1. EzBioCloud Database

2. Naming Convention

3. Analytics Methods
     Microbiome Taxonomic Profiling (MTP)    Whole Genome Analysis    16S Identification    Other Miscellaneous Bioinformatics Tools  

4. References

EzBioCloud^[1] is a microbial bioinformatics portal with its own database focusing on taxonomy, ecology, genomics, metagenomics, and microbiome of bacteria and archaea. The main databases are 16S rRNA DB and Genome DB analyzed through its own pipeline. All of these databases can be searched via EzBioCloud search engine.

EzBioCloud was published by ChunLab, Inc. in 2007 as EzTaxon^[2]. Although EzTaxon is mainly used for the routine identification of prokaryotic isolates, sequences from uncultured taxa were not included. Thus in 2012, it was extended to contain uncultured prokaryotes and the name of the database changed to EzTaxon-e^[3]. In the act of continuous updates in the database to cover bioinformatics tools and web-cloud services, Microbiome Taxonomic Profiling and Whole-genome analysis, the name changes once again to EzBioCloud in 2017.

EzBioCloud Database

• EzBioCloud database is consists of 62,988 species with 15,290 valid species and 121,767 whole genomes that were identified taxonomically at the genus, species, and subspecies level as of November 2018.
• The taxonomy hierarchical system of EzBioCloud database has the following principles.
• # All terminal taxa are represented by at least one 16S rRNA sequence.
• # All terminal taxa are assigned under their complete suprageneric ranks.
• # The taxonomic assignment is based on the phylogenetic relationship (maximum likelihood, OrthoANI).
• The database consists of the following sections:
• # EzBioCloud 16S DB: 16S rRNA gene provides a taxonomic framework for the whole EzBioCloud database. Basically, all species or subspecies are represented by a single 16S sequence, usually from type strains.
• # EzBioCloud Genome DB: Genomes are validated by various QC methods and are processed by the identical annotation pipeline. Taxonomic identities are checked by TrueBac database.
• # EzBioCloud Microbiome DB: An MTP (Microbiome Taxonomic Profiling) is a unit of data containing a taxonomic profile of a metagenomic sample.

Naming Convention

• Taxa names included in EzBioCloud have no standing in formal nomenclature but they were created to help in the comparison of microbial communities and diversity in nature.
• New names found in EzBioCloud are formed by adding special suffixes to GenBank sequence accession numbers of sequences (e.g. AB177171_s  → species of which the sequence entry AB177171 serves type; AB177171_g → genus; AB177171_f → family; AB177171_o → order; AB177171_c → class; AB177171_p → phylum).
• Well-known names have been preserved for historical reasons. SAR11, a famous marine inhabitant, is labeled as SAR11(order) and further divided into 4 families (SAR11-1_f to SAR11-4_f).
• Some misclassified species have been renamed using special suffixes based on 16S rRNA sequence phylogeny. For example, Bacteroides pectinophilus is not an authentic member of the genus Bacteroides, however, it may represent a novel genus in the family Lachnospiraceae. Therefore, in the EzTaxon-e database, Bacteroides pectinophilus is placed under a tentatively named new genus Bacteroides_g1.

Analytics Methods

Microbiome Taxonomic Profiling (MTP)

MTP analyzes the microbial community using data generated from various kinds of NGS platforms. It allows generating taxonomic profiles through the sequence quality filtering, chimera detection/calculation, identification process and clustering from the NGS data. It also provides functions that can easily group the taxonomic profiles and compare the profiles from different samples.

Whole Genome Analysis

It is for fast and accurate sequence assembly and annotation using NGS data. Genome contaminations are checked using ContEst16S^[4] and Bacterial Core Gene^[5]. All genome features can be navigated by various visualization tools such as genome browser. It can also compare up to 50 genomes to discover novel genomic islands, mutations, evidence for other evolutionary events.

16S Identification

The results of 16S rRNA sequences are listed in the order of high similarity that is calculated by pairwise sequence alignment against EzBioCloud 16S rRNA DB.

Other Miscellaneous Bioinformatics Tools

Several bioinformatics tools are provided for specific needs.

References

• List of Derry Gaelic footballers
• List of Desalination plants in Australia
• List of desalination plants in Australia
• List of descendants of Alfonso XIII of Spain
• List of Descendants of Darkness characters
• List of descendants of James II of England
• List of descendants of Louis XIV
• List of descendants of Louis XIV of France
• List of descendants of Philip V of Spain
• List of descendants of William Bradford (Plymouth governor)
• List of Descendents band members
• List of descriptions of Heaven in Abrahamic scriptures
• List of deserters from King James II to William of Orange
• List of Desert Island Discs episodes (1942 - 1946)
• List of Desert Island Discs episodes (1942 - 1950)
• List of Desert Island Discs episodes (1942 – 1946)
• List of Desert Island Discs episodes (1942–46)
• List of Desert Island Discs episodes (1951 - 1960)
• List of Desert Island Discs episodes (1951 – 1960)
• List of Desert Island Discs episodes (1951–60)
• List of Desert Island Discs episodes (1971 - 1980)
• List of Desert Island Discs episodes (1971 – 1980)
• List of Desert Island Discs episodes (1971–80)
• List of Desert Island Discs episodes (1981 - 1990)
• List of Desert Island Discs episodes (1981 – 1990)