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Article: Mining, analyzing, and integrating viral signals from metagenomic data

TitleMining, analyzing, and integrating viral signals from metagenomic data
Authors
Keywordsalgorithm
bacteriophage
Bacteroides
bioinformatics
community dynamics
Issue Date2019
PublisherBioMed Central Ltd. The Journal's web site is located at http://www.microbiomejournal.com/
Citation
Microbiome, 2019, v. 7, p. article no. 42 How to Cite?
AbstractBackground: Viruses are important components of microbial communities modulating community structure and function; however, only a couple of tools are currently available for phage identification and analysis from metagenomic sequencing data. Here we employed the random forest algorithm to develop VirMiner, a web-based phage contig prediction tool especially sensitive for high-abundances phage contigs, trained and validated by paired metagenomic and phagenomic sequencing data from the human gut flora. Results: VirMiner achieved 41.06%±17.51% sensitivity and 81.91%±4.04% specificity in the prediction of phage contigs. In particular, for the high-abundance phage contigs, VirMiner outperformed other tools (VirFinder and VirSorter) with much higher sensitivity (65.23%±16.94%) than VirFinder (34.63%±17.96%) and VirSorter (18.75%± 15.23%) at almost the same specificity. Moreover, VirMiner provides the most comprehensive phage analysis pipeline which is comprised of metagenomic raw reads processing, functional annotation, phage contig identification, and phage-host relationship prediction (CRISPR-spacer recognition) and supports two-group comparison when the input (metagenomic sequence data) includes different conditions (e.g., case and control). Application of VirMiner to an independent cohort of human gut metagenomes obtained from individuals treated with antibiotics revealed that 122 KEGG orthology and 118 Pfam groups had significantly differential abundance in the pre-treatment samples compared to samples at the end of antibiotic administration, including clustered regularly interspaced short palindromic repeats (CRISPR), multidrug resistance, and protein transport. The VirMiner webserver is available at http://sbb.hku.hk/VirMiner/. Conclusions: We developed a comprehensive tool for phage prediction and analysis for metagenomic samples. Compared to VirSorter and VirFinder—the most widely used tools—VirMiner is able to capture more highabundance phage contigs which could play key roles in infecting bacteria and modulating microbial community dynamics. Trial registration: The European Union Clinical Trials Register, EudraCT Number: 2013-003378-28. Registered on 9 April 2014 Keywords: Phage, Metagenome, Phage-host interaction, Antibiotics
Persistent Identifierhttp://hdl.handle.net/10722/273165
ISSN
2023 Impact Factor: 13.8
2023 SCImago Journal Rankings: 3.802
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorZheng, T-
dc.contributor.authorLi, J-
dc.contributor.authorNi, Y-
dc.contributor.authorKang, K-
dc.contributor.authorMisiakou, MA-
dc.contributor.authorImamovic, L-
dc.contributor.authorChow, BKC-
dc.contributor.authorRode, AA-
dc.contributor.authorBytzer, P-
dc.contributor.authorSommer, M-
dc.contributor.authorPanagiotou, G-
dc.date.accessioned2019-08-06T09:23:43Z-
dc.date.available2019-08-06T09:23:43Z-
dc.date.issued2019-
dc.identifier.citationMicrobiome, 2019, v. 7, p. article no. 42-
dc.identifier.issn2049-2618-
dc.identifier.urihttp://hdl.handle.net/10722/273165-
dc.description.abstractBackground: Viruses are important components of microbial communities modulating community structure and function; however, only a couple of tools are currently available for phage identification and analysis from metagenomic sequencing data. Here we employed the random forest algorithm to develop VirMiner, a web-based phage contig prediction tool especially sensitive for high-abundances phage contigs, trained and validated by paired metagenomic and phagenomic sequencing data from the human gut flora. Results: VirMiner achieved 41.06%±17.51% sensitivity and 81.91%±4.04% specificity in the prediction of phage contigs. In particular, for the high-abundance phage contigs, VirMiner outperformed other tools (VirFinder and VirSorter) with much higher sensitivity (65.23%±16.94%) than VirFinder (34.63%±17.96%) and VirSorter (18.75%± 15.23%) at almost the same specificity. Moreover, VirMiner provides the most comprehensive phage analysis pipeline which is comprised of metagenomic raw reads processing, functional annotation, phage contig identification, and phage-host relationship prediction (CRISPR-spacer recognition) and supports two-group comparison when the input (metagenomic sequence data) includes different conditions (e.g., case and control). Application of VirMiner to an independent cohort of human gut metagenomes obtained from individuals treated with antibiotics revealed that 122 KEGG orthology and 118 Pfam groups had significantly differential abundance in the pre-treatment samples compared to samples at the end of antibiotic administration, including clustered regularly interspaced short palindromic repeats (CRISPR), multidrug resistance, and protein transport. The VirMiner webserver is available at http://sbb.hku.hk/VirMiner/. Conclusions: We developed a comprehensive tool for phage prediction and analysis for metagenomic samples. Compared to VirSorter and VirFinder—the most widely used tools—VirMiner is able to capture more highabundance phage contigs which could play key roles in infecting bacteria and modulating microbial community dynamics. Trial registration: The European Union Clinical Trials Register, EudraCT Number: 2013-003378-28. Registered on 9 April 2014 Keywords: Phage, Metagenome, Phage-host interaction, Antibiotics-
dc.languageeng-
dc.publisherBioMed Central Ltd. The Journal's web site is located at http://www.microbiomejournal.com/-
dc.relation.ispartofMicrobiome-
dc.rightsMicrobiome. Copyright © BioMed Central Ltd.-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.subjectalgorithm-
dc.subjectbacteriophage-
dc.subjectBacteroides-
dc.subjectbioinformatics-
dc.subjectcommunity dynamics-
dc.titleMining, analyzing, and integrating viral signals from metagenomic data-
dc.typeArticle-
dc.identifier.emailChow, BKC: bkcc@hku.hk-
dc.identifier.authorityChow, BKC=rp00681-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1186/s40168-019-0657-y-
dc.identifier.pmid30890181-
dc.identifier.pmcidPMC6425642-
dc.identifier.scopuseid_2-s2.0-85063231120-
dc.identifier.hkuros299844-
dc.identifier.volume7-
dc.identifier.spagearticle no. 42-
dc.identifier.epagearticle no. 42-
dc.identifier.isiWOS:000462157900001-
dc.publisher.placeUnited Kingdom-
dc.identifier.issnl2049-2618-

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