Taxonomy

Summary

The summary gives a comprehensive report on any taxa in the EzBioCloud taxonomy database. The section comprises three parts.

Identification and Characteristics

Outlines the fundamental biological features and genetic markers of a taxa, detailing its initial discovery, physical attributes, and distinguishing biochemical properties.

Pathogenicity and Host Range

Describes the prokaryotes's ability to cause disease and potential impact on organisms, including insects, plants, and humans, highlighting its broader ecological and pathological significance.

Diagnostic Tools and Applications

Discusses the development of methods for detecting such taxa and explores potential uses in medicine and agriculture.

Nomenclature

The Nomenclature section discusses identifying and characterizing a prokaryote species through a comprehensive taxonomic study. It involves analyzing multiple isolates to determine their classification within a known genus, comparing their phenotypic traits, genetic content, and biochemical activities to closely related species. Methods such as fatty acid methyl ester (FAME) analysis, DNA-DNA relatedness, and genome analysis are used to establish the uniqueness of the new species. The findings lead to the formal proposal of a new species, supported by genetic and phenotypic evidence.

Clinical Relevance

The Clinical Relevance table displays any diseases associated with an organism.

Disease

This column lists the types of diseases caused by the bacterium.

Reference

This column provides citations for the reports of the diseases, including the year of publication and relevant context.

Country

This column indicates the country where each disease was reported.

Host

This column specifies the types of organisms affected by each disease.

Healthy Human Microbiome Plot

This informative plot indicates the average relative abundance of a taxon across multiple healthy human microbiome cohorts. It compares the microbial community structure and diversity across different countries, aiding in understanding regional variations in the human microbiome.

Subtree

Status

The validity of a bacterial name as determined by the Prokaryotic Code.

Type Taxon

A type taxon is a reference organism that defines a taxonomic group, such as a species or genus.

Authors

This refers to the scientists who first described the species or taxonomic group.

Taxonomy

Lists the taxonomic hierarchy of taxa from the Domain level all the way down to the Species level.

Subtree

Select to display the depth level of the taxonomic trees.

Levels

In a taxonomic tree, 'levels' refer to the hierarchical stages, such as kingdom, phylum, class, order, family, genus, species.

Taxonomy

Status

The validity of a bacterial name as determined by the Prokaryotic Code.

Basonym

The original name given to a species upon first description, which may change if the species is reclassified.

Authors

This refers to the scientists who first described the species or taxonomic group.

Taxonomy

Lists the taxonomic hierarchy of taxa from the Domain level all the way down to the Species level.

NCBI

The National Center for Biotechnology Information, a major source for genomic and genetic data.

Taxonomy ID

Unique identifiers used by NCBI’s database to track and organize information on species.

CheckM

Software that assesses the quality of microbial genomes recovered from isolates, single cells, or metagenomes.

Submitter

The individual or organization that submitted the genomic data to a database.

GTDB Taxonomy

Genome-based taxonomy from the Genome Taxonomy Database.

Representative 16S

The 16S ribosomal RNA sequence that represents the taxonomic identity of a microbial sample.

Strain Name

The identifier given to a particular strain of an organism.

Method

The technique or approach used to obtain genomic data, such as genome sequencing or shotgun sequencing.

Representative Genome

The genomic sequence that represents a species or strain.

Assembly Type

The state of completion of the representative genome, such as a complete genome assembly or a draft (partial) assembly.

Country

The country from which the representative genomic sample was collected.

Source

The origin of the biological sample, like a specific environment or host.

Year

The year in which the sample was collected or the data was submitted.

Genome Size

The total amount of DNA contained within the representative genome, measured in base pairs.

Number of Contigs

Contigs are sequences that have been assembled from overlapping reads. This count indicates how many such sequences are in the genome assembly.

N50

A measure of genome assembly quality; N50 represents the length at which 50% of the assembled genome is in contigs of that length or longer.

16S Copy Number

The number of 16S ribosomal RNA gene copies in the organism's genome.

UBCG

Up-to-date Bacterial Core Gene set used for bacterial phylogenies.

GC Content

The percentage of the genome that is made up of guanine (G) and cytosine (C) nucleotides.

BioProject

An identifier associated with a collection of biological data related to a single initiative in the NCBI database.

BioSample

An identifier for a biological sample in the NCBI database from a specific organism at a specific time and place with associated metadata.

Taxonomy Levels

Kingdom

One of the highest taxonomic ranks, grouping together all forms of life having certain fundamental characteristics in common.

Phylum

A taxonomic ranking below kingdom and above class that groups together organisms with similar body plans.

Class

A rank in taxonomic classification that is below phylum and above order.

Order

A taxonomic rank used in the classification of organisms, below class and above family.

Family

A taxonomic category ranking below order and above genus, which groups together genera sharing certain broad features.

Genus

A way to group species together based on a shared set of features, more specific than family but broader than species.

Species

The most specific major taxonomic classification, which groups individual prokaryotic organisms that are closely related based on genetic similarity and other characteristics. These groups share a high degree of similarity in their DNA sequences and often have similar physiological and morphological traits.

Subspecies

A taxonomic category that ranks below species, representing populations of prokaryotic organisms that are genetically distinct and often isolated by ecological or geographical factors. These populations exhibit specific genetic and phenotypic differences from other groups within the same species, while still maintaining enough similarity to be classified under the same species.