:  2006-03-16       Impact factor: 4.540

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  79 in total

Review 1.  A bioinformatician's guide to metagenomics.

Authors:  Victor Kunin; Alex Copeland; Alla Lapidus; Konstantinos Mavromatis; Philip Hugenholtz
Journal:  Microbiol Mol Biol Rev       Date:  2008-12       Impact factor: 11.056

2.  Revealing the hidden functional diversity of an enzyme family.

Authors:  Karine Bastard; Adam Alexander Thil Smith; Carine Vergne-Vaxelaire; Alain Perret; Anne Zaparucha; Raquel De Melo-Minardi; Aline Mariage; Magali Boutard; Adrien Debard; Christophe Lechaplais; Christine Pelle; Virginie Pellouin; Nadia Perchat; Jean-Louis Petit; Annett Kreimeyer; Claudine Medigue; Jean Weissenbach; François Artiguenave; Véronique De Berardinis; David Vallenet; Marcel Salanoubat
Journal:  Nat Chem Biol       Date:  2013-11-17       Impact factor: 15.040

3.  Bacterial and archaeal phylogenetic diversity associated with swine sludge from an anaerobic treatment lagoon.

Authors:  Juliana Cardinali-Rezende; Zelina L Pereira; José L Sanz; Edmar Chartone-Souza; Andréa M A Nascimento
Journal:  World J Microbiol Biotechnol       Date:  2012-07-25       Impact factor: 3.312

4.  Grape pomace compost harbors organohalide-respiring Dehalogenimonas species with novel reductive dehalogenase genes.

Authors:  Yi Yang; Steven A Higgins; Jun Yan; Burcu Şimşir; Karuna Chourey; Ramsunder Iyer; Robert L Hettich; Brett Baldwin; Dora M Ogles; Frank E Löffler
Journal:  ISME J       Date:  2017-08-15       Impact factor: 10.302

5.  Illuminating microbial dark matter in meromictic Sakinaw Lake.

Authors:  Esther A Gies; Kishori M Konwar; J Thomas Beatty; Steven J Hallam
Journal:  Appl Environ Microbiol       Date:  2014-08-29       Impact factor: 4.792

6.  MicroScope: a platform for microbial genome annotation and comparative genomics.

Authors:  D Vallenet; S Engelen; D Mornico; S Cruveiller; L Fleury; A Lajus; Z Rouy; D Roche; G Salvignol; C Scarpelli; C Médigue
Journal:  Database (Oxford)       Date:  2009-11-25       Impact factor: 3.451

7.  Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly.

Authors:  Bas E Dutilh; Martijn A Huynen; Marc Strous
Journal:  Bioinformatics       Date:  2009-06-19       Impact factor: 6.937

Review 8.  The dynamic genetic repertoire of microbial communities.

Authors:  Paul Wilmes; Sheri L Simmons; Vincent J Denef; Jillian F Banfield
Journal:  FEMS Microbiol Rev       Date:  2008-11-24       Impact factor: 16.408

9.  Community-wide analysis of microbial genome sequence signatures.

Authors:  Gregory J Dick; Anders F Andersson; Brett J Baker; Sheri L Simmons; Brian C Thomas; A Pepper Yelton; Jillian F Banfield
Journal:  Genome Biol       Date:  2009-08-21       Impact factor: 13.583

10.  Discovery and characterization of a new bacterial candidate division by an anaerobic sludge digester metagenomic approach.

Authors:  Sonda Guermazi; Patrick Daegelen; Catherine Dauga; Delphine Rivière; Théodore Bouchez; Jean Jacques Godon; Gábor Gyapay; Abdelghani Sghir; Eric Pelletier; Jean Weissenbach; Denis Le Paslier
Journal:  Environ Microbiol       Date:  2008-05-06       Impact factor: 5.491

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