Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples

Gut Pathogens

Volumn 8, Issue 1, 2016, Pages

  Glassing, Angela ^b   Dowd, Scot E ^c   Galandiuk, Susan ^d   Davis, Brian ^e   Chiodini, Rodrick J ^a,b  

^a St Vincent Healthcare Billings   (United States)

^b MONTANA STATE UNIVERSITY BILLINGS   (United States)

^c MR DNA Molecular Research   (United States)

^d University of Louisville School of Medicine   (United States)

^e Paul L Foster School of Medicine   (United States)

Author keywords

16S sequencing; Contamination; Inflammatory bowel disease; Metagenomics; Microbiota; PCR

Indexed keywords

EID: 84969940445     PISSN: None     EISSN: 17574749     Source Type: Journal    
DOI: 10.1186/s13099-016-0103-7     Document Type: Article

References (30)

1. Pace NR. A molecular view of microbial diversity and the biosphere. Science. 1997;276(5313):734-40.
2. Mojzsis SJ, Arrhenius G, McKeegan KD, Harrison TM, Nutman AP, Friend CR. Evidence for life on Earth before 3,800 million years ago. Nature. 1996;384(6604):55-9.
3. McAlister MB, Kulakov LA, O'Hanlon JF, Larkin MJ, Ogden KL. Survival and nutritional requirements of three bacteria isolated from ultrapure water. J Ind Microbiol Biotechnol. 2002;29(2):75-82.
4. McFeters GA, Broadaway SC, Pyle BH, Egozy Y. Distribution of bacteria within operating laboratory water purification systems. Appl Environ Microbiol. 1993;59(5):1410-5.
5. Shen H, Rogelj S, Kieft TL. Sensitive, real-time PCR detects low-levels of contamination by Legionella pneumophila in commercial reagents. Mol Cell Probes. 2006;20(3-4):147-53.
6. Rand KH, Houck H. Taq polymerase contains bacterial DNA of unknown origin. Mol Cell Probes. 1990;4(6):445-50.
7. Corless CE, Guiver M, Borrow R, Edwards-Jones V, Kaczmarski EB, Fox AJ. Contamination and sensitivity issues with a real-time universal 16S rRNA PCR. J Clin Microbiol. 2000;38(5):1747-52.
8. Chiodini RJ, Dowd SE, Chamberlin WM, Galandiuk S, Davis B, Glassing A. Microbial population differentials between mucosal and submucosal intestinal tissues in advanced Crohn's disease of the ileum. PLoS ONE. 2015;10(7):e0134382.
9. Quigley EM. Leaky gut - concept or clinical entity? Curr Opin Gastroenterol. 2016;32(2):74-9.
10. Patel P, Garson JA, Tettmar KI, Ancliff S, McDonald C, Pitt T, Coelho J, Tedder RS. Development of an ethidium monoazide-enhanced internally controlled universal 16S rDNA real-time polymerase chain reaction assay for detection of bacterial contamination in platelet concentrates. Transfusion. 2012;52(7):1423-32.
11. Hein I, Schneeweiss W, Stanek C, Wagner M. Ethidium monoazide and propidium monoazide for elimination of unspecific DNA background in quantitative universal real-time PCR. J Microbiol Methods. 2007;71(3):336-9.
12. Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO, Moffatt MF, Turner P, Parkhill J, Loman NJ, Walker AW. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 2014;12:87.
13. Xuan C, Shamonki JM, Chung A, Dinome ML, Chung M, Sieling PA, Lee DJ. Microbial dysbiosis is associated with human breast cancer. PLoS ONE. 2014;9(1):e83744.
14. Bhatt AS, Freeman SS, Herrera AF, Pedamallu CS, Gevers D, Duke F, Jung J, Michaud M, Walker BJ, Young S, et al. Sequence-based discovery of Bradyrhizobium enterica in cord colitis syndrome. N Engl J Med. 2013;369(6):517-28.
15. Nadkarni MA, Martin FE, Jacques NA, Hunter N. Determination of bacterial load by real-time PCR using a broad-range (universal) probe and primers set. Microbiology. 2002;148(Pt 1):257-66.
16. Horz HP, Vianna ME, Gomes BP, Conrads G. Evaluation of universal probes and primer sets for assessing total bacterial load in clinical samples: general implications and practical use in endodontic antimicrobial therapy. J Clin Microbiol. 2005;43(10):5332-7.
17. Chiodini RJ, Dowd SE, Davis B, Galandiuk S, Chamberlin WM, Kuenstner JT, McCallum RW, Zhang J. Crohn's disease may be differentiated into 2 distinct biotypes based on the detection of bacterial genomic sequences and virulence genes within submucosal tissues. J Clin Gastroenterol. 2013;47(7):612-20.
18. Garson JA, Patel P, McDonald C, Ball J, Rosenberg G, Tettmar KI, Brailsford SR, Pitt T, Tedder RS. Evaluation of an ethidium monoazide-enhanced 16S rDNA real-time polymerase chain reaction assay for bacterial screening of platelet concentrates and comparison with automated culture. Transfusion. 2014;54(3 Pt 2):870-8.
19. Raes J, Korbel JO, Lercher MJ, von Mering C, Bork P. Prediction of effective genome size in metagenomic samples. Genome Biol. 2007;8(1):R10.
20. Glassing A, Dowd SE, Galandiuk S, Davis B, Jorden JR, Chiodini RJ. Changes in 16S RNA gene microbial community profiling by concentration of prokaryotic DNA. J Microbiol Methods. 2015;119:239-42.
21. Willerslev E, Hansen AJ, Poinar HN. Isolation of nucleic acids and cultures from fossil ice and permafrost. Trends Ecol Evol. 2004;19(3):141-7.
22. Kearney MF, Spindler J, Wiegand A, Shao W, Anderson EM, Maldarelli F, Ruscetti FW, Mellors JW, Hughes SH, Le Grice SF, et al. Multiple sources of contamination in samples from patients reported to have XMRV infection. PLoS ONE. 2012;7(2):e30889.
23. Cooper A, Poinar HN. Ancient DNA: do it right or not at all. Science. 2000;289(5482):1139.
24. Human Microbiome Project. Core microbiome sampling. Protocol A. http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/GetPdf.cgi?id=phd003190.2.
25. Chiodini RJ, Chamberlin WM, Sarosiek J, McCallum RW. Crohn's disease and the mycobacterioses: a quarter century later. Causation or simple association? Crit Rev Microbiol. 2012;38(1):52-93.
26. Jervis-Bardy J, Leong LE, Marri S, Smith RJ, Choo JM, Smith-Vaughan HC, Nosworthy E, Morris PS, O'Leary S, Rogers GB, et al. Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data. Microbiome. 2015;3:19.
27. Walker AW, Martin JC, Scott P, Parkhill J, Flint HJ, Scott KP. 16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice. Microbiome. 2015;3:26.
28. Silva PE, Costa PS, Avila MP, Suhadolnik ML, Reis MP, Salgado AP, Lima MF, Chartone-Souza E, Nascimento AM. Leprous lesion presents enrichment of opportunistic pathogenic bacteria. Springerplus. 2015;4:187.
29. Burcelin R, Serino M, Chabo C, Garidou L, Pomie C, Courtney M, Amar J, Bouloumie A. Metagenome and metabolism: the tissue microbiota hypothesis. Diabetes Obes Metab. 2013;15(Suppl 3):61-70.
30. Lluch J, Servant F, Paisse S, Valle C, Valiere S, Kuchly C, Vilchez G, Donnadieu C, Courtney M, Burcelin R, et al. The characterization of novel tissue microbiota using an optimized 16S metagenomic sequencing pipeline. PLoS ONE. 2015;10(11):e0142334.