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

Assessing the distribution of 16S rRNA gene sequences within a biological sample represents the current state-of-the-art for determination of human gut microbiota composition. Advances in dissecting the microbial biodiversity of this ecosystem have very much been dependent on the development of nove...

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Published in	PloS one Vol. 8; no. 7; p. e68739
Main Authors	Milani, Christian, Hevia, Arancha, Foroni, Elena, Duranti, Sabrina, Turroni, Francesca, Lugli, Gabriele Andrea, Sanchez, Borja, Martín, Rebeca, Gueimonde, Miguel, van Sinderen, Douwe, Margolles, Abelardo, Ventura, Marco
Format	Journal Article
Language	English
Published	United States Public Library of Science 15.07.2013 Public Library of Science (PLoS)
Subjects	Analysis Animals Bacteria Biodiversity Bioinformatics Biological samples Biology Deoxyribonucleic acid DNA DNA sequencing Fecal microflora Feces Feces - microbiology Female Gastrointestinal diseases Gene sequencing Genes Health care Humans Intestinal microflora Laboratories Life Sciences Microbiota Microbiota (Symbiotic organisms) Microorganisms Nucleotide sequencing Phylogenetics Primers Rats RNA RNA, Ribosomal, 16S - chemistry RNA, Ribosomal, 16S - genetics rRNA 16S Sequence Analysis, DNA - methods
Online Access	Get full text
ISSN	1932-6203 1932-6203
DOI	10.1371/journal.pone.0068739

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Abstract	Assessing the distribution of 16S rRNA gene sequences within a biological sample represents the current state-of-the-art for determination of human gut microbiota composition. Advances in dissecting the microbial biodiversity of this ecosystem have very much been dependent on the development of novel high-throughput DNA sequencing technologies, like the Ion Torrent. However, the precise representation of this bacterial community may be affected by the protocols used for DNA extraction as well as by the PCR primers employed in the amplification reaction. Here, we describe an optimized protocol for 16S rRNA gene-based profiling of the fecal microbiota.
AbstractList	Assessing the distribution of 16S rRNA gene sequences within a biological sample represents the current state-of-the-art for determination of human gut microbiota composition. Advances in dissecting the microbial biodiversity of this ecosystem have very much been dependent on the development of novel high-throughput DNA sequencing technologies, like the Ion Torrent. However, the precise representation of this bacterial community may be affected by the protocols used for DNA extraction as well as by the PCR primers employed in the amplification reaction. Here, we describe an optimized protocol for 16S rRNA gene-based profiling of the fecal microbiota. Assessing the distribution of 16S rRNA gene sequences within a biological sample represents the current state-of-the-art for determination of human gut microbiota composition. Advances in dissecting the microbial biodiversity of this ecosystem have very much been dependent on the development of novel high-throughput DNA sequencing technologies, like the Ion Torrent. However, the precise representation of this bacterial community may be affected by the protocols used for DNA extraction as well as by the PCR primers employed in the amplification reaction. Here, we describe an optimized protocol for 16S rRNA gene-based profiling of the fecal microbiota.Assessing the distribution of 16S rRNA gene sequences within a biological sample represents the current state-of-the-art for determination of human gut microbiota composition. Advances in dissecting the microbial biodiversity of this ecosystem have very much been dependent on the development of novel high-throughput DNA sequencing technologies, like the Ion Torrent. However, the precise representation of this bacterial community may be affected by the protocols used for DNA extraction as well as by the PCR primers employed in the amplification reaction. Here, we describe an optimized protocol for 16S rRNA gene-based profiling of the fecal microbiota.
Audience	Academic
Author	van Sinderen, Douwe Sanchez, Borja Margolles, Abelardo Milani, Christian Duranti, Sabrina Foroni, Elena Turroni, Francesca Lugli, Gabriele Andrea Ventura, Marco Martín, Rebeca Gueimonde, Miguel Hevia, Arancha
AuthorAffiliation	3 Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland University of Glasgow, United Kingdom 1 Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy 4 INRA, 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 2 Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA – CSIC, Villaviciosa, Asturias, Spain
AuthorAffiliation_xml	– name: 1 Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy – name: University of Glasgow, United Kingdom – name: 2 Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA – CSIC, Villaviciosa, Asturias, Spain – name: 4 INRA, 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 – name: 3 Alimentary Pharmabiotic Centre and Department of Microbiology, Bioscience Institute, National University of Ireland, Western Road, Cork, Ireland
Author_xml	– sequence: 1 givenname: Christian surname: Milani fullname: Milani, Christian – sequence: 2 givenname: Arancha surname: Hevia fullname: Hevia, Arancha – sequence: 3 givenname: Elena surname: Foroni fullname: Foroni, Elena – sequence: 4 givenname: Sabrina surname: Duranti fullname: Duranti, Sabrina – sequence: 5 givenname: Francesca surname: Turroni fullname: Turroni, Francesca – sequence: 6 givenname: Gabriele Andrea surname: Lugli fullname: Lugli, Gabriele Andrea – sequence: 7 givenname: Borja surname: Sanchez fullname: Sanchez, Borja – sequence: 8 givenname: Rebeca surname: Martín fullname: Martín, Rebeca – sequence: 9 givenname: Miguel surname: Gueimonde fullname: Gueimonde, Miguel – sequence: 10 givenname: Douwe surname: van Sinderen fullname: van Sinderen, Douwe – sequence: 11 givenname: Abelardo surname: Margolles fullname: Margolles, Abelardo – sequence: 12 givenname: Marco surname: Ventura fullname: Ventura, Marco
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/23869230$$D View this record in MEDLINE/PubMed https://hal.science/hal-01190517$$DView record in HAL
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Cites_doi	10.1128/AEM.02036-12 10.1093/nar/gkn879 10.1038/nrmicro2576 10.1371/journal.pbio.0050177 10.1186/1471-2105-7-371 10.1073/pnas.0804812105 10.1073/pnas.0704189104 10.1093/nar/gkh293 10.1038/ismej.2011.82 10.1016/j.mimet.2012.07.008 10.1038/nature11053 10.1016/j.femsec.2005.03.012 10.1073/pnas.1115621109 10.1371/journal.pcbi.1002743 10.1073/pnas.1000081107 10.1186/1471-2164-13-341 10.1128/AEM.68.1.219-226.2002 10.1046/j.1365-2672.2000.01146.x 10.1038/nmeth.f.303 10.1016/j.cell.2012.01.035 10.1038/nrendo.2011.126 10.2174/1874285801105010014 10.1136/gut.53.1.1 10.1371/journal.pone.0006669 10.1097/MOG.0b013e32834d61e9 10.1371/journal.pone.0002836 10.1128/MMBR.00005-07 10.1038/nature10242 10.1038/ismej.2009.112 10.1038/nbt1360 10.1053/j.gastro.2007.04.005 10.1111/j.1651-2227.2003.tb00646.x 10.1073/pnas.1000097107 10.1038/nature08821 10.1016/j.mimet.2010.02.007 10.1371/journal.pone.0032543 10.1371/journal.pone.0041606 10.1371/journal.pone.0036957 10.1186/1475-2891-9-23 10.1038/nature05414 10.1126/science.1110591 10.1128/AEM.02216-08 10.1093/bioinformatics/btq461 10.1203/01.PDR.0000134251.45878.D5
ContentType	Journal Article
Copyright	COPYRIGHT 2013 Public Library of Science 2013 Milani et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. Distributed under a Creative Commons Attribution 4.0 International License 2013 Milani et al 2013 Milani et al
Copyright_xml	– notice: COPYRIGHT 2013 Public Library of Science – notice: 2013 Milani et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. – notice: Distributed under a Creative Commons Attribution 4.0 International License – notice: 2013 Milani et al 2013 Milani et al
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Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23 Conceived and designed the experiments: MV AM DV MG BS RM. Performed the experiments: CM AH EF SD FT GL. Analyzed the data: MV AM. Contributed reagents/materials/analysis tools: MV AM. Wrote the paper: MV AM DV. Competing Interests: GenProbio srl provided the financial support of the Laboratory of Probiogenomics for this study. There are no patents, products in development or marketed products to declare. This does not alter the authors’ adherence to all the PLOS ONE policies on sharing data and materials, as detailed online in the guide for authors.
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References	MW Ariefdjohan (ref41) 2010; 9 JM Rothberg (ref9) 2011; 475 AS Whiteley (ref13) 2012; 91 F Turroni (ref19) 2009; 75 MJ Claesson (ref28) 2009; 4 B Smith (ref42) 2011; 5 NM Delzenne (ref7) 2011; 7 MJ Kullen (ref24) 2000; 89 MF de la Cochetiere (ref8) 2004; 56 BS Samuel (ref38) 2007; 104 S Fanning (ref45) 2012; 109 PJ Turnbaugh (ref6) 2006; 444 S Junemann (ref14) 2012; 7 E Yergeau (ref12) 2012; 78 SV Albers (ref39) 2011; 9 C Palmer (ref22) 2007; 5 K Sim (ref15) 2012; 7 JC Clemente (ref2) 2012; 148 H Sokol (ref4) 2008; 105 T Yatsunenko (ref37) 2012; 486 ref20 D Field (ref26) 2008; 26 PB Eckburg (ref32) 2005; 308 M Ventura (ref34) 2007; 71 JJ Werner (ref35) 2012; 6 CF Favier (ref21) 2002; 68 CP Tamboli (ref3) 2004; 53 MA Quail (ref11) 2012; 13 SW Kembel (ref40) 2012; 8 A Salonen (ref16) 2010; 81 F Turroni (ref18) 2012; 7 RC Edgar (ref31) 2010; 26 M Wang (ref33) 2005; 54 AF Andersson (ref17) 2008; 3 A Kassinen (ref5) 2007; 133 VB Young (ref1) 2012; 28 JE Koenig (ref23) 2011; 108 JG Caporaso (ref29) 2010; 7 JR Cole (ref30) 2009; 37 L Liu (ref10) 2012; 2012 C Zhang (ref27) 2010; 4 C Lozupone (ref44) 2006; 7 MJ Claesson (ref43) 2011; 108 W Ludwig (ref25) 2004; 32 J Qin (ref36) 2010; 464 22424233 - Cell. 2012 Mar 16;148(6):1258-70 20709691 - Bioinformatics. 2010 Oct 1;26(19):2460-1 17594176 - PLoS Biol. 2007 Jul;5(7):e177 20571116 - Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4586-91 17631127 - Gastroenterology. 2007 Jul;133(1):24-33 22606315 - PLoS One. 2012;7(5):e36957 14599042 - Acta Paediatr Suppl. 2003 Sep;91(441):48-55 19693277 - PLoS One. 2009;4(8):e6669 20171997 - J Microbiol Methods. 2010 May;81(2):127-34 14684564 - Gut. 2004 Jan;53(1):1-4 22870235 - PLoS One. 2012;7(8):e41606 20383131 - Nat Methods. 2010 May;7(5):335-6 19865183 - ISME J. 2010 Feb;4(2):232-41 22849830 - J Microbiol Methods. 2012 Oct;91(1):80-8 11772630 - Appl Environ Microbiol. 2002 Jan;68(1):219-26 21826100 - Nat Rev Endocrinol. 2011 Nov;7(11):639-46 15831718 - Science. 2005 Jun 10;308(5728):1635-8 17804669 - Microbiol Mol Biol Rev. 2007 Sep;71(3):495-548 22923391 - Appl Environ Microbiol. 2012 Nov;78(21):7626-37 15201403 - Pediatr Res. 2004 Sep;56(3):366-70 21716311 - ISME J. 2012 Jan;6(1):94-103 18936492 - Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16731-6 14985472 - Nucleic Acids Res. 2004;32(4):1363-71 22080827 - Curr Opin Gastroenterol. 2012 Jan;28(1):63-9 19004872 - Nucleic Acids Res. 2009 Jan;37(Database issue):D141-5 22829749 - J Biomed Biotechnol. 2012;2012:251364 17563350 - Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10643-8 18464787 - Nat Biotechnol. 2008 May;26(5):541-7 17183312 - Nature. 2006 Dec 21;444(7122):1027-31 20668239 - Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4578-85 21572458 - Nat Rev Microbiol. 2011 Jun;9(6):414-26 22470420 - PLoS One. 2012;7(3):e32543 22699611 - Nature. 2012 Jun 14;486(7402):222-7 23133348 - PLoS Comput Biol. 2012;8(10):e1002743 20492702 - Nutr J. 2010;9:23 22308390 - Proc Natl Acad Sci U S A. 2012 Feb 7;109(6):2108-13 19168652 - Appl Environ Microbiol. 2009 Mar;75(6):1534-45 20203603 - Nature. 2010 Mar 4;464(7285):59-65 16893466 - BMC Bioinformatics. 2006;7:371 21643498 - Open Microbiol J. 2011;5:14-7 18665274 - PLoS One. 2008;3(7):e2836 22827831 - BMC Genomics. 2012;13:341 21776081 - Nature. 2011 Jul 21;475(7356):348-52 11021584 - J Appl Microbiol. 2000 Sep;89(3):511-6 16332321 - FEMS Microbiol Ecol. 2005 Oct 1;54(2):219-31
References_xml	– volume: 78 start-page: 7626 year: 2012 ident: ref12 article-title: Next-generation sequencing of microbial communities in the Athabasca River and its tributaries in relation to oil sands mining activities publication-title: Appl Environ Microbiol doi: 10.1128/AEM.02036-12 – volume: 37 start-page: D141 year: 2009 ident: ref30 article-title: The Ribosomal Database Project: improved alignments and new tools for rRNA analysis publication-title: Nucleic Acids Res doi: 10.1093/nar/gkn879 – volume: 9 start-page: 414 year: 2011 ident: ref39 article-title: The archaeal cell envelope publication-title: Nat Rev Microbiol doi: 10.1038/nrmicro2576 – volume: 5 start-page: e177 year: 2007 ident: ref22 article-title: Development of the human infant intestinal microbiota publication-title: PLoS Biol doi: 10.1371/journal.pbio.0050177 – volume: 7 start-page: 371 year: 2006 ident: ref44 article-title: UniFrac–an online tool for comparing microbial community diversity in a phylogenetic context publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-7-371 – volume: 105 start-page: 16731 year: 2008 ident: ref4 article-title: Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.0804812105 – volume: 104 start-page: 10643 year: 2007 ident: ref38 article-title: Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.0704189104 – volume: 32 start-page: 1363 year: 2004 ident: ref25 article-title: ARB: a software environment for sequence data publication-title: Nucleic Acids Res doi: 10.1093/nar/gkh293 – volume: 6 start-page: 94 year: 2012 ident: ref35 article-title: Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys publication-title: ISME J doi: 10.1038/ismej.2011.82 – volume: 91 start-page: 80 year: 2012 ident: ref13 article-title: Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform publication-title: J Microbiol Methods doi: 10.1016/j.mimet.2012.07.008 – volume: 486 start-page: 222 year: 2012 ident: ref37 article-title: Human gut microbiome viewed across age and geography publication-title: Nature doi: 10.1038/nature11053 – volume: 54 start-page: 219 year: 2005 ident: ref33 article-title: Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes publication-title: FEMS Microbiol Ecol doi: 10.1016/j.femsec.2005.03.012 – volume: 109 start-page: 2108 year: 2012 ident: ref45 article-title: Bifidobacterial surface-exopolysaccharide facilitates commensal-host interaction through immune modulation and pathogen protection publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.1115621109 – volume: 8 start-page: e1002743 year: 2012 ident: ref40 article-title: Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance publication-title: PLoS Comput Biol doi: 10.1371/journal.pcbi.1002743 – volume: 108 start-page: 4578 year: 2011 ident: ref23 article-title: Succession of microbial consortia in the developing infant gut microbiome publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.1000081107 – volume: 13 start-page: 341 year: 2012 ident: ref11 article-title: A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers publication-title: BMC Genomics doi: 10.1186/1471-2164-13-341 – volume: 68 start-page: 219 year: 2002 ident: ref21 article-title: Molecular monitoring of succession of bacterial communities in human neonates publication-title: Appl Environ Microbiol doi: 10.1128/AEM.68.1.219-226.2002 – volume: 2012 start-page: 251364 year: 2012 ident: ref10 article-title: Comparison of next-generation sequencing systems publication-title: J Biomed Biotechnol – volume: 89 start-page: 511 year: 2000 ident: ref24 article-title: 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 publication-title: J Appl Microbiol doi: 10.1046/j.1365-2672.2000.01146.x – volume: 7 start-page: 335 year: 2010 ident: ref29 article-title: QIIME allows analysis of high-throughput community sequencing data publication-title: Nat Methods doi: 10.1038/nmeth.f.303 – volume: 148 start-page: 1258 year: 2012 ident: ref2 article-title: The impact of the gut microbiota on human health: an integrative view publication-title: Cell doi: 10.1016/j.cell.2012.01.035 – volume: 7 start-page: 639 year: 2011 ident: ref7 article-title: Targeting gut microbiota in obesity: effects of prebiotics and probiotics publication-title: Nat Rev Endocrinol doi: 10.1038/nrendo.2011.126 – volume: 5 start-page: 14 year: 2011 ident: ref42 article-title: Optimising bacterial DNA extraction from faecal samples: comparison of three methods publication-title: Open Microbiol J doi: 10.2174/1874285801105010014 – volume: 53 start-page: 1 year: 2004 ident: ref3 article-title: Dysbiosis in inflammatory bowel disease publication-title: Gut doi: 10.1136/gut.53.1.1 – volume: 4 start-page: e6669 year: 2009 ident: ref28 article-title: Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine publication-title: PLoS One doi: 10.1371/journal.pone.0006669 – volume: 28 start-page: 63 year: 2012 ident: ref1 article-title: The intestinal microbiota in health and disease publication-title: Curr Opin Gastroenterol doi: 10.1097/MOG.0b013e32834d61e9 – volume: 3 start-page: e2836 year: 2008 ident: ref17 article-title: Comparative analysis of human gut microbiota by barcoded pyrosequencing publication-title: PLoS One doi: 10.1371/journal.pone.0002836 – volume: 71 start-page: 495 year: 2007 ident: ref34 article-title: Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum publication-title: Microbiol Mol Biol Rev doi: 10.1128/MMBR.00005-07 – volume: 475 start-page: 348 year: 2011 ident: ref9 article-title: An integrated semiconductor device enabling non-optical genome sequencing publication-title: Nature doi: 10.1038/nature10242 – volume: 4 start-page: 232 year: 2010 ident: ref27 article-title: Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice publication-title: ISME J doi: 10.1038/ismej.2009.112 – volume: 26 start-page: 541 year: 2008 ident: ref26 article-title: The minimum information about a genome sequence (MIGS) specification publication-title: Nat Biotechnol doi: 10.1038/nbt1360 – volume: 133 start-page: 24 year: 2007 ident: ref5 article-title: The fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjects publication-title: Gastroenterology doi: 10.1053/j.gastro.2007.04.005 – ident: ref20 doi: 10.1111/j.1651-2227.2003.tb00646.x – volume: 108 start-page: 4586 year: 2011 ident: ref43 article-title: Composition, variability, and temporal stability of the intestinal microbiota of the elderly publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.1000097107 – volume: 464 start-page: 59 year: 2010 ident: ref36 article-title: A human gut microbial gene catalogue established by metagenomic sequencing publication-title: Nature doi: 10.1038/nature08821 – volume: 81 start-page: 127 year: 2010 ident: ref16 article-title: Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: effective recovery of bacterial and archaeal DNA using mechanical cell lysis publication-title: J Microbiol Methods doi: 10.1016/j.mimet.2010.02.007 – volume: 7 start-page: e32543 year: 2012 ident: ref15 article-title: Improved detection of bifidobacteria with optimised 16S rRNA-gene based pyrosequencing publication-title: PLoS One doi: 10.1371/journal.pone.0032543 – volume: 7 start-page: e41606 year: 2012 ident: ref14 article-title: Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing publication-title: PLoS One doi: 10.1371/journal.pone.0041606 – volume: 7 start-page: e36957 year: 2012 ident: ref18 article-title: Diversity of bifidobacteria within the infant gut microbiota publication-title: PLoS One doi: 10.1371/journal.pone.0036957 – volume: 9 start-page: 23 year: 2010 ident: ref41 article-title: Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens publication-title: Nutr J doi: 10.1186/1475-2891-9-23 – volume: 444 start-page: 1027 year: 2006 ident: ref6 article-title: An obesity-associated gut microbiome with increased capacity for energy harvest publication-title: Nature doi: 10.1038/nature05414 – volume: 308 start-page: 1635 year: 2005 ident: ref32 article-title: Diversity of the human intestinal microbial flora publication-title: Science doi: 10.1126/science.1110591 – volume: 75 start-page: 1534 year: 2009 ident: ref19 article-title: Exploring the diversity of the bifidobacterial population in the human intestinal tract publication-title: Appl Environ Microbiol doi: 10.1128/AEM.02216-08 – volume: 26 start-page: 2460 year: 2010 ident: ref31 article-title: Search and clustering orders of magnitude faster than BLAST publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq461 – volume: 56 start-page: 366 year: 2004 ident: ref8 article-title: Early intestinal bacterial colonization and necrotizing enterocolitis in premature infants: the putative role of Clostridium publication-title: Pediatr Res doi: 10.1203/01.PDR.0000134251.45878.D5 – reference: 17631127 - Gastroenterology. 2007 Jul;133(1):24-33 – reference: 17804669 - Microbiol Mol Biol Rev. 2007 Sep;71(3):495-548 – reference: 22606315 - PLoS One. 2012;7(5):e36957 – reference: 14599042 - Acta Paediatr Suppl. 2003 Sep;91(441):48-55 – reference: 15831718 - Science. 2005 Jun 10;308(5728):1635-8 – reference: 16893466 - BMC Bioinformatics. 2006;7:371 – reference: 20709691 - Bioinformatics. 2010 Oct 1;26(19):2460-1 – reference: 21826100 - Nat Rev Endocrinol. 2011 Nov;7(11):639-46 – reference: 22308390 - Proc Natl Acad Sci U S A. 2012 Feb 7;109(6):2108-13 – reference: 22827831 - BMC Genomics. 2012;13:341 – reference: 20383131 - Nat Methods. 2010 May;7(5):335-6 – reference: 21643498 - Open Microbiol J. 2011;5:14-7 – reference: 18665274 - PLoS One. 2008;3(7):e2836 – reference: 19693277 - PLoS One. 2009;4(8):e6669 – reference: 20492702 - Nutr J. 2010;9:23 – reference: 15201403 - Pediatr Res. 2004 Sep;56(3):366-70 – reference: 17183312 - Nature. 2006 Dec 21;444(7122):1027-31 – reference: 21776081 - Nature. 2011 Jul 21;475(7356):348-52 – reference: 19168652 - Appl Environ Microbiol. 2009 Mar;75(6):1534-45 – reference: 20668239 - Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4578-85 – reference: 14985472 - Nucleic Acids Res. 2004;32(4):1363-71 – reference: 22470420 - PLoS One. 2012;7(3):e32543 – reference: 11021584 - J Appl Microbiol. 2000 Sep;89(3):511-6 – reference: 22849830 - J Microbiol Methods. 2012 Oct;91(1):80-8 – reference: 18936492 - Proc Natl Acad Sci U S A. 2008 Oct 28;105(43):16731-6 – reference: 20171997 - J Microbiol Methods. 2010 May;81(2):127-34 – reference: 22829749 - J Biomed Biotechnol. 2012;2012:251364 – reference: 22870235 - PLoS One. 2012;7(8):e41606 – reference: 19865183 - ISME J. 2010 Feb;4(2):232-41 – reference: 22699611 - Nature. 2012 Jun 14;486(7402):222-7 – reference: 19004872 - Nucleic Acids Res. 2009 Jan;37(Database issue):D141-5 – reference: 16332321 - FEMS Microbiol Ecol. 2005 Oct 1;54(2):219-31 – reference: 22923391 - Appl Environ Microbiol. 2012 Nov;78(21):7626-37 – reference: 17594176 - PLoS Biol. 2007 Jul;5(7):e177 – reference: 21716311 - ISME J. 2012 Jan;6(1):94-103 – reference: 11772630 - Appl Environ Microbiol. 2002 Jan;68(1):219-26 – reference: 22424233 - Cell. 2012 Mar 16;148(6):1258-70 – reference: 17563350 - Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10643-8 – reference: 22080827 - Curr Opin Gastroenterol. 2012 Jan;28(1):63-9 – reference: 20203603 - Nature. 2010 Mar 4;464(7285):59-65 – reference: 23133348 - PLoS Comput Biol. 2012;8(10):e1002743 – reference: 18464787 - Nat Biotechnol. 2008 May;26(5):541-7 – reference: 14684564 - Gut. 2004 Jan;53(1):1-4 – reference: 21572458 - Nat Rev Microbiol. 2011 Jun;9(6):414-26 – reference: 20571116 - Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4586-91
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Snippet	Assessing the distribution of 16S rRNA gene sequences within a biological sample represents the current state-of-the-art for determination of human gut...
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SubjectTerms	Analysis Animals Bacteria Biodiversity Bioinformatics Biological samples Biology Deoxyribonucleic acid DNA DNA sequencing Fecal microflora Feces Feces - microbiology Female Gastrointestinal diseases Gene sequencing Genes Health care Humans Intestinal microflora Laboratories Life Sciences Microbiota Microbiota (Symbiotic organisms) Microorganisms Nucleotide sequencing Phylogenetics Primers Rats RNA RNA, Ribosomal, 16S - chemistry RNA, Ribosomal, 16S - genetics rRNA 16S Sequence Analysis, DNA - methods
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Title	Assessing the Fecal Microbiota: An Optimized Ion Torrent 16S rRNA Gene-Based Analysis Protocol
URI	https://www.ncbi.nlm.nih.gov/pubmed/23869230 https://www.proquest.com/docview/1427353711 https://www.proquest.com/docview/1411631950 https://hal.science/hal-01190517 https://pubmed.ncbi.nlm.nih.gov/PMC3711900 https://doaj.org/article/80c5b2b1d73044a6ac3df96ae56b88a0 http://dx.doi.org/10.1371/journal.pone.0068739
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