Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Search research articles

Related Experiment Video

Updated: Oct 31, 2025

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

METAnnotatorX2: a Comprehensive Tool for Deep and Shallow Metagenomic Data Set Analyses.

Christian Milani^1,2, Gabriele Andrea Lugli¹, Federico Fontana^1,3

¹Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.

|June 29, 2021

Summary

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Concomitant Assessment of Oral and Gastric Microbiota Composition in Autoimmune Gastritis Patients: A Case-Control Study.

Microorganisms·2026

Same author

Exploring the molecular crosstalk between the sex steroids drospirenone and ethinylestradiol with vaginal lactobacilli.

Frontiers in microbiology·2026

Same author

Unveiling the genetic landscape and motility-associated functions of Type IV pili in the <i>Bifidobacterium</i> genus.

Microbiome research reports·2026

Same author

Assessment of genome evolution in <i>Bifidobacterium adolescentis</i> indicates genetic adaptation to the human gut.

mSystems·2026

Same author

Microbial BioRemediation Database: A Comprehensive Database of Genes Involved in Microbial Bioremediation Processes.

MicrobiologyOpen·2026

Same author

Disclosing the effects of pea-derived proteins on the human gut microbiota.

Microbiome research reports·2025

A new bioinformatic platform, METAnnotatorX2, enhances metagenomic analysis by integrating short and long DNA reads. It offers improved accuracy and user-friendliness for taxonomic and functional profiling, overcoming limitations of existing tools.

Area of Science:

Bioinformatics
Metagenomics
Computational Biology

Background:

Current bioinformatic tools for metagenomic analysis are fragmented and lack a gold standard.
Existing software often requires millions of reads and uses approximations, leading to suboptimal accuracy, sensitivity, and specificity.
Novel sequencing technologies like Nanopore and PacBio generate long reads, but lack integrated analysis tools for hybrid data.

Purpose of the Study:

To develop a comprehensive, user-friendly bioinformatic platform, METAnnotatorX2, for optimized metagenomic data analysis.
To enable integrated analysis of both short and long DNA reads.
To improve the accuracy and quality of taxonomic and functional profiling from metagenomic data.

Main Methods:

Development of METAnnotatorX2, a bioinformatic platform with adaptable pipelines.

Keywords:

deep functional profiling metagenomics shallow taxonomy

More Related Videos

Metagenomic Analysis of Silage

Metagenomic Analysis of Silage

Published on: January 13, 2017

Evaluating the Impact of Hydraulic Fracturing on Streams using Microbial Molecular Signatures

Evaluating the Impact of Hydraulic Fracturing on Streams using Microbial Molecular Signatures

Published on: April 4, 2021

Related Experiment Videos

Last Updated: Oct 31, 2025

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

Metagenomic Analysis of Silage

Metagenomic Analysis of Silage

Published on: January 13, 2017

Evaluating the Impact of Hydraulic Fracturing on Streams using Microbial Molecular Signatures

Evaluating the Impact of Hydraulic Fracturing on Streams using Microbial Molecular Signatures

Published on: April 4, 2021

Creation of custom, taxonomically revised genomic databases for viruses, prokaryotes, and eukaryotes.

Testing and validation using artificial and real biological samples with Illumina and Nanopore sequencing data.

Main Results:

METAnnotatorX2 demonstrated high performance in extracting taxonomic and functional information from sequence reads.
The platform successfully assembled and processed genomes from metagenomic data.
Validation on artificial and real-world datasets confirmed the robustness and accuracy of METAnnotatorX2 compared to other tools.

Conclusions:

METAnnotatorX2 provides an optimized solution for analyzing deep and shallow metagenomic datasets.
The platform supports integrated analysis of short and long reads with enhanced sensitivity and specificity.
METAnnotatorX2 offers a robust and user-friendly tool for comprehensive metagenomic analysis.