Characterization of bacterial communities in selected smokeless tobacco products using 16S rDNA analysis

PLoS ONE

Volumn 11, Issue 1, 2016, Pages

  Tyx, Robert E ^a   Stanfill, Stephen B ^a   Keong, Lisa M ^a,d   Rivera, Angel J ^a,c   Satten, Glen A ^b   Watson, Clifford H ^a  

^a CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^b NATIONAL CENTER FOR CHRONIC DISEASE PREVENTION AND HEALTH PROMOTION   (United States)

^c OAK RIDGE INSTITUTE FOR SCIENCE AND EDUCATION   (United States)

^d BATTELLE MEMORIAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL TOXIN; DNA 16S; NITRATE REDUCTASE; BACTERIAL DNA; RIBOSOME DNA; RNA 16S;

ACTINOBACTERIA; AEROCOCCACEAE; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIUM IDENTIFICATION; BACTEROIDETES; DNA DETERMINATION; ENTEROCOCCACEAE; GENETIC CODE; MICROBIAL COMMUNITY; NEXT GENERATION SEQUENCING; NONHUMAN; POPULATION ABUNDANCE; PROTEOBACTERIA; SMOKELESS TOBACCO; SPECIES DISTRIBUTION; STAPHYLOCOCCACEAE; ANTIBIOTIC RESISTANCE; BACTERIUM; CLASSIFICATION; GENETICS; HIGH THROUGHPUT SEQUENCING; METAGENOME; MICROBIOLOGY; PHYLOGENY; SOFTWARE; UNITED STATES;

BACTERIA; BACTERIAL TOXINS; DNA, BACTERIAL; DNA, RIBOSOMAL; DRUG RESISTANCE, BACTERIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; METAGENOME; PHYLOGENY; RNA, RIBOSOMAL, 16S; SOFTWARE; TOBACCO, SMOKELESS; UNITED STATES;

EID: 84958073794     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0146939     Document Type: Article

References (53)

1. NIH/CDC (2014) Smokeless Tobacco and Public Health: A Global Perspective. Bethesda, MD: US Department of Health and Human Services, Centers for Disease Control and Prevention and National Institutes of Health, National Cancer Institute. NIH Publication No. 14-7983.
2. Borgerding MF, Bodnar JA, Curtin GM, Swauger JE (2012) The chemical composition of smokeless tobacco: A survey of products sold in the United States in 2006 and 2007. Regulatory Toxicology and Pharmacology 64: 367-387. doi: 10.1016/j.yrtph.2012.09.003 PMID: 23000415
3. Zakiullah, Saeed M, Muhammad N, Khan SA, Gul F, Khuda F, et al. (2012) Assessment of potential toxicity of a smokeless tobacco product (naswar) available on the Pakistani market. Tobacco Control 21: 396-401. doi: 10.1136/tc.2010.042630 PMID: 21642445
4. Rickert WS, Joza PJ, Trivedi AH, Momin RA, Wagstaff WG, Lauterbach JH, et al. (2009) Chemical and toxicological characterization of commercial smokeless tobacco products available on the Canadian market. Regulatory Toxicology and Pharmacology 53: 121-133. doi: 10.1016/j.yrtph.2008.12.004 PMID: 19135498
5. Di Giacomo M, Paolino M, Silvestro D, Vigliotta G, Imperi F, Visca P, et al. (2007) Microbial community structure and dynamics of dark fire-cured tobacco fermentation. Applied and Environmental Microbiology 73: 825-837. PMID: 17142368
6. Sapkota AR, Berger S, Vogel TM (2010) Human Pathogens Abundant in the Bacterial Metagenome of Cigarettes. Environmental Health Perspectives 118: 351-356. doi: 10.1289/ehp.0901201 PMID: 20064769
7. Cockrell WTJ, Roberts J.S., Kane B.E., Fulghum R.S. (1989) Microbiology of Oral Smokeless Tobacco Products. Tobacco Science 33: 55-57.
8. Pauly JL, Paszkiewicz G (2011) Cigarette smoke, bacteria, mold, microbial toxins, and chronic lung inflammation. J Oncol 2011: 819129. doi: 10.1155/2011/819129 PMID: 21772847
9. Larsson L, Szponar B, Ridha B, Pehrson C, Dutkiewicz J, Krysińska-Traczyk E, et al. (2008) Identification of bacterial and fungal components in tobacco and tobacco smoke. Tob Induc Dis 4: 4. doi: 10.1186/1617-9625-4-4 PMID: 18822161
10. Wahlberg I, Wiernik A, Christakopoulos A, Johansson L (1999) Tobacco-specific nitrosamines. A multidisciplinary research area. Agro Food Industry Hi-Tech 10: 23-28.
11. IARC (2007) Smokeless tobacco and some tobacco-specific N-nitrosamines. Lyon, France: International Agency for Research of Cancer.
12. Lawler TS, Stanfill SB, Zhang L, Ashley DL, Watson CH (2013) Chemical characterization of domestic oral tobacco products: total nicotine, pH, unprotonated nicotine and tobacco-specific N-nitrosamines. Food Chem Toxicol 57: 380-386. doi: 10.1016/j.fct.2013.03.011 PMID: 23517910
13. Stepanov I, Jensen J, Hatsukami D, Hecht SS (2008) New and traditional smokeless tobacco: comparison of toxicant and carcinogen levels. Nicotine Tob Res 10: 1773-1782. doi: 10.1080/ 14622200802443544 PMID: 19023828
14. Richter P, Hodge K, Stanfill S, Zhang L, Watson C (2008) Surveillance of moist snuff: total nicotine, moisture, pH, un-ionized nicotine, and tobacco-specific nitrosamines. Nicotine & Tobacco Research 10: 1645-1652.
15. Idris AM, Ibrahim SO, Vasstrand EN, Johannessen AC, Lillehaug JR, Magnusson B, et al. (1998) The Swedish snus and the Sudanese toombak: are they different? Oral Oncol 34: 558-566. PMID: 9930371
16. Idris AM, Nair J, Ohshima H, Friesen M, Brouet I, Faustman EM, et al. (1991) Unusually High-Levels of Carcinogenic Tobacco-Specific Nitrosamines in Sudan Snuff (Toombak). Carcinogenesis 12: 1115-1118. PMID: 2044192
17. Fisher MT, Bennett CB, Hayes A, Kargalioglu Y, Knox BL, Xu D, et al. (2012) Sources of and technical approaches for the abatement of tobacco specific nitrosamine formation in moist smokeless tobacco products. Food and Chemical Toxicology 50: 942-948. doi: 10.1016/j.fct.2011.11.035 PMID: 22142690
18. Hempfling WP BG, Shulleeta M. (2004) Method for reduction of tobacco specific nitrosamines. In: Office USPaT, editor. USA.
19. Andersen RA, Fleming P.D., Burton H.R., Hamilton-Kemp T.R., Sutton T.G. (1991) Nitrosated, Acylated, and Oxidized Pyridine Alkaloids during Storage of Smokeless Tobaccos: Effects of Moisture, Temperature, and Thier Interactions. J Agric Food Chem 39: 1280-1287.
20. Rutqvist LE, Curvall M, Hassler T, Ringberger T, Wahlberg I (2011) Swedish snus and the GothiaTek (R) standard. Harm Reduction Journal 8:11. doi: 10.1186/1477-7517-8-11 PMID: 21575206
21. Huang JW, Yang JK, Duan YQ, Gu W, Gong XW, Zhe W, et al. (2010) Bacterial diversities on unaged and aging flue-cured tobacco leaves estimated by 16S rRNA sequence analysis. Applied Microbiology and Biotechnology 88: 553-562. doi: 10.1007/s00253-010-2763-4 PMID: 20645083
22. Su C, Gu W, Zhe W, Zhang KQ, Duan YQ, Yang J, et al. (2011) Diversity and phylogeny of bacteria on Zimbabwe tobacco leaves estimated by 16S rRNA sequence analysis. Applied Microbiology and Biotechnology 92: 1033-1044. doi: 10.1007/s00253-011-3367-3 PMID: 21660545
23. Bokulich NA, Joseph CML, Allen G, Benson AK, Mills DA (2012) Next-Generation Sequencing Reveals Significant Bacterial Diversity of Botrytized Wine. Plos One 7.
24. Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, et al. (2013) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41: e1. doi: 10.1093/nar/gks808 PMID: 22933715
25. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, et al. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196. PMID: 17947321
26. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. (2013) The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 41: D590-596. doi: 10.1093/nar/gks1219 PMID: 23193283
27. Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, et al. (2014) The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Nucleic Acids Res 42: D643-648. doi: 10.1093/nar/ gkt1209 PMID: 24293649
28. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nature Methods 7: 335-336. doi: 10.1038/nmeth.f.303 PMID: 20383131
29. Markowitz VM, Chen I-MA, Palaniappan K, Chu K, Szeto E, Grechkin Y, et al. (2012) IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Research 40: D115-D122. doi: 10.1093/nar/gkr1044 PMID: 22194640
30. Langille MGI, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, et al. (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotech 31: 814-821.
31. Kanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30. PMID: 10592173
32. Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M. (2014) Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res 42: D199-205. doi: 10.1093/nar/ gkt1076 PMID: 24214961
33. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanisha M. (1999) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research 27: 29-34. PMID: 9847135
34. Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin PR, O'Hara RB, et al. (2015) Vegan: Community Ecology Package.
35. Friedman J, Hastie T, Tibshirani R (2010) Regularization Paths for Generalized Linear Models via Coordinate Descent. J Stat Softw 33: 1-22. PMID: 20808728
36. Sohaskey CD, Wayne LG (2003) Role of narK2X and narGHJI in hypoxic upregulation of nitrate reduction by Mycobacterium tuberculosis. J Bacteriol 185: 7247-7256. PMID: 14645286
37. Rowe JJ, Ubbinkkok T, Molenaar D, Konings WN, Driessen AJM (1994) Nark Is a Nitrite-Extrusion System Involved in Anaerobic Nitrate Respiration by Escherichia-Coli. Molecular Microbiology 12: 579-586. PMID: 7934881
38. Moreno-Vivian C, Cabello P, Martinez-Luque M, Blasco R, Castillo F (1999) Prokaryotic nitrate reduction: molecular properties and functional distinction among bacterial nitrate reductases. J Bacteriol 181: 6573-6584. PMID: 10542156
39. Stewart V, Lu Y, Darwin AJ (2002) Periplasmic nitrate reductase (NapABC enzyme) supports anaerobic respiration by Escherichia coli K-12. J Bacteriol 184: 1314-1323. PMID: 11844760
40. Nishimura T, Vertes AA, Shinoda Y, Inui M, Yukawa H (2007) Anaerobic growth of Corynebacterium glutamicum using nitrate as a terminal electron acceptor. Appl Microbiol Biotechnol 75: 889-897. PMID: 17347820
41. Fast B, Lindgren P, Gotz F (1996) Cloning, sequencing, and characterization of a gene (narT) encoding a transport protein involved in dissimilatory nitrate reduction in Staphylococcus carnosus. Arch Microbiol 166: 361-367. PMID: 9082911
42. Luque-Almagro VM, Gates AJ, Moreno-Vivian C, Ferguson SJ, Richardson DJ, Roldán MD. (2011) Bacterial nitrate assimilation: gene distribution and regulation. Biochem Soc Trans 39: 1838-1843. doi: 10.1042/BST20110688 PMID: 22103536
43. Averill BA (1996) Dissimilatory Nitrite and Nitric Oxide Reductases. Chemical Reviews 96: 2951-2964. PMID: 11848847
44. Darwin A, Stewart V (1996) The NAR Modulon Systems: Nitrate and Nitrite Regulation of Anaerobic Gene Expression. Regulation of Gene Expression in Escherichia coli: Springer US. pp. 343-359.
45. Hartig E, Schiek U, Vollack KU, Zumft WG (1999) Nitrate and nitrite control of respiratory nitrate reduction in denitrifying Pseudomonas stutzeri by a two-component regulatory system homologous to NarXL of Escherichia coli. J Bacteriol 181: 3658-3665. PMID: 10368138
46. Mainar MS, Leroy F. (2015) Process-driven bacterial community dynamics are key to cured meat colour formation by coagulase-negative staphylococci via nitrate reductase or nitric oxide synthase activities. International Journal of Food Microbiology 212: 60-66. doi: 10.1016/j.ijfoodmicro.2015.03.009 PMID: 25805616
47. Bernard KA, Wiebe D, Burdz T, Reimer A, Ng B, Singh C, et al. (2010) Assignment of Brevibacterium stationis (ZoBell and Upham 1944) Breed 1953 to the genus Corynebacterium, as Corynebacterium stationis comb. nov., and emended description of the genus Corynebacterium to include isolates that can alkalinize citrate. International Journal of Systematic and Evolutionary Microbiology 60: 874-879. doi: 10.1099/ijs.0.012641-0 PMID: 19661509
48. Stanfill SB, Connolly GN, Zhang L, Jia LT, Henningfield JE, Richter P, et al. (2011) Global surveillance of oral tobacco products: total nicotine, unionised nicotine and tobacco-specific N-nitrosamines. Tobacco Control 20: e2.
49. Vigliotta G, Di Giacomo M, Carata E, Massardo DR, Tredici SM, Silvestro D, et al. (2007) Nitrite metabolism in Debaryomyces hansenii TOB-Y7, a yeast strain involved in tobacco fermentation. Applied Microbiology and Biotechnology 75: 633-645. PMID: 17318539
50. Zitomer N, Rybak ME, Li Z, Walters MJ, Holman MR (2015) Determination of Aflatoxin B in Smokeless Tobacco Products by Use of UHPLC-MS/MS. J Agric Food Chem.
51. Rubinstein I, PedersenGW (2002) Bacillus species are present in chewing tobacco sold in the United States and evoke plasma exudation from the oral mucosa. Clinical and Diagnostic Laboratory Immunology 9: 1057-1060. PMID: 12204959
52. Zheng H, Wisedchaisri G, Gonen T (2013) Crystal structure of a nitrate/nitrite exchanger. Nature 497: 647-651. doi: 10.1038/nature12139 PMID: 23665960
53. Spiegelhalder B, Fischer S (1991) Formation of Tobacco-Specific Nitrosamines. Critical Reviews in Toxicology 21: 241-241.