Poriferisocius anaerobius

Citation

Formal styling

Poriferisocius anaerobius Nguyen et al., 2023

Effective publication

Nguyen et al., 2023

SeqCode status

Valid (SeqCode)

Register List

seqco.de/r:v1sky3wb (validated)

Canonical URL

https://seqco.de/i:23659

Nomenclature

Rank

Species

Syllabication

a.nae.ro'bi.us

Etymology

Gr. pref. an-, not; Gr. masc. n. aer, air; Gr. masc. n. bios, life; N.L. masc. adj. anaerobius, one who lives without air

Nomenclatural type

NCBI Assembly: GCA_028278785.1

Nomenclatural status

Validly published under the SeqCode

Taxonomy

Description

Symbiont found to be enriched in sponge microbiomes, and no other environments. Predicted to be capable of growth under anoxic conditions with fumarate and hydrogen peroxide as electron acceptors 

Classification

Bacteria » Actinomycetota » Acidimicrobiia » Acidimicrobiales » Hopanoidiivorantaceae » Poriferisocius » Poriferisocius anaerobius

Parent

Poriferisocius gtdb

Genomics

Accession

NCBI Assembly:GCA_028278785.1

Type

Metagenome-Assembled Genome (MAG)

Estimated Quality Metrics

• Completeness: 85.9%
• Contamination: 4.27%
• Quality: 64.55

Ribosomal and transfer RNA genes

• 1 16S rRNA (up to 80.0%)
• 0 23S rRNAs
• tRNAs for 20 amino acids

Sequencing depth

11.0 ×

Source

• BioSample: SAMN31047475

Other features

• G+C Content: 65.92%
• Coding Density: 91.44%
• Codon Table: 11
• N50: 9,022 bp
• Contigs: 302
• Largest Contig: 48,813 bp
• Assembly Length: 2,243,157 bp
• Ambiguous Assembly Fraction: 0.0029%

Submitter comments

Completeness and contamination were assessed with CheckM v1.1.0 using a lineage-specific workflow.
This symbiont is from a sponge and we have seen previously seen that sponge-associated genomes which are closed (i.e. single, circular contig) have completeness estimates that are below the 90% threshold. For example, we have one completed MAG (2000x coverage, Q>50) for a sponge symbiont and gotten the following completeness estimates:
CheckM: 91 % complete

CheckM2: 81 % complete

Busco v5: 74 % complete

Clearly all pipelines are wrong and substantially underestimate the completeness. I believe this is also the case for this organisms.

We have not be able to reconstruct a better 16S rRNA gene sequence, but phylogenetic placement of the 16S rRNA gene is robust (see Nguyen et al., 2023).

Automated checks

Complete

See additional details

Metadata

Outside links and data sources

• GTDB Genome: GCA_028278785.1
• GTDB Tree: s__Poriferisocius anaerobius
• Global Biodiversity Information Facility (GBIF)
• Wikispecies: Poriferisocius anaerobius (see reference source)

Search sequences

• Seach in NCBI Nucleotide

Local history

• This name was last modified about 1 year ago
• Submission process status
• Quality checks before valid publication

Registered by

Thomas, Torsten about 2 years ago

Submitted by

Thomas, Torsten about 1 year ago

Curators

• Rodriguez-R, Luis M
• Palmer, Marike

Endorsed by

Palmer, Marike about 1 year ago

Validated by

Palmer, Marike about 1 year ago

Date of priority

2023-08-25 02:22 PM (UTC)