TRUC or the need for a new microbial classification

Intervirology

Volumn 56, Issue 6, 2013, Pages 349-353

  Raoult, Didier ^a  

^a AIX MARSEILLE UNIVERSITÉ   (France)

Author keywords

Archaea; Bacteria; Eukarya; Megavirales; Mimivirus; TRUC Things Resisting Uncompleted Classifications

Indexed keywords

ARCHAEON; BACTERIA; BACTERIAL GENE; CLASSIFICATION; DNA VIRUS; EUKARYOTE; GENE CLUSTER; GRAM POSITIVE BACTERIUM; GRAM STAINING; MEGAVIRALES; MICROBIOLOGY; MICROORGANISM; MIMIVIRUS; NONHUMAN; PRIORITY JOURNAL; PROKARYOTE; REVIEW; THING RESISTING UNCOMPLETED CLASSIFICATION; VERRUCOMICROBIA; VIRUS GENE;

EUKARYOTA; MIMIVIRUS; PROKARYOTA;

CLASSIFICATION; EUKARYOTA; PROKARYOTIC CELLS; VIRUSES;

EID: 84887055113     PISSN: 03005526     EISSN: 14230100     Source Type: Journal    
DOI: 10.1159/000354269     Document Type: Review

References (28)

1. Popper K: The Logic of Scientific Discovery, ed 2. New York, Routledge Classics, 2007.
2. Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, La SB, Suzan M, Claverie JM: The 1.2-megabase genome sequence of Mimivirus. Science 2004; 306: 1344-1350.
3. Colson P, de Lamballerie X, Fournous G, Raoult D: Reclassification of giant viruses composing a fourth domain of life in the new order Megavirales. Intervirology 2012; 55: 321-332.
4. Raoult D, Forterre P: Redefining viruses: lessons from Mimivirus. Nat Rev Microbiol 2008; 6: 315-319.
5. Chatton E: Pansporella perplexa. Réflexions sur la biologie et la phylogénie des protozoaires. Ann Sci Nat Zool 1925; 10(vii):1-84.
6. Woese CR: Bacterial evolution. Microbiol Rev 1987; 51: 222-270.
7. Fuerst JA, Sagulenko E: Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function. Nat Rev Microbiol 2011; 9: 403-413.
8. Dridi B, Fardeau ML, Ollivier B, Raoult D, Drancourt M: Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces. Int J Syst Evol Microbiol 2012; 62: 1902-1907.
9. Esser C, Ahmadinejad N, Wiegand C, Rotte C, Sebastiani F, Gelius-Dietrich G, Henze K, Kretschmann E, Richly E, Leister D, Bryant D, Steel MA, Lockhart PJ, Penny D, Martin W: A genome phylogeny for mitochondria among ?-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes. Mol Biol Evol 2004; 21: 1643-1660.
10. Georgiades K, Raoult D: The rhizome of Reclinomonas americana , Homo sapiens , Pediculus humanus and Saccharomyces cerevisiae mitochondria. Biol Direct 2011; 6: 55.
11. Dagan T, Martin W: The tree of one percent. Genome Biol 2006; 7: 118.
12. Raoult D: The post-Darwinist rhizome of life. Lancet 2010; 375: 104-105.
13. Moreira D, Lopez-Garcia P: Ten reasons to exclude viruses from the tree of life. Nat Rev Microbiol 2009; 7: 306-311.
14. Raoult D, La SB, Birtles R: The discovery and characterization of Mimivirus, the largest known virus and putative pneumonia agent. Clin Infect Dis 2007; 45: 95-102.
15. Iyer LM, Balaji S, Koonin EV, Aravind L: Evolutionary genomics of nucleocytoplasmic large DNA viruses. Virus Res 2006; 117: 156-184.
16. Boyer M, Madoui MA, Gimenez G, La SB, Raoult D: Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4 domain of life including giant viruses. PLoS One 2010; 5:e15530.
17. Boyer M, Madoui MA, Gimenez G, La SB, Raoult D: Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4 domain of life including giant viruses. PLoS One 2010; 5:e15530.
18. Wu D, Wu M, Halpern A, Rusch DB, Yooseph S, Frazier M, Venter JC, Eisen JA: Stalking the fourth domain in metagenomic data: searching for, discovering, and interpreting novel, deep branches in marker gene phylogenetic trees. PLoS One 2011; 6:e18011.
19. Nasir A, Kim KM, Caetano-Anolles G: Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya. BMC Evol Biol 2012; 12: 156.
20. LeGendre M, Arslan D, Abergel C, Claverie JM: Genomics of Megavirus and the elusive fourth domain of Life. Commun Integr Biol 2012; 5: 102-106.
21. Loftus B, Clarke M, Lohia A, et al: Genome of the environmental host Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of pattern recognition and tyrosine kinase signalling. Genome Res 2013, E-pub ahead of print.
22. La SB, Desnues C, Pagnier I, Robert C, Barrassi L, Fournous G, Merchat M, Suzan-Monti M, Forterre P, Koonin E, Raoult D: The virophage as a unique parasite of the giant Mimivirus. Nature 2008; 455: 100-104.
23. Desnues C, La SB, Yutin N, Fournous G, Robert C, Azza S, Jardot P, Monteil S, Campocasso A, Koonin EV, Raoult D: Provirophages and transpovirons as the diverse mobilome of giant viruses. Proc Natl Acad Sci USA 2012; 109: 18078-18083.
24. Forterre P: Giant viruses: conflicts in revisiting the virus concept. Intervirology 2010; 53: 362-378.
25. Boyer M, Gimenez G, Suzan-Monti M, Raoult D: Classification and determination of possible origins of ORFans through analysis of nucleocytoplasmic large DNA viruses. Intervirology 2010; 53: 310-320.
26. Edwards RA, Rohwer F: Viral metagenomics. Nat Rev Microbiol 2005; 3: 504-510.
27. Colson P, Fancello L, Gimenez G, Armoungom F, Desnues C, Fournous G, Yoosuf N, Million M, La Scola B, Raoult D: Evidence of the Megavirome in Humans. J Clin Virol 2013, E-pub ahead of print.
28. Woese CR, Kandler O, Wheelis ML: Towards a natural system of organisms: proposal for the domains Archae, Bacteria, and Eukarya. Proc Natl Acad Sci USA 1990; 87: 4576-4579.