Experts and Doctors on phylogeny in Marseille, Provence Alpes Côte d'Azur, France

Summary

Locale: Marseille, Provence Alpes Côte d'Azur, France
Topic: phylogeny

Top Publications

  1. Renesto P, Gautheret D, Drancourt M, Raoult D. Determination of the rpoB gene sequences of Bartonella henselae and Bartonella quintana for phylogenic analysis. Res Microbiol. 2000;151:831-6 pubmed
    ..Based on the bootstrap values derived from rpoB phylogenic analysis, we believe that this molecule should contribute to better understanding the evolutionary process. ..
  2. Fournier P, Gouriet F, Brouqui P, Lucht F, Raoult D. Lymphangitis-associated rickettsiosis, a new rickettsiosis caused by Rickettsia sibirica mongolotimonae: seven new cases and review of the literature. Clin Infect Dis. 2005;40:1435-44 pubmed
    ..quot; Lymphangitis-associated rickettsiosis should be considered in the differential diagnosis of tick-borne rickettsioses in Europe, Africa, and Asia. ..
  3. Dornas F, Assis F, Aherfi S, Arantes T, Abrahão J, Colson P, et al. A Brazilian Marseillevirus Is the Founding Member of a Lineage in Family Marseilleviridae. Viruses. 2016;8:76 pubmed publisher
    ..In addition, the BrMV genome encodes 29 ORFans. Here, we describe the isolation and genome analyses of the BrMV strain, and propose its classification as the prototype virus of a new lineage D within the family Marseilleviridae. ..
  4. Manuel M, Kruse M, Muller W, Le Parco Y. The comparison of beta-thymosin homologues among metazoa supports an arthropod-nematode clade. J Mol Evol. 2000;51:378-81 pubmed
    ..We argue that such discrete molecular character is phylogenetically very powerful and provides strong evidence for the monophyly of an arthropod-nematode clade. ..
  5. Charrel R, Fagbo S, Moureau G, Alqahtani M, Temmam S, de Lamballerie X. Alkhurma hemorrhagic fever virus in Ornithodoros savignyi ticks. Emerg Infect Dis. 2007;13:153-5 pubmed
    ..One Ornithodoros savignyi tick from Saudi Arabia contained AHFV RNA. This is the first direct evidence that AHFV is a tickborne flavivirus and confirms the association between human AHFV cases and tickbite history...
  6. Saisongkorh W, Robert C, La Scola B, Raoult D, Rolain J. Evidence of transfer by conjugation of type IV secretion system genes between Bartonella species and Rhizobium radiobacter in amoeba. PLoS ONE. 2010;5:e12666 pubmed publisher
    ..Based on this, we speculate that amoeba favor the transfer of genes as phagocytic protists, which allows for intraphagocytic survival and, as a consequence, promotes the creation of potential pathogenic organisms. ..
  7. Couturier M, Feliu J, Haon M, Navarro D, Lesage Meessen L, Coutinho P, et al. A thermostable GH45 endoglucanase from yeast: impact of its atypical multimodularity on activity. Microb Cell Fact. 2011;10:103 pubmed publisher
  8. Keita M, Padhmanabhan R, Robert C, Delaporte E, Raoult D, Fournier P, et al. Non-contiguous-Finished Genome Sequence and Description of Paenibacillus camerounensis sp. nov. Microb Ecol. 2016;71:990-8 pubmed publisher
    ..On the basis of these polyphasic data, consisting of phenotypic and genomic analyses, we propose the creation of Paenibacillus camerounensis sp. nov. that contains the strain G4(T). ..
  9. Brion C, Legrand S, Peter J, Caradec C, Pflieger D, Hou J, et al. Variation of the meiotic recombination landscape and properties over a broad evolutionary distance in yeasts. PLoS Genet. 2017;13:e1006917 pubmed publisher
    ..Identification of this major but underestimated evolutionary phenomenon illustrates the relevance of exploring non-model species. ..

More Information

Publications190 found, 100 shown here

  1. Renvoise A, Raoult D, Roux V. Actinomyces timonensis sp. nov., isolated from a human clinical osteo-articular sample. Int J Syst Evol Microbiol. 2010;60:1516-21 pubmed publisher
    ..On the basis of phenotypic data and phylogenetic inference, it is proposed that this strain should be designated Actinomyces timonensis sp. nov.; the type strain is strain 7400942(T) (=CSUR P35(T)=CCUG 55928(T))...
  2. Yoosuf N, Yutin N, Colson P, Shabalina S, Pagnier I, Robert C, et al. Related giant viruses in distant locations and different habitats: Acanthamoeba polyphaga moumouvirus represents a third lineage of the Mimiviridae that is close to the megavirus lineage. Genome Biol Evol. 2012;4:1324-30 pubmed publisher
    ..Comparative genome analysis of the three lineages of the Mimiviridae revealed significant mobility of Group I self-splicing introns, with the highest intron content observed in the moumouvirus genome. ..
  3. Zeaiter Z, Fournier P, Raoult D. Genomic variation of Bartonella henselae strains detected in lymph nodes of patients with cat scratch disease. J Clin Microbiol. 2002;40:1023-30 pubmed
    ..Patients infected with either one or the other genogroup did not exhibit different epidemiological or clinical characteristics. Our study highlights the genotypic heterogeneity of B. henselae in patients with CSD...
  4. Salinas M, Fardeau M, Cayol J, Casalot L, Patel B, Thomas P, et al. Petrobacter succinatimandens gen. nov., sp. nov., a moderately thermophilic, nitrate-reducing bacterium isolated from an Australian oil well. Int J Syst Evol Microbiol. 2004;54:645-9 pubmed
    ..thermoluteolus, it is proposed that it be assigned to a novel species of a novel genus, Petrobacter succinatimandens gen. nov., sp. nov. The type strain is 4BON(T) (=DSM 15512(T)=CIP 107790(T))...
  5. Enault F, Suhre K, Claverie J. Phydbac "Gene Function Predictor": a gene annotation tool based on genomic context analysis. BMC Bioinformatics. 2005;6:247 pubmed
    ..The "Gene Function predictor" is available at http://www.igs.cnrs-mrs.fr/phydbac/indexPS.html. ..
  6. Alboresi A, Caffarri S, Nogue F, Bassi R, Morosinotto T. In silico and biochemical analysis of Physcomitrella patens photosynthetic antenna: identification of subunits which evolved upon land adaptation. PLoS ONE. 2008;3:e2033 pubmed publisher
    ..The moss Physcomitrella patens is a member of a lineage that diverged from seed plants early after land colonization and therefore by studying this organism, we may gain insight into adaptations to the aerial environment...
  7. Drali R, Abi Rached L, Boutellis A, Djossou F, Barker S, Raoult D. Host switching of human lice to new world monkeys in South America. Infect Genet Evol. 2016;39:225-231 pubmed publisher
    ..Because this phylogenetic group forms a separate branch within the clade of lice from humans that were of American origin, this finding indicates that human lice have transferred to New World monkeys. ..
  8. Boissin E, Féral J, Chenuil A. Defining reproductively isolated units in a cryptic and syntopic species complex using mitochondrial and nuclear markers: the brooding brittle star, Amphipholis squamata (Ophiuroidea). Mol Ecol. 2008;17:1732-44 pubmed publisher
  9. Glazunova O, Raoult D, Roux V. Partial sequence comparison of the rpoB, sodA, groEL and gyrB genes within the genus Streptococcus. Int J Syst Evol Microbiol. 2009;59:2317-22 pubmed publisher
    ..3, 2.7, 0, 2.5 and 3.4 % for the 16S rRNA gene, rpoB, sodA, gyrB and groEL, respectively. In general, groEL partial gene sequence comparison represented the best tool for identifying species and subspecies and for phylogenetic analysis. ..
  10. Chiaroni J, Underhill P, Cavalli Sforza L. Y chromosome diversity, human expansion, drift, and cultural evolution. Proc Natl Acad Sci U S A. 2009;106:20174-9 pubmed publisher
  11. Grégoire P, Bohli M, Cayol J, Joseph M, Guasco S, Dubourg K, et al. Caldilinea tarbellica sp. nov., a filamentous, thermophilic, anaerobic bacterium isolated from a deep hot aquifer in the Aquitaine Basin. Int J Syst Evol Microbiol. 2011;61:1436-41 pubmed publisher
    ..nov. is proposed. The type strain is D1-25-10-4(T) (?=?DSM 22659(T) ?=?JCM 16120(T)). ..
  12. Desvignes T, Pontarotti P, Bobe J. Nme gene family evolutionary history reveals pre-metazoan origins and high conservation between humans and the sea anemone, Nematostella vectensis. PLoS ONE. 2010;5:e15506 pubmed publisher
    ..Future investigations of evolutionarily conserved Nme gene functions using the starlet sea anemone could shed new light on a wide variety of key developmental and cellular processes. ..
  13. Ben Hania W, Fraj B, Postec A, Fadhlaoui K, Hamdi M, Ollivier B, et al. Fusibacter tunisiensis sp. nov., isolated from an anaerobic reactor used to treat olive-mill wastewater. Int J Syst Evol Microbiol. 2012;62:1365-8 pubmed publisher
    ..nov. is proposed. The type strain is BELH1(T) ( = DSM 24436(T) = JCM 17481(T)). ..
  14. Luciano J, Agrebi R, Le Gall A, Wartel M, Fiegna F, Ducret A, et al. Emergence and modular evolution of a novel motility machinery in bacteria. PLoS Genet. 2011;7:e1002268 pubmed publisher
    ..Surprisingly, this motility machinery appears to be highly related to a sporulation system, underscoring unsuspected common mechanisms in these apparently distinct morphogenic phenomena...
  15. Colson P, Fancello L, Gimenez G, Armougom F, Desnues C, Fournous G, et al. Evidence of the megavirome in humans. J Clin Virol. 2013;57:191-200 pubmed publisher
    ..2-0.45-?m range. Concurrently, there has been accumulating evidence supporting the role of Mimivirus, discovered while investigating a pneumonia outbreak using amoebal coculture, as a causative agent in pneumonia...
  16. Llagonne Barets M, Icard V, Leparc Goffart I, Prat C, Perpoint T, André P, et al. A case of Mayaro virus infection imported from French Guiana. J Clin Virol. 2016;77:66-8 pubmed publisher
  17. Drancourt M, Bollet C, Carta A, Rousselier P. Phylogenetic analyses of Klebsiella species delineate Klebsiella and Raoultella gen. nov., with description of Raoultella ornithinolytica comb. nov., Raoultella terrigena comb. nov. and Raoultella planticola comb. nov. Int J Syst Evol Microbiol. 2001;51:925-32 pubmed
    ..The name Raoultella is proposed as a genus name for species of cluster II and emended definitions of Klebsiella species are proposed. ..
  18. Charrel R, Zaki A, Attoui H, Fakeeh M, Billoir F, Yousef A, et al. Complete coding sequence of the Alkhurma virus, a tick-borne flavivirus causing severe hemorrhagic fever in humans in Saudi Arabia. Biochem Biophys Res Commun. 2001;287:455-61 pubmed
  19. Marlétaz F, Le Parco Y. Careful with understudied phyla: the case of chaetognath. BMC Evol Biol. 2008;8:251 pubmed publisher
    ..However, the previous study came to incorrect conclusions on the basis of experiments that omitted validation procedures. ..
  20. Bonente G, Passarini F, Cazzaniga S, Mancone C, Buia M, Tripodi M, et al. The occurrence of the psbS gene product in Chlamydomonas reinhardtii and in other photosynthetic organisms and its correlation with energy quenching. Photochem Photobiol. 2008;84:1359-70 pubmed publisher
    ..By correlating growth habitat and PsbS accumulation in different species, we suggest that during the evolution the light environment has been a determinant factor for the conservation/loss of the PsbS function. ..
  21. Dridi B, Fardeau M, 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;62:1902-7 pubmed publisher
    ..nov., sp. nov. is proposed. The type strain of the type species is B10(T) (?=?DSM 24529(T)?=?CSUR P135(T)). ..
  22. Gazis R, Kuo A, Riley R, LaButti K, Lipzen A, Lin J, et al. The genome of Xylona heveae provides a window into fungal endophytism. Fungal Biol. 2016;120:26-42 pubmed publisher
    ..ITS data revealed that Trinosporium is also part of the Xylonomycetes, extending the taxonomic and ecological diversity of this group. ..
  23. Schenkelaars Q, Quintero O, Hall C, Fierro Constain L, Renard E, Borchiellini C, et al. ROCK inhibition abolishes the establishment of the aquiferous system in Ephydatia muelleri (Porifera, Demospongiae). Dev Biol. 2016;412:298-310 pubmed publisher
  24. Halfon P, Riflet H, Renou C, Quentin Y, Cacoub P. Molecular evidence of male-to-female sexual transmission of hepatitis C virus after vaginal and anal intercourse. J Clin Microbiol. 2001;39:1204-6 pubmed
    ..Based on HVR1 and phylogenetic tree analysis, the couple had closely related isolates. These findings confirm sexual transmission of HCV without other risk factors. ..
  25. Greub G, Raoult D. "Actinobaculum massiliae," a new species causing chronic urinary tract infection. J Clin Microbiol. 2002;40:3938-41 pubmed
    ..quot; ..
  26. Ad kambi T, Colson P, Drancourt M. rpoB-based identification of nonpigmented and late-pigmenting rapidly growing mycobacteria. J Clin Microbiol. 2003;41:5699-708 pubmed
    ..We conclude that molecular identification by analysis of the 723-bp rpoB sequence is a rapid and accurate tool for identification of RGM...
  27. Fenner L, Roux V, Mallet M, Raoult D. Bacteroides massiliensis sp. nov., isolated from blood culture of a newborn. Int J Syst Evol Microbiol. 2005;55:1335-7 pubmed
    ..8 % 16S rRNA similarity to Bacteroides vulgatus and a DNA G + C content of 49 mol%. The major cellular fatty acid is anteiso-branched C(15 : 0). The type strain of B. massiliensis sp. nov. is B84634(T) (=CIP 107942(T) = CCUG 48901(T))...
  28. La Scola B, Campocasso A, N Dong R, Fournous G, Barrassi L, Flaudrops C, et al. Tentative characterization of new environmental giant viruses by MALDI-TOF mass spectrometry. Intervirology. 2010;53:344-53 pubmed publisher
    ..We attempted herein to isolate new Acanthamoeba-growing giant viruses from environmental samples...
  29. Bonnefoy V, Holmes D. Genomic insights into microbial iron oxidation and iron uptake strategies in extremely acidic environments. Environ Microbiol. 2012;14:1597-611 pubmed publisher
    ..It is anticipated that integrated and complex regulatory networks sensing different environmental signals, such as the energy source and/or the redox state of the cell as well as the oxygen availability, are involved. ..
  30. Mounier A, Balzeau A, Caparrós M, Grimaud Hervé D. Brain, calvarium, cladistics: A new approach to an old question, who are modern humans and Neandertals?. J Hum Evol. 2016;92:22-36 pubmed publisher
    ..The combined study of endocranial and exocranial anatomy offers opportunities to further understand human evolution and the implication for the phylogeny of our genus. ..
  31. Andreani J, Khalil J, Sevvana M, Benamar S, Di Pinto F, Bitam I, et al. Pacmanvirus, a New Giant Icosahedral Virus at the Crossroads between Asfarviridae and Faustoviruses. J Virol. 2017;91: pubmed publisher
    ..These results highlight the emergence of previously unknown double-stranded DNA viruses which delineate and extend the diversity of a group around the asfarvirus members. ..
  32. Laugier Anfossi F, Villard L. Molecular characterization of a new human T-box gene (TBX22) located in xq21.1 encoding a protein containing a truncated T-domain. Gene. 2000;255:289-96 pubmed
    ..These data indicate that TBX22 may be the first identified member of a new family of T-domain-containing proteins. ..
  33. Baymann F, Brugna M, Muhlenhoff U, Nitschke W. Daddy, where did (PS)I come from?. Biochim Biophys Acta. 2001;1507:291-310 pubmed
    ..An evolutionary model trying to rationalise available data is presented. ..
  34. Gallian P, Biagini P, Attoui H, Cantaloube J, Dussol B, Berland Y, et al. High genetic diversity revealed by the study of TLMV infection in French hemodialysis patients. J Med Virol. 2002;67:630-5 pubmed
    ..5%). These data suggest that TLMV viral load is possibly related to the level of immunocompetence of hemodialysis patients; the genetic diversity of TLMV is extremely high; and co-infection by different strains is possible. ..
  35. Charrel R, de Lamballerie X, Emonet S. Phylogeny of the genus Arenavirus. Curr Opin Microbiol. 2008;11:362-8 pubmed publisher
  36. Crozat K, Guiton R, Contreras V, Feuillet V, Dutertre C, Ventre E, et al. The XC chemokine receptor 1 is a conserved selective marker of mammalian cells homologous to mouse CD8alpha+ dendritic cells. J Exp Med. 2010;207:1283-92 pubmed publisher
  37. Georgiades K, Madoui M, Le P, Robert C, Raoult D. Phylogenomic analysis of Odyssella thessalonicensis fortifies the common origin of Rickettsiales, Pelagibacter ubique and Reclimonas americana mitochondrion. PLoS ONE. 2011;6:e24857 pubmed publisher
    ..Recently, the whole genome of O. thessalonicensis has been sequenced, and 16S rDNA phylogeny and more robust and accurate phylogenomic analyses have been performed with 65 highly conserved proteins...
  38. Dubot Pérès A, Vongphrachanh P, Denny J, Phetsouvanh R, Linthavong S, Sengkeopraseuth B, et al. An epidemic of dengue-1 in a remote village in rural Laos. PLoS Negl Trop Dis. 2013;7:e2360 pubmed publisher
    ..More epidemiological and entomological investigations are required to understand dengue epidemiology and the importance of rural and forest dengue dynamics in Laos. ..
  39. D Amato F, Eldin C, Raoult D. The contribution of genomics to the study of Q fever. Future Microbiol. 2016;11:253-72 pubmed publisher
    ..An extensive pan-genomic analysis will allow for a comprehensive view of the clonal diversity of C. burnetii and its link with virulence. ..
  40. Aubry C, Socolovschi C, Raoult D, Parola P. Bacterial agents in 248 ticks removed from people from 2002 to 2013. Ticks Tick Borne Dis. 2016;7:475-81 pubmed publisher
    ..8%) and Rickettsia spp. (2%) were detected in Ixodes ticks. Among the bitten people for which clinical data and laboratory samples were available, tick borne diseases were confirmed in 11 symptomatic individuals. ..
  41. Amanzougaghene N, Fenollar F, Sangaré A, Sissoko M, Doumbo O, Raoult D, et al. Detection of bacterial pathogens including potential new species in human head lice from Mali. PLoS ONE. 2017;12:e0184621 pubmed publisher
    ..burnetii, R. aeschlimannii, Anaplasma and Ehrlichia is alarming and highlights the need for active survey programs to define the public health consequences of the detection of these emerging bacterial pathogens in human head lice. ..
  42. Mitchell M, Wilcox S, Watson J, Lerner J, Woods D, Scheffler J, et al. The origin and loss of the ubiquitin activating enzyme gene on the mammalian Y chromosome. Hum Mol Genet. 1998;7:429-34 pubmed
    ..Thus UBE1 illustrates the key steps of 'autosomal to X-specific' evolution of genes on the sex chromosomes...
  43. Matarazzo V, Tirard A, Renucci M, Belaich A, Clement J. Isolation of putative olfactory receptor sequences from pig nasal epithelium. Neurosci Lett. 1998;249:87-90 pubmed
    ..Ledbetter DH., Carrozzo R., Patel K., Sheer D., Lehrah H. and North M., Hum. Mol. Genet., 3 (1994) 229-235], the 11 receptors described here can be classified into three known families and seven subfamilies (one known and six new). ..
  44. Marqueze B, Berton F, Seagar M. Synaptotagmins in membrane traffic: which vesicles do the tagmins tag?. Biochimie. 2000;82:409-20 pubmed
    ..Therefore, to discuss the putative role of the various synaptotagmins we have examined in detail published data concerning their localization. ..
  45. Attoui H, Biagini P, Stirling J, Mertens P, Cantaloube J, Meyer A, et al. Sequence characterization of Ndelle virus genome segments 1, 5, 7, 8, and 10: evidence for reassignment to the genus Orthoreovirus, family Reoviridae. Biochem Biophys Res Commun. 2001;287:583-8 pubmed
    ..These findings, together with previous antigenic analyses, provide evidence that NDEV should be reclassified as a new serotype (designated MRV-4) within the Mammalian orthoreovirus species...
  46. Favre C, Gerard A, Clauzier E, Pontarotti P, Olive D, Nunes J. DOK4 and DOK5: new Dok-related genes expressed in human T cells. Genes Immun. 2003;4:40-5 pubmed
    ..So, Dok-4 and Dok-5 molecules constitute a new group of adapter proteins in T cells, requiring further functional analysis. ..
  47. Hua H, Bollet C, Tercian S, Drancourt M, Raoult D. Aeromonas popoffii urinary tract infection. J Clin Microbiol. 2004;42:5427-8 pubmed
    ..This is the first reported case of human infection attributed to this species. ..
  48. Emonet S, Lemasson J, Gonzalez J, de Lamballerie X, Charrel R. Phylogeny and evolution of old world arenaviruses. Virology. 2006;350:251-7 pubmed publisher
    ..No evidence for significant evolutionary events such as intra- or intersegmental recombination was obtained...
  49. Audic S, Robert C, Campagna B, Parinello H, Claverie J, Raoult D, et al. Genome analysis of Minibacterium massiliensis highlights the convergent evolution of water-living bacteria. PLoS Genet. 2007;3:e138 pubmed
    ..The M. massiliensis genome analyses strongly suggest that water-living bacteria are a common source for genes involved in heavy-metal resistance, antibiotics resistance, and virulence factors. ..
  50. Royer B, Soares D, Barlow P, Bontrop R, Roll P, Robaglia Schlupp A, et al. Molecular evolution of the human SRPX2 gene that causes brain disorders of the Rolandic and Sylvian speech areas. BMC Genet. 2007;8:72 pubmed publisher
    ..Further experiments are now required in order to evaluate the possible consequences of R75K on SRPX2 interactions and functioning...
  51. Brochier Armanet C, Boussau B, Gribaldo S, Forterre P. Mesophilic Crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota. Nat Rev Microbiol. 2008;6:245-52 pubmed publisher
    ..Our results indicate that C. symbiosum and its relatives are not Crenarchaeota, but should be considered as a third archaeal phylum, which we propose to name Thaumarchaeota (from the Greek 'thaumas', meaning wonder)...
  52. Vincent F, Molin D, Weiner R, Bourne Y, Henrissat B. Structure of a polyisoprenoid binding domain from Saccharophagus degradans implicated in plant cell wall breakdown. FEBS Lett. 2010;584:1577-84 pubmed publisher
    ..This unprecedented association coupling oxidoreduction and carbohydrate recognition events may have implications for effective nutrient uptake in the marine environment...
  53. Coumes Florens S, Brochier Armanet C, Guiseppi A, Denizot F, Foglino M. A new highly conserved antibiotic sensing/resistance pathway in firmicutes involves an ABC transporter interplaying with a signal transduction system. PLoS ONE. 2011;6:e15951 pubmed publisher
    ..Taken together our study suggests that this regulatory mechanism might constitute an important common antibiotic resistance mechanism in Firmicutes. [Supplemental material is available online at http://www.genome.org.]...
  54. Fancello L, Desnues C, Raoult D, Rolain J. Bacteriophages and diffusion of genes encoding antimicrobial resistance in cystic fibrosis sputum microbiota. J Antimicrob Chemother. 2011;66:2448-54 pubmed publisher
  55. Addou A, Schumann P, Sproer C, Hacene H, Cayol J, Fardeau M. Melghirimyces algeriensis gen. nov., sp. nov., a member of the family Thermoactinomycetaceae, isolated from a salt lake. Int J Syst Evol Microbiol. 2012;62:1491-8 pubmed publisher
    ..nov., sp. nov. is proposed. The type strain of Melghirimyces algeriensis, the type species of the genus, is NariEX(T) (=DSM 45474(T)=CCUG 59620(T)). ..
  56. Fancello L, Trape S, Robert C, Boyer M, Popgeorgiev N, Raoult D, et al. Viruses in the desert: a metagenomic survey of viral communities in four perennial ponds of the Mauritanian Sahara. ISME J. 2013;7:359-69 pubmed publisher
    ..We hypothesized that the differences observed in the structural and functional composition of the Hamdoun viral community resulted from the critically low water level experienced by the guelta. ..
  57. Paganini J, Campan Fournier A, Da Rocha M, Gouret P, Pontarotti P, Wajnberg E, et al. Contribution of lateral gene transfers to the genome composition and parasitic ability of root-knot nematodes. PLoS ONE. 2012;7:e50875 pubmed publisher
    ..Besides being involved in important processes regarding plant-parasitism, genes acquired via LGT now constitute a substantial proportion of protein-coding genes in these nematode genomes. ..
  58. McGregor N, Morar M, Fenger T, Stogios P, Lenfant N, Yin V, et al. Structure-Function Analysis of a Mixed-linkage β-Glucanase/Xyloglucanase from the Key Ruminal Bacteroidetes Prevotella bryantii B(1)4. J Biol Chem. 2016;291:1175-97 pubmed publisher
    ..Nonetheless, our results provide key enzyme functional and structural reference data for future bioinformatics analyses of (meta)genomes to elucidate the biology of complex gut ecosystems. ..
  59. York D, Vigne R, Verwoerd D, Querat G. Nucleotide sequence of the jaagsiekte retrovirus, an exogenous and endogenous type D and B retrovirus of sheep and goats. J Virol. 1992;66:4930-9 pubmed
    ..Southern blot studies show that closely related sequences are present in sheep and goat normal genomic DNA, indicating that JSRV could be endogenous in ovine and caprine species...
  60. Querat G, Audoly G, Sonigo P, Vigne R. Nucleotide sequence analysis of SA-OMVV, a visna-related ovine lentivirus: phylogenetic history of lentiviruses. Virology. 1990;175:434-47 pubmed
    ..BRU, ELI, and MAL HIV-1 isolates diverged in the early 1960s...
  61. Roux V, Bergoin M, Lamaze N, Raoult D. Reassessment of the taxonomic position of Rickettsiella grylli. Int J Syst Bacteriol. 1997;47:1255-7 pubmed
    ..Our results indicate that R. grylli should be removed from the order Rickettsiales. ..
  62. Brochier C, Forterre P, Gribaldo S. An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences. BMC Evol Biol. 2005;5:36 pubmed
    ..The identification and analysis of additional molecular markers not affected by LGT should continue defining the emerging picture of a genuine phylogenetic core for the third domain of life. ..
  63. Attoui H, Mohd Jaafar F, Belhouchet M, Aldrovandi N, Tao S, Chen B, et al. Yunnan orbivirus, a new orbivirus species isolated from Culex tritaeniorhynchus mosquitoes in China. J Gen Virol. 2005;86:3409-17 pubmed publisher
    ..The availability of the complete genome sequence will facilitate the development of sequence-specific PCR assays for the study of YUOV epidemiology in the field...
  64. Lebrun E, Santini J, Brugna M, Ducluzeau A, Ouchane S, Schoepp Cothenet B, et al. The Rieske protein: a case study on the pitfalls of multiple sequence alignments and phylogenetic reconstruction. Mol Biol Evol. 2006;23:1180-91 pubmed
    ..The obtained results are discussed against the background of hypotheses stipulating pervasive lateral gene transfer in prokaryotes. ..
  65. Leduc D, Battesti A, Bouveret E. The hotdog thioesterase EntH (YbdB) plays a role in vivo in optimal enterobactin biosynthesis by interacting with the ArCP domain of EntB. J Bacteriol. 2007;189:7112-26 pubmed
    ..This is the first description of such a role in the optimization of a nonribosomal biosynthesis pathway for a protein of the hotdog superfamily. ..
  66. Gérard K, Roby C, Chevalier N, Thomassin B, Chenuil A, Féral J. Assessment of three mitochondrial loci variability for the crown-of-thorns starfish: a first insight into Acanthaster phylogeography. C R Biol. 2008;331:137-43 pubmed publisher
    ..planci forming distinct clades in agreement with data from morphology and systematics. The A. planci clade split into a West Indian Ocean group and a Pacific group, in agreement with allozyme data on population differentiation. ..
  67. Claverie J, Grzela R, Lartigue A, Bernadac A, Nitsche S, Vacelet J, et al. Mimivirus and Mimiviridae: giant viruses with an increasing number of potential hosts, including corals and sponges. J Invertebr Pathol. 2009;101:172-80 pubmed publisher
  68. Abdelkafi S, Ogata H, Barouh N, Fouquet B, Lebrun R, Pina M, et al. Identification and biochemical characterization of a GDSL-motif carboxylester hydrolase from Carica papaya latex. Biochim Biophys Acta. 2009;1791:1048-56 pubmed publisher
  69. Dereeper A, Audic S, Claverie J, Blanc G. BLAST-EXPLORER helps you building datasets for phylogenetic analysis. BMC Evol Biol. 2010;10:8 pubmed publisher
    ..BLAST-Explorer is available at http://www.phylogeny.fr. ..
  70. Nitschke W, van Lis R, Schoepp Cothenet B, Baymann F. The "green" phylogenetic clade of Rieske/cytb complexes. Photosynth Res. 2010;104:347-55 pubmed publisher
    ..Structural and functional idiosyncrasies are (re-)interpreted in the framework of evolutionary biology and more specifically evolutionary bioenergetics. ..
  71. Gimenez G, Bertelli C, Moliner C, Robert C, Raoult D, Fournier P, et al. Insight into cross-talk between intra-amoebal pathogens. BMC Genomics. 2011;12:542 pubmed publisher
    ..Therefore it contributes to improve our knowledge on the intra-amoebal gene properties associated to their specific lifestyle. ..
  72. Mba Medie F, Davies G, Drancourt M, Henrissat B. Genome analyses highlight the different biological roles of cellulases. Nat Rev Microbiol. 2012;10:227-34 pubmed publisher
    ..We also discuss newly emerging roles of cellulases in such non-saprophytic organisms. ..
  73. Mediannikov O, Audoly G, Diatta G, Trape J, Raoult D. New Rickettsia sp. in tsetse flies from Senegal. Comp Immunol Microbiol Infect Dis. 2012;35:145-50 pubmed publisher
    ..The role of this probable fourth endosymbiotic bacterium of tsetse flies in Glossina lifecycle and possible pathogenecity for humans should be further investigated. ..
  74. Dubut V, Fouquet A, Voisin A, Costedoat C, Chappaz R, Gilles A. From Late Miocene to Holocene: processes of differentiation within the Telestes genus (Actinopterygii: Cyprinidae). PLoS ONE. 2012;7:e34423 pubmed publisher
    ..This study provides support for an evolutionary history of dispersal and vicariance with unprecedented resolution for any freshwater fish in this region. ..
  75. Lamrabet O, Merhej V, Pontarotti P, Raoult D, Drancourt M. The genealogic tree of mycobacteria reveals a long-standing sympatric life into free-living protozoa. PLoS ONE. 2012;7:e34754 pubmed publisher
    ..In conclusion, the results of this study support the hypothesis that protists can serve as a source and a place for gene transfer in mycobacteria. ..
  76. Parola P, Paddock C, Socolovschi C, Labruna M, Mediannikov O, Kernif T, et al. Update on tick-borne rickettsioses around the world: a geographic approach. Clin Microbiol Rev. 2013;26:657-702 pubmed publisher
    ..Here, we present the current knowledge on tick-borne rickettsiae and rickettsioses using a geographic approach toward the epidemiology of these diseases. ..
  77. Tidjani Alou M, Khelaifia S, Michelle C, Andrieu C, Armstrong N, Bittar F, et al. Anaerococcus rubiinfantis sp. nov., isolated from the gut microbiota of a Senegalese infant with severe acute malnutrition. Anaerobe. 2016;40:85-94 pubmed publisher
    ..We believe that the extension of the human anaerobic gut compendium by culturomics is one of the first steps that will improve the understanding of the links between the microbiome and health or disease. ..
  78. Smith D, Meyers G, Bukh J, Gould E, Monath T, Scott Muerhoff A, et al. Proposed revision to the taxonomy of the genus Pestivirus, family Flaviviridae. J Gen Virol. 2017;98:2106-2112 pubmed publisher
    ..A bat-derived virus and pestiviruses identified from sheep and goat (Tunisian sheep pestiviruses), which lack complete coding region sequences, may represent two additional species...
  79. Conte N, Delaval B, Ginestier C, Ferrand A, Isnardon D, Larroque C, et al. TACC1-chTOG-Aurora A protein complex in breast cancer. Oncogene. 2003;22:8102-16 pubmed
  80. Glazunova O, Raoult D, Roux V. Streptococcus massiliensis sp. nov., isolated from a patient blood culture. Int J Syst Evol Microbiol. 2006;56:1127-31 pubmed
    ..ferus and S. sanguinis, respectively, confirming it as belonging to a novel taxon, for which the name Streptococcus massiliensis sp. nov. is proposed. The type strain is 4401825T (=CIP 108498T=CCUG 49690T). ..
  81. Fournier P, Siritantikorn S, Rolain J, Suputtamongkol Y, Hoontrakul S, Charoenwat S, et al. Detection of new genotypes of Orientia tsutsugamushi infecting humans in Thailand. Clin Microbiol Infect. 2008;14:168-73 pubmed
    ..Other genotypes formed two other clusters that may also be associated with undescribed serotypes...
  82. Ben Salah I, Adekambi T, Raoult D, Drancourt M. rpoB sequence-based identification of Mycobacterium avium complex species. Microbiology. 2008;154:3715-23 pubmed publisher
    ..Partial rpoB gene sequencing using the Myco-F/Myco-R primers permits one-step identification of MAC isolates at the species level and the detection of potentially novel MAC species...
  83. Ninove L, Domart Y, Vervel C, Voinot C, Salez N, Raoult D, et al. Cowpox virus transmission from pet rats to humans, France. Emerg Infect Dis. 2009;15:781-4 pubmed publisher
    ..Pet rats, originating from the same pet store, were shown to be infected by a unique virus strain. Infection was then transmitted to humans who purchased or had contact with pet rats...
  84. Monier A, Pagarete A, de Vargas C, Allen M, Read B, Claverie J, et al. Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus. Genome Res. 2009;19:1441-9 pubmed publisher
  85. Ben Salah I, Cayrou C, Raoult D, Drancourt M. Mycobacterium marseillense sp. nov., Mycobacterium timonense sp. nov. and Mycobacterium bouchedurhonense sp. nov., members of the Mycobacterium avium complex. Int J Syst Evol Microbiol. 2009;59:2803-8 pubmed publisher
    ..nov., with strain 5351974(T) (=CCUG 56329(T) =CIP 109830(T) =CSUR P32(T)) as the type strain; and Mycobacterium bouchedurhonense sp. nov., with strain 4355387(T) (=CCUG 56331(T) =CIP 109827(T) =CSUR P34(T)) as the type strain. ..
  86. Grard G, Moureau G, Charrel R, Holmes E, Gould E, de Lamballerie X. Genomics and evolution of Aedes-borne flaviviruses. J Gen Virol. 2010;91:87-94 pubmed publisher
  87. Boyer M, Madoui M, Gimenez G, La Scola B, 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 pubmed publisher
    ..We hypothesize that the core genome of NCLDV is as ancient as the three currently accepted domains of life. ..
  88. Georgiades K, Merhej V, El Karkouri K, Raoult D, Pontarotti P. Gene gain and loss events in Rickettsia and Orientia species. Biol Direct. 2011;6:6 pubmed publisher
    ..Reviewed by Arcady Mushegian, Eugene V. Koonin and Patrick Forterre. For the full reviews please go to the Reviewers' comments section. ..
  89. Tan C, Ninove L, Gaudart J, Nougairede A, Zandotti C, Thirion Perrier L, et al. A retrospective overview of enterovirus infection diagnosis and molecular epidemiology in the public hospitals of Marseille, France (1985-2005). PLoS ONE. 2011;6:e18022 pubmed publisher
    ..Phylogenetic analysis in the VP1, 2C and 3D regions also provided evidence for recombination events amongst clinical isolates. In particular, it identified isolates with dissimilar VP1 but almost identical nonstructural regions...
  90. Santini S, Claverie J, Mouz N, Rousselle T, Maza C, Monchois V, et al. The conserved Candida albicans CA3427 gene product defines a new family of proteins exhibiting the generic periplasmic binding protein structural fold. PLoS ONE. 2011;6:e18528 pubmed publisher
    ..It was then lost by the Saccharomycetales which include Saccharomyces cerevisiae. ..
  91. Lemaire P. Evolutionary crossroads in developmental biology: the tunicates. Development. 2011;138:2143-52 pubmed publisher
    ..Tunicates are thus a powerful system for exploring chordate evolution and how extreme variation in genome sequence and gene regulatory network architecture is compatible with the preservation of an ancestral chordate body plan...
  92. Kaba M, Richet H, Ravaux I, Moreau J, Poizot Martin I, Motte A, et al. Hepatitis E virus infection in patients infected with the human immunodeficiency virus. J Med Virol. 2011;83:1704-16 pubmed publisher
    ..HEV RNA testing is necessary for such purposes...