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Taxonomy

Taxonomy

Taxonomy is the science of defining and naming groups of biological organisms based on shared characteristics. It uses a hierarchy of increasingly inclusive categories with Latin names. The smallest units of taxonomy, species and genus, are used to assign a formal, taxonomic name to each species in a system. This classification system, referred to as binomial nomenclature, was formalized by Carolus Linnaeus in the 18th century.
Hierarchy of Taxonomy
The hierarchy that Carolus Linnaeus first...

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

Phylogeny

Phylogeny

Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.

Phylogenetic Trees

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.

Receiver Operating Characteristic Plot

Receiver Operating Characteristic Plot

A ROC (Receiver Operating Characteristic) plot is a graphical tool used to assess the performance of a binary classification model by illustrating the trade-off between sensitivity (true positive rate) and specificity (false positive rate). By plotting sensitivity against 1 - specificity across various threshold settings, the ROC curve shows how well the model distinguishes between classes, with a curve closer to the top-left corner indicating a more accurate model. The area under the ROC curve...

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Related Experiment Video

Updated: Jul 1, 2025

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing

Published on: August 25, 2018

Updated RDP taxonomy and RDP Classifier for more accurate taxonomic classification.

Qiong Wang¹, James R Cole²

¹Health & Biosciences, International Flavors & Fragrances, Inc., Wilmington, Delaware, USA.

Microbiology Resource Announcements

|March 4, 2024

Summary

The Ribosomal Database Project (RDP) Classifier, a popular machine learning tool for taxonomic classification, has been updated. These updates incorporate new taxa and reflect recent changes in prokaryotic nomenclature, enhancing its accuracy.

Keywords:

16S rRNA microbiome taxonomic classification taxonomy

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Last Updated: Jul 1, 2025

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Area of Science:

Microbiology
Bioinformatics
Machine Learning

Background:

The Ribosomal Database Project (RDP) Classifier is a widely used machine learning method for microbial taxonomic classification.
Its popularity stems from its robustness and high accuracy in assigning sequences to taxa.

Purpose of the Study:

To announce updates to the RDP Classifier and its associated taxonomy.
To ensure the tool reflects the latest scientific understanding of prokaryotic diversity and nomenclature.

Main Methods:

The RDP Classifier utilizes machine learning algorithms for sequence-based taxonomic assignment.
Updates involve incorporating newly described species and phylogenetic revisions.

Main Results:

The RDP taxonomy and Classifier have been revised.
These updates improve the classification of newly discovered prokaryotic taxa.

Conclusions:

The updated RDP Classifier provides a more accurate and current tool for microbial taxonomy.
Researchers can now leverage these enhancements for more precise prokaryotic classification.