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A comprehensive repertoire of prokaryotic species identified in human beings

Hugon, Perrine, Dufour, Jean-Charles, Colson, Philippe, Fournier, Pierre-Edouard, Sallah, Kankoe, Raoult, Didier·2015·The Lancet Infectious Diseases
DOI 10.1016/s1473-3099(15)00293-5
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Research works printed but not linked: 102

  1. Drancourt, 2004, Systematic 16S rRNA gene sequencing of atypical clinical isolates identified 27 new bacterial species associated with humans, J Clin Microbiol, 42, 2197, 10.1128/JCM.42.5.2197-2202.2004 · DOI
  2. Lagier, 2015, Current and past strategies for bacterial culture in clinical microbiology, Clin Microbiol Rev, 28, 208, 10.1128/CMR.00110-14 · DOI · Paper page
  3. Fournier, 2013, Modern clinical microbiology: new challenges and solutions, Nat Rev Microbiol, 11, 574, 10.1038/nrmicro3068 · DOI
  4. Isenberg, 1988, Pathogenicity and virulence: another view, Clin Microbiol Rev, 1, 40, 10.1128/CMR.1.1.40 · DOI
  5. Vayssier-Taussat, 2014, Shifting the paradigm from pathogens to pathobiome: new concepts in the light of meta-omics, Front Cell Infect Microbiol, 4, 29, 10.3389/fcimb.2014.00029 · DOI · Paper page
  6. Dave, 2014, Opportunistic infections due to inflammatory bowel disease therapy, Inflamm Bowel Dis, 20, 196, 10.1097/MIB.0b013e3182a827d2 · DOI
  7. Fauci, 2001, Infectious diseases: considerations for the 21st century, Clin Infect Dis, 32, 675, 10.1086/319235 · DOI · Paper page
  8. Angelakis, 2014, Methods for the discovery of emerging pathogens, Microb Pathog, 77, 114, 10.1016/j.micpath.2014.06.007 · DOI
  9. Bittar, 2014, Gorilla gorilla gorilla gut: a potential reservoir of pathogenic bacteria as revealed using culturomics and molecular tools, Sci Rep, 4, 7174, 10.1038/srep07174 · DOI
  10. Vartoukian, 2010, Strategies for culture of ‘unculturable’ bacteria, FEMS Microbiol Lett, 309, 1
  11. Staley, 1985, Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats, Annu Rev Microbiol, 39, 321, 10.1146/annurev.mi.39.100185.001541 · DOI
  12. Pace, 1986, The analysis of natural microbial populations by ribosomal RNA sequences, Adv Microb Ecol, 9, 1, 10.1007/978-1-4757-0611-6_1 · DOI
  13. Hugenholtz, 1998, Impact of culture-independent studies on the emerging phylogenetic view of bacterial diversity, J Bacteriol, 180, 4765, 10.1128/JB.180.18.4765-4774.1998 · DOI
  14. Al-Awadhi, 2013, Bias problems in culture-independent analysis of environmental bacterial communities: a representative study on hydrocarbonoclastic bacteria, Springerplus, 2, 369, 10.1186/2193-1801-2-369 · DOI
  15. Hugon, 2013, Molecular studies neglect apparently gram-negative populations in the human gut microbiota, J Clin Microbiol, 51, 3286, 10.1128/JCM.00473-13 · DOI
  16. Drancourt, 2000, 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates, J Clin Microbiol, 38, 3623, 10.1128/JCM.38.10.3623-3630.2000 · DOI · Paper page
  17. Antranikian, 2005, Extreme environments as a resource for microorganisms and novel biocatalysts, Adv Biochem Eng Biotechnol, 96, 219
  18. Lagier, 2015, The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota, Clin Microbiol Rev, 28, 237, 10.1128/CMR.00014-14 · DOI · Paper page
  19. Horner-Devine, 2004, An ecological perspective on bacterial biodiversity, Proc Biol Sci, 271, 113, 10.1098/rspb.2003.2549 · DOI · Paper page
  20. Canganella, 2011, Extremophiles: from abyssal to terrestrial ecosystems and possibly beyond, Naturwissenschaften, 98, 253, 10.1007/s00114-011-0775-2 · DOI
  21. Moore, 1974, Human fecal flora: the normal flora of 20 Japanese-Hawaiians, Appl Microbiol, 27, 961, 10.1128/am.27.5.961-979.1974 · DOI · Paper page
  22. Van Houte, 1966, Studies of the cultivable flora of normal human feces, Antonie Van Leeuwenhoek, 32, 212, 10.1007/BF02097463 · DOI
  23. Fredricks, 2001, Microbial ecology of human skin in health and disease, J Investig Dermatol Symp Proc, 6, 167, 10.1046/j.0022-202x.2001.00039.x · DOI
  24. Schloss, 2004, Status of the microbial census, Microbiol Mol Biol Rev, 68, 686, 10.1128/MMBR.68.4.686-691.2004 · DOI · Paper page
  25. Curtis, 2002, Estimating prokaryotic diversity and its limits, Proc Natl Acad Sci USA, 99, 10494, 10.1073/pnas.142680199 · DOI · Paper page
  26. Rinke, 2013, Insights into the phylogeny and coding potential of microbial dark matter, Nature, 499, 431, 10.1038/nature12352 · DOI · Paper page
  27. Tindall, 2010, Notes on the characterization of prokaryote strains for taxonomic purposes, Int J Syst Evol Microbiol, 60, 249, 10.1099/ijs.0.016949-0 · DOI · Paper page
  28. Skerman, 1989, Approved lists of bacterial names, Int J Syst Bacteriol, 30, 225, 10.1099/00207713-30-1-225 · DOI
  29. Sentausa, 2013, Advantages and limitations of genomics in prokaryotic taxonomy, Clin Microbiol Infect, 19, 790, 10.1111/1469-0691.12181 · DOI
  30. Kämpfer, 2012, Prokaryotic taxonomy in the sequencing era—the polyphasic approach revisited, Environ Microbiol, 14, 291, 10.1111/j.1462-2920.2011.02615.x · DOI
  31. Schleifer, 2009, Classification of Bacteria and Archaea: past, present and future, Syst Appl Microbiol, 32, 533, 10.1016/j.syapm.2009.09.002 · DOI
  32. Oren, 2014, Then and now: a systematic review of the systematics of prokaryotes in the last 80 years, Antonie Van Leeuwenhoek, 106, 43, 10.1007/s10482-013-0084-1 · DOI
  33. Ramasamy, 2014, A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species, Int J Syst Evol Microbiol, 64, 384, 10.1099/ijs.0.057091-0 · DOI · Paper page
  34. Ramasamy, 2012, Genome sequence and description of Aeromicrobium massiliense sp. nov, Stand Genomic Sci, 7, 246, 10.4056/sigs.3306717 · DOI
  35. Lagier, 2012, Non-contiguous finished genome sequence and description of Alistipes timonensis sp. nov, Stand Genomic Sci, 6, 315, 10.4056/sigs.2685971 · DOI
  36. Lagier, 2012, Non-contiguous finished genome sequence and description of Anaerococcus senegalensis sp. nov, Stand Genomic Sci, 6, 116, 10.4056/sigs.2415480 · DOI
  37. Hugon, 2013, Non-contiguous finished genome sequence and description of Brevibacillus massiliensis sp. nov, Stand Genomic Sci, 8, 1, 10.4056/sigs.3466975 · DOI
  38. Kokcha, 2012, Non-contiguous finished genome sequence and description of Brevibacterium senegalense sp. nov, Stand Genomic Sci, 7, 233, 10.4056/sigs.3256677 · DOI
  39. Lagier, 2013, Non contiguous-finished genome sequence and description of Enterobacter massiliensis sp. nov, Stand Genomic Sci, 7, 399, 10.4056/sigs.3396830 · DOI
  40. Lagier, 2012, Non-contiguous finished genome sequence and description of Herbaspirillum massiliense sp. nov, Stand Genomic Sci, 7, 200, 10.4056/sigs.3086474 · DOI
  41. Roux, 2012, Non-contiguous finished genome sequence and description of Kurthia massiliensis sp. nov, Stand Genomic Sci, 7, 221, 10.4056/sigs.3206554 · DOI
  42. Mishra, 2012, Non contiguous-finished genome sequence and description of Paenibacillus senegalensis sp. nov, Stand Genomic Sci, 7, 70, 10.4056/sigs.3056450 · DOI
  43. Lagier, 2012, Non contiguous-finished genome sequence and description of Cellulomonas massiliensis, sp. nov, Stand Genomic Sci, 7, 258, 10.4056/sigs.3316719 · DOI
  44. Mishra, 2012, Non contiguous-finished genome sequence and description of Peptoniphilus timonensis sp. nov, Stand Genomic Sci, 7, 1, 10.4056/sigs.2956294 · DOI
  45. Mishra, 2012, Non contiguous-finished genome sequence and description of Clostridium senegalense sp. nov, Stand Genomic Sci, 6, 386
  46. Lagier, 2013, Non contiguous-finished genome sequence and description of Senegalemassilia anaerobia gen. nov., sp. nov, Stand Genomic Sci, 7, 343, 10.4056/sigs.3246665 · DOI
  47. Foxman, 2010, Why the human microbiome project should motivate epidemiologists to learn ecology, Epidemiology, 21, 757, 10.1097/EDE.0b013e3181f4e1f9 · DOI
  48. Zoetendal, 2003, Victivallis vadensis gen. nov., sp. nov., a sugar-fermenting anaerobe from human faeces, Int J Syst Evol Microbiol, 53, 211, 10.1099/ijs.0.02362-0 · DOI
  49. Lagier, 2012, Microbial culturomics: paradigm shift in the human gut microbiome study, Clin Microbiol Infect, 18, 1185, 10.1111/1469-0691.12023 · DOI · Paper page
  50. Nagy, 2010, Anaerobic infections: update on treatment considerations, Drugs, 70, 841, 10.2165/11534490-000000000-00000 · DOI
  51. Nair, 2014, Impact of Staphylococcus aureus on pathogenesis in polymicrobial infections, Infect Immun, 82, 2162, 10.1128/IAI.00059-14 · DOI
  52. Hungate, 1969, Roll-tube method for the cultivation of strict anaerobes, 117, 10.1016/S0580-9517(08)70503-8 · DOI · Paper page
  53. Summanen, 1999, Comparison of recovery of anaerobic bacteria using the Anoxomat, anaerobic chamber, and GasPak jar systems, Anaerobe, 5, 5, 10.1006/anae.1999.0184 · DOI
  54. Sonnenwirth, 1972, Evolution of anaerobic methodology, Am J Clin Nutr, 25, 1295, 10.1093/ajcn/25.12.1295 · DOI
  55. La Scola, 2014, Aerobic culture of anaerobic bacteria using antioxidants: a preliminary report, Eur J Clin Microbiol Infect Dis, 33, 1781, 10.1007/s10096-014-2137-4 · DOI
  56. DiBaise, 2008, Gut microbiota and its possible relationship with obesity, Mayo Clin Proc, 83, 460, 10.4065/83.4.460 · DOI · Paper page
  57. Loesche, 1969, Oxygen sensitivity of various anaerobic bacteria, Appl Microbiol, 18, 723, 10.1128/am.18.5.723-727.1969 · DOI · Paper page
  58. Tally, 1977, Superoxide dismutase in anaerobic bacteria of clinical significance, Infect Immun, 16, 20, 10.1128/iai.16.1.20-25.1977 · DOI
  59. Hurst, 2005, Divining the future of microbiology, ASM News, 71, 262
  60. Turnbaugh, 2007, The human microbiome project, Nature, 449, 804, 10.1038/nature06244 · DOI · Paper page
  61. Fraher, 2012, Techniques used to characterize the gut microbiota: a guide for the clinician, Nat Rev Gastroenterol Hepatol, 9, 312, 10.1038/nrgastro.2012.44 · DOI · Paper page
  62. Xie, 2010, Community and gene composition of a human dental plaque microbiota obtained by metagenomic sequencing, Mol Oral Microbiol, 25, 391, 10.1111/j.2041-1014.2010.00587.x · DOI
  63. Seng, 2013, Identification of rare pathogenic bacteria in a clinical microbiology laboratory: impact of matrix-assisted laser desorption ionization-time of flight mass spectrometry, J Clin Microbiol, 51, 2182, 10.1128/JCM.00492-13 · DOI · Paper page
  64. Fock, 2013, Helicobacter pylori research: historical insights and future directions, Nat Rev Gastroenterol Hepatol, 10, 495, 10.1038/nrgastro.2013.96 · DOI
  65. Lazarevic, 2009, Metagenomic study of the oral microbiota by Illumina high-throughput sequencing, J Microbiol Methods, 79, 266, 10.1016/j.mimet.2009.09.012 · DOI
  66. Mansfield, 2012, Molecular analysis of 16S rRNA genes identifies potentially periodontal pathogenic bacteria and archaea in the plaque of partially erupted third molars, J Oral Maxillofac Surg, 70, 1507, 10.1016/j.joms.2011.09.049 · DOI
  67. Tamaki, 2011, Armatimonas rosea gen. nov., sp. nov., of a novel bacterial phylum, Armatimonadetes phyl. nov., formally called the candidate phylum OP10, Int J Syst Evol Microbiol, 61, 1442, 10.1099/ijs.0.025643-0 · DOI
  68. Hutter, 2003, Molecular analysis of bacteria in periodontitis: evaluation of clone libraries, novel phylotypes and putative pathogens, Microbiology, 149, 67, 10.1099/mic.0.25791-0 · DOI
  69. Siqueira, 2005, Novel bacterial phylotypes in endodontic infections, J Dent Res, 84, 565, 10.1177/154405910508400615 · DOI
  70. Hunter, 1992, Cyanobacteria and human health, J Med Microbiol, 36, 301, 10.1099/00222615-36-5-301 · DOI
  71. 1991, Outbreaks of diarrheal illness associated with cyanobacteria (blue–green algae)-like bodies—Chicago and Nepal, 1989 and 1990, MMWR Morb Mortal Wkly Rep, 40, 325
  72. Drancourt, 2014, Planctomycetes DNA in febrile aplastic patients with leukemia, rash, diarrhea, and micronodular pneumonia, J Clin Microbiol, 52, 3453, 10.1128/JCM.01207-14 · DOI
  73. Bollmann, 2007, Incubation of environmental samples in a diffusion chamber increases the diversity of recovered isolates, Appl Environ Microbiol, 73, 6386, 10.1128/AEM.01309-07 · DOI
  74. Sizova, 2012, New approaches for isolation of previously uncultivated oral bacteria, Appl Environ Microbiol, 78, 194, 10.1128/AEM.06813-11 · DOI
  75. Epstein, 2013, The phenomenon of microbial uncultivability, Curr Opin Microbiol, 16, 636, 10.1016/j.mib.2013.08.003 · DOI
  76. Kaeberlein, 2002, Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment, Science, 296, 1127, 10.1126/science.1070633 · DOI · Paper page
  77. Jung, 2014, Application of a new cultivation technology, I-tip, for studying microbial diversity in freshwater sponges of Lake Baikal, Russia, FEMS Microbiol Ecol, 90, 417
  78. Ferrari, 2005, Microcolony cultivation on a soil substrate membrane system selects for previously uncultured soil bacteria, Appl Environ Microbiol, 71, 8714, 10.1128/AEM.71.12.8714-8720.2005 · DOI
  79. Boyer, 2010, Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4 domain of life including giant viruses, PLoS One, 5, e15530, 10.1371/journal.pone.0015530 · DOI
  80. Chaban, 2006, Archaeal habitats—from the extreme to the ordinary, Can J Microbiol, 52, 73, 10.1139/w05-147 · DOI
  81. Raoult, 2013, TRUC or the need for a new microbial classification, Intervirology, 56, 349, 10.1159/000354269 · DOI
  82. DeLong, 2001, Environmental diversity of bacteria and archaea, Syst Biol, 50, 470, 10.1080/106351501750435040 · DOI
  83. DeLong, 1998, Everything in moderation: archaea as ‘non-extremophiles’, Curr Opin Genet Dev, 8, 649, 10.1016/S0959-437X(98)80032-4 · DOI · Paper page
  84. Khelaifia, 2012, Susceptibility of archaea to antimicrobial agents: applications to clinical microbiology, Clin Microbiol Infect, 18, 841, 10.1111/j.1469-0691.2012.03913.x · DOI
  85. Drancourt, 2012, Archaea as emerging, fastidious members of the human microbiota, Clin Microbiol Infect, 18, 823, 10.1111/j.1469-0691.2012.03904.x · DOI
  86. Zhang, 2009, Human gut microbiota in obesity and after gastric bypass, Proc Natl Acad Sci USA, 106, 2365, 10.1073/pnas.0812600106 · DOI · Paper page
  87. Dridi, 2011, Archaea as emerging organisms in complex human microbiomes, Anaerobe, 17, 56, 10.1016/j.anaerobe.2011.03.001 · DOI · Paper page
  88. Nguyen-Hieu, 2013, Methanogenic archaea in subgingival sites: a review, APMIS, 121, 467, 10.1111/apm.12015 · DOI
  89. Miller, 1982, Isolation of Methanobrevibacter smithii from human feces, Appl Environ Microbiol, 43, 227, 10.1128/aem.43.1.227-232.1982 · DOI
  90. Khelaifia, 2013, A versatile medium for cultivating methanogenic archaea, PLoS One, 8, e61563, 10.1371/journal.pone.0061563 · DOI
  91. Miller, 1985, Methanosphaera stadtmaniae gen. nov., sp. nov.: a species that forms methane by reducing methanol with hydrogen, Arch Microbiol, 141, 116, 10.1007/BF00423270 · DOI · Paper page
  92. Gouriet, 2005, Use of shell-vial cell culture assay for isolation of bacteria from clinical specimens: 13 years of experience, J Clin Microbiol, 43, 4993, 10.1128/JCM.43.10.4993-5002.2005 · DOI
  93. Yukawa, 2013, Nested culture method improves detection of Fusobacterium from stool in patients with ulcerative colitis, Jpn J Infect Dis, 66, 109, 10.7883/yoken.66.109 · DOI
  94. Siew, 2003, Analysis of singleton ORFans in fully sequenced microbial genomes, Proteins, 53, 241, 10.1002/prot.10423 · DOI
  95. Olsen, 2012, Bacterial genomics in infectious disease and the clinical pathology laboratory, Arch Pathol Lab Med, 136, 1414, 10.5858/arpa.2012-0025-RA · DOI
  96. Bryant, 2013, Culture-free club, Nat Rev Microbiol, 11, 434, 10.1038/nrmicro3052 · DOI
  97. Rajilić-Stojanović, 2014, The first 1000 cultured species of the human gastrointestinal microbiota, FEMS Microbiol Rev, 38, 996, 10.1111/1574-6976.12075 · DOI · Paper page
  98. Dubourg, 2013, High-level colonisation of the human gut by Verrucomicrobia following broad-spectrum antibiotic treatment, Int J Antimicrob Agents, 41, 149, 10.1016/j.ijantimicag.2012.10.012 · DOI
  99. Dubourg, 2014, Culturomics and pyrosequencing evidence of the reduction in gut microbiota diversity in patients with broad-spectrum antibiotics, Int J Antimicrob Agents, 44, 117, 10.1016/j.ijantimicag.2014.04.020 · DOI
  100. Dubourg, 2013, The gut microbiota of a patient with resistant tuberculosis is more comprehensively studied by culturomics than by metagenomics, Eur J Clin Microbiol Infect Dis, 32, 637, 10.1007/s10096-012-1787-3 · DOI
  101. Pfleiderer, 2013, Culturomics identified 11 new bacterial species from a single anorexia nervosa stool sample, Eur J Clin Microbiol Infect Dis, 32, 1471, 10.1007/s10096-013-1900-2 · DOI
  102. Samb-Ba, 2014, MALDI-TOF identification of the human gut microbiome in people with and without diarrhea in Senegal, PLoS One, 9, e87419, 10.1371/journal.pone.0087419 · DOI

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Metadata

Authors
Hugon, P., Dufour, J.-C., Colson, P., Fournier, P.-E., Sallah, K., & Raoult, D.
Venue
The Lancet Infectious Diseases
Publisher
Elsevier BV
Published
2015-10
Volume
15
Issue
10
Pages
1211-1219
ISSN
1473-3099 (ISSN-L)
DOI
10.1016/s1473-3099(15)00293-5
OpenAlex
W2160017126
Cited by
403
References
5
FWCI
9.52
Type
journal article
Language
en
Open access
closed
Licence
  • www.elsevier.com/tdm/userlicense/1.0/ (tdm)
  • www.elsevier.com/legal/tdmrep-license (tdm)

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Hugon, P., Dufour, J.-C., Colson, P., Fournier, P.-E., Sallah, K., & Raoult, D. (2015). A comprehensive repertoire of prokaryotic species identified in human beings. The Lancet Infectious Diseases. https://doi.org/10.1016/s1473-3099(15)00293-5

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