Host-associated bacterial taxa from Chlorobi, Chloroflexi, GN02, Synergistetes, SR1, TM7, and WPS-2 Phyla/candidate divisions

Journal of Oral Microbiology

Volumn 6, Issue 1, 2014, Pages

  Camanocha, Anuj ^a   Dewhirst, Floyd E ^a,b  

^a HARVARD SCHOOL OF DENTAL MEDICINE   (United States)

^b FORSYTH INSTITUTE   (United States)

Author keywords

16S rRNA; Cloning; Microbiome; Phylogeny; Primers

Indexed keywords

RNA 16S;

AMPLICON; ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTERIUM IDENTIFICATION; CHLOROBI; CHLOROFLEXI; GENE AMPLIFICATION; GENE IDENTIFICATION; GENE SEQUENCE; HOST PATHOGEN INTERACTION; HUMAN; METAGENOMICS; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PHYLOGENY; PHYLUM; PROTEOMICS; SEQUENCE ALIGNMENT; TAXONOMY; TRANSCRIPTOMICS;

EID: 84939235410     PISSN: None     EISSN: 20002297     Source Type: Journal    
DOI: 10.3402/jom.v6.25468     Document Type: Article

References (63)

1. Dewhirst FE, Chen T, Izard J, Paster BJ, Tanner AC, Yu WH, et al. The human oral microbiome. J Bacteriol 2010; 192: 5002-17.
2. Dewhirst FE, Klein EA, Thompson EC, Blanton JM, Chen T, Milella L, et al. The canine oral microbiome. PLoS One 2012; 7: e36067.
3. Human Microbiome Project C. A framework for human microbiome research. Nature 2012; 486: 215-21.
4. Overmann J, Tuschak C. Phylogeny and molecular fingerprinting of green sulfur bacteria. Arch Microbiol 1997; 167: 302-9.
5. Iino T, Mori K, Uchino Y, Nakagawa T, Harayama S, Suzuki K. Ignavibacterium album gen. nov., sp. nov., a moderately thermophilic anaerobic bacterium isolated from microbial mats at a terrestrial hot spring and proposal of Ignavibacteria classis nov., for a novel lineage at the periphery of green sulfur bacteria. Int J Syst Evol Microbiol 2010; 60: 1376-82.
6. Podosokorskaya OA, Kadnikov VV, Gavrilov SN, Mardanov AV, Merkel AY, Karnachuk OV, et al. Characterization of Melioribacter roseus gen. nov., sp. nov., a novel facultatively anaerobic thermophilic cellulolytic bacterium from the class Ignavibacteria, and a proposal of a novel bacterial phylum Ignavibacteriae. Environ Microbiol 2013; 15: 1759-71.
7. Kadnikov VV, Mardanov AV, Podosokorskaya OA, Gavrilov SN, Kublanov IV, Beletsky AV, et al. Genomic analysis of Melioribacter roseus, facultatively anaerobic organotrophic bacterium representing a novel deep lineage within Bacteriodetes/ Chlorobi group. PLoS One 2013; 8: e53047.
8. Liu Z, Frigaard NU, Vogl K, Iino T, Ohkuma M, Overmann J, et al. Complete genome of Ignavibacterium album, a metabolically versatile, flagellated, facultative anaerobe from the Phylum Chlorobi. Front Microbiol 2012; 3: 185.
9. Bjornsson L, Hugenholtz P, Tyson GW, Blackall LL. Filamentous Chloroflexi (green non-sulfur bacteria) are abundant in wastewater treatment processes with biological nutrient removal. Microbiology 2002; 148: 2309-18.
10. Garrity GM, Holt JG. Phylum BVI Chloroblexi phy. nov. In: Boon DR, Castenholtz RW, Garrity GM, editors. Bergey's manual of systematic bacteriology, second ed. New York: Springer; 2001. pp. 427-46.
11. Hugenholtz P, Stackebrandt E. Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description). Int J Syst Evol Microbiol 2004; 54: 2049-51.
12. Yamada T, Sekiguchi Y, Hanada S, Imachi H, Ohashi A, Harada H, et al. Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. Int J Syst Evol Microbiol 2006; 56: 1331-40.
13. Yabe S, Aiba Y, Sakai Y, Hazaka M, Yokota A. Thermosporothrix hazakensis gen. nov., sp. nov., isolated from compost, description of Thermosporotrichaceae fam. nov. within the class Ktedonobacteria Cavaletti et al. 2007 and emended description of the class Ktedonobacteria. Int J Syst Evol Microbiol 2010; 60: 1794-801.
14. Kawaichi S, Ito N, Kamikawa R, Sugawara T, Yoshida T, Sako Y. Ardenticatena maritima gen. nov., sp. nov., a ferric iron-and nitrate-reducing bacterium of the phylum 'Chloroflexi' isolated from an iron-rich coastal hydrothermal field, and description of Ardenticatenia classis nov. Int J Syst Evol Microbiol 2013; 63: 2992-3002.
15. Morris RM, Rappe MS, Urbach E, Connon SA, Giovannoni SJ. Prevalence of the Chloroflexi-related SAR202 bacterioplankton cluster throughout the mesopelagic zone and deep ocean. Appl Environ Microbiol 2004; 70: 2836-42.
16. Ley RE, Harris JK, Wilcox J, Spear JR, Miller SR, Bebout BM, et al. Unexpected diversity and complexity of the Guerrero Negro hypersaline microbial mat. Appl Environ Microbiol 2006; 72: 3685-95.
17. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006; 72: 5069-72.
18. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 2013; 499: 431-7.
19. Harris JK, Kelley ST, Pace NR. New perspective on uncultured bacterial phylogenetic division OP11. Appl Environ Microbiol 2004; 70: 845-9.
20. Paster BJ, Boches SK, Galvin JL, Ericson RE, Lau CN, Levanos VA, et al. Bacterial diversity in human subgingival plaque. J Bacteriol 2001; 183: 3770-83.
21. Segata N, Haake SK, Mannon P, Lemon KP, Waldron L, Gevers D, et al. Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol 2012; 13: R42.
22. Kantor RS, Wrighton KC, Handley KM, Sharon I, Hug LA, Castelle CJ, et al. Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla. mBio 2013; 4: e00708-13.
23. Campbell JH, O'Donoghue P, Campbell AG, Schwientek P, Sczyrba A, Woyke T, et al. UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota. Proc Natl Acad Sci USA 2013; 110: 5540-5.
24. Jumas-Bilak E, Roudiere L, Marchandin H. Description of 'Synergistetes' phyl. nov. and emended description of the phylum 'Deferribacteres' and of the family Syntrophomonadaceae, phylum 'Firmicutes'. Int J Syst Evol Microbiol 2009; 59: 1028-35.
25. Hugenholtz P, Hooper SD, Kyrpides NC. Focus: Synergistetes. Environment Microbiol 2009; 11: 1327-9.
26. Allison JJ, Mayberry WR, McSweeney CS, Stahl DA. Synergistes jonesii, gen. nov.: a rumen bacterium that degrades toxic pyridinediols. Syst Appl Microbiol 1992; 15: 522-9.
27. Marchandin H, Damay A, Roudiere L, Teyssier C, Zorgniotti I, Dechaud H, et al. Phylogeny, diversity and host specialization in the phylum Synergistetes with emphasis on strains and clones of human origin. Res Microbiol 2010; 161: 91-100.
28. Vartoukian SR, Palmer RM, Wade WG. Diversity and morphology of members of the phylum ''Synergistetes'' in periodontal health and disease. Appl Environ Microbiol 2009; 75: 3777-86.
29. Jumas-Bilak E, Carlier JP, Jean-Pierre H, Citron D, Bernard K, Damay A, et al. Jonquetella anthropi gen. nov., sp. nov., the first member of the candidate phylum 'Synergistetes' isolated from man. Int J Syst Evol Microbiol 2007; 57: 2743-8.
30. Downes J, Vartoukian SR, Dewhirst FE, Izard J, Chen T, Yu WH, et al. Pyramidobacter piscolens gen. nov., sp. nov., a member of the phylum 'Synergistetes' isolated from the human oral cavity. Int J Syst Evol Microbiol 2009; 59: 972-80.
31. Vartoukian SR, Downes J, Palmer RM,WadeWG. Fretibacterium fastidiosum gen. nov., sp. nov., isolated from the human oral cavity. Int J Syst Evol Microbiol 2013; 63: 458-63.
32. Hugenholtz P, Tyson GW, Webb RI, Wagner AM, Blackall LL. Investigation of candidate division TM7, a recently recognized major lineage of the domain Bacteria with no known pureculture representatives. Appl Environ Microbiol 2001; 67: 411-19.
33. Brinig MM, Lepp PW, Ouverney CC, Armitage GC, Relman DA. Prevalence of bacteria of division TM7 in human subgingival plaque and their association with disease. Appl Environ Microbiol 2003; 69: 1687-94.
34. Marcy Y, Ouverney C, Bik EM, Losekann T, Ivanova N, Martin HG, et al. Dissecting biological ''dark matter'' with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci USA 2007; 104: 11889-94.
35. Aas JA, Paster BJ, Stokes LN, Olsen I, Dewhirst FE. Defining the normal bacterial flora of the oral cavity. J Clin Microbiol 2005; 43: 5721-32.
36. Pei Z, Bini EJ, Yang L, Zhou M, Francois F, Blaser MJ. Bacterial biota in the human distal esophagus. Proc Natl Acad Sci USA 2004; 101: 4250-5.
37. Nogales B, Moore ER, Llobet-Brossa E, Rossello-Mora R, Amann R, Timmis KN. Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil. Appl Environ Microbiol 2001; 67: 1874-84.
38. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4: 406-25.
39. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39: 783-91.
40. Jukes TH, Cantor CR. Evolution of protein molecules. New York: Academic Press; 1969.
41. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 2013; 30: 2725-9.
42. Dewhirst FE, Shen Z, Scimeca MS, Stokes LN, Boumenna T, Chen T, et al. Discordant 16S and 23S rRNA gene phylogenies for the genus Helicobacter: implications for phylogenetic inference and systematics. J Bacteriol 2005; 187: 6106-18.
43. Hugenholtz P, Pitulle C, Hershberger KL, Pace NR. Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 1998; 180: 366-76.
44. Yamada T, Imachi H, Ohashi A, Harada H, Hanada S, Kamagata Y, et al. Bellilinea caldifistulae gen. nov., sp. nov. and Longilinea arvoryzae gen. nov., sp. nov., strictly anaerobic, filamentous bacteria of the phylum Chloroflexi isolated from methanogenic propionate-degrading consortia. Int J Syst Evol Microbiol 2007; 57: 2299-306.
45. Imachi H, Sakai S, Lipp JS, Miyazaki M, Saito Y, Yamanaka Y, et al. Pelolinea submarina gen. nov., sp. nov., an anaerobic, filamentous bacterium of the phylum Chloroflexi isolated from subseafloor sediment offshore Shimokita, Japan. Int J Syst Evol Microbiol 2014; 64: 812-18. doi: 10.1099/ijs.0.057547-0.
46. Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, et al. Evolution of mammals and their gut microbes. Science 2008; 320: 1647-51.
47. Sekiguchi Y, Yamada T, Hanada S, Ohashi A, Harada H, Kamagata Y. Anaerolinea thermophila gen. nov., sp. nov. and Caldilinea aerophila gen. nov., sp. nov., novel filamentous thermophiles that represent a previously uncultured lineage of the domain Bacteria at the subphylum level. Int J Syst Evol Microbiol 2003; 53: 1843-51.
48. Gregoire P, Fardeau ML, Joseph M, Guasco S, Hamaide F, Biasutti S, et al. Isolation and characterization of Thermanaerothrix daxensis gen. nov., sp. nov., a thermophilic anaerobic bacterium pertaining to the phylum ''Chloroflexi,'' isolated from a deep hot aquifer in the Aquitaine Basin. Syst Appl Microbiol 2011; 34: 494-7.
49. Nunoura T, Hirai M, Miyazaki M, Kazama H, Makita H, Hirayama H, et al. Isolation and characterization of a thermophilic, obligately anaerobic and heterotrophic marine Chloroflexi bacterium from a Chloroflexi-dominated microbial community associated with a Japanese shallow hydrothermal system, and proposal for Thermomarinilinea lacunofontalis gen. nov., sp. nov. Microbes Environ/JSME 2013; 28: 228-35.
50. Podosokorskaya OA, Bonch-Osmolovskaya EA, Novikov AA, Kolganova TV, Kublanov IV. Ornatilinea apprima gen. nov., sp. nov., a cellulolytic representative of the class Anaerolineae. Int J Syst Evol Microbiol 2013; 63: 86-92.
51. Bik EM, Long CD, Armitage GC, Loomer P, Emerson J, Mongodin EF, et al. Bacterial diversity in the oral cavity of 10 healthy individuals. Isme J. 2010; 4: 962-74.
52. Kong HH, Oh J, Deming C, Conlan S, Grice EA, Beatson MA, et al. Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis. Genome Res 2012; 22: 850-9.
53. Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 2013; 499: 431-7.
54. Davis JP, Youssef NH, Elshahed MS. Assessment of the diversity, abundance, and ecological distribution of members of candidate division SR1 reveals a high level of phylogenetic diversity but limited morphotypic diversity. Appl Environ Microbiol 2009; 75: 4139-48.
55. Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ, VerBerkmoes NC, et al. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science 2012; 337: 1661-5.
56. Ivanova NN, Schwientek P, Tripp HJ, Rinke C, Pati A, Huntemann M, et al. Stop codon reassignments in the wild. Science 2014; 344: 909-13.
57. Miyoshi T, Iwatsuki T, Naganuma T. Phylogenetic characterization of 16S rRNA gene clones from deep-groundwater microorganisms that pass through 0.2-micrometer-pore-size filters. Appl Environ Microbiol 2005; 71: 1084-8.
58. Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, et al. Topographical and temporal diversity of the human skin microbiome. Science 2009; 324: 1190-2.
59. Jurica MS, Monnat RJ, Jr, Stoddard BL. DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-CreI. Mol Cell 1998; 2: 469-76.
60. Bertin PN, Heinrich-Salmeron A, Pelletier E, Goulhen-Chollet F, Arsene-Ploetze F, Gallien S, et al. Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta-and proteo-genomics. Isme J. 2011; 5: 1735-47.
61. Dinis JM, Barton DE, Ghadiri J, Surendar D, Reddy K, Velasquez F, et al. In search of an uncultured human-associated TM7 bacterium in the environment. PLoS One 2011; 6: e21280.
62. Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol 2013; 31: 533-8.
63. Qiu YL, Hanada S, Kamagata Y, Guo RB, Sekiguchi Y. Lactivibrio alcoholicus gen. nov., sp. nov., an anaerobic, mesophilic, lactate-, alcohol-, carbohydrate-and amino-aciddegrading bacterium in the phylum Synergistetes. Int J Syst Evol Microbiol 2014; 64: 2137-45.