Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX

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dc.contributor.authorMilani, Christian
dc.contributor.authorCaballero-Fonseca, F.
dc.contributor.authorLugli, Gabriele Andrea
dc.contributor.authorMoore, Rebecca
dc.contributor.authorKaczorowska, Joanna
dc.contributor.authorFeehily, Conor
dc.contributor.authorMangifesta, Marta
dc.contributor.authorMancabelli, Leonardo
dc.contributor.authorDuranti, Sabrina
dc.contributor.authorTurroni, Francesca
dc.contributor.authorBottacini, Francesca
dc.contributor.authorMahony, Jennifer
dc.contributor.authorCotter, Paul D.
dc.contributor.authorMcAuliffe, Fionnuala M.
dc.contributor.authorvan Sinderen, Douwe
dc.contributor.authorVentura, Marco
dc.contributor.funderScience Foundation Irelanden
dc.contributor.funderAlimentary Healthen
dc.contributor.funderEuropean Commissionen
dc.contributor.funderMinistero dell’Istruzione, dell’Università e della Ricercaen
dc.contributor.funderFondazione Cariparmaen
dc.date.accessioned2019-11-23T07:23:17Z
dc.date.available2019-11-23T07:23:17Z
dc.date.issued2018-08-20
dc.description.abstractBackground: Despite the relevance of viral populations, our knowledge of (bacterio) phage populations, i.e., the phageome, suffers from the absence of a “gold standard” protocol for viral DNA extraction with associated in silico sequence processing analyses. To overcome this apparent hiatus, we present here a comprehensive performance evaluation of various protocols and propose an optimized pipeline that covers DNA extraction, sequencing, and bioinformatic analysis of phageome data. Results: Five widely used protocols for viral DNA extraction from fecal samples were tested for their performance in removal of non-viral DNA. Moreover, we developed a novel bioinformatic platform, METAnnotatorX, for metagenomic dataset analysis. This in silico tool facilitates a range of read- and assembly-based analyses, including taxonomic profiling using an iterative multi-database pipeline, classification of contigs at genus and species level, as well as functional characterizations of reads and assembled data. Performances of METAnnotatorX were assessed through investigation of seven mother-newborn pairs, leading to the identification of shared phage genotypes, of which two were genomically decoded and characterized. METAnnotatorX was furthermore employed to evaluate a protocol for the identification of contaminant non-viral DNA in sequenced datasets and was exploited to determine the amount of metagenomic data needed for robust evaluation of human adult-derived (fecal) phageomes. Conclusions: Results obtained in this study demonstrate that a comprehensive pipeline for analysis of phageomes will be pivotal for future explorations of the ecology of phages in the gut environment as well as for understanding their impact on the physiology and bacterial community kinetics as players of dysbiosis and homeostasis in the gut microbiota.en
dc.description.sponsorshipScience Foundation Ireland (16/SP/3827, 15/JP-HDHL/3280); Fondazione Cariparma (TeachInParma project)en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.articleid145en
dc.identifier.citationMilani, C., Casey, E., Lugli, G.A., Moore, R., Kaczorowska, J., Feehily, C., Mangifesta, M., Mancabelli, L., Duranti, S., Turroni, F. and Bottacini, F. (2018) 'Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX'. Microbiome, 6(1), 145. (16pp). doi:10.1186/s40168-018-0527-zen
dc.identifier.doi10.1186/s40168-018-0527-zen
dc.identifier.eissn2049-2618
dc.identifier.endpage16en
dc.identifier.issued1en
dc.identifier.journaltitleMicrobiomeen
dc.identifier.startpage1en
dc.identifier.urihttps://hdl.handle.net/10468/9205
dc.identifier.volume6en
dc.language.isoenen
dc.publisherBioMed Central, Springer Natureen
dc.relation.projectinfo:eu-repo/grantAgreement/EC/H2020::CSA/696300/EU/The second coordination and support action for the JPI Healthy Diet for a Healthy Life/CSA JPI HDHL 2.0en
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Starting Investigator Research Grant (SIRG)/15/SIRG/3430/IE/Phage-host interactome of the dairy bacterium Streptococcus thermophilus (PHIST)/en
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/en
dc.relation.urihttps://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0527-z
dc.rights© The Author(s) 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectGut microbiotaen
dc.subjectMetagenomicsen
dc.subjectMetagenomeen
dc.subjectViromeen
dc.subjectGastro intestinal tracten
dc.subjectVertical transmissionen
dc.titleTracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorXen
dc.typeArticle (peer-reviewed)en
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