ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores

Orellana, Luis H.; Rodriguez-R, Luis M.; Konstantinidis, Konstantinos T.

doi:10.1093/nar/gkw900

Title: ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores

Journal Article · Fri Oct 07 00:00:00 EDT 2016 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkw900· OSTI ID:1356171

^[1];

^[2];

^[3]

Georgia Inst. of Technology, Atlanta, GA (United States). School of Civil and Environmental Engineering
Georgia Inst. of Technology, Atlanta, GA (United States). Center for Bioinformatics and Computational Genomics. School of Biological Sciences
Georgia Inst. of Technology, Atlanta, GA (United States). School of Civil and Environmental Engineering. Center for Bioinformatics and Computational Genomics. School of Biological Sciences

Functional annotation of metagenomic and metatranscriptomic data sets relies on similarity searches based on e-value thresholds resulting in an unknown number of false positive and negative matches. To overcome these limitations, we introduce ROCker, aimed at identifying position-specific,most-discriminant thresholds in sliding windows along the sequence of a target protein, accounting for non-discriminative domains shared by unrelated proteins. ROCker employs the receiver operating characteristic (ROC) curve to minimize false discovery rate (FDR) and calculate the best thresholds based on how simulated shotgun metagenomic reads of known composition map onto well-curated reference protein sequences and thus, differs from HMM profiles and related methods. We showcase ROCker using ammonia monooxygenase (amoA) and nitrous oxide reductase (nosZ) genes, mediating oxidation of ammonia and the reduction of the potent greenhouse gas, N2O, to inert N2, respectively. ROCker typically showed 60-fold lower FDR when compared to the common practice of using fixed e-values. Previously uncounted ‘atypical’ nosZ genes were found to be two times more abundant, on average, than their typical counterparts in most soil metagenomes and the abundance of bacterial amoA was quantified against the highly-related particulate methane monooxygenase (pmoA). Therefore, ROCker can reliably detect and quantify target genes in short-read metagenomes.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Georgia Institute of Technology, Atlanta, GA (United States)

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

Grant/Contract Number:: SC0006662; 1241046; 1356288

OSTI ID:: 1356171

Alternate ID(s):: OSTI ID: 1362281

Journal Information:: Nucleic Acids Research, Vol. 45, Issue 3; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 31 works

Citation information provided by
Web of Science

References (47)

Grinder: a versatile amplicon and shotgun sequence simulator Angly, Florent E.; Willner, Dana; Rohwer, Forest Nucleic Acids Research, Vol. 40, Issue 12 https://doi.org/10.1093/nar/gks251	journal	March 2012
pROC: an open-source package for R and S+ to analyze and compare ROC curves Robin, Xavier; Turck, Natacha; Hainard, Alexandre BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-77	journal	March 2011
Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill Mason, Olivia U.; Scott, Nicole M.; Gonzalez, Antonio The ISME Journal, Vol. 8, Issue 7 https://doi.org/10.1038/ismej.2013.254	journal	January 2014
MEGAN analysis of metagenomic data Huson, D. H.; Auch, A. F.; Qi, J. Genome Research, Vol. 17, Issue 3 https://doi.org/10.1101/gr.5969107	journal	February 2007
A Format for Phylogenetic Placements Matsen, Frederick A.; Hoffman, Noah G.; Gallagher, Aaron PLoS ONE, Vol. 7, Issue 2 https://doi.org/10.1371/journal.pone.0031009	journal	February 2012
Cross-biome metagenomic analyses of soil microbial communities and their functional attributes Fierer, N.; Leff, J. W.; Adams, B. J. Proceedings of the National Academy of Sciences, Vol. 109, Issue 52 https://doi.org/10.1073/pnas.1215210110	journal	December 2012
GRASP: Guided Reference-based Assembly of Short Peptides Zhong, Cuncong; Yang, Youngik; Yooseph, Shibu Nucleic Acids Research, Vol. 43, Issue 3 https://doi.org/10.1093/nar/gku1210	journal	November 2014
Archaea predominate among ammonia-oxidizing prokaryotes in soils Leininger, S.; Urich, T.; Schloter, M. Nature, Vol. 442, Issue 7104 https://doi.org/10.1038/nature04983	journal	August 2006
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega Sievers, Fabian; Wilm, Andreas; Dineen, David Molecular Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1038/msb.2011.75	journal	January 2011
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
MUSCLE: multiple sequence alignment with high accuracy and high throughput Edgar, R. C. Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797 https://doi.org/10.1093/nar/gkh340	journal	March 2004
UProC: tools for ultra-fast protein domain classification Meinicke, Peter Bioinformatics, Vol. 31, Issue 9 https://doi.org/10.1093/bioinformatics/btu843	journal	December 2014
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
Opitutus terrae gen. nov., sp. nov., to accommodate novel strains of the division 'Verrucomicrobia' isolated from rice paddy soil Chin, K. J.; Liesack, W.; Janssen, P. H. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 51, Issue 6 https://doi.org/10.1099/00207713-51-6-1965	journal	November 2001
Bacteria rather than Archaea dominate microbial ammonia oxidation in an agricultural soil Jia, Zhongjun; Conrad, Ralf Environmental Microbiology, Vol. 11, Issue 7 https://doi.org/10.1111/j.1462-2920.2009.01891.x	journal	July 2009
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy Letunic, I.; Bork, P. Nucleic Acids Research, Vol. 39, Issue suppl https://doi.org/10.1093/nar/gkr201	journal	April 2011
FunGene: the functional gene pipeline and repository Fish, Jordan A.; Chai, Benli; Wang, Qiong Frontiers in Microbiology, Vol. 4 https://doi.org/10.3389/fmicb.2013.00291	journal	January 2013
The human microbiome: there is much left to do Ley, Ruth Nature, Vol. 606, Issue 7914 https://doi.org/10.1038/d41586-022-01610-5	journal	June 2022
The ammonia monooxygenase structural gene amoA as a functional marker: molecular fine-scale analysis of natural ammonia-oxidizing populations. Rotthauwe, J. H.; Witzel, K. P.; Liesack, W. Applied and environmental microbiology, Vol. 63, Issue 12 https://doi.org/10.1128/aem.63.12.4704-4712.1997	journal	January 1997
‘Candidatus Competibacter’-lineage genomes retrieved from metagenomes reveal functional metabolic diversity McIlroy, Simon J.; Albertsen, Mads; Andresen, Eva K. The ISME Journal, Vol. 8, Issue 3 https://doi.org/10.1038/ismej.2013.162	journal	October 2013
Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw Mackelprang, Rachel; Waldrop, Mark P.; DeAngelis, Kristen M. Nature, Vol. 480, Issue 7377 https://doi.org/10.1038/nature10576	journal	November 2011
A Bioinformatician's Guide to Metagenomics Kunin, V.; Copeland, A.; Lapidus, A. Microbiology and Molecular Biology Reviews, Vol. 72, Issue 4 https://doi.org/10.1128/MMBR.00009-08	journal	December 2008
Taxonomic classification of metagenomic shotgun sequences with CARMA3 Gerlach, Wolfgang; Stoye, Jens Nucleic Acids Research, Vol. 39, Issue 14 https://doi.org/10.1093/nar/gkr225	journal	May 2011
Detecting Nitrous Oxide Reductase (nosZ) Genes in Soil Metagenomes: Method Development and Implications for the Nitrogen Cycle Orellana, L. H.; Rodriguez-R, L. M.; Higgins, S. mBio, Vol. 5, Issue 3 https://doi.org/10.1128/mBio.01193-14	journal	June 2014
Analysis Tool Web Services from the EMBL-EBI McWilliam, Hamish; Li, Weizhong; Uludag, Mahmut Nucleic Acids Research, Vol. 41, Issue W1 https://doi.org/10.1093/nar/gkt376	journal	May 2013
BLAST+: architecture and applications Camacho, Christiam; Coulouris, George; Avagyan, Vahram BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-421	journal	January 2009
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
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
FragGeneScan: predicting genes in short and error-prone reads Rho, Mina; Tang, Haixu; Ye, Yuzhen Nucleic Acids Research, Vol. 38, Issue 20 https://doi.org/10.1093/nar/gkq747	journal	August 2010
Soil Microbial Community Responses to a Decade of Warming as Revealed by Comparative Metagenomics Luo, Chengwei; Rodriguez-R, Luis M.; Johnston, Eric R. Applied and Environmental Microbiology, Vol. 80, Issue 5 https://doi.org/10.1128/AEM.03712-13	journal	December 2013
Microbial community successional patterns in beach sands impacted by the Deepwater Horizon oil spill Rodriguez-R, Luis M.; Overholt, Will A.; Hagan, Christopher The ISME Journal, Vol. 9, Issue 9 https://doi.org/10.1038/ismej.2015.5	journal	February 2015
SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data Cox, Murray P.; Peterson, Daniel A.; Biggs, Patrick J. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-485	journal	September 2010
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models Stamatakis, Alexandros Bioinformatics, Vol. 22, Issue 21 https://doi.org/10.1093/bioinformatics/btl446	journal	August 2006
Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils Sanford, R. A.; Wagner, D. D.; Wu, Q. Proceedings of the National Academy of Sciences, Vol. 109, Issue 48 https://doi.org/10.1073/pnas.1211238109	journal	November 2012
The unaccounted yet abundant nitrous oxide-reducing microbial community: a potential nitrous oxide sink Jones, Christopher M.; Graf, Daniel RH; Bru, David The ISME Journal, Vol. 7, Issue 2 https://doi.org/10.1038/ismej.2012.125	journal	November 2012
Xander: employing a novel method for efficient gene-targeted metagenomic assembly Wang, Qiong; Fish, Jordan A.; Gilman, Mariah Microbiome, Vol. 3, Issue 1 https://doi.org/10.1186/s40168-015-0093-6	journal	August 2015
Type-2 copper-containing enzymes MacPherson, I. S.; Murphy, M. E. P. Cellular and Molecular Life Sciences, Vol. 64, Issue 22 https://doi.org/10.1007/s00018-007-7310-9	journal	September 2007
Crystal structure of a membrane-bound metalloenzyme that catalyses the biological oxidation of methane Lieberman, Raquel L.; Rosenzweig, Amy C. Nature, Vol. 434, Issue 7030 https://doi.org/10.1038/nature03311	journal	January 2005
Isolation of an autotrophic ammonia-oxidizing marine archaeon Könneke, Martin; Bernhard, Anne E.; de la Torre, José R. Nature, Vol. 437, Issue 7058 https://doi.org/10.1038/nature03911	journal	September 2005
A novel family of functional operons encoding methane/ammonia monooxygenase-related proteins in gammaproteobacterial methanotrophs: Novel monooxygenase in Gamma-MOB Tavormina, Patricia L.; Orphan, Victoria J.; Kalyuzhnaya, Marina G. Environmental Microbiology Reports, Vol. 3, Issue 1 https://doi.org/10.1111/j.1758-2229.2010.00192.x	journal	February 2011
Structural conservation of the B subunit in the ammonia monooxygenase/particulate methane monooxygenase superfamily: Structure of an Archaeal amoB Domain Lawton, Thomas J.; Ham, Jungwha; Sun, Tianlin Proteins: Structure, Function, and Bioinformatics, Vol. 82, Issue 9 https://doi.org/10.1002/prot.24535	journal	March 2014
Comparative in silico analysis of PCR primers suited for diagnostics and cloning of ammonia monooxygenase genes from ammonia-oxidizing bacteria Junier, Pilar; Kim, Ok-Sun; Molina, VerÃ³nica FEMS Microbiology Ecology, Vol. 64, Issue 1 https://doi.org/10.1111/j.1574-6941.2007.00437.x	journal	April 2008
Evidence that participate methane monooxygenase and ammonia monooxygenase may be evolutionarily related Holmes, Andrew J.; Costello, Andria; Lidstrom, Mary E. FEMS Microbiology Letters, Vol. 132, Issue 3 https://doi.org/10.1111/j.1574-6968.1995.tb07834.x	journal	October 1995
Quantitative Detection of the nosZ Gene, Encoding Nitrous Oxide Reductase, and Comparison of the Abundances of 16S rRNA, narG, nirK, and nosZ Genes in Soils Henry, S.; Bru, D.; Stres, B. Applied and Environmental Microbiology, Vol. 72, Issue 8 https://doi.org/10.1128/AEM.00231-06	journal	August 2006
Insights into the Effect of Soil pH on N2O and N2 Emissions and Denitrifier Community Size and Activity Cuhel, J.; Simek, M.; Laughlin, R. J. Applied and Environmental Microbiology, Vol. 76, Issue 6 https://doi.org/10.1128/AEM.02484-09	journal	January 2010
Abundance of microbial genes associated with nitrogen cycling as indices of biogeochemical process rates across a vegetation gradient in Alaska: Functional genes predict potential N cycling rates Petersen, Dorthe Groth; Blazewicz, Steven J.; Firestone, Mary Environmental Microbiology, Vol. 14, Issue 4 https://doi.org/10.1111/j.1462-2920.2011.02679.x	journal	January 2012
Characterization and Description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an Aryl-Halorespiring Facultative Anaerobic Myxobacterium Sanford, R. A.; Cole, J. R.; Tiedje, J. M. Applied and Environmental Microbiology, Vol. 68, Issue 2 https://doi.org/10.1128/AEM.68.2.893-900.2002	journal	February 2002

Cited By (4)

Quantification of nosZ genes and transcripts in activated sludge microbiomes with novel group-specific qPCR methods validated with metagenomic analyses Kim, DaeHyun D.; Park, Doyoung; Yoon, Hyun Water Research https://doi.org/10.1101/710483	journal	January 2020
Comparing DNA, RNA and protein levels for measuring microbial dynamics in soil microcosms amended with nitrogen fertilizer Orellana, Luis H.; Hatt, Janet K.; Iyer, Ramsunder Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-53679-0	journal	November 2019
Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes Guo, Jiarong; Quensen, John F.; Sun, Yanni Frontiers in Genetics, Vol. 10 https://doi.org/10.3389/fgene.2019.00957	journal	October 2019
Niche differentiation among annually recurrent coastal Marine Group II Euryarchaeota Orellana, Luis H.; Ben Francis, T.; Krüger, Karen The ISME Journal, Vol. 13, Issue 12 https://doi.org/10.1038/s41396-019-0491-z	journal	August 2019

Similar Records

Detecting Nitrous Oxide Reductase (nosZ) Genes in Soil Metagenomes: Method Development and Implications for the Nitrogen Cycle

Journal Article · Tue Jun 03 00:00:00 EDT 2014 · mBio (Online) · OSTI ID:1356171

Orellana, L. H.; Rodriguez-R, L. M.; Higgins, S.; +5 more

Year-Round Shotgun Metagenomes Reveal Stable Microbial Communities in Agricultural Soils and Novel Ammonia Oxidizers Responding to Fertilization

Journal Article · Fri Nov 03 00:00:00 EDT 2017 · Applied and Environmental Microbiology · OSTI ID:1356171

Orellana, Luis H.; Chee-Sanford, Joanne C.; Sanford, Robert A.; +2 more

MetaFunPrimer: an Environment-Specific, High-Throughput Primer Design Tool for Improved Quantification of Target Genes

Journal Article · Tue Oct 26 00:00:00 EDT 2021 · mSystems · OSTI ID:1356171

Liu, Jia; Villanueva, Paul; Choi, Jinlyung; +12 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
97 MATHEMATICS AND COMPUTING
genes
soil
false-positive results
candidate disease gene
datasets

Title: ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores

Citation Formats

References (47)

Cited By (4)

Similar Records

Related Subjects