GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes

Boyd, Joel A.; Woodcroft, Ben J.; Tyson, Gene W.

doi:10.1093/nar/gky174

Title: GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes

Journal Article · Mon Mar 19 00:00:00 EDT 2018 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gky174· OSTI ID:1439479

Boyd, Joel A. ^[1]; Woodcroft, Ben J. ^[1]; Tyson, Gene W. ^[1]

Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia 4072, Queensland, Australia

Large-scale metagenomic datasets enable the recovery of hundreds of population genomes from environmental samples. However, these genomes do not typically represent the full diversity of complex microbial communities. Gene-centric approaches can be used to gain a comprehensive view of diversity by examining each read independently, but traditional pairwise comparison approaches typically over-classify taxonomy and scale poorly with increasing metagenome and database sizes. Here we introduce GraftM, a tool that uses gene specific packages to rapidly identify gene families in metagenomic data using hidden Markov models (HMMs) or DIAMOND databases, and classifies these sequences using placement into pre-constructed gene trees. The speed and accuracy of GraftM was benchmarked with in silico and in vitro mock communities using taxonomic markers, and was found to have higher accuracy at the family level with a processing time 2.0–3.7× faster than currently available software. Exploration of a wetland metagenome using 16S rRNA- and methyl-coenzyme M reductase (McrA)-specific gpkgs revealed taxonomic and functional shifts across a depth gradient. Analysis of the NCBI nr database using the McrA gpkg allowed the detection of novel sequences belonging to phylum-level lineages. A growing collection of gpkgs is available online (https://github.com/geronimp/graftM_gpkgs), where curated packages can be uploaded and exchanged.

View Journal Article

Cite

Export

Save

Research Organization:: Univ. of Arizona, Tucson, AZ (United States); The Ohio State Univ., Columbus, OH (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0004632; SC0010580; SC0016440

OSTI ID:: 1439479

Alternate ID(s):: OSTI ID: 1502447

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Vol. 46 Journal Issue: 10; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United Kingdom

Language:: English

Citation Metrics:

Cited by: 69 works

Citation information provided by
Web of Science

References (43)

Adaptive seeds tame genomic sequence comparison Kielbasa, S. M.; Wan, R.; Sato, K. Genome Research, Vol. 21, Issue 3 https://doi.org/10.1101/gr.113985.110	journal	January 2011
Quantitative Phylogenetic Assessment of Microbial Communities in Diverse Environments von Mering, C.; Hugenholtz, P.; Raes, J. Science, Vol. 315, Issue 5815 https://doi.org/10.1126/science.1133420	journal	February 2007
Prokka: rapid prokaryotic genome annotation Seemann, T. Bioinformatics, Vol. 30, Issue 14 https://doi.org/10.1093/bioinformatics/btu153	journal	March 2014
Tackling soil diversity with the assembly of large, complex metagenomes Howe, Adina Chuang; Jansson, Janet K.; Malfatti, Stephanie A. Proceedings of the National Academy of Sciences, Vol. 111, Issue 13 https://doi.org/10.1073/pnas.1402564111	journal	March 2014
Using the Metagenomics RAST Server (MG-RAST) for Analyzing Shotgun Metagenomes Glass, E. M.; Wilkening, J.; Wilke, A. Cold Spring Harbor Protocols, Vol. 2010, Issue 1 https://doi.org/10.1101/pdb.prot5368	journal	January 2010
Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics Evans, P. N.; Parks, D. H.; Chadwick, G. L. Science, Vol. 350, Issue 6259 https://doi.org/10.1126/science.aac7745	journal	October 2015
Phylogeny-aware identification and correction of taxonomically mislabeled sequences Kozlov, Alexey M.; Zhang, Jiajie; Yilmaz, Pelin Nucleic Acids Research, Vol. 44, Issue 11 https://doi.org/10.1093/nar/gkw396	journal	May 2016
The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity Galagan, J. E. Genome Research, Vol. 12, Issue 4 https://doi.org/10.1101/gr.223902	journal	April 2002
Phylogenetic classification of short environmental DNA fragments Krause, Lutz; Diaz, Naryttza N.; Goesmann, Alexander Nucleic Acids Research, Vol. 36, Issue 7 https://doi.org/10.1093/nar/gkn038	journal	February 2008
ARB: a software environment for sequence data Ludwig, W. Nucleic Acids Research, Vol. 32, Issue 4 https://doi.org/10.1093/nar/gkh293	journal	February 2004
Climate change and the permafrost carbon feedback Schuur, E. A. G.; McGuire, A. D.; Schädel, C. Nature, Vol. 520, Issue 7546 https://doi.org/10.1038/nature14338	journal	April 2015
Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics Rinke, Christian; Low, Serene; Woodcroft, Ben J. PeerJ, Vol. 4 https://doi.org/10.7717/peerj.2486	journal	January 2016
Accelerated Profile HMM Searches Eddy, Sean R. PLoS Computational Biology, Vol. 7, Issue 10 https://doi.org/10.1371/journal.pcbi.1002195	journal	October 2011
Unusual biology across a group comprising more than 15% of domain Bacteria Brown, Christopher T.; Hug, Laura A.; Thomas, Brian C. Nature, Vol. 523, Issue 7559 https://doi.org/10.1038/nature14486	journal	June 2015
Edge Principal Components and Squash Clustering: Using the Special Structure of Phylogenetic Placement Data for Sample Comparison Matsen IV, Frederick A.; Evans, Steven N. PLoS ONE, Vol. 8, Issue 3 https://doi.org/10.1371/journal.pone.0056859	journal	March 2013
Fast and accurate short read alignment with Burrows-Wheeler transform Li, H.; Durbin, R. Bioinformatics, Vol. 25, Issue 14 https://doi.org/10.1093/bioinformatics/btp324	journal	May 2009
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes Albertsen, Mads; Hugenholtz, Philip; Skarshewski, Adam Nature Biotechnology, Vol. 31, Issue 6 https://doi.org/10.1038/nbt.2579	journal	May 2013
Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla Wrighton, K. C.; Thomas, B. C.; Sharon, I. Science, Vol. 337, Issue 6102 https://doi.org/10.1126/science.1224041	journal	September 2012
Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software Sczyrba, Alexander; Hofmann, Peter; Belmann, Peter Nature Methods, Vol. 14, Issue 11 https://doi.org/10.1038/nmeth.4458	journal	October 2017
Decadal vegetation changes in a northern peatland, greenhouse gas fluxes and net radiative forcing Johansson, TorbjÖRn; Malmer, Nils; Crill, Patrick M. Global Change Biology, Vol. 12, Issue 12 https://doi.org/10.1111/j.1365-2486.2006.01267.x	journal	December 2006
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea McDonald, Daniel; Price, Morgan N.; Goodrich, Julia The ISME Journal, Vol. 6, Issue 3 https://doi.org/10.1038/ismej.2011.139	journal	December 2011
Community structure and metabolism through reconstruction of microbial genomes from the environment Tyson, Gene W.; Chapman, Jarrod; Hugenholtz, Philip Nature, Vol. 428, Issue 6978 https://doi.org/10.1038/nature02340	journal	February 2004
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2	journal	October 1990
Treephyler: fast taxonomic profiling of metagenomes Schreiber, F.; Gumrich, P.; Daniel, R. Bioinformatics, Vol. 26, Issue 7 https://doi.org/10.1093/bioinformatics/btq070	journal	February 2010
OrfM: a fast open reading frame predictor for metagenomic data Woodcroft, Ben J.; Boyd, Joel A.; Tyson, Gene W. Bioinformatics, Vol. 32, Issue 17 https://doi.org/10.1093/bioinformatics/btw241	journal	May 2016
Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota Vanwonterghem, Inka; Evans, Paul N.; Parks, Donovan H. Nature Microbiology, Vol. 1, Issue 12 https://doi.org/10.1038/nmicrobiol.2016.170	journal	October 2016
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009490	journal	March 2010
RefSeq: an update on prokaryotic genome annotation and curation Haft, Daniel H.; DiCuccio, Michael; Badretdin, Azat Nucleic Acids Research, Vol. 46, Issue D1 https://doi.org/10.1093/nar/gkx1068	journal	November 2017
PhyloSift: phylogenetic analysis of genomes and metagenomes Darling, Aaron E.; Jospin, Guillaume; Lowe, Eric PeerJ, Vol. 2 https://doi.org/10.7717/peerj.243	journal	January 2014
Hidden Markov Models in Computational Biology Krogh, Anders; Brown, Michael; Mian, I. Saira Journal of Molecular Biology, Vol. 235, Issue 5 https://doi.org/10.1006/jmbi.1994.1104	journal	February 1994
Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood Berger, Simon A.; Krompass, Denis; Stamatakis, Alexandros Systematic Biology, Vol. 60, Issue 3 https://doi.org/10.1093/sysbio/syr010	journal	March 2011
IMG: the integrated microbial genomes database and comparative analysis system Markowitz, V. M.; Chen, I. -M. A.; Palaniappan, K. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1044	journal	December 2011
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities Kang, Dongwan D.; Froula, Jeff; Egan, Rob PeerJ, Vol. 3 https://doi.org/10.7717/peerj.1165	journal	January 2015
Integrative analysis of environmental sequences using MEGAN4 Huson, D. H.; Mitra, S.; Ruscheweyh, H. -J. Genome Research, Vol. 21, Issue 9 https://doi.org/10.1101/gr.120618.111	journal	June 2011
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree Matsen, Frederick A.; Kodner, Robin B.; Armbrust, E. Virginia BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-538	journal	October 2010
Rapid identification of high-confidence taxonomic assignments for metagenomic data MacDonald, Norman J.; Parks, Donovan H.; Beiko, Robert G. Nucleic Acids Research, Vol. 40, Issue 14 https://doi.org/10.1093/nar/gks335	journal	April 2012
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T. Genome Research, Vol. 25, Issue 7 https://doi.org/10.1101/gr.186072.114	journal	May 2015
MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes Petrenko, Pavel; Lobb, Briallen; Kurtz, Daniel A. BMC Biology, Vol. 13, Issue 1 https://doi.org/10.1186/s12915-015-0195-4	journal	November 2015
Fast and sensitive protein alignment using DIAMOND Buchfink, Benjamin; Xie, Chao; Huson, Daniel H. Nature Methods, Vol. 12, Issue 1 https://doi.org/10.1038/nmeth.3176	journal	November 2014
Interactive metagenomic visualization in a Web browser Ondov, Brian D.; Bergman, Nicholas H.; Phillippy, Adam M. BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-385	journal	September 2011
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm Wu, Yu-Wei; Tang, Yung-Hsu; Tringe, Susannah G. Microbiome, Vol. 2, Issue 1 https://doi.org/10.1186/2049-2618-2-26	journal	August 2014
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability Katoh, K.; Standley, D. M. Molecular Biology and Evolution, Vol. 30, Issue 4 https://doi.org/10.1093/molbev/mst010	journal	January 2013
Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies Schnoes, Alexandra M.; Brown, Shoshana D.; Dodevski, Igor PLoS Computational Biology, Vol. 5, Issue 12 https://doi.org/10.1371/journal.pcbi.1000605	journal	December 2009

Cited By (18)

Methanotrophy across a natural permafrost thaw environment Singleton, Caitlin M.; McCalley, Carmody K.; Woodcroft, Ben J. The ISME Journal, Vol. 12, Issue 10 https://doi.org/10.1038/s41396-018-0065-5	journal	June 2018
iMicrobe: Tools and data-driven discovery platform for the microbiome sciences Youens-Clark, Ken; Bomhoff, Matt; Ponsero, Alise J. GigaScience, Vol. 8, Issue 7 https://doi.org/10.1093/gigascience/giz083	journal	July 2019
Distinct Taxonomic and Functional Profiles of the Microbiome Associated With Different Soil Horizons of a Moist Tussock Tundra in Alaska Tripathi, Binu M.; Kim1, Hye Min; Jung, Ji Young Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01442	journal	June 2019
Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi Boyd, Joel A.; Jungbluth, Sean P.; Leu, Andy O. The ISME Journal, Vol. 13, Issue 5 https://doi.org/10.1038/s41396-018-0343-2	journal	January 2019
Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae Leu, Andy O.; Cai, Chen; McIlroy, Simon J. The ISME Journal, Vol. 14, Issue 4 https://doi.org/10.1038/s41396-020-0590-x	journal	January 2020
Characterization of a sponge microbiome using an integrative genome-centric approach Engelberts, J. Pamela; Robbins, Steven J.; de Goeij, Jasper M. The ISME Journal, Vol. 14, Issue 5 https://doi.org/10.1038/s41396-020-0591-9	journal	January 2020
Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments Dong, Xiyang; Greening, Chris; Rattray, Jayne E. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-09747-0	journal	April 2019
Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea Hua, Zheng-Shuang; Wang, Yu-Lin; Evans, Paul N. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-12574-y	journal	October 2019
Bacterial fermentation and respiration processes are uncoupled in anoxic permeable sediments Kessler, Adam J.; Chen, Ya-Jou; Waite, David W. Nature Microbiology, Vol. 4, Issue 6 https://doi.org/10.1038/s41564-019-0391-z	journal	March 2019
Defining the human gut host–phage network through single-cell viral tagging Džunková, Mária; Low, Soo Jen; Daly, Joshua N. Nature Microbiology, Vol. 4, Issue 12 https://doi.org/10.1038/s41564-019-0526-2	journal	August 2019
A genomic view of the reef-building coral Porites lutea and its microbial symbionts Robbins, Steven J.; Singleton, Caitlin M.; Chan, Cheong Xin Nature Microbiology, Vol. 4, Issue 12 https://doi.org/10.1038/s41564-019-0532-4	journal	September 2019
An evolving view of methane metabolism in the Archaea Evans, Paul N.; Boyd, Joel A.; Leu, Andy O. Nature Reviews Microbiology, Vol. 17, Issue 4 https://doi.org/10.1038/s41579-018-0136-7	journal	January 2019
Genome-centric view of carbon processing in thawing permafrost Woodcroft, Ben J.; Singleton, Caitlin M.; Boyd, Joel A. Nature, Vol. 560, Issue 7716 https://doi.org/10.1038/s41586-018-0338-1	journal	July 2018
PhyloMagnet: fast and accurate screening of short-read meta-omics data using gene-centric phylogenetics Schön, Max E.; Eme, Laura; Ettema, Thijs J. G. Bioinformatics https://doi.org/10.1093/bioinformatics/btz799	journal	October 2019
Heliorhodopsins are absent in diderm (Gram‐negative) bacteria: Some thoughts and possible implications for activity Flores‐Uribe, José; Hevroni, Gur; Ghai, Rohit Environmental Microbiology Reports, Vol. 11, Issue 3 https://doi.org/10.1111/1758-2229.12730	journal	January 2019
Predominance of Anaerobic, Spore-Forming Bacteria in Metabolically Active Microbial Communities from Ancient Siberian Permafrost Liang, Renxing; Lau, Maggie; Vishnivetskaya, Tatiana Applied and Environmental Microbiology, Vol. 85, Issue 15 https://doi.org/10.1128/aem.00560-19	journal	May 2019
Draft Genome Sequence of “Candidatus Bathyarchaeota” Archaeon BE326-BA-RLH, an Uncultured Denitrifier and Putative Anaerobic Methanotroph from South Africa’s Deep Continental Biosphere Harris, Rachel L.; Lau, Maggie C. Y.; Cadar, Andreia Microbiology Resource Announcements, Vol. 7, Issue 20 https://doi.org/10.1128/mra.01295-18	journal	November 2018
Archaea dominate the microbial community in an ecosystem with low-to-moderate temperature and extreme acidity Korzhenkov, Aleksei A.; Toshchakov, Stepan V.; Bargiela, Rafael Microbiome, Vol. 7, Issue 1 https://doi.org/10.1186/s40168-019-0623-8	journal	January 2019