Sphingorhabdus communis


Citation

Formal styling
Sphingorhabdus communis Salcher et al., 2025
Effective publication
Salcher et al., 2025
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:opjv7zsc (validated)
Canonical URL
https://seqco.de/i:48711

Nomenclature

Rank
Species
Syllabication
com.mu'nis
Etymology
L. fem. adj. communis, common, referring to a widespread distribution in freshwater lakes.
Nomenclatural type
NCBI Assembly: GCA_965234695.1
Reference strain
Strain sc|0038959: GE-11 Lookup StrainInfo
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
Type strain is Sphingorhabdus commune GE-11 (GCA_965234695.1), isolated from 5 m depth from Lake Greifensee, Switzerland (date: 2019-04-03), via high-throughput dilution to extinction cultivation. GE-11 has a genome size of 2.4 Mbp with a genomic GC content of 54.9%, contains 3 rRNA genes and 42 tRNAs. The genome is complete, consisting of a circular chromosome. The genome contains genes encoding rhodopsins and the biosynthetic pathway for retinal biosynthesis. No genes for flagellar or pilus assembly and chemotaxis were annotated. Pathways for assimilatory sulfate reduction and methane/alkanesulfonate oxidation and the biosynthesis of all amino acids were predicted. Further, pathways for riboflavin, NAD, coenzyme A, THF, and heme biosynthesis were identified. The closest cultivated relative is Sphingorhabdus wooponensis 03SU3-P (GCF_003933235.1), with an average amino acid identity of 87.4% and average nucleotide identity of 80.5%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Alphaproteobacteria; o__Sphingomonadales; f__Sphingomonadaceae; g__Sphingorhabdus_B; s__Sphingorhabdus_B sp903821685.
Classification
Bacteria » Pseudomonadota » Alphaproteobacteria » Sphingomonadales » Sphingomonadaceae » Sphingorhabdus » Sphingorhabdus communis
Parent
Sphingorhabdus

Genomics

Accession
NCBI Assembly:GCA_965234695.1
Cultures
Strain sc|0038959
Type
Isolate Genome
Estimated Quality Metrics
  • Completeness: 100.0%
  • Contamination: 0.0%
  • Quality: 100.0
Ribosomal and transfer RNA genes
  • 1 16S rRNA (up to 100.0%)
  • 1 23S rRNA (up to 100.0%)
  • tRNAs for 20 amino acids
Sequencing depth
397.082 ×
Source
Other features
  • G+C Content: 54.9%
  • Coding Density: 92.38%
  • Codon Table: 11
  • N50: 2,358,504 bp
  • Contigs: 1
  • Largest Contig: 2,358,504 bp
  • Assembly Length: 2,358,504 bp
  • Ambiguous Assembly Fraction: 0.0%
Submitter comments
Genome of a culture that was harvested by filtration on 0.22 µm filters; DNA was extracted with the Quiagen MagAttract HMW DNA kit. Sequencing was done with Illuminia Novaseq 6000, trimming of reads with BBMap v36.x, assembly with SPAdes v3.12.0. The genome was manually curated to a circular chromosome in Geneious 10 by repeated rounds of read mapping. Completeness and contamination were assessed with CheckM.
Automated checks
Complete

Last modified 6 months ago

Metadata

Outside links and data sources
Search sequences
Local history
Registered
Over 1 year ago by Layoun, Paul
Submitted
7 months ago by Layoun, Paul
Curators
Endorsed
5 months ago by Rodriguez-R, Luis M
Validated
3 months ago by Valero Tebar, Juan
Date of priority
2025-08-28 03:27 PM (UTC)

Publications
1

Citation Title
Salcher et al., 2025, Nature Communications Bringing the uncultivated microbial majority of freshwater ecosystems into culture
Effective publication



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seqco.de/r:opjv7zsc