Characterization of oral bacterial diversity of irradiated patients by high-throughput sequencing

Abstract

Radiation therapy for cancer can alter the type and number of microbes in patients’ mouths, research by Zheng-Wei Huang and colleagues of the Ninth People’s Hospital in Shanghai, China has shown. Diverse oral microbial communities play an important role in maintaining human oral health, and changes in composition can contribute to side-effects such as radiation caries and soft tissue necrosis. Huang and colleagues sampled plaque from 8 patients and used high-throughput sequencing to produce detailed microbial maps for 7 time points during the course of radiotherapy. This technique averts the need for inefficient and unreliable culturing. Overall, 50% of all microbes detected belonged to just 5 genera, although many species were present in low numbers. As radiotherapy progressed, the composition of patients’ microbial communities changed. Understanding these community shifts may help researchers design effective therapies.

Keywords

dental plaque / head-and-neck radiotherapy / microbial diversity / oral microbiota / pyrosequencing

References

[1] Walker MP, Wichman B, Cheng AL. Impact of radiotherapy dose on dentition breakdown in head and neck cancer patients. Pract Radiat Oncol, 2011, 1(3): 142-148.

[2] Shih A, Miaskowski C, Dodd MJ. Mechanisms for radiation-induced oral mucositis and the consequences. Cancer Nurs, 2003, 26(3): 222-229.

[3] Rothwell BR. Prevention and treatment of the orofacial complications of radiotherapy. J Am Dent Assoc, 1987, 114(3): 316-322.

[4] Whitmyer CC, Waskowski JC, Iffland HA. Radiotherapy and oral sequelae: preventive and management protocols. J Dent Hyg, 1997, 71(1): 23-29.

[5] Nederfors T. Xerostomia and hyposalivation. Adv Dent Res, 2000, 14: 48-56.

[6] MacFarlane TW, Mason DK. Changes in the oral flora in Sjögren’s syndrome. J Clin Pathol, 1974, 27: 416-419.

[7] Leung WK, Jin LJ, Samaranayake LP. Subgingival microbiota of shallow periodontal pockets in individuals after head and neck irradiation. Oral Microbiol Immunol, 1998, 13(1): 1-10.

[8] Aas JA, Paster BJ, Stokes LN. Defining the normal bacterial flora of the oral cavity. J Clin Microbiol, 2005, 43(11): 5721-5732.

[9] He XS, Shi WY. Oral microbiology: past, present and future. Int J Oral Sci, 2009, 1(2): 47-58.

[10] Li Y, Ku CY, Xu J. Survey of oral microbial diversity using PCR-based denaturing gradient gel electrophoresis. J Dent Res, 2005, 84(6): 559-564.

[11] Rasiah IA, Wong L, Anderson SA. Variation in bacterial DGGE patterns from human saliva: over time, between individuals and in corresponding dental plaque microcosms. Arch Oral Biol, 2005, 50(9): 779-787.

[12] Lazarevic V, Whiteson K, Hernandez D. Study of inter- and intra-individual variations in the salivary microbiota. BMC Genomics, 2010, 11: 523.

[13] Carr AJ, Ng WF, Figueiredo F. Sjogren’s syndrome—an update for dental practitioners. Br Dent J, 2012, 213(7): 353-357.

[14] Shao ZY, Tang ZS, Yan C. Effects of intensity-modulated radiotherapy on human oral microflora. J Radiat Res, 2011, 52(6): 834-839.

[15] Margulies M, Egholm M, Altman WE. Genome sequencing in open microfabricated high density picolitre reactors. Nature, 2005, 437(7057): 376-380.

[16] Ling Z, Kong J, Jia P. Analysis of oral microbiota in children with dental caries by PCR-DGGE and barcoded pyrosequencing. Microb Ecol, 2010, 60(3): 677-690.

[17] Ley RE, Hamady M, Lozupone C. Evolution of mammals and their gut microbes. Science, 2008, 320(5883): 1647-1651.

[18] Hamady M, Knight R. Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res, 2009, 19(7): 1141-1152.

[19] Siqueira JJ, Fouad AF, Rocas IN . Pyrosequencing as a tool for better understanding of human microbiomes. J Oral Microbiol 2012; 4: 10.3402/jom.v4i0.10743. Epub 2012 Jan. 23.

[20] Aas JA, Griffen AL, Dardis SR. Bacteria of dental caries in primary and permanent teeth in children and young adults. J Clin Microbiol, 2008, 46(4): 1407-1417.

[21] Huang Z, Meric G, Liu Z. luxS-based quorum-sensing signaling affects biofilm formation in Streptococcus mutans. . J Mol Microbiol Biotechnol, 2009, 17(1): 12-19.

[22] He Z, Wang Q, Hu Y. Use of the quorum sensing inhibitor furanone C-30 to interfere with biofilm formation by Streptococcus mutans and its luxS mutant strain. Int J Antimicrob Agents, 2012, 40(1): 30-35.

[23] Xie CH, Yokota A. Phylogenetic analyses of the nitrogen-fixing genus Derxia. J Gen Appl Microbiol, 2004, 50(3): 129-135.

[24] Collins MD, Lawson PA, Nikolaitchouk N. Luteococcus peritonei sp. nov., isolated from the human peritoneum. Int J Syst Evol Microbiol, 2000, 50(Pt 1): 179-181.

[25] Collins MD, Hutson RA, Nikolaitchouk N. Luteococcus sanguinis sp. nov., isolated from human blood. Int J Syst Evol Microbiol, 2003, 53(Pt 6): 1889-1891.

[26] Kumar PS, Brooker MR, Dowd SE. Target region selection is a critical determinant of community fingerprints generated by 16S pyrosequencing. PLoS ONE, 2011, 6(6): e20956.

[27] Wittebolle L, Marzorati M, Clement L. Initial community evenness favours functionality under selective stress. Nature, 2009, 458(7238): 623-626.

[28] Chang Q, Luan Y, Sun F. Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny. BMC Bioinformatics, 2011, 12: 118.