Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

4.3K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
4.3K
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

834
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
834
Methods to Assess Microbial Communities01:19

Methods to Assess Microbial Communities

33
Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...
33
Applications of Molecular Taxonomy01:20

Applications of Molecular Taxonomy

653
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
653
Methods to Assess Microbial Populations01:30

Methods to Assess Microbial Populations

56
Assessing microbial populations is crucial for understanding microbial roles in health, ecology, and industry. Various complementary techniques—both culture-based and molecular—enable detailed analysis of microbial abundance, diversity, and function.Viable Plate CountThe viable plate count is a traditional culture-based method used to estimate the number of living microbes in a sample. After serial dilution, the sample is spread onto nutrient agar plates. Each viable cell forms a...
56
Microbial Classification System01:24

Microbial Classification System

1.6K
Classification is the process of organizing organisms into hierarchically inclusive groups based on their phenotypic similarities or evolutionary relationships. A species comprises one or more strains, and closely related species are grouped into genera. Genera are further classified into families, families into orders, orders into classes, and so forth, up to the domain level, which is the broadest taxonomic rank derived from a combination of phenotypic and genotypic data.The nomenclature of...
1.6K

You might also read

Related Articles

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

Sort by
Same author

The transcriptome of dendritic cells redraws the boundaries between pathogenicity and commensalism in yeast.

Microbial cell (Graz, Austria)·2026
Same author

Characterization of ovine abortion in Uruguay reveals extensive non-clonal diversity and multiple evolutionary origins of Toxoplasma gondii.

Scientific reports·2026
Same author

Deciphering Trypanosoma lainsoni kDNA minicircles: insights into genetic diversity, mRNA editing, and molecular diagnosis.

Parasite (Paris, France)·2026
Same author

Updated European Reference Network for rare Inherited and Congenital Digestive and Gastrointestinal Anomalies guidelines for the management of rectosigmoid Hirschsprung's disease 2025.

Journal of pediatric gastroenterology and nutrition·2026
Same author

Energy-efficient selection of high-yield PHA producers via microaerophilic uncoupled feeding.

Bioresource technology·2026
Same author

Linking microbial function and remote sensing for understanding drylands.

Trends in ecology & evolution·2026

Related Experiment Video

Updated: Mar 29, 2026

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
11:22

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

Published on: October 15, 2019

31.6K

riboFrame: An Improved Method for Microbial Taxonomy Profiling from Non-Targeted Metagenomics.

Matteo Ramazzotti1, Luisa Berná2, Claudio Donati3

  • 1Dipartimento di Scienze Biomediche Sperimentali e Cliniche, Università degli Studi di Firenze Firenze, Italy.

Frontiers in Genetics
|December 5, 2015
PubMed
Summary

RiboFrame enhances microbial profiling in non-targeted metagenomics by analyzing 16S rDNA sequences. This novel method improves taxonomic accuracy for understanding microbial communities.

Keywords:
16S rDNA genecommunity profilingmetagenomicsnon-targeted approachshort readsvariable region

More Related Videos

RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
12:05

RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing

Published on: August 7, 2021

9.5K
De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

4.3K

Related Experiment Videos

Last Updated: Mar 29, 2026

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
11:22

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

Published on: October 15, 2019

31.6K
RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
12:05

RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing

Published on: August 7, 2021

9.5K
De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

4.3K

Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Non-targeted metagenomics allows simultaneous investigation of microbial communities and their genetic potential.
  • Current microbial taxonomic profiling relies on mapping reads to genomic databases, which are often limited and biased.
  • Accurate microbial profiling is crucial for understanding complex biological systems.

Purpose of the Study:

  • To introduce riboFrame, a novel computational procedure for microbial profiling using 16S ribosomal DNA (rDNA) sequences within non-targeted metagenomics datasets.
  • To improve the accuracy and reliability of microbial community assessment in metagenomic samples.
  • To leverage the conserved yet variable nature of the 16S rDNA gene for enhanced taxonomic resolution.

Main Methods:

  • Identification and classification of 16S rDNA sequences using Hidden Markov Models (HMMs) and Naïve Bayesian classification.
  • Coherent positioning of identified ribosomal reads within the 16S rDNA gene sequence.
  • Utilizing the secondary structure and variable regions of the 16S rDNA gene to guide abundance analysis.

Main Results:

  • RiboFrame effectively identifies and classifies 16S rDNA sequences in non-targeted metagenomic data.
  • The method demonstrated accuracy on simulated ribosomal data, simulated metagenomes, and a real-world dataset.
  • Coherent read positioning and gene topology analysis improved abundance estimations.

Conclusions:

  • RiboFrame provides an accurate and robust method for microbial profiling in non-targeted metagenomics.
  • The procedure effectively exploits the taxonomic information within 16S rDNA sequences.
  • This approach offers a valuable tool for gaining deeper insights into microbial community composition.