Accurate read-based metagenome characterization using a hierarchical suite of unique signatures

Nucleic Acids Research
Tracey Allen K FreitasPatrick S G Chain

Abstract

A major challenge in the field of shotgun metagenomics is the accurate identification of organisms present within a microbial community, based on classification of short sequence reads. Though existing microbial community profiling methods have attempted to rapidly classify the millions of reads output from modern sequencers, the combination of incomplete databases, similarity among otherwise divergent genomes, errors and biases in sequencing technologies, and the large volumes of sequencing data required for metagenome sequencing has led to unacceptably high false discovery rates (FDR). Here, we present the application of a novel, gene-independent and signature-based metagenomic taxonomic profiling method with significantly and consistently smaller FDR than any other available method. Our algorithm circumvents false positives using a series of non-redundant signature databases and examines Genomic Origins Through Taxonomic CHAllenge (GOTTCHA). GOTTCHA was tested and validated on 20 synthetic and mock datasets ranging in community composition and complexity, was applied successfully to data generated from spiked environmental and clinical samples, and robustly demonstrates superior performance compared with other available tools.

References

Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Oct 4, 2002·Microbes and Infection·Ruiting Lan, Peter R Reeves
Oct 18, 2002·Proceedings of the National Academy of Sciences of the United States of America·Mya BreitbartForest Rohwer
Jan 23, 2003·Bioinformatics·Paul Pavlidis, William Stafford Noble
May 26, 2004·Proceedings. Biological Sciences·Mya BreitbartForest Rohwer
May 12, 2005·Nature Reviews. Microbiology·Robert A Edwards, Forest Rohwer
Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Mar 7, 2009·Clinical Chemistry·Joseph F PetrosinoJames Versalovic
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Aug 12, 2009·International Journal of Systematic and Evolutionary Microbiology·A GeigerG Cuny
Oct 10, 2009·Science·P S G ChainJ C Detter
Dec 25, 2009·Nature·Dongying WuJonathan A Eisen
Mar 26, 2010·The ISME Journal·Bánk BeszteriStephen J Giovannoni
Aug 11, 2010·FEMS Microbiology Letters·David J StudholmeJonathan D G Jones
Sep 28, 2010·Applied and Environmental Microbiology·Yao PanPaul L E Bodelier
Jan 11, 2011·Bioinformatics·Guillaume Marçais, Carl Kingsford
Jun 3, 2011·FEMS Microbiology Ecology·Nathalie LombardPascal Simonet
Jun 17, 2011·The ISME Journal·Patrick H Degnan, Howard Ochman
Dec 14, 2011·Current Opinion in Biotechnology·Matthew B ScholzPatrick S G Chain
Jan 24, 2012·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Roy R Chaudhuri, Ian R Henderson
Apr 18, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Sophie SchbathJean-François Gibrat
Jun 13, 2012·Nature Methods·Nicola SegataCurtis Huttenhower
Jun 16, 2012·Nature·UNKNOWN Human Microbiome Project Consortium
Jun 16, 2012·Nature·UNKNOWN Human Microbiome Project Consortium
Jun 22, 2012·PloS One·Kristine M WylieKatherine S Pollard
May 15, 2013·BMC Genomics·Sergei A SolonenkoMatthew B Sullivan
Jun 14, 2013·BMC Bioinformatics·Ayat HatemÜmit V Çatalyürek
Jul 3, 2013·Methods : a Companion to Methods in Enzymology·Matthew P A DavisAnton J Enright
Jul 12, 2013·PloS One·Vladimir LazarevicJacques Schrenzel
Oct 22, 2013·Nature Methods·Shinichi SunagawaPeer Bork

❮ Previous
Next ❯

Citations

May 15, 2015·Computational and Structural Biotechnology Journal·Sevasti FilippidouPilar Junier
Jun 18, 2016·Health Security·Norman A DoggettSegaran Pillai
Jan 21, 2017·Microbiome·Jeremy W CoxAleksey Porollo
Jan 19, 2016·Scientific Reports·Stinus LindgreenPaul P Gardner
Mar 18, 2017·Scientific Reports·Ashish YeriKendall Van Keuren-Jensen
Mar 23, 2017·GigaScience·Bonnie L BrownRima B Franklin
Dec 14, 2016·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·G R ThompsonD M Engelthaler
Jul 3, 2017·Intervirology·Andriniaina Andy Nkili-MeyongNicolas Berthet
Nov 9, 2016·MSystems·Nicholas A BokulichJ Gregory Caporaso
Aug 12, 2016·Journal of Clinical Microbiology·Amy S GargisIra M Lubin
Apr 4, 2019·GigaScience·Stuart M BrownKonstantinos Krampis
Sep 25, 2017·Genome Biology·Alexa B R McIntyreChristopher E Mason
Apr 11, 2019·BMC Genomics·Kui Hua, Xuegong Zhang
Jul 12, 2016·Nature Reviews. Microbiology·Jun Wang, Huijue Jia
Aug 10, 2017·Nature Reviews. Gastroenterology & Hepatology·Marcus J ClaessonPaul W O'Toole
Dec 19, 2019·Briefings in Bioinformatics·Richa Bharti, Dominik G Grimm
Feb 6, 2017·Indian Journal of Microbiology·Anukriti Sharma, Rup Lal
Apr 4, 2017·PeerJ·Temesgen Hailemariam DadiKnut Reinert
Aug 16, 2017·Microbiome·Vitor C PiroBernhard Y Renard
Oct 14, 2017·Briefings in Bioinformatics·Florian P BreitwieserSteven L Salzberg
Nov 9, 2018·PeerJ·Juan C CastroKonstantinos T Konstantinidis
May 10, 2018·Frontiers in Microbiology·Sam NooijMarion P G Koopmans
Dec 20, 2019·Emerging Infectious Diseases·Huahua YiMin Zhou
Oct 31, 2019·International Journal of Genomics·Andrew HatchMomchilo Vuyisich
Feb 7, 2020·International Journal of Molecular Sciences·Valery V PanyukovOlga N Ozoline
Sep 12, 2020·Genome Biology·Nathan LaPierreSerghei Mangul
Apr 13, 2018·Viruses·Casandra W PhilipsonKimberly A Bishop-Lilly
May 26, 2017·Frontiers in Microbiology·Danillo O AlvarengaAlessandro M Varani
Nov 18, 2018·Genome Biology·F P BreitwieserS L Salzberg

❮ Previous
Next ❯

Methods Mentioned

BETA
profiler
MDA
PCR
RNA
chips

Software Mentioned

Bowtie2
MetaPhlAn
MetaPhyler
PhyloPythiaS
samtools view
Jellyfish
MetaCV
GOTTCHA
MetaSim
Phymm

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.