Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles

Maria T. Nelson; Christopher E. Pope; Robyn L. Marsh; Daniel J. Wolter; Eli J. Weiss; Kyle R. Hager; Anh T. Vo; Mitchell J. Brittnacher; Matthew C. Radey; Hillary S. Hayden; Alexander Eng; Samuel I. Miller; Elhanan Borenstein; Lucas R. Hoffman

doi:10.1016/j.celrep.2019.01.091

Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles

Maria T. Nelson, Christopher E. Pope, Robyn L. Marsh, Daniel J. Wolter, Eli J. Weiss, Kyle R. Hager, Anh T. Vo, Mitchell J. Brittnacher, Matthew C. Radey, Hillary S. Hayden, Alexander Eng, Samuel I. Miller, Elhanan Borenstein, Lucas R. Hoffman

School of Computer Sciences

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

Abstract

Nelson et al. describe a method for reducing both human cellular DNA and extracellular DNA (human and bacterial) in a complex respiratory sample using hypotonic lysis and endonuclease digestion. This method increases effective microbial sequencing depth and minimizes bias introduced into subsequent phylogenetic analysis by bacterial extracellular DNA.

Original language	English
Pages (from-to)	2227-2240.e5
Journal	Cell Reports
Volume	26
Issue number	8
DOIs	https://doi.org/10.1016/j.celrep.2019.01.091
State	Published - 19 Feb 2019

Keywords

clinical samples
cystic fibrosis
extracellular DNA
human DNA
infection samples
metagenome
microbiome
microbiota
polymicrobial infections
sputum

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10.1016/j.celrep.2019.01.091

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Nelson, M. T., Pope, C. E., Marsh, R. L., Wolter, D. J., Weiss, E. J., Hager, K. R., Vo, A. T., Brittnacher, M. J., Radey, M. C., Hayden, H. S., Eng, A., Miller, S. I., Borenstein, E., & Hoffman, L. R. (2019). Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles. Cell Reports, 26(8), 2227-2240.e5. https://doi.org/10.1016/j.celrep.2019.01.091

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title = "Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles",

abstract = "Nelson et al. describe a method for reducing both human cellular DNA and extracellular DNA (human and bacterial) in a complex respiratory sample using hypotonic lysis and endonuclease digestion. This method increases effective microbial sequencing depth and minimizes bias introduced into subsequent phylogenetic analysis by bacterial extracellular DNA.",

keywords = "clinical samples, cystic fibrosis, extracellular DNA, human DNA, infection samples, metagenome, microbiome, microbiota, polymicrobial infections, sputum",

author = "Nelson, {Maria T.} and Pope, {Christopher E.} and Marsh, {Robyn L.} and Wolter, {Daniel J.} and Weiss, {Eli J.} and Hager, {Kyle R.} and Vo, {Anh T.} and Brittnacher, {Mitchell J.} and Radey, {Matthew C.} and Hayden, {Hillary S.} and Alexander Eng and Miller, {Samuel I.} and Elhanan Borenstein and Hoffman, {Lucas R.}",

note = "Publisher Copyright: {\textcopyright} 2019 The Author(s)",

year = "2019",

month = feb,

day = "19",

doi = "10.1016/j.celrep.2019.01.091",

language = "אנגלית",

volume = "26",

pages = "2227--2240.e5",

journal = "Cell Reports",

issn = "2211-1247",

publisher = "Cell Press",

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Nelson, MT, Pope, CE, Marsh, RL, Wolter, DJ, Weiss, EJ, Hager, KR, Vo, AT, Brittnacher, MJ, Radey, MC, Hayden, HS, Eng, A, Miller, SI, Borenstein, E & Hoffman, LR 2019, 'Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles', Cell Reports, vol. 26, no. 8, pp. 2227-2240.e5. https://doi.org/10.1016/j.celrep.2019.01.091

TY - JOUR

T1 - Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles

AU - Nelson, Maria T.

AU - Pope, Christopher E.

AU - Marsh, Robyn L.

AU - Wolter, Daniel J.

AU - Weiss, Eli J.

AU - Hager, Kyle R.

AU - Vo, Anh T.

AU - Brittnacher, Mitchell J.

AU - Radey, Matthew C.

AU - Hayden, Hillary S.

AU - Eng, Alexander

AU - Miller, Samuel I.

AU - Borenstein, Elhanan

AU - Hoffman, Lucas R.

PY - 2019/2/19

Y1 - 2019/2/19

N2 - Nelson et al. describe a method for reducing both human cellular DNA and extracellular DNA (human and bacterial) in a complex respiratory sample using hypotonic lysis and endonuclease digestion. This method increases effective microbial sequencing depth and minimizes bias introduced into subsequent phylogenetic analysis by bacterial extracellular DNA.

AB - Nelson et al. describe a method for reducing both human cellular DNA and extracellular DNA (human and bacterial) in a complex respiratory sample using hypotonic lysis and endonuclease digestion. This method increases effective microbial sequencing depth and minimizes bias introduced into subsequent phylogenetic analysis by bacterial extracellular DNA.

KW - clinical samples

KW - cystic fibrosis

KW - extracellular DNA

KW - human DNA

KW - infection samples

KW - metagenome

KW - microbiome

KW - microbiota

KW - polymicrobial infections

KW - sputum

UR - http://www.scopus.com/inward/record.url?scp=85061317990&partnerID=8YFLogxK

U2 - 10.1016/j.celrep.2019.01.091

DO - 10.1016/j.celrep.2019.01.091

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AN - SCOPUS:85061317990

VL - 26

SP - 2227-2240.e5

JO - Cell Reports

JF - Cell Reports

SN - 2211-1247

IS - 8

ER -

Human and Extracellular DNA Depletion for Metagenomic Analysis of Complex Clinical Infection Samples Yields Optimized Viable Microbiome Profiles

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