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

RNA-seq03:21

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

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...
Ribosome Profiling02:24

Ribosome Profiling

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 helps...

You might also read

Related Articles

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

Sort by
Same author

Evaluation of Oscillatory Flow Conditions for Microalgal CO<sub>2</sub> Capture and Biomass Sedimentation Kinetics: Experimental and Mathematical Approach.

Biotech (Basel (Switzerland))·2026
Same author

On the Design of <i>Chlorella vulgaris</i> Composition for Potential Food Uses via Manipulation of Cultivation Conditions.

Marine drugs·2026
Same author

Sustainable Nutrient Recovery from Wastewater Mixture to Optimize Microalgal Lipid Production: A Vision of Zero Water Footprint.

Bioengineering (Basel, Switzerland)·2025
Same author

Comparing Growth Models Dependent on Irradiation and Nutrient Consumption on Closed Outdoor Cultivations of <i>Nannochloropsis</i> sp.

Bioengineering (Basel, Switzerland)·2025
Same author

Amino Acid and Carotenoid Profiles of <i>Chlorella vulgaris</i> During Two-Stage Cultivation at Different Salinities.

Bioengineering (Basel, Switzerland)·2025
Same author

Surfactant-Mediated Microalgal Flocculation: Process Efficiency and Kinetic Modelling.

Bioengineering (Basel, Switzerland)·2024
Same journal

Anti-Inflammatory Activity of a Phycocyanin-Protein Complex in THP-1 Cells: Implications for Dermocosmetic Applications.

Biotech (Basel (Switzerland))·2026
Same journal

Clinical Outcomes of Metronidazole Monotherapy Versus Metronidazole Plus <i>Clostridium butyricum</i> MIYAIRI 588 Combination Therapy in Non-Severe <i>Clostridioides difficile</i> Infection: A Retrospective Cohort Study.

Biotech (Basel (Switzerland))·2026
Same journal

The Gut Microbiome Dependency Continuum in Drug Discovery: A Unified Pharmacology Framework Linking Clinical Drugs, Natural Products, and Engineered Microbial Therapeutics.

Biotech (Basel (Switzerland))·2026
Same journal

Optimizing Light Intensity for the Co-Production of Fucoxanthin and Polyunsaturated Fatty Acids in <i>Isochrysis galbana</i>.

Biotech (Basel (Switzerland))·2026
Same journal

Regioselective Oxidation of D-Galacturonic Acid to Provide Crystallized Mucic Acid Using Engineered <i>Gluconobacter oxydans</i>.

Biotech (Basel (Switzerland))·2026
Same journal

Rabbit Immune Cell Function: In Vitro Assays for Immunological Assessment Studies Using Flow Cytometry.

Biotech (Basel (Switzerland))·2026
See all related articles

Related Experiment Video

Updated: Jun 26, 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

Bioinformatics Strategy for 16s and 23s rRNA Metabarcoding Data.

Rita Domingues1, José C M Pires1

  • 1LEPABE (Laboratory for Process Engineering, Environment, Biotechnology and Energy), ALiCE (Associate Laboratory in Chemical Engineering), Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal.

Biotech (Basel (Switzerland))
|June 25, 2026
PubMed
Summary
This summary is machine-generated.

A new bioinformatics pipeline, SOMBA, simplifies the analysis of 16S and 23S ribosomal RNA (rRNA) gene metabarcoding data. This user-friendly tool integrates essential steps for bacterial and microalgal community analysis, making complex data accessible.

Keywords:
16S rRNA23S rRNAOTU clusteringVSEARCHbioinformaticsmetagenomics

More Related Videos

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons
10:24

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Published on: August 29, 2014

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization
12:37

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization

Published on: April 14, 2016

Related Experiment Videos

Last Updated: Jun 26, 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

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons
10:24

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Published on: August 29, 2014

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization
12:37

Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization

Published on: April 14, 2016

Area of Science:

  • Microbiology
  • Bioinformatics
  • Ecology

Background:

  • Metabarcoding using ribosomal RNA (rRNA) genes (16S and 23S) is crucial for studying bacterial and microalgal communities.
  • Analyzing high-throughput sequencing data is complex due to fragmented tools and limited user accessibility.

Purpose of the Study:

  • To develop a user-friendly, comprehensive bioinformatics pipeline for analyzing 16S and 23S paired-end metabarcoding data.
  • To provide a standardized and accessible solution for processing dual-marker metabarcoding data.

Main Methods:

  • Developed a Python 3.11 pipeline integrating read merging, trimming, quality filtering, dereplication, chimaera removal, and Operational Taxonomic Unit (OTU) clustering.
  • Utilized VSEARCH and Cutadapt tools for robustness and efficiency.
  • Incorporated taxonomic assignment using EZBioCloud and µgreen databases.
  • Included modules for alpha and beta diversity analysis.

Main Results:

  • The pipeline, SOMBA, offers a unified, GUI-based framework for standardized processing of 16S/23S metabarcoding data.
  • Ensures consistency in parameterization, processing steps, and output structure across separate but harmonized workflows for each marker.
  • Facilitates robust and computationally efficient analysis.

Conclusions:

  • SOMBA provides an accessible and standardized solution for transforming raw sequencing data into reliable biological insights.
  • Supports applications in environmental microbiology and biotechnology by bridging the gap for non-specialist users.
  • Enables comprehensive ecological interpretation through integrated diversity analyses.