High-resolution phylogenetic microbial community profiling
Abstract
Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structures at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake's water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communitiesmore »
- Authors:
-
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); USDA-ARS, Albanay, CA (United States)
- Pacific Biosciences, Menlo Park, CA (United States)
- Univ. of British Columbia, Vancouver, BC (Canada)
- Newcastle Univ. (United Kingdom). School of Biology
- Univ. of Queensland, St. Lucia, QLD (Australia). Australian Centre for Ecogenomics
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1379539
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- The ISME Journal
- Additional Journal Information:
- Journal Volume: 10; Journal Issue: 8; Journal ID: ISSN 1751-7362
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 54 ENVIRONMENTAL SCIENCES
Citation Formats
Singer, Esther, Bushnell, Brian, Coleman-Derr, Devin, Bowman, Brett, Bowers, Robert M., Levy, Asaf, Gies, Esther A., Cheng, Jan -Fang, Copeland, Alex, Klenk, Hans -Peter, Hallam, Steven, Hugenholtz, Philip, Tringe, Susannah G., and Woyke, Tanja. High-resolution phylogenetic microbial community profiling. United States: N. p., 2016.
Web. doi:10.1038/ismej.2015.249.
Singer, Esther, Bushnell, Brian, Coleman-Derr, Devin, Bowman, Brett, Bowers, Robert M., Levy, Asaf, Gies, Esther A., Cheng, Jan -Fang, Copeland, Alex, Klenk, Hans -Peter, Hallam, Steven, Hugenholtz, Philip, Tringe, Susannah G., & Woyke, Tanja. High-resolution phylogenetic microbial community profiling. United States. https://doi.org/10.1038/ismej.2015.249
Singer, Esther, Bushnell, Brian, Coleman-Derr, Devin, Bowman, Brett, Bowers, Robert M., Levy, Asaf, Gies, Esther A., Cheng, Jan -Fang, Copeland, Alex, Klenk, Hans -Peter, Hallam, Steven, Hugenholtz, Philip, Tringe, Susannah G., and Woyke, Tanja. Tue .
"High-resolution phylogenetic microbial community profiling". United States. https://doi.org/10.1038/ismej.2015.249. https://www.osti.gov/servlets/purl/1379539.
@article{osti_1379539,
title = {High-resolution phylogenetic microbial community profiling},
author = {Singer, Esther and Bushnell, Brian and Coleman-Derr, Devin and Bowman, Brett and Bowers, Robert M. and Levy, Asaf and Gies, Esther A. and Cheng, Jan -Fang and Copeland, Alex and Klenk, Hans -Peter and Hallam, Steven and Hugenholtz, Philip and Tringe, Susannah G. and Woyke, Tanja},
abstractNote = {Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structures at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake's water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential.},
doi = {10.1038/ismej.2015.249},
journal = {The ISME Journal},
number = 8,
volume = 10,
place = {United States},
year = {Tue Feb 09 00:00:00 EST 2016},
month = {Tue Feb 09 00:00:00 EST 2016}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 178 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Microbial diversity in the deep sea and the underexplored "rare biosphere"
journal, July 2006
- Sogin, M. L.; Morrison, H. G.; Huber, J. A.
- Proceedings of the National Academy of Sciences, Vol. 103, Issue 32
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
journal, November 2011
- Pruitt, K. D.; Tatusova, T.; Brown, G. R.
- Nucleic Acids Research, Vol. 40, Issue D1
Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
journal, July 2006
- DeSantis, T. Z.; Hugenholtz, P.; Larsen, N.
- Applied and Environmental Microbiology, Vol. 72, Issue 7, p. 5069-5072
A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers
journal, January 2012
- Quail, Michael; Smith, Miriam E.; Coupland, Paul
- BMC Genomics, Vol. 13, Article No. 341
Comparison of Species Richness Estimates Obtained Using Nearly Complete Fragments and Simulated Pyrosequencing-Generated Fragments in 16S rRNA Gene-Based Environmental Surveys
journal, June 2009
- Youssef, N.; Sheik, C. S.; Krumholz, L. R.
- Applied and Environmental Microbiology, Vol. 75, Issue 16
The Human Microbiome Project
journal, October 2007
- Turnbaugh, Peter J.; Ley, Ruth E.; Hamady, Micah
- Nature, Vol. 449, Issue 7164
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
journal, June 2007
- Wang, Q.; Garrity, G. M.; Tiedje, J. M.
- Applied and Environmental Microbiology, Vol. 73, Issue 16
Improved performance of the PacBio SMRT technology for 16S rDNA sequencing
journal, September 2014
- Mosher, Jennifer J.; Bowman, Brett; Bernberg, Erin L.
- Journal of Microbiological Methods, Vol. 104
Illuminating Microbial Dark Matter in Meromictic Sakinaw Lake
journal, August 2014
- Gies, Esther A.; Konwar, Kishori M.; Beatty, J. Thomas
- Applied and Environmental Microbiology, Vol. 80, Issue 21
RStudio: A Platform-Independent IDE for R and Sweave: SOFTWARE REVIEW
journal, October 2011
- Racine, Jeffrey S.
- Journal of Applied Econometrics, Vol. 27, Issue 1
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences
journal, January 2012
- Soergel, David A. W.; Dey, Neelendu; Knight, Rob
- The ISME Journal, Vol. 6, Issue 7
Molecular Evidence for Genus Level Diversity of Bacteria Capable of Catalyzing Anaerobic Ammonium Oxidation
journal, April 2000
- Schmid, Markus; Twachtmann, Ulf; Klein, Michael
- Systematic and Applied Microbiology, Vol. 23, Issue 1, p. 93-106
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes
journal, May 2012
- Pruesse, Elmar; Peplies, Jörg; Glöckner, Frank Oliver
- Bioinformatics, Vol. 28, Issue 14
Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat
journal, January 2014
- Babauta, Jerome T.; Atci, Erhan; Ha, Phuc T.
- Frontiers in Microbiology, Vol. 5
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
journal, October 2009
- Schloss, P. D.; Westcott, S. L.; Ryabin, T.
- Applied and Environmental Microbiology, Vol. 75, Issue 23, p. 7537-7541
Purification and Concentration of DNA from Aqueous Solutions
journal, July 2002
- Moore, David; Dowhan, Dennis
- Current Protocols in Molecular Biology, Vol. 59, Issue 1
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
journal, December 2011
- Pagani, I.; Liolios, K.; Jansson, J.
- Nucleic Acids Research, Vol. 40, Issue D1
Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex
journal, February 2008
- Hamady, Micah; Walker, Jeffrey J.; Harris, J. Kirk
- Nature Methods, Vol. 5, Issue 3, p. 235-237
Insights into the phylogeny and coding potential of microbial dark matter
journal, July 2013
- Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander
- Nature, Vol. 499, Issue 7459
Novel methylotrophic isolates from lake sediment, description of Methylotenera versatilis sp. nov. and emended description of the genus Methylotenera
journal, February 2011
- Kalyuzhnaya, M. G.; Beck, D. A. C.; Vorobev, A.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 62, Issue 1
A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing
journal, October 2007
- Parameswaran, Poornima; Jalili, Roxana; Tao, Li
- Nucleic Acids Research, Vol. 35, Issue 19
Competition betweenNitrospira spp. andNitrobacter spp. in nitrite-oxidizing bioreactors
journal, January 2006
- Nogueira, Regina; Melo, Luís F.
- Biotechnology and Bioengineering, Vol. 95, Issue 1
Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing
journal, May 2011
- Bolhuis, Henk; Stal, Lucas J.
- The ISME Journal, Vol. 5, Issue 11
Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences
journal, August 2014
- Yarza, Pablo; Yilmaz, Pelin; Pruesse, Elmar
- Nature Reviews Microbiology, Vol. 12, Issue 9
The integrated microbial genomes (IMG) system
journal, January 2006
- Markowitz, V. M.
- Nucleic Acids Research, Vol. 34, Issue 90001
DNA Extraction from 0.22 μM Sterivex Filters and Cesium Chloride Density Gradient Centrifugation
journal, January 2009
- Wright, Jody J.; Lee, Sangwon; Zaikova, Elena
- Journal of Visualized Experiments, Issue 31
Identifying the Dominant Soil Bacterial Taxa in Libraries of 16S rRNA and 16S rRNA Genes
journal, March 2006
- Janssen, P. H.
- Applied and Environmental Microbiology, Vol. 72, Issue 3
Genetic diversity in Sargasso Sea bacterioplankton
journal, May 1990
- Giovannoni, Stephen J.; Britschgi, Theresa B.; Moyer, Craig L.
- Nature, Vol. 345, Issue 6270
Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes
journal, January 2011
- Kim, Minseok; Morrison, Mark; Yu, Zhongtang
- Journal of Microbiological Methods, Vol. 84, Issue 1
Revised Taxonomy of the Methanotrophs: Description of Methylobacter gen. nov., Emendation of Methylococcus, Validation of Methylosinus and Methylocystis Species, and a Proposal that the Family Methylococcaceae Includes Only the Group I Methanotrophs
journal, October 1993
- Bowman, J. P.; Sly, L. I.; Nichols, P. D.
- International Journal of Systematic Bacteriology, Vol. 43, Issue 4
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
journal, November 2012
- Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin
- Nucleic Acids Research, Vol. 41, Issue D1
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers
journal, February 2011
- Walters, William A.; Caporaso, J. Gregory; Lauber, Christian L.
- Bioinformatics, Vol. 27, Issue 8
A renaissance for the pioneering 16S rRNA gene
journal, October 2008
- Tringe, Susannah G.; Hugenholtz, Philip
- Current Opinion in Microbiology, Vol. 11, Issue 5
Short pyrosequencing reads suffice for accurate microbial community analysis
journal, August 2007
- Liu, Z.; Lozupone, C.; Hamady, M.
- Nucleic Acids Research, Vol. 35, Issue 18
Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing
journal, August 2014
- Takahashi, Shunsuke; Tomita, Junko; Nishioka, Kaori
- PLoS ONE, Vol. 9, Issue 8
FunGene: the functional gene pipeline and repository
journal, January 2013
- Fish, Jordan A.; Chai, Benli; Wang, Qiong
- Frontiers in Microbiology, Vol. 4
Human gut microbiome viewed across age and geography
journal, May 2012
- Yatsunenko, Tanya; Rey, Federico E.; Manary, Mark J.
- Nature, Vol. 486, Issue 7402
Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples: Primers for marine microbiome studies
journal, October 2015
- Parada, Alma E.; Needham, David M.; Fuhrman, Jed A.
- Environmental Microbiology, Vol. 18, Issue 5
One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly
journal, February 2015
- Koren, Sergey; Phillippy, Adam M.
- Current Opinion in Microbiology, Vol. 23
Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance
journal, October 2012
- Kembel, Steven W.; Wu, Martin; Eisen, Jonathan A.
- PLoS Computational Biology, Vol. 8, Issue 10
Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions
journal, September 2010
- Claesson, Marcus J.; Wang, Qiong; O'Sullivan, Orla
- Nucleic Acids Research, Vol. 38, Issue 22
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
journal, March 2012
- Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A.
- The ISME Journal, Vol. 6, Issue 8
Methane formation and oxidation in the meromictic oligotrophic Lake Gek-Gel (Azerbaijan)
journal, April 2010
- Pimenov, N. V.; Kallistova, A. Yu.; Rusanov, I. I.
- Microbiology, Vol. 79, Issue 2
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing
journal, December 2009
- Lazarevic, Vladimir; Whiteson, Katrine; Huse, Susan
- Journal of Microbiological Methods, Vol. 79, Issue 3
Impact of Culture-Independent Studies on the Emerging Phylogenetic View of Bacterial Diversity
journal, September 1998
- Hugenholtz, Philip; Goebel, Brett M.; Pace, Norman R.
- Journal of Bacteriology, Vol. 180, Issue 18
Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA.
journal, January 1993
- Muyzer, G.; de Waal, E. C.; Uitterlinden, A. G.
- Applied and Environmental Microbiology, Vol. 59, Issue 3
Analysis of immune, microbiota and metabolome maturation in infants in a clinical trial of Lactobacillus paracasei CBA L74-fermented formula
journal, June 2020
- Roggero, Paola; Liotto, Nadia; Pozzi, Chiara
- Nature Communications, Vol. 11, Issue 1
Reconstruction of ancient microbial genomes from the human gut
journal, May 2021
- Wibowo, Marsha C.; Yang, Zhen; Borry, Maxime
- Nature, Vol. 594, Issue 7862
Microbial Dysbiosis During Simian Immunodeficiency Virus Infection is Partially Reverted with Combination Anti-retroviral Therapy
journal, April 2020
- Blum, Faith C.; Hardy, Britney L.; Bishop-Lilly, Kimberly A.
- Scientific Reports, Vol. 10, Issue 1
Revised Taxonomy of the Methanotrophs: Description of Methylobacter gen. nov., Emendation of Methylococcus, Validation of Methylosinus and Methylocystis Species, and a Proposal that the Family Methylococcaceae Includes Only the Group I Methanotrophs
journal, April 1994
- Bowman, J. P.; Sly, L. I.; Nichols, P. D.
- International Journal of Systematic Bacteriology, Vol. 44, Issue 2
Purification and Concentration of DNA from Aqueous Solutions
journal, September 2007
- Moore, David; Dowhan, Dennis
- Current Protocols in Pharmacology, Vol. 38, Issue 1
Competition betweenNitrospira spp. andNitrobacter spp. in nitrite-oxidizing bioreactors
journal, January 2006
- Nogueira, Regina; Melo, Luís F.
- Biotechnology and Bioengineering, Vol. 95, Issue 1
A renaissance for the pioneering 16S rRNA gene
journal, October 2008
- Tringe, Susannah G.; Hugenholtz, Philip
- Current Opinion in Microbiology, Vol. 11, Issue 5
One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly
journal, February 2015
- Koren, Sergey; Phillippy, Adam M.
- Current Opinion in Microbiology, Vol. 23
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing
journal, December 2009
- Lazarevic, Vladimir; Whiteson, Katrine; Huse, Susan
- Journal of Microbiological Methods, Vol. 79, Issue 3
Evaluation of different partial 16S rRNA gene sequence regions for phylogenetic analysis of microbiomes
journal, January 2011
- Kim, Minseok; Morrison, Mark; Yu, Zhongtang
- Journal of Microbiological Methods, Vol. 84, Issue 1
Improved performance of the PacBio SMRT technology for 16S rDNA sequencing
journal, September 2014
- Mosher, Jennifer J.; Bowman, Brett; Bernberg, Erin L.
- Journal of Microbiological Methods, Vol. 104
Selection of primers for optimal taxonomic classification of environmental 16S rRNA gene sequences
journal, January 2012
- Soergel, David A. W.; Dey, Neelendu; Knight, Rob
- The ISME Journal, Vol. 6, Issue 7
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
journal, March 2012
- Caporaso, J. Gregory; Lauber, Christian L.; Walters, William A.
- The ISME Journal, Vol. 6, Issue 8
Human gut microbiome viewed across age and geography
journal, May 2012
- Yatsunenko, Tanya; Rey, Federico E.; Manary, Mark J.
- Nature, Vol. 486, Issue 7402
Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex
journal, February 2008
- Hamady, Micah; Walker, Jeffrey J.; Harris, J. Kirk
- Nature Methods, Vol. 5, Issue 3, p. 235-237
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers
journal, February 2011
- Walters, William A.; Caporaso, J. Gregory; Lauber, Christian L.
- Bioinformatics, Vol. 27, Issue 8
Short pyrosequencing reads suffice for accurate microbial community analysis
journal, August 2007
- Liu, Z.; Lozupone, C.; Hamady, M.
- Nucleic Acids Research, Vol. 35, Issue 18
A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing
journal, October 2007
- Parameswaran, Poornima; Jalili, Roxana; Tao, Li
- Nucleic Acids Research, Vol. 35, Issue 19
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
journal, November 2011
- Pruitt, K. D.; Tatusova, T.; Brown, G. R.
- Nucleic Acids Research, Vol. 40, Issue D1
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata
journal, December 2011
- Pagani, I.; Liolios, K.; Jansson, J.
- Nucleic Acids Research, Vol. 40, Issue D1
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
journal, November 2012
- Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin
- Nucleic Acids Research, Vol. 41, Issue D1
Novel methylotrophic isolates from lake sediment, description of Methylotenera versatilis sp. nov. and emended description of the genus Methylotenera
journal, February 2011
- Kalyuzhnaya, M. G.; Beck, D. A. C.; Vorobev, A.
- INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 62, Issue 1
Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance
journal, October 2012
- Kembel, Steven W.; Wu, Martin; Eisen, Jonathan A.
- PLoS Computational Biology, Vol. 8, Issue 10
Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing
journal, August 2014
- Takahashi, Shunsuke; Tomita, Junko; Nishioka, Kaori
- PLoS ONE, Vol. 9, Issue 8
Primer and platform effects on 16S rRNA tag sequencing
text, January 2015
- Alison, Fern,; Feng, Chen,; Julien, Tremblay,
- The University of North Carolina at Chapel Hill University Libraries
FunGene: the functional gene pipeline and repository
journal, January 2013
- Fish, Jordan A.; Chai, Benli; Wang, Qiong
- Frontiers in Microbiology, Vol. 4
Molecular characterization of vulnibactin biosynthesis in Vibrio vulnificus indicates the existence of an alternative siderophore
journal, January 2014
- Tan, Wenzhi; Verma, Vivek; Jeong, Kwangjoon
- Frontiers in Microbiology, Vol. 5
Works referencing / citing this record:
Effect of biosurfactant derived from Vibrio natriegens MK3 against Vibrio harveyi biofilm and virulence
journal, July 2019
- Kannan, Suganya; Krishnamoorthy, Govindan; Kulanthaiyesu, Arunkumar
- Journal of Basic Microbiology, Vol. 59, Issue 9
Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis
journal, July 2019
- Klemetsen, Terje; Willassen, Nils Peder; Karlsen, Christian René
- MicrobiologyOpen, Vol. 8, Issue 10
Anaerobic Biodegradation of Hydrocarbons: Metagenomics and Metabolomics
book, January 2016
- Gieg, Lisa M.; Toth, Courtney R. A.
- Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation
Combination of probiotics with different functions alleviate DSS-induced colitis by regulating intestinal microbiota, IL-10, and barrier function
journal, November 2019
- Wang, Yanbo; Xie, Qiuhong; Zhang, Ying
- Applied Microbiology and Biotechnology, Vol. 104, Issue 1
Analysis of soil microbial communities based on amplicon sequencing of marker genes
journal, May 2017
- Schöler, Anne; Jacquiod, Samuel; Vestergaard, Gisle
- Biology and Fertility of Soils, Vol. 53, Issue 5
Retrieval of a million high-quality, full-length microbial 16S and 18S rRNA gene sequences without primer bias
journal, January 2018
- Karst, Søren M.; Dueholm, Morten S.; McIlroy, Simon J.
- Nature Biotechnology, Vol. 36, Issue 2
Reference standards for next-generation sequencing
journal, June 2017
- Hardwick, Simon A.; Deveson, Ira W.; Mercer, Tim R.
- Nature Reviews Genetics, Vol. 18, Issue 8
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
Mycobiome diversity: high-throughput sequencing and identification of fungi
journal, November 2018
- Nilsson, R. Henrik; Anslan, Sten; Bahram, Mohammad
- Nature Reviews Microbiology, Vol. 17, Issue 2
Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies
journal, November 2019
- Sevim, Volkan; Lee, Juna; Egan, Robert
- Scientific Data, Vol. 6, Issue 1
High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system
journal, June 2017
- Pootakham, Wirulda; Mhuantong, Wuttichai; Yoocha, Thippawan
- Scientific Reports, Vol. 7, Issue 1
Insight into the microbial world of Bemisia tabaci cryptic species complex and its relationships with its host
journal, April 2019
- Wang, Hua-Ling; Lei, Teng; Xia, Wen-Qiang
- Scientific Reports, Vol. 9, Issue 1
Next generation sequencing data of a defined microbial mock community
journal, September 2016
- Singer, Esther; Andreopoulos, Bill; Bowers, Robert M.
- Scientific Data, Vol. 3, Issue 1
The effects of sequencing platforms on phylogenetic resolution in 16 S rRNA gene profiling of human feces
journal, April 2018
- Whon, Tae Woong; Chung, Won-Hyong; Lim, Mi Young
- Scientific Data, Vol. 5, Issue 1
From hairballs to hypotheses–biological insights from microbial networks
journal, July 2018
- Röttjers, Lisa; Faust, Karoline
- FEMS Microbiology Reviews, Vol. 42, Issue 6
NanoAmpli-Seq: a workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform
journal, November 2018
- Calus, Szymon T.; Ijaz, Umer Z.; Pinto, Ameet J.
- GigaScience, Vol. 7, Issue 12
Systematic processing of ribosomal RNA gene amplicon sequencing data
journal, December 2019
- Tremblay, Julien; Yergeau, Etienne
- GigaScience, Vol. 8, Issue 12
High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution
journal, July 2019
- Callahan, Benjamin J.; Wong, Joan; Heiner, Cheryl
- Nucleic Acids Research, Vol. 47, Issue 18
Thousands of primer-free, high-quality, full-length SSU rRNA sequences from all domains of life
journal, August 2016
- Karst, Søren M.; Dueholm, Morten S.; McIlroy, Simon J.
- Nature Biotechnology
Using MinION ™ to characterize dog skin microbiota through full-length 16S rRNA gene sequencing approach
posted_content, July 2017
- Cuscó, Anna; Viñes, Joaquim; D’Andreano, Sara
- bioRxiv
Interpretations of microbial community studies are biased by the selected 16S rRNA gene amplicon sequencing pipeline
posted_content, December 2019
- Straub, Daniel; Blackwell, Nia; Fuentes, Adrian Langarica
CaptureSeq: Capture-based enrichment of cpn60 gene fragments empowers pan-Domain profiling of microbial communities without universal PCR
preprint, August 2020
- Links, Matthew G.; Dumonceaux, Tim J.; McCarthy, Luke
Combining the 5.8S and ITS2 gene regions to improve classification of fungi
preprint, February 2019
- Heeger, Felix; Wurzbacher, Christian; Bourne, Elizabeth C.
Highly Multiplexed Spatial Mapping of Microbial Communities
posted_content, June 2019
- Shi, Hao; Zipfel, Warren; Brito, Ilana
- bioRxiv
High-resolution sequencing reveals unexplored archaeal diversity in freshwater wetland soils: Freshwater wetland archaeal diversity
journal, March 2017
- Narrowe, Adrienne B.; Angle, Jordan C.; Daly, Rebecca A.
- Environmental Microbiology, Vol. 19, Issue 6
Comparative genomics and physiology of the genus Methanohalophilus , a prevalent methanogen in hydraulically fractured shale
journal, December 2018
- Borton, Mikayla A.; Daly, Rebecca A.; O'Banion, Bridget
- Environmental Microbiology, Vol. 20, Issue 12
Dietary polysaccharides: fermentation potentials of a primitive gut ecosystem
journal, March 2019
- Zeibich, Lydia; Schmidt, Oliver; Drake, Harold L.
- Environmental Microbiology, Vol. 21, Issue 4
Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S‐ITS‐23S rRNA operon
journal, May 2019
- Martijn, Joran; Lind, Anders E.; Schön, Max E.
- Environmental Microbiology, Vol. 21, Issue 7
Interkingdom microbial consortia mechanisms to guide biotechnological applications
journal, July 2018
- Zhang, Shu; Merino, Nancy; Okamoto, Akihiro
- Microbial Biotechnology, Vol. 11, Issue 5
Long-read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments
journal, September 2018
- Heeger, Felix; Bourne, Elizabeth C.; Baschien, Christiane
- Molecular Ecology Resources, Vol. 18, Issue 6
Introducing ribosomal tandem repeat barcoding for fungi
journal, October 2018
- Wurzbacher, Christian; Larsson, Ellen; Bengtsson‐Palme, Johan
- Molecular Ecology Resources, Vol. 19, Issue 1
Combining the 5.8S and ITS2 to improve classification of fungi
journal, August 2019
- Heeger, Felix; Wurzbacher, Christian; Bourne, Elizabeth C.
- Methods in Ecology and Evolution, Vol. 10, Issue 10
Delineation of ecologically distinct units of marine Bacteroidetes in the Northwestern Mediterranean Sea
journal, May 2019
- Díez‐Vives, Cristina; Nielsen, Shaun; Sánchez, Pablo
- Molecular Ecology
High-resolution community profiling of arbuscular mycorrhizal fungi
journal, July 2016
- Schlaeppi, Klaus; Bender, S. Franz; Mascher, Fabio
- New Phytologist, Vol. 212, Issue 3
PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives
journal, September 2017
- Tedersoo, Leho; Tooming-Klunderud, Ave; Anslan, Sten
- New Phytologist, Vol. 217, Issue 3
Probing promise versus performance in longer read fungal metabarcoding
journal, January 2018
- Kennedy, Peter G.; Cline, Lauren C.; Song, Zewei
- New Phytologist, Vol. 217, Issue 3
Relative Performance of MinION (Oxford Nanopore Technologies) versus Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens
journal, August 2019
- Loit, Kaire; Adamson, Kalev; Bahram, Mohammad
- Applied and Environmental Microbiology, Vol. 85, Issue 21
Studying microbial functionality within the gut ecosystem by systems biology
journal, March 2018
- Hornung, Bastian; Martins dos Santos, Vitor A. P.; Smidt, Hauke
- Genes & Nutrition, Vol. 13, Issue 1
Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification
journal, November 2016
- Wagner, Josef; Coupland, Paul; Browne, Hilary P.
- BMC Microbiology, Vol. 16, Issue 1
Profiling of koumiss microbiota and organic acids and their effects on koumiss taste
journal, April 2020
- Tang, Hai; Ma, Huimin; Hou, Qiangchuan
- BMC Microbiology, Vol. 20, Issue 1
Hybridization capture reveals microbial diversity missed using current profiling methods
journal, March 2018
- Gasc, Cyrielle; Peyret, Pierre
- Microbiome, Vol. 6, Issue 1
Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes
journal, October 2018
- Earl, Joshua P.; Adappa, Nithin D.; Krol, Jaroslaw
- Microbiome, Vol. 6, Issue 1
From Vineyard Soil to Wine Fermentation: Microbiome Approximations to Explain the “terroir” Concept
journal, May 2017
- Belda, Ignacio; Zarraonaindia, Iratxe; Perisin, Matthew
- Frontiers in Microbiology, Vol. 8
High Throughput Sequencing for Detection of Foodborne Pathogens
journal, October 2017
- Sekse, Camilla; Holst-Jensen, Arne; Dobrindt, Ulrich
- Frontiers in Microbiology, Vol. 8
Belowground Microbiota and the Health of Tree Crops
journal, June 2018
- Mercado-Blanco, Jesús; Abrantes, Isabel; Barra Caracciolo, Anna
- Frontiers in Microbiology, Vol. 9
The Not-so-Sterile Womb: Evidence That the Human Fetus Is Exposed to Bacteria Prior to Birth
journal, June 2019
- Stinson, Lisa F.; Boyce, Mary C.; Payne, Matthew S.
- Frontiers in Microbiology, Vol. 10
Identification of Microbial Profiles in Heavy-Metal-Contaminated Soil from Full-Length 16S rRNA Reads Sequenced by a PacBio System
journal, September 2019
- Hur, Moonsuk; Park, Soo-Je
- Microorganisms, Vol. 7, Issue 9
Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system
journal, January 2016
- Schloss, Patrick D.; Jenior, Matthew L.; Koumpouras, Charles C.
- PeerJ, Vol. 4
A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq
journal, January 2016
- Burke, Catherine M.; Darling, Aaron E.
- PeerJ, Vol. 4
How conserved are the conserved 16S-rRNA regions?
journal, January 2017
- Martinez-Porchas, Marcel; Villalpando-Canchola, Enrique; Ortiz Suarez, Luis Enrique
- PeerJ, Vol. 5
Anaerobic Biodegradation of Hydrocarbons: Metagenomics and Metabolomics
book, January 2019
- Gieg, Lisa M.; Toth, Courtney R. A.
- Consequences of Microbial Interactions with Hydrocarbons, Oils, and Lipids: Biodegradation and Bioremediation
Introducing ribosomal tandem repeat barcoding for fungi
posted_content, April 2018
- Wurzbacher, Christian; Larsson, Ellen; Bengtsson-Palme, Johan
- bioRxiv
Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification.
journalarticle, January 2016
- Wagner, Josef; Coupland, Paul; Browne, Hilary P.
- Springer Science and Business Media LLC
Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system
preprint, February 2016
- Schloss, Patrick D.; Jenior, Matthew L.; Koumpouras, Charles C. .
High-resolution community profiling of arbuscular mycorrhizal fungi
text, January 2016
- Schlaeppi, Klaus; Bender, S. Franz; Mascher, Fabio
- Wiley-Blackwell Publishing, Inc.
CAMISIM: simulating metagenomes and microbial communities
journal, February 2019
- Fritz, Adrian; Hofmann, Peter; Majda, Stephan
- Microbiome, Vol. 7, Issue 1
The Role of Land Use Types and Water Chemical Properties in Structuring the Microbiomes of a Connected Lake System
journal, February 2020
- Marmen, Sophi; Blank, Lior; Al-Ashhab, Ashraf
- Frontiers in Microbiology, Vol. 11
Profiling of Koumiss Microbiota and Organic Acids and their Effects on Koumiss Taste
preprint, April 2020
- Tang, Hai; Ma, Huimin; Hou, Qiangchuan
Profiling of Koumiss Microbiota and Organic Acids and their Effects on Koumiss Taste
preprint, April 2020
- Tang, Hai; Ma, Huimin; Hou, Qiangchuan
- Research Square
Full‐length 16S rRNA gene classification of Atlantic salmon bacteria and effects of using different 16S variable regions on community structure analysis
journal, July 2019
- Klemetsen, Terje; Willassen, Nils Peder; Karlsen, Christian René
- MicrobiologyOpen, Vol. 8, Issue 10
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
Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies
journal, November 2019
- Sevim, Volkan; Lee, Juna; Egan, Robert
- Scientific Data, Vol. 6, Issue 1
High resolution profiling of coral-associated bacterial communities using full-length 16S rRNA sequence data from PacBio SMRT sequencing system
journal, June 2017
- Pootakham, Wirulda; Mhuantong, Wuttichai; Yoocha, Thippawan
- Scientific Reports, Vol. 7, Issue 1
Next generation sequencing data of a defined microbial mock community
journal, September 2016
- Singer, Esther; Andreopoulos, Bill; Bowers, Robert M.
- Scientific Data, Vol. 3, Issue 1
The effects of sequencing platforms on phylogenetic resolution in 16 S rRNA gene profiling of human feces
journal, April 2018
- Whon, Tae Woong; Chung, Won-Hyong; Lim, Mi Young
- Scientific Data, Vol. 5, Issue 1
Large-scale 16S gene assembly using metagenomics shotgun sequences
journal, January 2017
- Zeng, Feng; Wang, Zicheng; Wang, Ying
- Bioinformatics, Vol. 33, Issue 10
From hairballs to hypotheses–biological insights from microbial networks
journal, July 2018
- Röttjers, Lisa; Faust, Karoline
- FEMS Microbiology Reviews, Vol. 42, Issue 6
Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies
journal, October 2018
- Gardner, Paul P.; Watson, Renee J.; Morgan, Xochitl C.
- PeerJ
Combining the 5.8S and ITS2 gene regions to improve classification of fungi
preprint, February 2019
- Heeger, Felix; Wurzbacher, Christian; Bourne, Elizabeth C.
Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S‐ITS‐23S rRNA operon
journal, May 2019
- Martijn, Joran; Lind, Anders E.; Schön, Max E.
- Environmental Microbiology, Vol. 21, Issue 7
Interkingdom microbial consortia mechanisms to guide biotechnological applications
journal, July 2018
- Zhang, Shu; Merino, Nancy; Okamoto, Akihiro
- Microbial Biotechnology, Vol. 11, Issue 5
Introducing ribosomal tandem repeat barcoding for fungi
journal, October 2018
- Wurzbacher, Christian; Larsson, Ellen; Bengtsson‐Palme, Johan
- Molecular Ecology Resources, Vol. 19, Issue 1
Protein- and RNA-Enhanced Fermentation by Gut Microbiota of the Earthworm Lumbricus terrestris
journal, June 2018
- Zeibich, Lydia; Schmidt, Oliver; Drake, Harold L.
- Applied and Environmental Microbiology, Vol. 84, Issue 11
Amino Acids and Ribose: Drivers of Protein and RNA Fermentation by Ingested Bacteria of a Primitive Gut Ecosystem
journal, October 2019
- Zeibich, Lydia; Staege, Maraike; Schmidt, Oliver
- Applied and Environmental Microbiology, Vol. 85, Issue 19
Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification
journal, November 2016
- Wagner, Josef; Coupland, Paul; Browne, Hilary P.
- BMC Microbiology, Vol. 16, Issue 1
G3 PhyloChip Analysis Confirms the Promise of Plant-Based Culture Media for Unlocking the Composition and Diversity of the Maize Root Microbiome and for Recovering Unculturable Candidate Divisions/Phyla
journal, January 2018
- Sarhan, Mohamed S.; Patz, Sascha; Hamza, Mervat A.
- Microbes and Environments, Vol. 33, Issue 3
From Vineyard Soil to Wine Fermentation: Microbiome Approximations to Explain the “terroir” Concept
journal, May 2017
- Belda, Ignacio; Zarraonaindia, Iratxe; Perisin, Matthew
- Frontiers in Microbiology, Vol. 8
High Throughput Sequencing for Detection of Foodborne Pathogens
journal, October 2017
- Sekse, Camilla; Holst-Jensen, Arne; Dobrindt, Ulrich
- Frontiers in Microbiology, Vol. 8
The Not-so-Sterile Womb: Evidence That the Human Fetus Is Exposed to Bacteria Prior to Birth
journal, June 2019
- Stinson, Lisa F.; Boyce, Mary C.; Payne, Matthew S.
- Frontiers in Microbiology, Vol. 10
A Bioinformatics Guide to Plant Microbiome Analysis
journal, October 2019
- Lucaciu, Rares; Pelikan, Claus; Gerner, Samuel M.
- Frontiers in Plant Science, Vol. 10
Full-Length Multi-Barcoding: DNA Barcoding from Single Ingredient to Complex Mixtures
journal, May 2019
- Zhang, Peng; Liu, Chunsheng; Zheng, Xiasheng
- Genes, Vol. 10, Issue 5
Identification of Microbial Profiles in Heavy-Metal-Contaminated Soil from Full-Length 16S rRNA Reads Sequenced by a PacBio System
journal, September 2019
- Hur, Moonsuk; Park, Soo-Je
- Microorganisms, Vol. 7, Issue 9
The Root Nodule Microbiome of Cultivated and Wild Halophytic Legumes Showed Similar Diversity but Distinct Community Structure in Yellow River Delta Saline Soils
journal, February 2020
- Zheng, Yanfen; Liang, Jing; Zhao, Dong-Lin
- Microorganisms, Vol. 8, Issue 2
Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system
journal, January 2016
- Schloss, Patrick D.; Jenior, Matthew L.; Koumpouras, Charles C.
- PeerJ, Vol. 4
A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq
journal, January 2016
- Burke, Catherine M.; Darling, Aaron E.
- PeerJ, Vol. 4
How conserved are the conserved 16S-rRNA regions?
journal, January 2017
- Martinez-Porchas, Marcel; Villalpando-Canchola, Enrique; Ortiz Suarez, Luis Enrique
- PeerJ, Vol. 5