Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics
Abstract
High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. For this study, we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (~100–1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities.more »
- Authors:
-
[1];
- Univ. of Queensland, Brisbane (Australia). Australian Centre for Ecogenomics and School of Chemistry and Molecular Biosciences
- Univ. of Technology Sydney, NSW (Australia). Climate Change Cluster
- ETH Zurich (Switzerland). Dept. of Civil, Environmental, and Geomatic Engineering
- Univ. of Queensland, Brisbane (Australia). Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, and Advanced Water Management Centre
- Univ. of Queensland, Brisbane (Australia). Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences and Inst. for Molecular Bioscience
- Publication Date:
- Research Org.:
- Univ. of Arizona, Tucson, AZ (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); Gordon and Betty Moore Foundation; Australian Research Council (ARC)
- OSTI Identifier:
- 1435770
- Grant/Contract Number:
- SC0004632; GBMF3801; FL150100038; 160100248
- Resource Type:
- Accepted Manuscript
- Journal Name:
- PeerJ
- Additional Journal Information:
- Journal Volume: 4; Journal ID: ISSN 2167-8359
- Publisher:
- PeerJ Inc.
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Nextera XT; 100 fg; Low input DNA library; Picogram; Reagent contamination; Low biomass; Low volume; Microscale metagenomics; Marine microheterogeneity; Illumina
Citation Formats
Rinke, Christian, Low, Serene, Woodcroft, Ben J., Raina, Jean-Baptiste, Skarshewski, Adam, Le, Xuyen H., Butler, Margaret K., Stocker, Roman, Seymour, Justin, Tyson, Gene W., and Hugenholtz, Philip. Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics. United States: N. p., 2016.
Web. doi:10.7717/peerj.2486.
Rinke, Christian, Low, Serene, Woodcroft, Ben J., Raina, Jean-Baptiste, Skarshewski, Adam, Le, Xuyen H., Butler, Margaret K., Stocker, Roman, Seymour, Justin, Tyson, Gene W., & Hugenholtz, Philip. Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics. United States. https://doi.org/10.7717/peerj.2486
Rinke, Christian, Low, Serene, Woodcroft, Ben J., Raina, Jean-Baptiste, Skarshewski, Adam, Le, Xuyen H., Butler, Margaret K., Stocker, Roman, Seymour, Justin, Tyson, Gene W., and Hugenholtz, Philip. Thu .
"Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics". United States. https://doi.org/10.7717/peerj.2486. https://www.osti.gov/servlets/purl/1435770.
@article{osti_1435770,
title = {Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics},
author = {Rinke, Christian and Low, Serene and Woodcroft, Ben J. and Raina, Jean-Baptiste and Skarshewski, Adam and Le, Xuyen H. and Butler, Margaret K. and Stocker, Roman and Seymour, Justin and Tyson, Gene W. and Hugenholtz, Philip},
abstractNote = {High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. For this study, we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (~100–1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.},
doi = {10.7717/peerj.2486},
journal = {PeerJ},
number = ,
volume = 4,
place = {United States},
year = {Thu Sep 22 00:00:00 EDT 2016},
month = {Thu Sep 22 00:00:00 EDT 2016}
}
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Works referenced in this record:
Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community
journal, October 2015
- Bowers, Robert M.; Clum, Alicia; Tice, Hope
- BMC Genomics, Vol. 16, Issue 1
Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples
journal, November 2014
- Strong, Michael J.; Xu, Guorong; Morici, Lisa
- PLoS Pathogens, Vol. 10, Issue 11
Ecology and Physics of Bacterial Chemotaxis in the Ocean
journal, November 2012
- Stocker, Roman; Seymour, Justin R.
- Microbiology and Molecular Biology Reviews, Vol. 76, Issue 4
Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments
journal, August 2014
- Smith, Erin N.; Jepsen, Kristen; Khosroheidari, Mahdieh
- Genome Biology, Vol. 15, Issue 7
Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition
journal, January 2010
- Adey, Andrew; Morrison, Hilary G.; (no last name), Asan
- Genome Biology, Vol. 11, Issue 12
Tn5/IS50 target recognition
journal, September 1998
- Goryshin, I. Y.; Miller, J. A.; Kil, Y. V.
- Proceedings of the National Academy of Sciences, Vol. 95, Issue 18
Microbial Metagenomics: Beyond the Genome
journal, January 2011
- Gilbert, Jack A.; Dupont, Christopher L.
- Annual Review of Marine Science, Vol. 3, Issue 1
Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
journal, October 2011
- Kircher, Martin; Sawyer, Susanna; Meyer, Matthias
- Nucleic Acids Research, Vol. 40, Issue 1
UniRef: comprehensive and non-redundant UniProt reference clusters
journal, March 2007
- Suzek, B. E.; Huang, H.; McGarvey, P.
- Bioinformatics, Vol. 23, Issue 10
Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method: Linker amplification for ultra-low DNA samples
journal, June 2012
- Duhaime, Melissa B.; Deng, Li; Poulos, Bonnie T.
- Environmental Microbiology, Vol. 14, Issue 9
Archaea on Human Skin
journal, June 2013
- Probst, Alexander J.; Auerbach, Anna K.; Moissl-Eichinger, Christine
- PLoS ONE, Vol. 8, Issue 6
Taxonomic binning of metagenome samples generated by next-generation sequencing technologies
journal, July 2012
- Droge, J.; McHardy, A. C.
- Briefings in Bioinformatics, Vol. 13, Issue 6
A field guide to whole-genome sequencing, assembly and annotation
journal, June 2014
- Ekblom, Robert; Wolf, Jochen B. W.
- Evolutionary Applications, Vol. 7, Issue 9
Bias from removing read duplication in ultra-deep sequencing experiments
journal, January 2014
- Zhou, Wanding; Chen, Tenghui; Zhao, Hao
- Bioinformatics, Vol. 30, Issue 8
Systematic artifacts in metagenomes from complex microbial communities
journal, July 2009
- Gomez-Alvarez, Vicente; Teal, Tracy K.; Schmidt, Thomas M.
- The ISME Journal, Vol. 3, Issue 11
New Perspectives on Microbial Community Distortion after Whole-Genome Amplification
journal, May 2015
- Probst, Alexander J.; Weinmaier, Thomas; DeSantis, Todd Z.
- PLOS ONE, Vol. 10, Issue 5
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
journal, November 2014
- Salter, Susannah J.; Cox, Michael J.; Turek, Elena M.
- BMC Biology, Vol. 12, Issue 1
Diverse and Widespread Contamination Evident in the Unmapped Depths of High Throughput Sequencing Data
journal, October 2014
- Lusk, Richard W.
- PLoS ONE, Vol. 9, Issue 10
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
journal, January 2015
- Kang, Dongwan D.; Froula, Jeff; Egan, Rob
- PeerJ, Vol. 3
Characterization of the Tn5 transposase and inhibitor proteins: a model for the inhibition of transposition.
journal, November 1993
- de la Cruz, N. B.; Weinreich, M. D.; Wiegand, T. W.
- Journal of Bacteriology, Vol. 175, Issue 21
Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes
journal, March 2009
- Kozarewa, Iwanka; Ning, Zemin; Quail, Michael A.
- Nature Methods, Vol. 6, Issue 4
Fast and sensitive protein alignment using DIAMOND
journal, November 2014
- Buchfink, Benjamin; Xie, Chao; Huson, Daniel H.
- Nature Methods, Vol. 12, Issue 1
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities: Metagenomic and rRNA diversity characterization
journal, February 2013
- Shakya, Migun; Quince, Christopher; Campbell, James H.
- Environmental Microbiology, Vol. 15, Issue 6
WebLogo: A Sequence Logo Generator
journal, May 2004
- Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc
- Genome Research, Vol. 14, Issue 6, p. 1188-1190
Microbial structuring of marine ecosystems
journal, October 2007
- Azam, Farooq; Malfatti, Francesca
- Nature Reviews Microbiology, Vol. 5, Issue 10
Use of simulated data sets to evaluate the fidelity of metagenomic processing methods
journal, April 2007
- Mavromatis, Konstantinos; Ivanova, Natalia; Barry, Kerrie
- Nature Methods, Vol. 4, Issue 6
Next-Generation Sequencing on Metagenomic Data: Assembly and Binning
book, January 2013
- Leung, Henry C. M.; Wang, Yi; Yiu, S. M.
- Encyclopedia of Metagenomics
Global distribution of microbial abundance and biomass in subseafloor sediment
journal, August 2012
- Kallmeyer, J.; Pockalny, R.; Adhikari, R. R.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 40
New perspectives on viable microbial communities in low-biomass cleanroom environments
journal, October 2012
- Vaishampayan, Parag; Probst, Alexander J.; La Duc, Myron T.
- The ISME Journal, Vol. 7, Issue 2
Determination of DNA Content of Aquatic Bacteria by Flow Cytometry
journal, April 2001
- Button, D. K.; Robertson, B. R.
- Applied and Environmental Microbiology, Vol. 67, Issue 4
Sequencing platform and library preparation choices impact viral metagenomes
journal, January 2013
- Solonenko, Sergei A.; Ignacio-Espinoza, J.; Alberti, Adriana
- BMC Genomics, Vol. 14, Issue 1
Decontamination of MDA Reagents for Single Cell Whole Genome Amplification
journal, October 2011
- Woyke, Tanja; Sczyrba, Alexander; Lee, Janey
- PLoS ONE, Vol. 6, Issue 10
Defining characteristics of Tn5 Transposase non-specific DNA binding
journal, January 2006
- Steiniger, M.; Adams, C. D.; Marko, J. F.
- Nucleic Acids Research, Vol. 34, Issue 9
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification
journal, October 2014
- Reddy, T. B. K.; Thomas, Alex D.; Stamatis, Dimitri
- Nucleic Acids Research, Vol. 43, Issue D1
Marine Microbes See a Sea of Gradients
journal, November 2012
- Stocker, R.
- Science, Vol. 338, Issue 6107
Reconstructing each cell's genome within complex microbial communities—dream or reality?
journal, January 2015
- Clingenpeel, Scott; Clum, Alicia; Schwientek, Patrick
- Frontiers in Microbiology, Vol. 5
Multiple displacement amplification compromises quantitative analysis of metagenomes
journal, November 2010
- Yilmaz, Suzan; Allgaier, Martin; Hugenholtz, Philip
- Nature Methods, Vol. 7, Issue 12
OCEANOGRAPHY: Microbial Control of Oceanic Carbon Flux: The Plot Thickens
journal, May 1998
- Azam, F.
- Science, Vol. 280, Issue 5364
Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA
journal, November 2011
- Parkinson, N. J.; Maslau, S.; Ferneyhough, B.
- Genome Research, Vol. 22, Issue 1
Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assembly
journal, April 2013
- Chen, Yen-Chun; Liu, Tsunglin; Yu, Chun-Hui
- PLoS ONE, Vol. 8, Issue 4
Methylobacterium iners sp. nov. and Methylobacterium aerolatum sp. nov., isolated from air samples in Korea
journal, January 2008
- Weon, H. -Y.; Kim, B. -Y.; Joa, J. -H.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 1
Microscale patchiness of bacterioplankton assemblage richness in seawater
journal, January 2001
- Long, Ra; Azam, F.
- Aquatic Microbial Ecology, Vol. 26
Staphylococcus colonization of the skin and antimicrobial peptides
journal, April 2010
- Otto, Michael
- Expert Review of Dermatology, Vol. 5, Issue 2
Sequence logos: a new way to display consensus sequences
journal, January 1990
- Schneider, Thomas D.; Stephens, R. Michael
- Nucleic Acids Research, Vol. 18, Issue 20
GC-Content Normalization for RNA-Seq Data
journal, January 2011
- Risso, Davide; Schwartz, Katja; Sherlock, Gavin
- BMC Bioinformatics, Vol. 12, Issue 1
Improved workflows for high throughput library preparation using the transposome-based nextera system
journal, November 2013
- Lamble, Sarah; Batty, Elizabeth; Attar, Moustafa
- BMC Biotechnology, Vol. 13, Issue 1
The Sequence Alignment/Map format and SAMtools
journal, June 2009
- Li, H.; Handsaker, B.; Wysoker, A.
- Bioinformatics, Vol. 25, Issue 16
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014
- Love, Michael I.; Huber, Wolfgang; Anders, Simon
- Genome Biology, Vol. 15, Issue 12
The effects of variable sample biomass on comparative metagenomics: Metagenomics of low biomass microbial communities
journal, January 2015
- Chafee, Meghan; Maignien, Loïs; Simmons, Sheri L.
- Environmental Microbiology, Vol. 17, Issue 7
The Uncultured Microbial Majority
journal, October 2003
- Rappé, Michael S.; Giovannoni, Stephen J.
- Annual Review of Microbiology, Vol. 57, Issue 1
Genomic DNA Amplification from a Single Bacterium
journal, June 2005
- Raghunathan, A.; Ferguson, H. R.; Bornarth, C. J.
- Applied and Environmental Microbiology, Vol. 71, Issue 6
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
journal, May 2015
- Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T.
- Genome Research, Vol. 25, Issue 7
Datura genome reveals duplications of psychoactive alkaloid biosynthetic genes and high mutation rate following tissue culture
journal, March 2021
- Rajewski, Alex; Carter-House, Derreck; Stajich, Jason
- BMC Genomics, Vol. 22, Issue 1
Polinton-like viruses are abundant in aquatic ecosystems
journal, January 2021
- Bellas, Christopher M.; Sommaruga, Ruben
- Microbiome, Vol. 9, Issue 1
An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities.
text, January 2021
- O'Sullivan, Denise M.; Doyle, Ronan M.; Temisak, Sasithon
- Apollo - University of Cambridge Repository
Archaea on human skin
text, January 2013
- Probst, Alexander J.; Auerbach, Anna K.; Moissl-Eichinger, Christine
- Universität Regensburg
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.
text, January 2014
- Salter, Susannah; Cox, Michael J.; Turek, Elena M.
- Apollo - University of Cambridge Repository
Diverse and widespread contamination evident in the unmapped depths of high throughput sequencing data
text, January 2014
- Lusk, Richard W.
- arXiv
A mini-review of microbial consortia: Their roles in aquatic production and biogeochemical cycling
journal, January 1996
- Paerl, H. W.; Pinckney, J. L.
- Microbial Ecology, Vol. 31, Issue 3
Systematic artifacts in metagenomes from complex microbial communities
journal, July 2009
- Gomez-Alvarez, Vicente; Teal, Tracy K.; Schmidt, Thomas M.
- The ISME Journal, Vol. 3, Issue 11
Multiple displacement amplification compromises quantitative analysis of metagenomes
journal, November 2010
- Yilmaz, Suzan; Allgaier, Martin; Hugenholtz, Philip
- Nature Methods, Vol. 7, Issue 12
Microbial structuring of marine ecosystems
journal, October 2007
- Azam, Farooq; Malfatti, Francesca
- Nature Reviews Microbiology, Vol. 5, Issue 10
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing
journal, January 2021
- Karst, Søren M.; Ziels, Ryan M.; Kirkegaard, Rasmus H.
- Nature Methods, Vol. 18, Issue 2
Global distribution of microbial abundance and biomass in subseafloor sediment
journal, August 2012
- Kallmeyer, J.; Pockalny, R.; Adhikari, R. R.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 40
Tn5/IS50 target recognition
journal, September 1998
- Goryshin, I. Y.; Miller, J. A.; Kil, Y. V.
- Proceedings of the National Academy of Sciences, Vol. 95, Issue 18
Taxonomic binning of metagenome samples generated by next-generation sequencing technologies
journal, July 2012
- Droge, J.; McHardy, A. C.
- Briefings in Bioinformatics, Vol. 13, Issue 6
Sequence logos: a new way to display consensus sequences
journal, January 1990
- Schneider, Thomas D.; Stephens, R. Michael
- Nucleic Acids Research, Vol. 18, Issue 20
Defining characteristics of Tn5 Transposase non-specific DNA binding
journal, January 2006
- Steiniger, M.; Adams, C. D.; Marko, J. F.
- Nucleic Acids Research, Vol. 34, Issue 9
Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
journal, October 2011
- Kircher, Martin; Sawyer, Susanna; Meyer, Matthias
- Nucleic Acids Research, Vol. 40, Issue 1
The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification
journal, October 2014
- Reddy, T. B. K.; Thomas, Alex D.; Stamatis, Dimitri
- Nucleic Acids Research, Vol. 43, Issue D1
Methylobacterium iners sp. nov. and Methylobacterium aerolatum sp. nov., isolated from air samples in Korea
journal, January 2008
- Weon, H. -Y.; Kim, B. -Y.; Joa, J. -H.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 1
Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA
journal, November 2011
- Parkinson, N. J.; Maslau, S.; Ferneyhough, B.
- Genome Research, Vol. 22, Issue 1
A field guide to whole-genome sequencing, assembly and annotation
journal, June 2014
- Ekblom, Robert; Wolf, Jochen B. W.
- Evolutionary Applications, Vol. 7, Issue 9
Towards quantitative metagenomics of wild viruses and other ultra-low concentration DNA samples: a rigorous assessment and optimization of the linker amplification method: Linker amplification for ultra-low DNA samples
journal, June 2012
- Duhaime, Melissa B.; Deng, Li; Poulos, Bonnie T.
- Environmental Microbiology, Vol. 14, Issue 9
Marine Microbes See a Sea of Gradients
journal, November 2012
- Stocker, R.
- Science, Vol. 338, Issue 6107
Evaluation of a Transposase Protocol for Rapid Generation of Shotgun High-Throughput Sequencing Libraries from Nanogram Quantities of DNA
journal, September 2011
- Marine, Rachel; Polson, Shawn W.; Ravel, Jacques
- Applied and Environmental Microbiology, Vol. 77, Issue 22
Characterization of the Tn5 transposase and inhibitor proteins: a model for the inhibition of transposition.
journal, November 1993
- de la Cruz, N. B.; Weinreich, M. D.; Wiegand, T. W.
- Journal of Bacteriology, Vol. 175, Issue 21
Microbial Metagenomics: Beyond the Genome
journal, January 2011
- Gilbert, Jack A.; Dupont, Christopher L.
- Annual Review of Marine Science, Vol. 3, Issue 1
GC-Content Normalization for RNA-Seq Data
journal, January 2011
- Risso, Davide; Schwartz, Katja; Sherlock, Gavin
- BMC Bioinformatics, Vol. 12, Issue 1
Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition
journal, January 2010
- Adey, Andrew; Morrison, Hilary G.; (no last name), Asan
- Genome Biology, Vol. 11, Issue 12
Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community
journal, October 2015
- Bowers, Robert M.; Clum, Alicia; Tice, Hope
- BMC Genomics, Vol. 16, Issue 1
Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments
journal, August 2014
- Smith, Erin N.; Jepsen, Kristen; Khosroheidari, Mahdieh
- Genome Biology, Vol. 15, Issue 7
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014
- Love, Michael I.; Huber, Wolfgang; Anders, Simon
- Genome Biology, Vol. 15, Issue 12
Decontamination of MDA Reagents for Single Cell Whole Genome Amplification
journal, October 2011
- Woyke, Tanja; Sczyrba, Alexander; Lee, Janey
- PLoS ONE, Vol. 6, Issue 10
Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assembly
journal, April 2013
- Chen, Yen-Chun; Liu, Tsunglin; Yu, Chun-Hui
- PLoS ONE, Vol. 8, Issue 4
Microbial Contamination in Next Generation Sequencing: Implications for Sequence-Based Analysis of Clinical Samples
journal, November 2014
- Strong, Michael J.; Xu, Guorong; Morici, Lisa
- PLoS Pathogens, Vol. 10, Issue 11
Microscale patchiness of bacterioplankton assemblage richness in seawater
journal, January 2001
- Long, Ra; Azam, F.
- Aquatic Microbial Ecology, Vol. 26
Reconstructing each cell's genome within complex microbial communities—dream or reality?
journal, January 2015
- Clingenpeel, Scott; Clum, Alicia; Schwientek, Patrick
- Frontiers in Microbiology, Vol. 5
Archaea on human skin
text, January 2013
- Probst, Alexander J.; Auerbach, Anna K.; Moissl-Eichinger, Christine
- Universität Regensburg
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
journal, January 2015
- Kang, Dongwan D.; Froula, Jeff; Egan, Rob
- PeerJ, Vol. 3
Works referencing / citing this record:
Exploring the Viral Ecology of High Latitude Aquatic Systems
book, January 2017
- Chénard, Caroline; Lauro, Federico M.
- Microbial Ecology of Extreme Environments
MetaSort untangles metagenome assembly by reducing microbial community complexity
journal, January 2017
- Ji, Peifeng; Zhang, Yanming; Wang, Jinfeng
- Nature Communications, Vol. 8, Issue 1
Zooming in on the phycosphere: the ecological interface for phytoplankton–bacteria relationships
journal, May 2017
- Seymour, Justin R.; Amin, Shady A.; Raina, Jean-Baptiste
- Nature Microbiology, Vol. 2, Issue 7
Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis
journal, August 2018
- Hardwick, Simon A.; Chen, Wendy Y.; Wong, Ted
- Nature Communications, Vol. 9, Issue 1
Defining the human gut host–phage network through single-cell viral tagging
journal, August 2019
- Džunková, Mária; Low, Soo Jen; Daly, Joshua N.
- Nature Microbiology, Vol. 4, Issue 12
Detection of mixed-strain infections by FACS and ultra-low input genome sequencing
journal, October 2018
- Džunková, Mária; Moya, Andrés; Chen, Xinhua
- Gut Microbes, Vol. 11, Issue 3
GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes
journal, March 2018
- Boyd, Joel A.; Woodcroft, Ben J.; Tyson, Gene W.
- Nucleic Acids Research, Vol. 46, Issue 10
Morphology of obligate ectosymbionts reveals Paralaxus gen. nov., a new circumtropical genus of marine stilbonematine nematodes
posted_content, August 2019
- Scharhauser, Florian; Zimmermann, Judith; Ott, Jörg A.
- bioRxiv
Microbial ecology of mountain glacier ecosystems: biodiversity, ecological connections and implications of a warming climate
journal, May 2017
- Hotaling, Scott; Hood, Eran; Hamilton, Trinity L.
- Environmental Microbiology, Vol. 19, Issue 8
Enrichment of Clinically Relevant Organisms in Spontaneous Preterm-Delivered Placentas and Reagent Contamination across All Clinical Groups in a Large Pregnancy Cohort in the United Kingdom
journal, May 2018
- Leon, Lydia J.; Doyle, Ronan; Diez-Benavente, Ernest
- Applied and Environmental Microbiology, Vol. 84, Issue 14
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads
journal, October 2019
- Sanders, Jon G.; Nurk, Sergey; Salido, Rodolfo A.
- Genome Biology, Vol. 20, Issue 1
A pipeline for targeted metagenomics of environmental bacteria
journal, February 2020
- Grieb, Anissa; Bowers, Robert M.; Oggerin, Monike
- Microbiome, Vol. 8, Issue 1
Evaluation of Sequencing Library Preparation Protocols for Viral Metagenomic Analysis from Pristine Aquifer Groundwaters
journal, May 2019
- Kallies, René; Hölzer, Martin; Brizola Toscan, Rodolfo
- Viruses, Vol. 11, Issue 6
Optimizing de novo genome assembly from PCR-amplified metagenomes
journal, January 2019
- Roux, Simon; Trubl, Gareth; Goudeau, Danielle
- PeerJ, Vol. 7
Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils
journal, January 2019
- Trubl, Gareth; Roux, Simon; Solonenko, Natalie
- PeerJ, Vol. 7
Morphology of obligate ectosymbionts reveals Paralaxus gen. nov.: A new circumtropical genus of marine stilbonematine nematodes
journal, February 2020
- Scharhauser, Florian; Zimmermann, Judith; Ott, Jörg A.
- Zoologica Scripta, Vol. 49, Issue 3
MetaSort untangles metagenome assembly by reducing microbial community complexity
journal, January 2017
- Ji, Peifeng; Zhang, Yanming; Wang, Jinfeng
- Nature Communications, Vol. 8, Issue 1
Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis
journal, August 2018
- Hardwick, Simon A.; Chen, Wendy Y.; Wong, Ted
- Nature Communications, Vol. 9, Issue 1
GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes
journal, March 2018
- Boyd, Joel A.; Woodcroft, Ben J.; Tyson, Gene W.
- Nucleic Acids Research, Vol. 46, Issue 10
Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads
journal, October 2019
- Sanders, Jon G.; Nurk, Sergey; Salido, Rodolfo A.
- Genome Biology, Vol. 20, Issue 1
Library Construction from Subnanogram DNA for Pelagic Sea Water and Deep-Sea Sediments
journal, January 2017
- Hirai, Miho; Nishi, Shinro; Tsuda, Miwako
- Microbes and Environments, Vol. 32, Issue 4
Evaluation of Sequencing Library Preparation Protocols for Viral Metagenomic Analysis from Pristine Aquifer Groundwaters
journal, May 2019
- Kallies, René; Hölzer, Martin; Brizola Toscan, Rodolfo
- Viruses, Vol. 11, Issue 6
Bioreactor virome metagenomics sequencing using DNA spike-ins
journal, January 2018
- Cremers, Geert; Gambelli, Lavinia; van Alen, Theo
- PeerJ, Vol. 6