Poriferisocius anaerobius


Citation

Formal styling
Poriferisocius anaerobius Nguyen et al., 2023
Proposed in
Nguyen et al., 2023
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:v1sky3wb (validated)
Cannonical 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

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
Other features
  • G+C Content: 65.92%
  • Coding Density: 91.44%
  • Codon Table: 11
  • N50: 9,022 bp
  • Contigs: 302
  • Largest Contig: 48,813bp
  • 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
Search sequences
Local history
Registered by
Thomas, Torsten over 1 year ago
Submitted by
Thomas, Torsten 6 months ago
Curators
Endorsed by
Palmer, Marike 6 months ago
Validated by
Palmer, Marike 6 months ago

Publications
1

Citation Title
Nguyen et al., 2023, Systematic and Applied Microbiology Identification, classification, and functional characterization of novel sponge-associated acidimicrobiial species
Proposed this name



© 2022-2024 The SeqCode Initiative
  All information contributed to the SeqCode Registry is released under the terms of the Creative Commons Attribution (CC BY) 4.0 license