Pedobacter colombiensis

Citation

Formal styling

Pedobacter colombiensis Díaz-García et al., 2024

Effective publication

Díaz-García et al., 2024

SeqCode status

Valid (SeqCode)

Register List

seqco.de/r:-kiq_w89 (validated)

Canonical URL

https://seqco.de/i:24104

Nomenclature

Rank

Species

Syllabication

co.lom.bi.en'sis

Etymology

N.L. masc. adj. colombiensis, belonging to Colombia

Nomenclatural type

INSDC Nucleotide: CP119313.1

Nomenclatural status

Validly published under the SeqCode

Taxonomy

Description

A species established on the basis of MiGA taxonomic novelty analyses, AAI, dDDH, 16S rRNA gene phylogenetic reconstruction and the type material is the genome MAG_3858. Genomic metrics include ANI (81.7), AAI (81.02) and dDDH d4 (29.6). The MAG was reconstructed from lignocellulolytic bacterial consortium and encoded for 254 CAZymes, 63 of them involved in lignocellulose degradation. In addition, putative genes for PET and PUR hydrolisis were found within the MAG.

Classification

Bacteria » Bacteroidota » Sphingobacteriia » Sphingobacteriales » Sphingobacteriaceae » Pedobacter » Pedobacter colombiensis

Parent

Pedobacter gtdb

Genomics

Accession

INSDC Nucleotide:CP119313.1

Type

Metagenome-Assembled Genome (MAG)

Estimated Quality Metrics

• Completeness: 100.0%
• Contamination: 0.0%
• Quality: 100.0

Ribosomal and transfer RNA genes

• 5 16S rRNAs (up to 100.0%)
• 5 23S rRNAs (up to 100.0%)
• tRNAs for 20 amino acids

Sequencing depth

20.0 ×

Source

• BioSample: SAMN33481879
• BioSample: SAMN33438288

Other features

• G+C Content: 38.78%
• Coding Density: 91.6%
• Codon Table: 11
• N50: 5,388,978 bp
• Contigs: 1
• Largest Contig: 5,388,978 bp
• Assembly Length: 5,388,978 bp
• Ambiguous Assembly Fraction: 0.0%

Submitter comments

Dfast was used to identify rRNA genes. Completion and contamination were estimated by CheckM.

Automated checks

Complete

See additional details

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Last modified about 1 month ago

Metadata

Outside links and data sources

• GTDB Tree: s__Pedobacter colombiensis
• Global Biodiversity Information Facility (GBIF)
• Wikispecies: Pedobacter colombiensis (see reference source)

Search sequences

• Seach in NCBI Nucleotide

Local history

• This name was last modified 7 months ago
• Submission process status
• Quality checks before valid publication

Registered by

Díaz-García, Laura almost 2 years ago

Submitted by

Díaz-García, Laura over 1 year ago

Curators

• Palmer, Marike (nomenclature) (genomics)

Endorsed by

Palmer, Marike over 1 year ago

Validated by

Palmer, Marike 11 months ago

Date of priority

2024-01-25 09:26 AM (UTC)