Strain identifier
BacDive ID: 130515
Type strain:
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)
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
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 96.82 | |
69480 | 100 | positive |
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
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | yes | 100 |
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
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Paenibacillus abyssi CGMCC 1.12987 | GCA_014640295 | contig | ncbi | 1340531 |
66792 | Paenibacillus abyssi strain CGMCC 1.12987 | 1340531.3 | wgs | patric | 1340531 |
GC content
- @ref: 21717
- GC-content: 45.5
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
motile | yes | 86.509 | no |
gram-positive | yes | 85.834 | no |
anaerobic | no | 98.413 | no |
halophile | no | 89.985 | no |
spore-forming | yes | 95.285 | no |
thermophile | no | 96.038 | no |
glucose-util | yes | 88.204 | no |
aerobic | yes | 89.481 | no |
flagellated | yes | 79.359 | no |
glucose-ferment | no | 91.85 | no |
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
@id | authors | title | doi/url | catalogue |
---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |
21717 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26238 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26238) | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
69479 | João 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 beta | https://microbeatlas.org/ | |
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | |
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
89037 | Reimer, 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 identifiers | 10.60712/SI-ID407547.1 |