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Characterization of Tobacco Microbiome by Metagenomics Approach

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Cancer Biomarkers

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2413))

Abstract

Chronic consumption of tobacco in all forms, either smoked/smokeless forms, causes major health hazards to humans that include cancer, cardiovascular, lung diseases, diabetes, fertility issues, etc. Among tobacco-mediated cancers, the prominent one being the oral cancers are caused due to chronic tobacco chewing. The biochemicals present in tobacco are involved in carcinogenesis, and their presence is partly mediated by the existence of microbes in tobacco products. The microbial characterization has been evolved from classical microscopical observation to the recent development of 16S rRNA sequencing by next-generation sequencing methods. The metagenomics approach using 16S rRNA-based next-generation sequencing methods enables the detection and characterization of the complete microbial community of tobacco, including both cultivable and non-cultivable microorganisms. Identification of microbes will help in devising strategies to limit the carcinogenic compounds present in tobacco.

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References

  1. Mehrotra R, Yadav A, Sinha DN, Parascandola M, John RM, Ayo-Yusuf O, Nargis N, Hatsukami DK, Warnakulasuriya S, Straif K, Siddiqi K, Gupta PC (2019) Smokeless tobacco control in 180 countries across the globe: call to action for full implementation of WHO FCTC measures. Lancet Oncol 20(4):E208–E217

    Article  Google Scholar 

  2. IARC (2007) Monographs on the evaluation of carcinogenic risks to humans smokeless tobacco and some tobacco-specific N-nitrosamines. IARC Monogr Eval Carcinog Risks Hum 89:1–592

    Google Scholar 

  3. Gregory LG, Bond PL, Richardson DJ, Spiro S (2003) Characterization of a nitrate-respiring bacterial community using the nitrate reductase gene (narG) as a functional marker. Microbiology (Reading) 149:229–237

    Article  CAS  Google Scholar 

  4. Sleiman M, Gundel LA, Pankow JF, Jacob P III, Singer BC, Destaillats H (2010) Formation of carcinogens indoors by surface-mediated reactions of nicotine with nitrous acid, leading to potential thirdhand smoke hazards. Proc Natl Acad Sci U S A 107:6576–6581

    Article  CAS  Google Scholar 

  5. Klus H, Kunze M, Koenig S, Poeschl E (2009) Smokeless tobacco—an overview. Contributions Tob Res 23:248–276

    CAS  Google Scholar 

  6. Berlanga M (2010) Brock biology of microorganisms (11th edn). Madigan MT, Martinko JM (eds) Prentice Hall, Upper Saddle River, NJ, USA ISBN 0-13-144329

    Google Scholar 

  7. Whitman WB, Suzuki K (2015) Solirubrobacterales. In: Whitman WB (ed) Bergey’s Manual of Systematics of Archaea and Bacteria. John Wiley & Sons, Chichester, pp 1–3

    Google Scholar 

  8. Willey JM, Sherwood LM, Woolverton CJ (2011) Epidemiology and public health microbiology: nosocomial infections. In: Willey JM, Sherwood LM, Woolverton CJ (eds) Edited Prescott’s Microbiology, 8th edn. The McGraw Hill companies. International edition., New York, pp 873,884–873,886

    Google Scholar 

  9. Chung KT, Ferris DH (1996) "Martinus Willem Beijerinck (1851–1931): Pioneer of general microbiology (PDF). ASM news. Washington, D.C.: American Society For Microbiology 62(10): 539––543

    Google Scholar 

  10. Overmann J (2013) Principles of enrichment, isolation, cultivation, and preservation of bacteria. In: Rosenberg E, DeLong EF, Stackebrandt E, Lory S, Thompson F (eds) The prokaryotes: prokaryotic biology and symbiotic associations, 4th edn. Springer, NY, pp 149–207

    Chapter  Google Scholar 

  11. Curtis TP, Sloan WT, Scannell JW (2002) Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci U S A 99:10494–10499

    Article  CAS  Google Scholar 

  12. Pace NR, Sapp J, Goldenfeld N (2012) Phylogeny and beyond: scientific, historical, and conceptual significance of the first tree of life. Proc Natl Acad Sci U S A 109(4):1011–1018

    Article  CAS  Google Scholar 

  13. Fukuda K, Ogawa M, Taniguchi H, Saito M (2016) Molecular approaches to studying microbial communities: targeting the 16S ribosomal RNA gene. J UOEH 38(3):223–232

    Article  CAS  Google Scholar 

  14. Handelsman J (2004) Metagenomics: application of genomics to uncultured micro-organisms. Microbiol Mol Biol Rev 68(4):669–685

    Article  CAS  Google Scholar 

  15. Schloss PD, Handelsman J (2005) Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol 71:1501

    Article  CAS  Google Scholar 

  16. Prescott ML, Harley PJ, Klein AD (eds) (2004) Microbiology, sixth edition. McGraw-Hill Higher Education, NY

    Google Scholar 

  17. Huang J, Yang J, Duan Y, Gu W, Gong X, Zhe W, Su C, Zhang K (2010) Bacterial diversities on unaged and aging flue-cured tobacco leaves estimated by 16S rRNA sequence analysis. Appl Microbiol Biotechnol 88:553–562

    Article  CAS  Google Scholar 

  18. Vanwonterghem I, Jensen PD, Dennis PG, Hugenholtz P, Rabaey K, Tyson GW (2014) Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters. ISME J 8(10):2015–2028

    Article  CAS  Google Scholar 

  19. Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glöckner FO (2013) Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res 41(1):e1

    Article  CAS  Google Scholar 

  20. Fadrosh DW, Ma B, Gajer P, Sengamalay N, Ott S, Brotman RM, Ravel J (2014) An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. Microbiome 2(1):6. https://doi.org/10.1186/2049-2618-2-6

    Article  PubMed  PubMed Central  Google Scholar 

  21. Schloss PD, Westcott SL, Ryabin T et al (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75(23):7537–7541

    Article  CAS  Google Scholar 

  22. Caporaso JG, Kuczynski J, Stombaugh J et al (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7(5):335–336

    Article  CAS  Google Scholar 

  23. Pylro VS, Roesch LF, Morais DK et al (2014) Data analysis for 16S microbial profiling from different benchtop sequencing platforms. J Microbiol Methods 107:30–37

    Article  CAS  Google Scholar 

  24. Wood DE, Salzberg SL (2014) Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 15(3):R46

    Article  Google Scholar 

  25. Ounit R, Wanamaker S, Close TJ, Lonardi S (2015) CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. BMC Genomics 16(1):236

    Article  Google Scholar 

  26. Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP (2016) DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods 7:581–583

    Google Scholar 

  27. Amir A, McDonald D, Navas-Molina JA, Kopylova E, Morton JT, Zech Xu Z, Kightley EP, Thompson LR, Hyde ER, Gonzalez A, Knight R (2017) Deblur rapidly resolves single-nucleotide community sequence patterns. mSystems 2:e00191-16

    Google Scholar 

  28. Willis AD (2019) Rarefaction, alpha diversity, and statistics. Front Microbiol 10:2407.3

    Google Scholar 

  29. Katoh K, Misawa K, Kuma K-I, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059–3066

    Google Scholar 

  30. Price MN, Dehal PS, Arkin AP, FastTree (2009) Computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26:1641–1650

    Google Scholar 

  31. Plassais J, Gbikpi-Benissan G, Figarol M, Scheperjans F, Gorochov G, Derkinderen P, Cervino ACL (2021) Gut microbiome alpha-diversity is not a marker of Parkinson’s disease and multiple sclerosis. Brain commun 3:fcab113

    Google Scholar 

  32. Lozupone CA, Hamady M, Kelley ST, Knight R (2009) Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities. Appl Environ Microbiol 73:1576–1585

    Google Scholar 

  33. Mandal S, Van TW, White RA, Eggesbø M, Knight R, Peddada SD (2015) Analysis of composition of microbiomes: a novel method for studying microbial composition. Microb Ecol Health Dis 26:27663

    Google Scholar 

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Acknowledgments

We thank Ms. Sanchita, Dr. Archana, and Dr. Anita Kumari (ICMR-PDF, NICPR) for reading and correcting the write-up.

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Authors and Affiliations

  1. Molecular Genetics Lab, Molecular Biology Group, National Institute of Cancer Prevention and Research (ICMR), Noida, Uttar Pradesh, India

    R. Suresh Kumar & Nivedita Mishra

  2. ICMR-AIIMS Computational Genomics Center, Division of Biomedical Informatics, Indian Council of Medical Research, New Delhi, India

    Amit Kumar

Authors
  1. R. Suresh Kumar
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  2. Nivedita Mishra
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  3. Amit Kumar
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Editor information

Editors and Affiliations

  1. Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA

    Gagan Deep

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Kumar, R.S., Mishra, N., Kumar, A. (2022). Characterization of Tobacco Microbiome by Metagenomics Approach. In: Deep, G. (eds) Cancer Biomarkers. Methods in Molecular Biology, vol 2413. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1896-7_22

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  • DOI: https://doi.org/10.1007/978-1-0716-1896-7_22

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1895-0

  • Online ISBN: 978-1-0716-1896-7

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