Rise of microbial culturomics: Noncontiguous finished genome sequence and description of Beduini massiliensis gen. Nov., sp. Nov.

OMICS A Journal of Integrative Biology

Volumn 19, Issue 12, 2015, Pages 766-776

  Mourembou, Gaël ^a,b   Yasir, Muhammad ^c   Azhar, Esam Ibraheem ^c   Lagier, Jean Christophe ^a   Bibi, Fehmida ^c   Jiman Fatani, Asif Ahmad ^c   Helmy, Nayel ^d   Robert, Catherine ^a   Rathored, Jaishriram ^a   Fournier, Pierre Edouard ^a   Raoult, Didier ^a,c   Million, Matthieu ^a  

^a AIX MARSEILLE UNIVERSITÉ   (France)

^b Regional Doctoral School of Central Africa   (Gabon)

^c KING ABDULAZIZ UNIVERSITY   (Saudi Arabia)

^d Suliman Fageeh Hospital   (Saudi Arabia)

Author keywords

[No Author keywords available]

Indexed keywords

AMIKACIN; AMOXICILLIN; AMOXICILLIN PLUS CLAVULANIC ACID; BACTERIAL PROTEIN; BACTERIAL RNA; CIPROFLOXACIN; CLINDAMYCIN; CONTIG; COTRIMOXAZOLE; DOXYCYCLINE; ERYTHROMYCIN; GENTAMICIN; IMIPENEM; METRONIDAZOLE; NITROFURANTOIN; RNA 16S; TOBRAMYCIN; TRANSFER RNA; VANCOMYCIN;

ANTIBIOTIC SENSITIVITY; ARTICLE; BACILLI; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM ISOLATE; BASE PAIRING; BEDUINI MASSILIENSIS; BIOMICS; DNA BASE COMPOSITION; GENOME ANALYSIS; GRAM NEGATIVE ANAEROBIC BACTERIA; INTESTINE FLORA; MICROBIAL CULTUROMICS; MICROBIAL DIVERSITY; MICROBIAL GENETICS; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PRIORITY JOURNAL; ADULT; BACILLUS; CLASSIFICATION; DRUG EFFECTS; FEMALE; GENETICS; GENOMICS; HUMAN; METAGENOME; METAGENOMICS; PHENOTYPE; PHYLOGENY; PROCEDURES; ULTRASTRUCTURE;

ADULT; BACILLUS; FEMALE; GASTROINTESTINAL MICROBIOME; GENOME, BACTERIAL; GENOMICS; HUMANS; METAGENOME; METAGENOMICS; PHENOTYPE; PHYLOGENY; RNA, RIBOSOMAL, 16S;

EID: 84951780456     PISSN: 15362310     EISSN: 15578100     Source Type: Journal    
DOI: 10.1089/omi.2015.0143     Document Type: Article

References (44)

1. Adams SH, Barnes KM, and Odle J. (2013). Comparative metabolic physiology in the omics era: A call to arms, paws, flippers, and claws. Adv Nutr 4, 568-569.
2. Akondi KB, and Lakshmi VV. (2013). Emerging trends in genomic approaches for microbial bioprospecting. OMICS 17, 61-70.
3. Aziz RK, Bartels D, Best AA, et al. (2008). The RAST Server: Rapid annotations using subsystems technology. BMC Genomics 9, 75.
4. Bendtsen JD, Nielsen H, von Heijne G, and Brunak S. (2004). Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340, 783-795.
5. Benson DA, Karsch-Mizrachi I, Clark K, Lipman DJ, Ostell J, and Sayers EW. (2012). GenBank. Nucl Acids Res 40, D48-D53.
6. Borriello SP, and Carman RJ. (1983). Association of iota-like toxin and Clostridium spiroforme with both spontaneous and antibiotic-associated diarrhea and colitis in rabbits. J Clin Microbiol 17, 414-418.
7. Canuel V, Rance B, Avillach P, Degoulet P, and Burgun A. (2015). Translational research platforms integrating clinical and omics data: A review of publicly available solutions. Brief Bioinform 16, 280-290.
8. Carver T, Thomson N, Bleasby A, Berriman M, and Parkhill J. (2009). DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 25, 119-120.
9. Clavel T, Lippman R, Gavini F, Dore J, and Blaut M. (2007). Clostridium saccharogumia sp. Nov. and Lactonifactor longoviformis gen. Nov., sp. Nov., two novel human faecal bacteria involved in the conversion of the dietary phytoestrogen secoisolariciresinol diglucoside. Syst Appl Microbiol 30, 16-26.
10. Darling AC, Mau B, Blattner FR, and Perna NT. (2004). Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14, 1394-1403.
11. Edouard S, Bibi F, Dhamodharan R, et al. (2014). Non-contiguous finished genome sequence and description of Corynebacterium jeddahense sp. Nov. Stand Genomic Sci 9, 987-1002.
12. Fournier PE, Lagier JC, Dubourg G, and Raoult D. (2015). From culturomics to taxonomogenomics: A need to change the taxonomy of prokaryotes in clinical microbiology. Anaerobe. In press.
13. Gouret P, Paganini J, Dainat J, Louati D, Darbo E, Pontarotti P, and Levasseur A. (2011). Integration of evolutionary biology concepts for functional annotation and automation of complex research. In: Evolution: The Multi-Agent Software System DAGOBAH, Evolutionary Biology-Concepts. Biodiversity, Macroevolution and Genome Evolution, pp. 71-87.
14. Gouret P, Vitiello V, Balandraud N, Gilles A, Pontarotti P, and Danchin EG. (2005). FIGENIX: Intelligent automation of genomic annotation: Expertise integration in a new software platform. BMC Bioinformatics 6, 198.
15. Kaneuchi C, Miyazato T, Shinjo T, and Mitsuoka T. (1979). Taxonomic study of helically coiled, sporeforming anaerobes isolated from the intestines of humans and other animals: Clostridium cocleatum sp. Nov. and Clostridium spiroforme sp. Nov. Int J Syst Bacteriol 29, 1-12.
16. Kokcha S, Mishra AK, Lagier JC, et al. (2012). Non-contiguousfinished genome sequence and description of Bacillus timonensis sp. Nov. Stand Genomic Sci 6, 346-355.
17. Krogh A, Larsson B, von Heijne G, and Sonnhammer EL. (2001). Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J Mol Biol 305, 567-580.
18. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, and Ussery DW. (2007). RNAmmer: Consistent and rapid annotation of ribosomal RNA genes. Nucl Acids Res 35, 3100-3108.
19. Lagier JC, Armougom F, Million M, et al. (2012a). Microbial culturomics: Paradigm shift in the human gut microbiome study. Clin Microbiol Infect 18, 1185-1193.
20. Lagier J C, Armougom F, Mishra AK, Nguyen TT, Raoult D, and Fournier PE. (2012b). Non-contiguous-finished genome sequence and description of Alistipes timonensis sp. Nov. Stand Genomic Sci 6, 315-324.
21. Lagier JC, Bibi F, Ramasany D, et al. (2014). Non contiguousfinished genome sequence and description of Clostridium jeddahense sp. Nov. Stand Genomic Sci 9, 1003-1019.
22. Lagier JC, Hugon P, Khelaifia S, Fournier PE, La Scola B, and Raoult D. (2015). The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Rev 28, 237-264.
23. Lagier JC, El Karkouri K, Nguyen TT, Armougom F, Raoult D, and Fournier PE. (2012c). Non-contiguous-finished genome sequence and description of Anaerococcus senegalensis sp. Nov. Stand Genomic Sci 6, 116-125.
24. Lagier JC, Million M, Hugon P, Armougom F, and Raoult D. (2012d). Human gut microbiota: Repertoire and variations. Front Cell Infect Microbiol 2, 136.
25. Lechner M, Findeib S, Steiner L, Marz M, Stadler PF, and Prohaska SJ. (2011). Proteinortho: Detection of (Co-)orthologs in large-scale analysis. BMC Bioinformatics 12, 124.
26. Lowe TM, and Eddy SR. (1997). tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucl Acids Res 25, 955-964.
27. Mishra AK, Lagier JC, Robert C, Raoult D, and Fournier PE. (2013). Non-contiguous-finished genome sequence and description of Peptinophilus senegalensis sp. Nov. Stand Genomic Sci 7, 370-381.
28. Mishra AK, Gimenez G, Lagier JC, Robert C, Raoult D, and Fournier PE. (2012a). Non-contiguous-finished genome sequence and description of Alistipes senegalensis sp. Nov. Stand Genomic Sci 6, 304-314.
29. Mishra AK, Lagier JC, Robert C, Raoult D, and Fournier PE. (2012b). Non-contiguous-finished genome sequence and description of Clostridium senegalense sp. Nov. Stand Genomic Sci 6, 386-395.
30. Mishra AK, Lagier JC, Robert C, Raoult D, and Fournier PE. (2012c). Non-contiguous-finished genome sequence and description of Peptinophilus timonensis sp. Nov. Stand Genomic Sci 7, 1-11.
31. Nkamga VD, Huynh HT, Aboudharam G, Ruimy R, and Drancourt M. (2015). Diversity of human-associated Methanobrevibacter smithii isolates revealed by multispacer sequence typing. Curr Microbiol 70, 810-815.
32. Pribram E. (1933). Klassification der Schizomyceten. Leipzig, pp. 1-143. Edited by Deuticke, F. Deuticke, Leipzig. Prodigal (http://prodigal.ornl.gov/). Last access: October, 2015.
33. Ramasamy D, Mishra AK, Lagier JC, et al. (2014). A polyphasic strategy incorporating genomic data for the taxonomic description of new bacterial species. Int J Syst Evol Microbiol 64, 384-391.
34. Rossello-Mora R. (2006). DNA-DNA reassociation methods applied to microbial taxonomy and their critical evaluation. In: Molecular Identification, Systematics, and Population Structure of Prokaryotes. Edited by E. Stackebrandt. pp.23-50. Springer, Berlin.
35. Rutherford K, Parkhill J, Crook J, et al. (2000). Artemis: Sequence visualization and annotation. Bioinformatics 16, 944-945.
36. Seng P, Rolain JM, Fournier PE, La Scola B, Drancourt M, and Raoult D. (2010).MALDI-TOF-mass spectrometry applications in clinical microbiology. Future Microbiol 5, 1733-1754.
37. SinghA,MahtoKK, and Prasad R. (2013). Lipidomics and in vitro azole resistance in Candida albicans. OMICS 17, 84-93.
38. Spor A, Koren O, and Ley R. (2011). Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol 9, 279-290.
39. Stackebrandt E, and Ebers J. (2006). Taxonomic parameters revisited: Tarnished gold standards. Microbiol Today 33, 152-155.
40. Tindall BJ, Rosselló-Móra R, Busse HJ, Ludwig W, and Kämpfer P. (2010). Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60, 249-266.
41. Wayne LG, Brenner DJ, Colwell PR, et al. (1987). Report of the ad hoc committee on reconciliation of approaches to bacterial systematic. Int J Syst Bacteriol 37, 463-464.
42. Weinstein MP. (2003). Blood culture contamination: Persisting problems and partial progress. J Clin Microbiol 41, 2275-2278.
43. Welker M, and Moore ER. (2011). Applications of whole-cell matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry in systematic microbiology. Syst Appl Microbiol 34, 2-11.
44. Zhou Y, Liang Y, Lynch KH, Dennis JJ, and Wishart DS. (2011). PHAST:Afast phage search tool.NuclAcids Res 39, W347-352.