Strain identifier

BacDive ID: 130515

Type strain: Yes

Species: Paenibacillus abyssi

Strain history: <- X.-P. Tian, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; SCSIO N0306 <- X.-P. Tian and X.-F. Huang

NCBI tax ID(s): 1340531 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 21717

BacDive-ID: 130515

DSM-Number: 26238

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, motile

description: Paenibacillus abyssi DSM 26238 is a spore-forming, mesophilic, motile bacterium that was isolated from abyssal sediment.

NCBI tax id

  • NCBI tax id: 1340531
  • Matching level: species

strain history

  • @ref: 21717
  • history: <- X.-P. Tian, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; SCSIO N0306 <- X.-P. Tian and X.-F. Huang

doi: 10.13145/bacdive130515.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Paenibacillaceae
  • genus: Paenibacillus
  • species: Paenibacillus abyssi
  • full scientific name: Paenibacillus abyssi Huang et al. 2015

@ref: 21717

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus abyssi

full scientific name: Paenibacillus abyssi Huang et al. 2015

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes96.82
69480100positive

Culture and growth conditions

culture medium

  • @ref: 21717
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

  • @ref: 21717
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

Isolation, sampling and environmental information

isolation

  • @ref: 21717
  • sample type: abyssal sediment
  • geographic location: (10.0575°N; 82.985°E) at a depth of 3636 m
  • latitude: 10.0575
  • longitude: 82.985

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_72190.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_30764;97_38913;98_50596;99_72190&stattab=map
  • Last taxonomy: Paenibacillus abyssi subclade
  • 16S sequence: KC978082
  • Sequence Identity:
  • Total samples: 446
  • soil counts: 345
  • aquatic counts: 47
  • animal counts: 41
  • plant counts: 13

Safety information

risk assessment

  • @ref: 21717
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21717
  • description: Paenibacillus abyssi strain SCSIO N0306 16S ribosomal RNA gene, partial sequence
  • accession: KC978082
  • length: 1453
  • database: ena
  • NCBI tax ID: 1340531

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus abyssi CGMCC 1.12987GCA_014640295contigncbi1340531
66792Paenibacillus abyssi strain CGMCC 1.129871340531.3wgspatric1340531

GC content

  • @ref: 21717
  • GC-content: 45.5
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes86.509no
gram-positiveyes85.834no
anaerobicno98.413no
halophileno89.985no
spore-formingyes95.285no
thermophileno96.038no
glucose-utilyes88.204no
aerobicyes89.481no
flagellatedyes79.359no
glucose-fermentno91.85no

External links

@ref: 21717

culture collection no.: DSM 26238, CGMCC 1.12987, SCSIO N0306

straininfo link

  • @ref: 89037
  • straininfo: 407547

literature

  • topic: Phylogeny
  • Pubmed-ID: 25249446
  • title: Paenibacillus abyssi sp. nov., isolated from an abyssal sediment sample from the Indian Ocean.
  • authors: Huang XF, Wang FZ, Zhang W, Li J, Ling J, Yang J, Dong JD, Tian XP
  • journal: Antonie Van Leeuwenhoek
  • DOI: 10.1007/s10482-014-0277-2
  • year: 2014
  • mesh: Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Indian Ocean, Microscopy, Electron, Transmission, Molecular Sequence Data, Paenibacillus/*classification/genetics/*isolation & purification/physiology, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
21717Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-26238Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26238)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
89037Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID407547.1