Methylophilus medardensis

Citation

Formal styling

Methylophilus medardensis corrig. Salcher et al., 2019 (priority 2025)

Effective publication

Salcher et al., 2019

Corrigendum

In SeqCode Registry from “Methylophilus medardicus” (sic)

SeqCode status

Valid (SeqCode)

Register List

seqco.de/r:y_q1qhwb (validated)

Canonical URL

https://seqco.de/i:39350

Nomenclature

Rank

Species

Syllabication

me.dar.den'sis

Etymology

N.L. masc. adj. medardensis, pertaining to Lake Medard (Czechia), the isolation source of the type strain.

Nomenclatural type

NCBI Assembly: GCF_006363915.1

Reference strain

Strain sc|0038982: MMS-M-51 Lookup StrainInfo

Nomenclatural status

Validly published under the SeqCode

Taxonomy

Description

Type genome is Methylophilus medardensis MMS-M-51 (GCF_006363915.1), that was isolated by dilution-to-extinction cultivation from the water column of Lake Medard, Czechia. MMS-M-51 has a genome size of 2.6 Mb with a genomic GC content of 49.8%, contains 6 rRNA genes and 42 tRNAs. The genome is complete, consisting of 1 circular chromosome. The closest cultivated relatives are Methylophilus sp. Q8 (GCF_000800115.1) with an average amino acid identity of 85.53% and average nucleotide identity of 78.73% and Methylophilus sp. OH31 (GCF_000576615.1) with an AAI of 85.28% and an ANI of 78.71%.

Classification

Bacteria » Pseudomonadota » Betaproteobacteria » Nitrosomonadales » Methylophilaceae » Methylophilus » Methylophilus medardensis

Parent

Methylophilus ncbigtdb

Pseudonyms

• Methylophilus medaricus (Misspelling or other orthographic variants)
• Methylophilus medardicus (Original, corrected name)

Genomics

Accession

NCBI Assembly:GCF_006363915.1

Cultures

Strain sc|0038982

Type

Isolate Genome

Estimated Quality Metrics

• Completeness: 100.0%
• Contamination: 2.88%
• Quality: 85.6

Ribosomal and transfer RNA genes

• 2 16S rRNAs (up to 100.0%)
• 2 23S rRNAs (up to 100.0%)
• tRNAs for 20 amino acids

Sequencing depth

352.0 ×

Source

• BioSample: SAMN11964623

Other features

• G+C Content: 49.8%
• Coding Density: 90.93%
• Codon Table: 11
• N50: 2,603,080 bp
• Contigs: 1
• Largest Contig: 2,603,080 bp
• Assembly Length: 2,603,080 bp
• Ambiguous Assembly Fraction: 0.0038%

Submitter comments

Genome of a culture that was harvested by centrifugation; DNA was extracted with the Quiagen MagAttract HMW DNA kit. Sequencing was done with Illuminia MiSeq (PE250), trimming of reads with trimmomatic, assembly with SPAdes. The genome was manually polished in Geneious 9 by repeated rounds of read mapping. Completeness and contamination were assessed with CheckM, but as the genome consists of a circular chromosome, it should be complete without any contamination. 

Automated checks

Complete

See additional details

---

Last modified 6 months ago

Metadata

Outside links and data sources

• NCBI Taxonomy: 2588534
• GTDB Genome: GCF_006363915.1
• GTDB Tree: s__Methylophilus medardicus
• Wikispecies: Methylophilus medardensis
• Wikidata: Q136031451

Search sequences

• Seach in NCBI Nucleotide
• NCBI Genomes table

Local history

• This name was last modified 3 months ago
• Submission process status
• Quality checks before valid publication

Registered

Almost 2 years ago and claimed 7 months ago by Salcher, Michaela M

Submitted

7 months ago by Salcher, Michaela M

Curators

• Rodriguez-R, Luis M
• Palmer, Marike (nomenclature)
• Valero Tebar, Juan (genomics)

Validated

3 months ago by Palmer, Marike

Date of priority

2025-05-02 12:27 PM (UTC)