ArticleMicrobiome2018
Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX.
Article in Microbiome, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers, 1 of them a synthesis that pooled it.
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Who cites it
50 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Investigating the infant gut microbiota in developing countries: worldwide metagenomic meta-analysis involving infants living in sub-urban areas of Côte d'Ivoire.Environmental microbiology reports · 2021Pooled it
- Intestinal Microbial Composition of Children in a Randomized Controlled Trial of Probiotics to Treat Acute Gastroenteritis.Frontiers in cellular and infection microbiology · 2022Trial
- Fecal calprotectin and gut microbiome in a cohort without intestinal pathologies from northern Italy.iScience · 2026Article
- Artificial Intelligence in Bacteriophage Science: A Comprehensive Narrative Review of Applications, Challenges, and Translational Opportunities.Antibiotics (Basel, Switzerland) · 2026Review
- Optimizing methods for virome analysis based on studies of a synthetic viral community.mSystems · 2026Article
- Review
- Impact of phage enrichment on the observed infant gut phageome.Microbiology spectrum · 2026Article
- Severity of Depressive Symptoms by Perceived Stress and Gut Microbiota Composition: A Sex-Stratified Bayesian Approach in a Non-Clinical Sample.Stress and health : journal of the International Society for the Investigation of Stress · 2026Article
- Optimizing methods for virome analysis based on studies of a synthetic viral community.bioRxiv : the preprint server for biology · 2025Article
- Identification of bacteriophage DNA in human umbilical cord blood.JCI insight · 2025Article
- Functional modulation of the human gut microbiome by bacteria vehicled by cheese.Applied and environmental microbiology · 2025Article
- Heart rate variability, daily cortisol indices and their association with psychometric characteristics and gut microbiota composition in an Italian community sample.Scientific reports · 2025Article
- Exploring diversity and functional contribution of the microbiome of traditional Italian dry-cured hams.Current research in microbial sciences · 2025Article
- Relationship between Infant Feeding and the Microbiome: Implications for Allergies and Food Intolerances.Children (Basel, Switzerland) · 2024Review
- Viromic and Metagenomic Analyses of Commercial Spirulina Fermentations Reveal Remarkable Microbial Diversity.Viruses · 2024Article
- Species-level characterization of saliva and dental plaque microbiota reveals putative bacterial and functional biomarkers of periodontal diseases in dogs.FEMS microbiology ecology · 2024Article
- Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation.mSystems · 2024Article
- Saponin treatment for eukaryotic DNA depletion alters the microbial DNA profiles by reducing the abundance of Gram-negative bacteria in metagenomics analyses.Microbiome research reports · 2024Article
- A Metagenomics Approach to Enumerate Bacteriophages in a Food Niche.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Review
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Authors and funding
16 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDespite 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.
resultsFive 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.
conclusionsResults 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.
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