Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

J. Gregory Caporaso; Christian L. Lauber; William A. Walters; Donna Berg-Lyons; James Huntley; Noah Fierer; Sarah M. Owens; Jason Betley; Louise Fraser; Markus Bauer; Niall Gormley; Jack A. Gilbert; Geoff Smith; Rob Knight

doi:10.1038/ismej.2012.8

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

J. Gregory Caporaso, Christian L. Lauber, William A. Walters, Donna Berg-Lyons, James Huntley, Noah Fierer, Sarah M. Owens, Jason Betley, Louise Fraser, Markus Bauer, Niall Gormley, Jack A. Gilbert, Geoff Smith, Rob Knight

Informatics, Computing, and Cyber Systems, School of

Research output: Contribution to journal › Article › peer-review

6600 Scopus citations

Abstract

DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600 Gb of paired-end 100 base reads in a ten-day run. Here we present a protocol for community amplicon sequencing on the HiSeq2000 and MiSeq Illumina platforms, and apply that protocol to sequence 24 microbial communities from host-associated and free-living environments. A critical question as more sequencing platforms become available is whether biological conclusions derived on one platform are consistent with what would be derived on a different platform. We show that the protocol developed for these instruments successfully recaptures known biological results, and additionally that biological conclusions are consistent across sequencing platforms (the HiSeq2000 versus the MiSeq) and across the sequenced regions of amplicons.

Original language	English (US)
Pages (from-to)	1621-1624
Number of pages	4
Journal	ISME Journal
Volume	6
Issue number	8
DOIs	https://doi.org/10.1038/ismej.2012.8
State	Published - Aug 2012

Keywords

QIIME
barcoded sequencing
illumine

ASJC Scopus subject areas

Microbiology
Ecology, Evolution, Behavior and Systematics

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10.1038/ismej.2012.8

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title = "Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms",

abstract = "DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600 Gb of paired-end 100 base reads in a ten-day run. Here we present a protocol for community amplicon sequencing on the HiSeq2000 and MiSeq Illumina platforms, and apply that protocol to sequence 24 microbial communities from host-associated and free-living environments. A critical question as more sequencing platforms become available is whether biological conclusions derived on one platform are consistent with what would be derived on a different platform. We show that the protocol developed for these instruments successfully recaptures known biological results, and additionally that biological conclusions are consistent across sequencing platforms (the HiSeq2000 versus the MiSeq) and across the sequenced regions of amplicons.",

keywords = "QIIME, barcoded sequencing, illumine",

author = "Caporaso, {J. Gregory} and Lauber, {Christian L.} and Walters, {William A.} and Donna Berg-Lyons and James Huntley and Noah Fierer and Owens, {Sarah M.} and Jason Betley and Louise Fraser and Markus Bauer and Niall Gormley and Gilbert, {Jack A.} and Geoff Smith and Rob Knight",

note = "Funding Information: We wish to thank the National Ecological Observatory Network (a project sponsored by the National Science Foundation and managed under cooperative agreement by NEON, Inc.) for donation of the soil samples; and Aurelie Breton and Joshua Quick for running the MiSeq instrument. This work was funded in part by Amazon Web Services, NIH, Crohn{\textquoteright}s and Colitis Foundation of America, The Bill and Melinda Gates Foundation, and the Howard Hughes Medical Institute.",

year = "2012",

month = aug,

doi = "10.1038/ismej.2012.8",

language = "English (US)",

volume = "6",

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AU - Caporaso, J. Gregory

AU - Lauber, Christian L.

AU - Walters, William A.

AU - Berg-Lyons, Donna

AU - Huntley, James

AU - Fierer, Noah

AU - Owens, Sarah M.

AU - Betley, Jason

AU - Fraser, Louise

AU - Bauer, Markus

AU - Gormley, Niall

AU - Gilbert, Jack A.

AU - Smith, Geoff

AU - Knight, Rob

N1 - Funding Information: We wish to thank the National Ecological Observatory Network (a project sponsored by the National Science Foundation and managed under cooperative agreement by NEON, Inc.) for donation of the soil samples; and Aurelie Breton and Joshua Quick for running the MiSeq instrument. This work was funded in part by Amazon Web Services, NIH, Crohn’s and Colitis Foundation of America, The Bill and Melinda Gates Foundation, and the Howard Hughes Medical Institute.

PY - 2012/8

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N2 - DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600 Gb of paired-end 100 base reads in a ten-day run. Here we present a protocol for community amplicon sequencing on the HiSeq2000 and MiSeq Illumina platforms, and apply that protocol to sequence 24 microbial communities from host-associated and free-living environments. A critical question as more sequencing platforms become available is whether biological conclusions derived on one platform are consistent with what would be derived on a different platform. We show that the protocol developed for these instruments successfully recaptures known biological results, and additionally that biological conclusions are consistent across sequencing platforms (the HiSeq2000 versus the MiSeq) and across the sequenced regions of amplicons.

AB - DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600 Gb of paired-end 100 base reads in a ten-day run. Here we present a protocol for community amplicon sequencing on the HiSeq2000 and MiSeq Illumina platforms, and apply that protocol to sequence 24 microbial communities from host-associated and free-living environments. A critical question as more sequencing platforms become available is whether biological conclusions derived on one platform are consistent with what would be derived on a different platform. We show that the protocol developed for these instruments successfully recaptures known biological results, and additionally that biological conclusions are consistent across sequencing platforms (the HiSeq2000 versus the MiSeq) and across the sequenced regions of amplicons.

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Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

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Keywords

ASJC Scopus subject areas

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