Conservation of streptococcal CRISPRs on human skin and saliva

BMC Microbiology

Volumn 14, Issue 1, 2014, Pages

  Robles Sikisaka, Refugio ^a   Naidu, Mayuri ^a   Ly, Melissa ^a   Salzman, Julia ^b   Abeles, Shira R ^c   Boehm, Tobias K ^d   Pride, David T ^a,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^d WESTERN UNIVERSITY OF HEALTH SCIENCES   (United States)

Author keywords

CRISPR; Saliva microbiome; Skin microbiome; Virome; Virus

Indexed keywords

ARTICLE; BACTERIAL STRAIN; BIOGEOGRAPHIC REGION; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; GENE LOCUS; HUMAN; LACTOCOCCUS; METAGENOME; MICROBIAL COMMUNITY; MOUTH CAVITY; MOUTH HYGIENE; SALIVA; SKIN; SKIN FLORA; SPECIES CONSERVATION; STREPTOCOCCUS; STREPTOCOCCUS PNEUMONIAE; STREPTOCOCCUS THERMOPHILUS; CLASSIFICATION; GENETICS; HETEROZYGOTE; ISOLATION AND PURIFICATION; MICROBIOLOGY; NUCLEOTIDE SEQUENCE; STREPTOCOCCUS INFECTION;

CARRIER STATE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEATS; CONSERVED SEQUENCE; HUMANS; SALIVA; SKIN; STREPTOCOCCAL INFECTIONS; STREPTOCOCCUS;

EID: 84903274696     PISSN: None     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-14-146     Document Type: Article

References (55)

1. Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. Pride DT, Salzman J, Haynes M, Rohwer F, Davis-Long C, White RA, Loomer P, Armitage GC, Relman DA, ISME J 2012 6 5 915 926
2. Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity. Willner D, Furlan M, Schmieder R, Grasis JA, Pride DT, Relman DA, Angly FE, McDole T, Mariella RP Jr, Rohwer F, Haynes M, Proc Natl Acad Sci U S A 2011 108 Suppl 1 4547 4553
3. Viruses in the faecal microbiota of monozygotic twins and their mothers. Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, Rohwer F, Gordon JI, Nature 2010 466 7304 334 U381
4. The human gut virome: inter-individual variation and dynamic response to diet. Minot S, Sinha R, Chen J, Li H, Keilbaugh SA, Wu GD, Lewis JD, Bushman FD, Genome Res 2011 21 10 1616 1625
5. Characterization of the viral microbiome in patients with severe lower respiratory tract infections, using metagenomic sequencing. Lysholm F, Wetterbom A, Lindau C, Darban H, Bjerkner A, Fahlander K, Lindberg AM, Persson B, Allander T, Andersson B, PLoS One 2012 7 2 30875
6. Viral diversity and dynamics in an infant gut. Breitbart M, Haynes M, Kelley S, Angly F, Edwards RA, Felts B, Mahaffy JM, Mueller J, Nulton J, Rayhawk S, Rodriguez-Brito B, Salamon P, Rohwer F, Res Microbiol 2008 159 5 367 373
7. Metagenomic analyses of an uncultured viral community from human feces. Breitbart M, Hewson I, Felts B, Mahaffy JM, Nulton J, Salamon P, Rohwer F, J Bacteriol 2003 185 20 6220 6223 (Pubitemid 37248478)
8. Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. Pride DT, Salzman J, Haynes M, Rohwer F, Davis-Long C, White RA 3rd, Loomer P, Armitage GC, Relman DA, ISME J 2011 6 5 915 926
9. Sequence analysis of the human virome in febrile and afebrile children. Wylie KM, Mihindukulasuriya KA, Sodergren E, Weinstock GM, Storch GA, PLoS One 2012 7 6 27735
10. Association between living environment and human oral viral ecology. Robles-Sikisaka RLM, Boehm T, Naudi M, Salzman J, Pride DT, ISME J 2013 7 9 1710 1724
11. CRISPR provides acquired resistance against viruses in prokaryotes. Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P, Science 2007 315 5819 1709 1712 (Pubitemid 46515624)
12. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Garneau JE, Dupuis M-E, Villion M, Romero DA, Barrangou R, Boyaval P, Fremaux C, Horvath P, Magadan AH, Moineau S, Nature 2010 468 7320 67 71
13. Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Tyson GW, Banfield JF, Environ Microbiol 2008 10 1 200 207
14. Comparisons of clustered regularly interspaced short palindromic repeats and viromes in human saliva reveal bacterial adaptations to salivary viruses. Pride DT, Salzman J, Relman DA, Environ Microbiol 2012 14 9 2564 2576
15. Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time. Pride DT, Sun CL, Salzman J, Rao N, Loomer P, Armitage GC, Banfield JF, Relman DA, Genome Res 2011 21 1 126 136
16. Virus population dynamics and acquired virus resistance in natural microbial communities. Andersson AF, Banfield JF, Science 2008 320 5879 1047 1050 (Pubitemid 351929541)
17. Diverse CRISPRs evolving in human microbiomes. Rho M, Wu YW, Tang H, Doak TG, Ye Y, PLoS Genet 2012 8 6 1002441
18. Strong bias in the bacterial CRISPR elements that confer immunity to phage. Paez-Espino D, Morovic W, Sun CL, Thomas BC, Ueda K, Stahl B, Barrangou R, Banfield JF, Nat Commun 2013 4 1430
19. Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. Willner D, Furlan M, Haynes M, Schmieder R, Angly FE, Silva J, Tammadoni S, Nosrat B, Conrad D, Rohwer F, PLoS One 2009 4 10 7370
20. Quantitation of major human cutaneous bacterial and fungal populations. Gao Z, Perez-Perez GI, Chen Y, Blaser MJ, J Clin Microbiol 2010 48 10 3575 3581
21. Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents. Blaser MJ, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Estrada I, Gao Z, Clemente JC, Costello EK, Knight R, ISME J 2013 7 1 85 95
22. Topographical and temporal diversity of the human skin microbiome. Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, Bouffard GG, Blakesley RW, Murray PR, Green ED, Turner ML, Segre JA, Science 2009 324 5931 1190 1192
23. Human Skin Microbiota: High Diversity of DNA Viruses Identified on the Human Skin by High Throughput Sequencing. Foulongne V, Sauvage V, Hebert C, Dereure O, Cheval J, Gouilh MA, Pariente K, Segondy M, Burguière A, Manuguerra J-C, Caro V, Eloit M, PLoS One 2012 7 6 38499
24. What happened to the streptococci: overview of taxonomic and nomenclature changes. Facklam R, Clin Microbiol Rev 2002 15 4 613 630 (Pubitemid 41184081)
25. Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood. Stahringer SS, Clemente JC, Corley RP, Hewitt J, Knights D, Walters WA, Knight R, Krauter KS, Genome Res 2012 22 11 2146 2152
26. Analyses of the microbial diversity across the human microbiome. Li K, Bihan M, Yooseph S, Methe BA, PLoS One 2012 7 6 32118
27. Biogeography of the ecosystems of the healthy human body. Zhou Y, Gao H, Mihindukulasuriya KA, La Rosa PS, Wylie KM, Vishnivetskaya T, Podar M, Warner B, Tarr PI, Nelson DE, Fortenberry JD, Holland MJ, Burr SE, Shannon WD, Sodergren E, Weinstock GM, Genome Biol 2013 14 1 1
28. Bacterial community variation in human body habitats across space and time. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R, Science 2009 326 5960 1694 1697
29. Quantitation and composition of cutaneous microbiota in diabetic and nondiabetic men. Redel H, Gao Z, Li H, Alekseyenko AV, Zhou Y, Perez-Perez GI, Weinstock G, Sodergren E, Blaser MJ, J Infect Dis 2013 207 7 1105 1114
30. A core human microbiome as viewed through 16S rRNA sequence clusters. Huse SM, Ye Y, Zhou Y, Fodor AA, PLoS One 2012 7 6 34242
31. Molecular analysis of human forearm superficial skin bacterial biota. Gao Z, Tseng CH, Pei Z, Blaser MJ, Proc Natl Acad Sci U S A 2007 104 8 2927 2932 (Pubitemid 46327980)
32. The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Fierer N, Hamady M, Lauber CL, Knight R, Proc Natl Acad Sci U S A 2008 105 46 17994 17999
33. A diversity profile of the human skin microbiota. Grice EA, Kong HH, Renaud G, Young AC, Bouffard GG, Blakesley RW, Wolfsberg TG, Turner ML, Segre JA, Genome Res 2008 18 7 1043 1050 (Pubitemid 351931155)
34. Basic local alignment search tool. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, J Mol Biol 1990 215 3 403 410
35. Environmental biodiversity, human microbiota, and allergy are interrelated. Hanski I, von Hertzen L, Fyhrquist N, Koskinen K, Torppa K, Laatikainen T, Karisola P, Auvinen P, Paulin L, Makela MJ, Vartiainen E, Kosunen TU, Alenius H, Haahtela T, Proc Natl Acad Sci U S A 2012 109 21 8334 8339
36. An integrated semiconductor device enabling non-optical genome sequencing. Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, Leamon JH, Johnson K, Milgrew MJ, Edwards M, Hoon J, Simons JF, Marran D, Myers JW, Davidson JF, Branting A, Nobile JR, Puc BP, Light D, Clark TA, Huber M, Branciforte JT, Stoner IB, Cawley SE, Lyons M, Fu Y, Homer N, Sedova M, Miao X, Reed B, et al. Nature 2011 475 7356 348 352
37. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Mojica FJ, Diez-Villasenor C, Garcia-Martinez J, Almendros C, Microbiology 2009 155 Pt 3 733 740
38. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. Grissa I, Vergnaud G, Pourcel C, BMC Bioinforma 2007 8 172
39. The oral metagenome in health and disease. Belda-Ferre P, Alcaraz LD, Cabrera-Rubio R, Romero H, Simon-Soro A, Pignatelli M, Mira A, ISME J 2012 6 1 46 56
40. Gut metagenome in European women with normal, impaired and diabetic glucose control. Karlsson FH, Tremaroli V, Nookaew I, Bergstrom G, Behre CJ, Fagerberg B, Nielsen J, Backhed F, Nature 2013 498 7452 99 103
41. Recruiting human microbiome shotgun data to site-specific reference genomes. Xie G, Lo CC, Scholz M, Chain PS, PLoS One 2014 9 1 84963
42. Evolution and classification of the CRISPR-Cas systems. Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin AF, van der Oost J, Koonin EV, Nat Rev Microbiol 2011 9 6 467 477
43. Java Treeview-extensible visualization of microarray data. Saldanha AJ, Bioinformatics 2004 20 17 3246 3248 (Pubitemid 39619217)
44. QIIME allows analysis of high-throughput community sequencing data. Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R, Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, et al. Nat Meth 2010 7 5 335 336
45. Development of a software tool for in silico simulation of Escherichia coli using a visual programming environment. Lee SG, Kim CM, Hwang KS, J Biotechnol 2005 119 1 87 92 (Pubitemid 41112620)
46. Murphy FA, Fauquet CM, Bishop DHL, Ghabrial SA, Jarvis AW, Martelli GP, Mayo MA, Summers MD, Virus Taxonomy: Sizth Report of the International Committee on Taxonomy of Viruses New York: Springer-Verlag 1995 Vol. Supplement 10
47. The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM, Nucleic Acids Res 2009 37 141 D145
48. Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform. Whiteley AS, Jenkins S, Waite I, Kresoje N, Payne H, Mullan B, Allcock R, O'Donnell A, J Microbiol Methods 2012 91 1 80 88
49. Search and clustering orders of magnitude faster than BLAST. Edgar RC, Bioinformatics 2010 26 19 2460 2461
50. PyNAST: a flexible tool for aligning sequences to a template alignment. Caporaso JG, Bittinger K, Bushman FD, DeSantis TZ, Andersen GL, Knight R, Bioinformatics 2010 26 2 266 267
51. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL, Appl Environ Microbiol 2006 72 7 5069 5072 (Pubitemid 44078840)
52. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Li W, Godzik A, Bioinformatics 2006 22 13 1658 1659 (Pubitemid 43985301)
53. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Price MN, Dehal PS, Arkin AP, Mol Biol Evol 2009 26 7 1641 1650
54. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Wang Q, Garrity GM, Tiedje JM, Cole JR, Appl Environ Microbiol 2007 73 16 5261 5267 (Pubitemid 47326658)
55. UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context. Lozupone C, Hamady M, Knight R, BMC Bioinforma 2006 7 371