Tag: NCBI Taxonomy

ASM Microbe 2022 was a success!

NCBI had the pleasure of attending and participating in this year’s American Society of Microbiology (ASM) Microbe conference, June 9-13 in Washington, D.C. NCBI staff participated in activities and events throughout the three-day conference. Over 4,500 attendees gathered in the exhibit hall and joined a variety of poster presentations and talks!

Reflections from a few of our NCBI experts

“It was a great honor for me to receive the ASM Elizabeth O. King Lecturer Award. Thank you to my colleagues, without whom so much of my work would not have been possible, and to all of those who attended my presentation on Making Genomics Accessible to Aid Public Health and Research.”

~Michael Feldgarden, Ph.D. Continue reading “ASM Microbe 2022 was a success!” →

Announcing an updated prokaryotic representative genomes collection with 706 new species!

An updated bacterial and archaeal representative genomes collection is available! A total of 16,105 assemblies among the 249,000 prokaryotic assemblies in RefSeq were selected to represent their respective species. The collection has grown by 3.7% since January 2022. A total of 706 species are represented for the first time. In addition, 186 species are represented by a better assembly, and 124 species were removed because of changes in NCBI Taxonomy or uncertainty in their species assignment.

We updated the database on the Microbial Nucleotide BLAST page as well as the basic nucleotide BLAST RefSeq Representative genomes database (fourth in the menu) to reflect these changes. Finally, remember that you can now run BLAST searches against the proteins annotated on representative genomes (second in the menu). See more info here.

Come see NCBI at the ASM Microbe Conference 2022

The American Society of Microbiology (ASM) Microbe conference is back, and scheduled to take place in-person, June 9th-13th in Washington, D.C.

NCBI staff member Dr. Michael Feldgarden will be recognized by ASM with an award for his research. Other NCBI staff will present posters on NCBI resources and will also be available at our booth (#1128) to address your questions. Drop by to see what’s new and provide your feedback. We hope to see you there! Check out NCBI’s schedule of activities: Continue reading “Come see NCBI at the ASM Microbe Conference 2022” →

NCBI Taxonomy to include phylum rank in taxonomic names

NCBI Taxonomy will append a list of 42 names of prokaryote phyla published for validation purposes as required under the International Code of Nomenclature for Prokaryotes (ICNP). You can still search for previous informal names, and any informal phylum rank names not addressed in the validation list will remain unchanged.

The largest named groups affected by this change are:

Current name	New name
Firmicutes	Bacillota
Proteobacteria	Pseudomonadota
Actinobacteria	Actinomycetota
Bacteroidetes	Bacteroidota

In the first half of 2021, the International Committee on Systematics of Prokaryotes (ICSP) voted to include the rank of phylum under taxonomic names covered by the International Code of Nomenclature of Prokaryotes (ICNP) (2008 Revision). The rank phylum was previously widely used in literature for prokaryotic names, and included in the NCBI Taxonomy, but not formally recognized in the ICNP. Currently, this rank is assigned to 167 bacterial and 39 archaeal informal names in NCBI Taxonomy. The newly adjusted rule (Rule 8) in the ICNP requires all formal rank names to be formed by the addition of the suffix ” -ota” to the stem of the name of the designated type genus. NCBI Taxonomy adheres to the rules stipulated in several codes of nomenclature and this means that several names in long standing use will be changed accordingly.

NCBI Taxonomy is a curated classification and nomenclature for all of the organisms in public sequence databases. This currently represents about 10% of the described life on the planet.

March 10 Webinar: Where to find data for your research organism!

Do you work with data from organisms outside the traditional set of model organisms? Join us on March 10, 2021 to learn how to use NCBI resources including NCBI’s Taxonomy and BLAST that can help you find information from your organism and closely related taxa. You will see an example that shows you how to retrieve and download gene sequences for a set of species, generate multiple sequence alignments, and design primers using Primer-Blast.

Date and time: Wed, March 10, 2021 12:00 PM – 12:45 PM EST
Register

After registering, you will receive a confirmation email with information about attending the webinar. A few days after the live presentation, you can view the recording on the NCBI YouTube channel. You can learn about future webinars on the Webinars and Courses page.

Enhanced prokaryote type strain report now with details on needed type strain data

The Prokaryote type strain report provides information on type-strains for over 18,000 species. We revised and expanded the report to make it easier to identify cases where sequencing or establishing type material would have the biggest impact on improving prokaryote taxonomy and accurate identification. These cases include species with designated type strains but without a sequenced type strain assembly and species without designated type material. We hope that the community will prioritize sequencing type strains for the former set of species (Table 1) and establishing a neotype or reftype, where applicable (as defined in Cuifo et al 2018) for the latter set (Table 2).

Other changes from the old format file are detailed in a recent genomes announce post.

Scientific Name	Type material/co-identical strains	Assemblies
Burkholderia ubonensis	CCUG:48852, CIP:1070, …	308
Escherichia albertii	Albert 19982, BCCM/LMG:20976, …	181
Xanthomonas perforans	AATCC:BAA-983, DSM:18975, …	153
Listeria innocua	ATCC:33090, BCCM/LMG:11387, …	106
Streptococcus iniae	ATCC:29178, BCCM/LMG:14520, …	94
Vibrio lentus	CECT:5110, CIP:107166, …	87
Vibrio cyclitrophicus	ATCC:700982, BCCM/LMG:21359, …	83
Pseudomonas coronafaciens	BCCM/LMG:5060, CFPB:2216, …	77
Aliivibrio fischeri	ATCC:7744, BCCM/LMG:4414, …	66
Xanthomonas fragariae	ATCC:33239, BCCM/LMG:708, …	61

Table 1. The top 10 candidate species for sequencing type-strains sorted by the number of assemblies. These have designated type strains but no type strain assembly. We generated the list by sorting by “number of assemblies from type materials per species”, then by decreasing “number of assemblies per taxon”, then filtering out “type materials and coidentical strains” = “na”.

Scientific name	Assemblies
Nostoc linckia	14
Blattabacterium punctulatus	10
Microcystis flos-aquae	10
Microcystis panniformis	9
Microcystis wesenbergii	8
Aphanizomenon flos-aquae	6
Arthrobacter bacterium	6
Denitromonas halophilus	6
Ensifer aridi	6
Methylacidiphilum fumariolicum	6

Table 2. The top 10 candidates for proposing a reftype assembly, or neotype where applicable sorted by the number of assemblies. These species have no designated type strain. We generated the list by selecting for “type materials and coidentical strains” = “na”, “number of assemblies from type materials per species” = 0, and sorting by decreasing “number of assemblies per taxon”, then filtering out Candidatus.

Please contact info@ncbi.nlm.nih.gov if you want to provide information about missing type-strains.

Expanded average nucleotide identity analysis now available for prokaryotic genome assemblies

As we described in an earlier post, GenBank uses average nucleotide identity (ANI) analysis to find and correct misidentified prokaryotic genome assemblies. You can now access ANI data for the more than 600,000 GenBank bacterial and archaeal genome assemblies through a downloadable report (ANI_report_prokaryotes.txt) available from the genomes/ASSEMBLY_REPORTS area of the FTP site. The README describes the contents of the report in detail. You can use the ANI data to evaluate the taxonomic identity of genome assemblies of interest for yourself.

The new ANI_report_prokaryotes.txt replaces the older ANI_report_bacteria.txt in the same directory. We are no longer updating the ANI_report_bacteria.txt file and will remove it after 31st May 2020.

Improving the Display of Type Material in the NCBI TaxBrowser

Have you ever been confused by multiple taxonomic names for a single organism? You’re not alone! It’s one of the challenges in maintaining any biological database. Recently we updated the NCBI TaxBrowser to assist with this.

Let’s start with a brief word about how investigators name species in the first place. For any new species, the reporting author declares a “type.” They then deposit a specimen, or “type material,” in a publicly available biorepository. This type material is tied to the new species name and serves as a reference for future comparisons. Researchers can then use DNA sequences obtained from type material to identify other samples from the same species. NCBI currently uses such an approach to verify the taxonomic assignment of prokaryotic genomes.

Our Taxonomy group has been curating type material records in the Taxonomy database since 2013 using a common vocabulary accepted by our international partners (the INSDC). For example, the Entrez query “type material[prop]” in the Taxonomy database will return all type material at NCBI.

So what are the improvements to the TaxBrowser?

Continue reading “Improving the Display of Type Material in the NCBI TaxBrowser” →

May 16 webinar: Improved Standalone BLAST database and programs: now with taxonomic information

Next Wednesday, May 16, 2018, we’ll show you how to download and use the latest standalone BLAST databases, dbv5. You’ll learn how to use BLASTdbv5 and the new BLAST programs to limit searches to taxonomic groups and to retrieve sequences from the database by taxonomy.

Date and time: Wed, May 16, 2018 12:00 PM – 12:30 PM EDT

BLAST+ database improved

We’ve made some recent enhancements to the BLAST+ applications that allow you to:

Limit your search by taxonomy using information built into the BLAST databases
Search sequences by accession faster
Use blastdbcmd to retrieve sequences by taxonomy from a BLAST database

The new version of the BLAST databases (version 5, release notes) supports the items listed above. You can access the new executables on FTP. Sample version 5 databases are also available.

Note: This is an alpha release to allow users to test and comment on new features.

Problems/Feedback

Please send problem reports and feedback to blast-help@ncbi.nlm.nih.gov or write to the Help Desk.