Related Experiment Video
Updated: Oct 14, 2025
07:21
Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
Published on: August 25, 2018
13.0K
RESCRIPt: Reproducible sequence taxonomy reference database management
Michael S Robeson1, Devon R O'Rourke2, Benjamin D Kaehler3
1University of Arkansas for Medical Sciences, Department of Biomedical Informatics, Little Rock, Arkansas, United States of America.
Plos Computational Biology
|November 8, 2021
Summary
RESCRIPt software democratizes reference database creation for microbiome, eDNA, and genome studies. It enables reproducible generation and management of sequence databases, improving research transparency and comparability.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Nucleotide sequence and taxonomy reference databases are essential for microbiome analysis, metabarcoding, and environmental DNA (eDNA) surveys.
- Generating, managing, and evaluating these databases present significant challenges, hindering reproducibility and cross-study comparisons due to varying database compositions.
Purpose of the Study:
- To develop a robust software package (RESCRIPt) for reproducible generation and management of reference sequence taxonomy databases.
- To provide tools for evaluating, comparing, and exploring characteristics of different reference databases.
Main Methods:
- Developed RESCRIPt, a Python 3 software package and QIIME 2 plugin.
- Implemented functions for streamlined database creation from popular sources.
- Included functionalities for database evaluation, comparison, and interactive exploration.
Main Results:
- Demonstrated RESCRIPt's utility with popular databases (SILVA, Greengenes, NCBI-RefSeq, GTDB, BOLD, GenBank) for various applications.
- Showcased that database size is not the sole determinant of quality; standardized taxonomies and type strain focus offer advantages.
- Found that curation (quality filtering) benefits databases, while sequence clustering can be detrimental.
Conclusions:
- RESCRIPt empowers researchers to reproducibly and transparently create custom reference databases.
- The software addresses bottlenecks in database management, enhancing the reliability of microbiome, eDNA, and genomic analyses.
- RESCRIPt facilitates standardized and reproducible research workflows across diverse biological applications.
Related Concept Videos
01:24Microbial Classification System
304
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...
304
01:29Modern Molecular Taxonomy
262
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...
262
02:51Multi-species Conserved Sequences
4.3K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.3K
01:20Applications of Molecular Taxonomy
196
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...
196
02:54Evolutionary Relationships through Genome Comparisons
6.4K
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...
6.4K
02:40The Tree of Life - Bacteria, Archaea, Eukaryotes
35.8K
The “tree of life” describes the evolution of life and the evolutionary relationships between organisms. The root of the tree is the common ancestor to all life on Earth. All other species radiate from this point, much like the branches of a tree. The numerous tips of these branches on the tree of life represent every living, or extant, species. Extinct species, which are species that no longer exist, can be found towards the center of the tree. Currently, these organisms, both...
35.8K