Type

Journal Article

Authors

Marco Ventura
Douwe van Sinderen
Fionnuala M McAuliffe
Paul D. Cotter
Jennifer Mahony
Francesca Bottacini
Francesca Turroni
Sabrina Duranti
Leonardo Mancabelli
Marta Mangifesta
and 6 others

Subjects

Veterinary

Topics
gut microbiota performance evaluation metagenomics dna viral gastro intestinal tract metagenome virome vertical transmission

Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX (2018)

Abstract Background: 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.
Collections Ireland -> University College Cork -> APC Microbiome Institute
Ireland -> University College Cork -> College of Science, Engineering and Food Science
Ireland -> University College Cork -> APC Microbiome Institute- Journal Articles
Ireland -> University College Cork -> Microbiology
Ireland -> University College Cork -> Research Institutes and Centres
Ireland -> University College Cork -> Microbiology - Journal Articles

Full list of authors on original publication

Marco Ventura, Douwe van Sinderen, Fionnuala M McAuliffe, Paul D. Cotter, Jennifer Mahony, Francesca Bottacini, Francesca Turroni, Sabrina Duranti, Leonardo Mancabelli, Marta Mangifesta and 6 others

Experts in our system

1
Marco Ventura
University College Cork
Total Publications: 52
 
2
Douwe van Sinderen
University College Cork
Total Publications: 144
 
3
Fionnuala M McAuliffe
University College Dublin
Total Publications: 176
 
4
Paul D. Cotter
Teagasc
Total Publications: 296
 
5
Jennifer Mahony
University College Cork
Total Publications: 87
 
6
Francesca Bottacini
University College Cork
Total Publications: 32
 
7
Francesca Turroni
University College Cork
Total Publications: 24
 
8
Sabrina Duranti
University College Cork
Total Publications: 19
 
9
Leonardo Mancabelli
University College Cork
Total Publications: 16
 
10
Marta Mangifesta
University College Cork