SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data

Silva, Genivaldo Gueiros Z.; Green, Kevin T.; Dutilh, Bas E.; Edwards, Robert A.

doi:10.1093/bioinformatics/btv584

Title: SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data

Journal Article · 08 October 2015 · Bioinformatics

DOI: https://doi.org/10.1093/bioinformatics/btv584 · OSTI ID:1261146

Silva, Genivaldo Gueiros Z. ^[1]; Green, Kevin T. ^[2]; Dutilh, Bas E. ^[3]; Edwards, Robert A. ^[4]

San Diego State Univ. San Diego, CA (United States). Computational Science Research Center
San Diego State Univ. San Diego, CA (United States). Dept. of Biology
Univ. of Utrecht (Netherlands); Radboud Univ., Nijmegen (Netherlands); Federal Univ. of Rio de Janeiro (Brazil)
San Diego State Univ. San Diego, CA (United States). Computational Science Research Center; San Diego State Univ. San Diego, CA (United States). Dept. of Biology; Federal Univ. of Rio de Janeiro (Brazil); San Diego State Univ. San Diego, CA (United States). Dept. of of Computer Science; Argonne National Lab. (ANL), Argonne, IL (United States)

Analyzing the functional profile of a microbial community from unannotated shotgun sequencing reads is one of the important goals in metagenomics. Functional profiling has valuable applications in biological research because it identifies the abundances of the functional genes of the organisms present in the original sample, answering the question what they can do. Currently, available tools do not scale well with increasing data volumes, which is important because both the number and lengths of the reads produced by sequencing platforms keep increasing. Here, we introduce SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances. We tested SUPER-FOCUS with over 70 real metagenomes, the results showing that it accurately predicts the subsystems present in the profiled microbial communities, and is up to 1000 times faster than other tools.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: National Science Foundation (NSF); USDOE

OSTI ID:: 1261146

Journal Information:: Bioinformatics, Journal Name: Bioinformatics Journal Issue: 3 Vol. 32; ISSN 1367-4803

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Metagenomic Analysis of Healthy and White Plague-Affected Mussismilia braziliensis Corals Garcia, Gizele D.; Gregoracci, Gustavo B.; de O. Santos, Eidy Microbial Ecology, Vol. 65, Issue 4 https://doi.org/10.1007/s00248-012-0161-4	journal	January 2013
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Closely-related Photobacterium strains comprise the majority of bacteria in the gut of migrating Atlantic cod (Gadus morhua) Le Doujet, Typhaine; De Santi, Concetta; Klemetsen, Terje Microbiome, Vol. 7, Issue 1 https://doi.org/10.1186/s40168-019-0681-y	journal	April 2019
The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge Doane, Michael P.; Morris, Megan M.; Papudeshi, Bhavya Microbiome, Vol. 8, Issue 1 https://doi.org/10.1186/s40168-020-00840-x	journal	June 2020
The skin microbiome of elasmobranchs follows phylosymbosis, but in teleost fishes the microbiomes converge Doane, Michael; Morris, Megan M.; Papudeshi, Bhavya https://doi.org/10.21203/rs.2.19644/v1	preprint	December 2019
The skin microbiome of elasmobranchs follows phylosymbosis, but in teleost fishes the microbiomes converge Doane, Michael; Morris, Megan M.; Papudeshi, Bhavya https://doi.org/10.21203/rs.2.19644/v2	posted_content	April 2020
Metagenomics of Thermophiles with a Focus on Discovery of Novel Thermozymes DeCastro, María-Eugenia; Rodríguez-Belmonte, Esther; González-Siso, María-Isabel Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.01521	journal	September 2016
Bacterial Community Associated with the Reef Coral Mussismilia braziliensis's Momentum Boundary Layer over a Diel Cycle Silveira, Cynthia B.; Gregoracci, Gustavo B.; Coutinho, Felipe H. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00784	journal	May 2017
Metagenomic Functional Potential Predicts Degradation Rates of a Model Organophosphorus Xenobiotic in Pesticide Contaminated Soils Jeffries, Thomas C.; Rayu, Smriti; Nielsen, Uffe N. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00147	journal	February 2018
Taxon-Function Decoupling as an Adaptive Signature of Lake Microbial Metacommunities Under a Chronic Polymetallic Pollution Gradient Cheaib, Bachar; Le Boulch, Malo; Mercier, Pierre-Luc Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00869	journal	May 2018
Gut Microbiome Biomarkers and Functional Diversity Within an Amazonian Semi-Nomadic Hunter–Gatherer Group Conteville, Liliane Costa; Oliveira-Ferreira, Joseli; Vicente, Ana Carolina Paulo Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01743	journal	July 2019
Metagenomics-Guided Survey, Isolation, and Characterization of Uranium Resistant Microbiota from the Savannah River Site, USA Genes, Vol. 10, Issue 5 https://doi.org/10.3390/genes10050325	journal	April 2019
Intermediate-Salinity Systems at High Altitudes in the Peruvian Andes Unveil a High Diversity and Abundance of Bacteria and Viruses Castelán-Sánchez, Hugo Gildardo; Elorrieta, Paola; Romoacca, Pedro Genes, Vol. 10, Issue 11 https://doi.org/10.3390/genes10110891	journal	November 2019
Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard Pratas, Diogo; Hosseini, Morteza; Grilo, Gonçalo Genes, Vol. 9, Issue 9 https://doi.org/10.3390/genes9090445	journal	September 2018
Metagenomics of Atacama Lithobiontic Extremophile Life Unveils Highlights on Fungal Communities, Biogeochemical Cycles and Carbohydrate-Active Enzymes Gómez-Silva, Benito; Vilo-Muñoz, Claudia; Galetović, Alexandra Microorganisms, Vol. 7, Issue 12 https://doi.org/10.3390/microorganisms7120619	journal	November 2019

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