Omnitrophus fodinaeTs


Citation

Formal styling
Omnitrophus fodinaeTs Rinke et al., 2013 (valid 2023)
Effective publication
Rinke et al., 2013
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:d841ck02 (validated)
Cannonical URL
https://seqco.de/i:23567

Nomenclature

Rank
Species
Syllabication
fo.di'nae
Etymology
L. gen. n. fodinae, of a mine, coal mine
Nomenclatural type
NCBI Assembly: GCA_000405945.1
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
This species is the type of the genus Omnitrophus. No data on cell size in the species is available. This species is represented by only one medium-quality genome, however, for historical significance, this genome serves as the nomenclatural type for the species. The %GC content of the genome is 49.56%. The estimated genome size is 2.9 Mb, with the available genome estimated to be 65 % complete. The genome available for this species encodes 2 very large ORFs with domains typically implicated in eukaryotic cell adhesion. This organism originated from groundwater sampled at Homestake Mine (Sanford Lab Homestake), South Dakota. The nomenclatural type for the species is the genome GCA_000405945.1.
Notes
Classification
Bacteria » Omnitrophota » “Omnitrophia” » “Omnitrophales” » “Omnitrophaceae” » Omnitrophus » Omnitrophus fodinaeTs
Parent
Omnitrophus gtdb

Genomics

Accession
NCBI Assembly:GCA_000405945.1
Type
Single-Cell Amplified Genome (SAG)
Estimated Quality Metrics
  • Completeness: 65.01%
  • Contamination: 0.56%
  • Quality: 62.21
Ribosomal and transfer RNA genes
  • 1 16S rRNA (up to 100.0%)
  • 1 23S rRNA (up to 100.0%)
  • tRNAs for 17 amino acids
Source
Other features
  • G+C Content: 49.56%
  • Coding Density: 93.69%
  • Codon Table: 11
  • N50: 20,345 bp
  • Contigs: 150
  • Largest Contig: 75,002 bp
  • Assembly Length: 2,037,078 bp
  • Ambiguous Assembly Fraction: 0.001%
Submitter comments
Quality metrics were assessed using CheckM v. 2. This genome has lower completeness than suggested by standards but we request lowering of the requirement here, because this is a historical name and allows us to keep the nomenclature for the entire phylum. Despite several attempts at recovering a higher completeness genome from metagenomic data, there has been no other genomes recovered for the genus, thus in order to retain the historical genus through phylum names with the least amount of confusion, we request special consideration for validation with this genome as type. 
Automated checks
Complete
See additional details

Metadata

Outside links and data sources
Search sequences
Local history
Registered by
Rinke, Chris over 1 year ago
Submitted by
Rinke, Chris over 1 year ago
Curators
Validated by
Rodriguez-R, Luis M 3 months ago
Date of priority
2023-02-22 12:07 AM (UTC)

Publications
3

Citation Title
Seymour et al., 2023, Nature Microbiology Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota
SeqCode Reconciliation Commission, 2023, Zenodo Official decision on "Omnitrophus fodinae" request (seqco.de/r:d841ck02)
Rinke et al., 2013, Nature Insights into the phylogeny and coding potential of microbial dark matter
Effective publication



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