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

PLoS ONE - Tập 8 Số 7 - Trang e68739
Christian Milani1, Arancha Hevia2, Elena Foroni1, Sabrina Duranti1, Francesca Turroni3, Gabriele Andrea Lugli1, Borja Sánchez2, Rebeca Martín4, Miguel Gueimonde2, Douwe van Sinderen3, Abelardo Margollés2, Marco Ventura1
1Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy
2Departamento de Microbiologia y Bioquimica de Productos Lacteos IPLA – CSIC, Villaviciosa, Asturias, Spain
3Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland
4INRA, UMR 1319 MICALIS-Microbiologie de l’Alimentation au Service de la Santé humaine, Pôle Ecosystèmes: Interactions des bactéries commensales et probiotiques avec l’hôte, Domaine de Vilvert, Bât 440 R-2 78352, Jouy en Josas, France

Tóm tắt

Từ khóa


Tài liệu tham khảo

VB Young, 2012, The intestinal microbiota in health and disease, Curr Opin Gastroenterol, 28, 63, 10.1097/MOG.0b013e32834d61e9

JC Clemente, 2012, The impact of the gut microbiota on human health: an integrative view, Cell, 148, 1258, 10.1016/j.cell.2012.01.035

CP Tamboli, 2004, Dysbiosis in inflammatory bowel disease, Gut, 53, 1, 10.1136/gut.53.1.1

H Sokol, 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, 10.1073/pnas.0804812105

A Kassinen, 2007, The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects, Gastroenterology, 133, 24, 10.1053/j.gastro.2007.04.005

PJ Turnbaugh, 2006, An obesity-associated gut microbiome with increased capacity for energy harvest, Nature, 444, 1027, 10.1038/nature05414

NM Delzenne, 2011, Targeting gut microbiota in obesity: effects of prebiotics and probiotics, Nat Rev Endocrinol, 7, 639, 10.1038/nrendo.2011.126

MF de la Cochetiere, 2004, Early intestinal bacterial colonization and necrotizing enterocolitis in premature infants: the putative role of Clostridium, Pediatr Res, 56, 366, 10.1203/01.PDR.0000134251.45878.D5

JM Rothberg, 2011, An integrated semiconductor device enabling non-optical genome sequencing, Nature, 475, 348, 10.1038/nature10242

L Liu, 2012, Comparison of next-generation sequencing systems, J Biomed Biotechnol, 2012, 251364

MA Quail, 2012, A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers, BMC Genomics, 13, 341, 10.1186/1471-2164-13-341

E Yergeau, 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, 10.1128/AEM.02036-12

AS Whiteley, 2012, Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform, J Microbiol Methods, 91, 80, 10.1016/j.mimet.2012.07.008

S Junemann, 2012, Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing, PLoS One, 7, e41606, 10.1371/journal.pone.0041606

K Sim, 2012, Improved detection of bifidobacteria with optimised 16S rRNA-gene based pyrosequencing, PLoS One, 7, e32543, 10.1371/journal.pone.0032543

A Salonen, 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, 10.1016/j.mimet.2010.02.007

AF Andersson, 2008, Comparative analysis of human gut microbiota by barcoded pyrosequencing, PLoS One, 3, e2836, 10.1371/journal.pone.0002836

F Turroni, 2012, Diversity of bifidobacteria within the infant gut microbiota, PLoS One, 7, e36957, 10.1371/journal.pone.0036957

F Turroni, 2009, Exploring the diversity of the bifidobacterial population in the human intestinal tract, Appl Environ Microbiol, 75, 1534, 10.1128/AEM.02216-08

Fanaro S, Chierici R, Guerrini P, Vigi V (2003) Intestinal microflora in early infancy: composition and development. Acta Paediatr Suppl 91: 48–55.

CF Favier, 2002, Molecular monitoring of succession of bacterial communities in human neonates, Appl Environ Microbiol, 68, 219, 10.1128/AEM.68.1.219-226.2002

C Palmer, 2007, Development of the human infant intestinal microbiota, PLoS Biol, 5, e177, 10.1371/journal.pbio.0050177

JE Koenig, 2011, Succession of microbial consortia in the developing infant gut microbiome, Proc Natl Acad Sci U S A, 108, 4578, 10.1073/pnas.1000081107

MJ Kullen, 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, 10.1046/j.1365-2672.2000.01146.x

W Ludwig, 2004, ARB: a software environment for sequence data, Nucleic Acids Res, 32, 1363, 10.1093/nar/gkh293

D Field, 2008, The minimum information about a genome sequence (MIGS) specification, Nat Biotechnol, 26, 541, 10.1038/nbt1360

C Zhang, 2010, Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice, ISME J, 4, 232, 10.1038/ismej.2009.112

MJ Claesson, 2009, Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine, PLoS One, 4, e6669, 10.1371/journal.pone.0006669

JG Caporaso, 2010, QIIME allows analysis of high-throughput community sequencing data, Nat Methods, 7, 335, 10.1038/nmeth.f.303

JR Cole, 2009, The Ribosomal Database Project: improved alignments and new tools for rRNA analysis, Nucleic Acids Res, 37, D141, 10.1093/nar/gkn879

RC Edgar, 2010, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, 26, 2460, 10.1093/bioinformatics/btq461

PB Eckburg, 2005, Diversity of the human intestinal microbial flora, Science, 308, 1635, 10.1126/science.1110591

M Wang, 2005, Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes, FEMS Microbiol Ecol, 54, 219, 10.1016/j.femsec.2005.03.012

M Ventura, 2007, Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum, Microbiol Mol Biol Rev, 71, 495, 10.1128/MMBR.00005-07

JJ Werner, 2012, Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys, ISME J, 6, 94, 10.1038/ismej.2011.82

J Qin, 2010, A human gut microbial gene catalogue established by metagenomic sequencing, Nature, 464, 59, 10.1038/nature08821

T Yatsunenko, 2012, Human gut microbiome viewed across age and geography, Nature, 486, 222, 10.1038/nature11053

BS Samuel, 2007, Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut, Proc Natl Acad Sci U S A, 104, 10643, 10.1073/pnas.0704189104

SV Albers, 2011, The archaeal cell envelope, Nat Rev Microbiol, 9, 414, 10.1038/nrmicro2576

SW Kembel, 2012, Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance, PLoS Comput Biol, 8, e1002743, 10.1371/journal.pcbi.1002743

MW Ariefdjohan, 2010, Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens, Nutr J, 9, 23, 10.1186/1475-2891-9-23

B Smith, 2011, Optimising bacterial DNA extraction from faecal samples: comparison of three methods, Open Microbiol J, 5, 14, 10.2174/1874285801105010014

MJ Claesson, 2011, Composition, variability, and temporal stability of the intestinal microbiota of the elderly, Proc Natl Acad Sci U S A, 108, 4586, 10.1073/pnas.1000097107

C Lozupone, 2006, UniFrac–an online tool for comparing microbial community diversity in a phylogenetic context, BMC Bioinformatics, 7, 371, 10.1186/1471-2105-7-371

S Fanning, 2012, Bifidobacterial surface-exopolysaccharide facilitates commensal-host interaction through immune modulation and pathogen protection, Proc Natl Acad Sci U S A, 109, 2108, 10.1073/pnas.1115621109