Species Core Genome (SCG)
Definition The Species Core Genome (SCG) is the artificially generated genome sequence that contains the set of core genes within a species. How to construct
Tag: Taxonomy
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True taxonomic identities of ATCC Microbiome Standards
Microbiome standards are important both for the evaluation and effective standardization of methodologies used in microbiome sequencing and bioinformatics analysis. In this document, the genomes
Course: Prokaryotic Taxonomy and Microbiome
This is a collection of articles and resources for prokaryotic taxonomy and microbiome study. This is developed by Jon Jongsik Chun at Seoul National University,
Identification of Lachnospiraceae bacterium 5_1_63FAA
The genome sequence that is labeled as “Lachnospiraceae bacterium 5_1_63FAA” has been included in most microbiome taxonomic profiling software tools, and has therefore appeared in
Bacterial Nomenclature 101 and How to Describe a New Species
A short survival guide for microbiologists How are names controlled? Bacterial nomenclature and naming are regulated by the  International Code of Nomenclature of Prokaryotes (shortly the
Identification of Ruminococcus sp. 5_1_39BFAA
Many genome sequences in public databases are used in metagenomic studies to understand the human microbiome. Unfortunately, many of the taxonomic identities of these genomes
[Tutorial] Discover Biomarkers Facilitating Anti-PD-L1 Efficacy
Discover Biomarkers Facilitating Anti-PD-L1 Efficacy The gut microbiota plays an important role in shaping systemic immune responses. In a study published in the journal Science,
Type strain and reference strain
There is significant confusion between bacterial type strains and reference strains. The type strain is defined in the context of formal bacterial taxonomy whereas reference
[Tutorial] Exploring kimchi microbiota
Kimchi is a traditional side dish made from salted and fermented vegetables. When the fermentation is right, the pH of the cabbage kimchi reaches ~4.2.
Taxonomy of Clostridium clusters XIVa and IV
Clostridium clusters XIVa and IV are groups of bacteria that have been known as major players in the human microbiome(Hold et al., 2002;Frank et al.,
[Tutorial] Identifying a bacterial strain using a genome sequence
Welcome! The purpose of this tutorial is to get familiar with EzBioCloud’s many functions, and to be able to apply that knowledge to a scenario
[Quiz] Identification of bacterium in a probiotic product
Probiotics are defined as live microorganisms that are thought to provide health benefits when consumed. The most popular probiotic organisms are bacteria belonging to a
Taxonomic group
“Taxonomic group” in EzBioCloud 16S database Even though 16S rRNA gene has been widely used in the classification and identification of Bacteria and Archaea, it has
[Tutorial] Comparison of respiratory tract microbiomes between healthy and diseased humans
Welcome! In this tutorial, we will work with you to compare human respiratory samples between diseased and healthy subjects to get you familiarized with EzBioCloud’s microbiome taxonomic
Pairwise nucleotide sequence alignment for taxonomy
Pairwise DNA sequence alignment is achieved by adding gaps (-) into sequences, so two sequences are aligned each other according to their homology. Two bases aligned
[Quiz] Sequence similarities of small subunit rRNA genes
Objectives: Small subunit ribosomal RNA (rRNA) gene is one of the most widely used phylogenetic markers or DNA barcodes. A similarity between two DNA sequences is
Genomes in this data set
This table contains the following information (only selected columns are explained): Title of column Description  Download CLG CLG is a data file with a special
Erroneous DNA G+C content data determined by HPLC and thermal melting experiments are no longer required for species descriptions
In the recent paper (Kim et al., 2015), we evaluated DNA G+C content data obtained by HPLC and thermal melting experiments (Tm) with more accurate
How to calculate 16S rRNA sequence similarity values for bacterial taxonomy: Why BLAST should be avoided
Nucleotide sequence similarity values are widely used for identification and description of novel species among bacterial taxonomists. There are many different algorithms available for calculating
