Assessing the Fecal Microbiota: An Optimized Ion Torrent 16S rRNA Gene-Based Analysis Protocol

PLoS ONE

Volumn 8, Issue 7, 2013, Pages

  Milani, Christian ^a   Hevia, Arancha ^b   Foroni, Elena ^a   Duranti, Sabrina ^a   Turroni, Francesca ^c   Lugli, Gabriele Andrea ^a   Sanchez, Borja ^b   Martín, Rebeca ^d   Gueimonde, Miguel ^b   van Sinderen, Douwe ^c   Margolles, Abelardo ^b   Ventura, Marco ^a  

^a UNIVERSITY OF PARMA   (Italy)

^b DEPARTMENT OF MICROBIOLOGY AND BIOCHEMISTRY OF DAIRY PRODUCTS   (Spain)

^c UNIVERSITY COLLEGE CORK   (Ireland)

^d UMR1319 MICALIS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 16S;

AMPLICON; ARTICLE; CLINICAL PROTOCOL; CONTROLLED STUDY; FECES MICROFLORA; FEMALE; GENE AMPLIFICATION; GENE EXPRESSION PROFILING; GENE SEQUENCE; HUMAN; MALE; MICROBIAL DIVERSITY; MOUSE; NONHUMAN; POLYMERASE CHAIN REACTION; RAT; RNA ANALYSIS;

ANIMALS; BIODIVERSITY; FECES; FEMALE; HUMANS; MICROBIOTA; RATS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

EID: 84880286399     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0068739     Document Type: Article

References (45)

1. Young VB, (2012) The intestinal microbiota in health and disease. Curr Opin Gastroenterol 28: 63-69.
2. Clemente JC, Ursell LK, Parfrey LW, Knight R, (2012) The impact of the gut microbiota on human health: an integrative view. Cell 148: 1258-1270.
3. Tamboli CP, Neut C, Desreumaux P, Colombel JF, (2004) Dysbiosis in inflammatory bowel disease. Gut 53: 1-4.
4. Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermudez-Humaran LG, et al. (2008) Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A 105: 16731-16736.
5. Kassinen A, Krogius-Kurikka L, Makivuokko H, Rinttila T, Paulin L, et al. (2007) The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects. Gastroenterology 133: 24-33.
6. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, et al. (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-1031.
7. Delzenne NM, Neyrinck AM, Backhed F, Cani PD, (2011) Targeting gut microbiota in obesity: effects of prebiotics and probiotics. Nat Rev Endocrinol 7: 639-646.
8. de la Cochetiere MF, Piloquet H, des Robert C, Darmaun D, Galmiche JP, et al. (2004) Early intestinal bacterial colonization and necrotizing enterocolitis in premature infants: the putative role of Clostridium. Pediatr Res 56: 366-370.
9. Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, et al. (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475: 348-352.
10. Liu L, Li Y, Li S, Hu N, He Y, et al. (2012) Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012: 251364.
11. Quail MA, Smith M, Coupland P, Otto TD, Harris SR, et al. (2012) A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 13: 341.
12. Yergeau E, Lawrence JR, Sanschagrin S, Waiser MJ, Korber DR, et al. (2012) Next-generation sequencing of microbial communities in the Athabasca River and its tributaries in relation to oil sands mining activities. Appl Environ Microbiol 78: 7626-7637.
13. Whiteley AS, Jenkins S, Waite I, Kresoje N, Payne H, et al. (2012) Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform. J Microbiol Methods 91: 80-88.
14. Junemann S, Prior K, Szczepanowski R, Harks I, Ehmke B, et al. (2012) Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing. PLoS One 7: e41606.
15. Sim K, Cox MJ, Wopereis H, Martin R, Knol J, et al. (2012) Improved detection of bifidobacteria with optimised 16S rRNA-gene based pyrosequencing. PLoS One 7: e32543.
16. Salonen A, Nikkila J, Jalanka-Tuovinen J, Immonen O, Rajilic-Stojanovic M, et al. (2010) Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis. J Microbiol Methods 81: 127-134.
17. Andersson AF, Lindberg M, Jakobsson H, Backhed F, Nyren P, et al. (2008) Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS One 3: e2836.
18. Turroni F, Peano C, Pass DA, Foroni E, Severgnini M, et al. (2012) Diversity of bifidobacteria within the infant gut microbiota. PLoS One 7: e36957.
19. Turroni F, Foroni E, Pizzetti P, Giubellini V, Ribbera A, et al. (2009) Exploring the diversity of the bifidobacterial population in the human intestinal tract. Appl Environ Microbiol 75: 1534-1545.
20. Fanaro S, Chierici R, Guerrini P, Vigi V (2003) Intestinal microflora in early infancy: composition and development. Acta Paediatr Suppl 91: 48-55.
21. Favier CF, Vaughan EE, De Vos WM, Akkermans AD, (2002) Molecular monitoring of succession of bacterial communities in human neonates. Appl Environ Microbiol 68: 219-226.
22. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO, (2007) Development of the human infant intestinal microbiota. PLoS Biol 5: e177.
23. Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, et al. (2011) Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci U S A 108Suppl 1: 4578-4585.
24. Kullen MJ, Sanozky-Dawes RB, Crowell DC, Klaenhammer TR, (2000) Use of the DNA sequence of variable regions of the 16S rRNA gene for rapid and accurate identification of bacteria in the Lactobacillus acidophilus complex. J Appl Microbiol 89: 511-516.
25. Ludwig W, Strunk O, Westram R, Richter L, Meier H, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
26. Field D, Garrity G, Gray T, Morrison N, Selengut J, et al. (2008) The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 26: 541-547.
27. Zhang C, Zhang M, Wang S, Han R, Cao Y, et al. (2010) Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice. ISME J 4: 232-241.
28. Claesson MJ, O'Sullivan O, Wang Q, Nikkila J, Marchesi JR, et al. (2009) Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS One 4: e6669.
29. Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, et al. (2010) QIIME allows analysis of high-throughput community sequencing data. Nat Methods 7: 335-336.
30. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, et al. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-145.
31. Edgar RC, (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
32. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, et al. (2005) Diversity of the human intestinal microbial flora. Science 308: 1635-1638.
33. Wang M, Ahrne S, Jeppsson B, Molin G, (2005) Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes. FEMS Microbiol Ecol 54: 219-231.
34. Ventura M, Canchaya C, Tauch A, Chandra G, Fitzgerald GF, et al. (2007) Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol Mol Biol Rev 71: 495-548.
35. Werner JJ, Koren O, Hugenholtz P, DeSantis TZ, Walters WA, et al. (2012) Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys. ISME J 6: 94-103.
36. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65.
37. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, et al. (2012) Human gut microbiome viewed across age and geography. Nature 486: 222-227.
38. Samuel BS, Hansen EE, Manchester JK, Coutinho PM, Henrissat B, et al. (2007) Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut. Proc Natl Acad Sci U S A 104: 10643-10648.
39. Albers SV, Meyer BH, (2011) The archaeal cell envelope. Nat Rev Microbiol 9: 414-426.
40. Kembel SW, Wu M, Eisen JA, Green JL, (2012) Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance. PLoS Comput Biol 8: e1002743.
41. Ariefdjohan MW, Savaiano DA, Nakatsu CH, (2010) Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens. Nutr J 9: 23.
42. Smith B, Li N, Andersen AS, Slotved HC, Krogfelt KA, (2011) Optimising bacterial DNA extraction from faecal samples: comparison of three methods. Open Microbiol J 5: 14-17.
43. Claesson MJ, Cusack S, O'Sullivan O, Greene-Diniz R, de Weerd H, et al. (2011) Composition, variability, and temporal stability of the intestinal microbiota of the elderly. Proc Natl Acad Sci U S A 108Suppl 1: 4586-4591.
44. Lozupone C, Hamady M, Knight R, (2006) UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics 7: 371.
45. Fanning S, Hall LJ, Cronin M, Zomer A, MacSharry J, et al. (2012) Bifidobacterial surface-exopolysaccharide facilitates commensal-host interaction through immune modulation and pathogen protection. Proc Natl Acad Sci U S A 109: 2108-2113.