Strain identifier
BacDive ID: 132384
Type strain:
Species: Paenibacillus cavernae
Strain Designation: C4-5
Strain history: <- Soon Dong Lee, Jeju Univ.
NCBI tax ID(s): 1660197 (species)
General
@ref: 24173
BacDive-ID: 132384
DSM-Number: 100100
keywords: 16S sequence, Bacteria, obligate aerobe, spore-forming, Gram-variable, motile, rod-shaped, colony-forming
description: Paenibacillus cavernae C4-5 is an obligate aerobe, spore-forming, Gram-variable bacterium that forms circular colonies and was isolated from soil inside a natural cave.
NCBI tax id
- NCBI tax id: 1660197
- Matching level: species
strain history
@ref | history |
---|---|
24173 | <- S. D. Lee, Jeju National Univ., Rep. of Korea; C4-5 |
67771 | <- Soon Dong Lee, Jeju Univ. |
doi: 10.13145/bacdive132384.20230509.8.1
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 cavernae
- full scientific name: Paenibacillus cavernae Lee 2016
@ref: 24173
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Paenibacillaceae
genus: Paenibacillus
species: Paenibacillus cavernae
full scientific name: Paenibacillus cavernae Lee 2016
strain designation: C4-5
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement |
---|---|---|---|---|---|---|
43809 | variable | 2.7-3.2 µm | 0.9-1.1 µm | rod-shaped | yes | |
67771 | rod-shaped | yes | monotrichous, polar | |||
67771 | variable |
colony morphology
- @ref: 43809
- colony size: 1-2 mm
- colony color: White-cream
- colony shape: circular
- incubation period: 3 days
- medium used: Nutrient agar
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
43809 | Nutrient agar (NA) | yes | ||
43809 | Reasoner's 2A agar (R2A) | yes | ||
43809 | Trypticase soy agar | yes | ||
24173 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
43809 | positive | growth | 20-42 | |
43809 | positive | optimum | 30 | mesophilic |
24173 | positive | growth | 30 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
43809 | positive | growth | 6-10 | alkaliphile |
43809 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
43809 | obligate aerobe |
67771 | aerobe |
spore formation
- @ref: 43809
- spore description: Ellipsoidal; formed in sporangia and at subterminal position of cells
- type of spore: endospore
- spore formation: yes
halophily
@ref | salt | growth | tested relation | concentration | halophily level |
---|---|---|---|---|---|
43809 | NaCl | positive | growth | 0-1 %(w/v) | |
43809 | NaCl | positive | optimum | 0 %(w/v) | non-halophilic |
observation
- @ref: 67771
- observation: quinones: MK-7
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43809 | 17128 | adipate | - | assimilation |
43809 | 27689 | decanoate | - | assimilation |
43809 | 16947 | citrate | - | assimilation |
43809 | 17108 | D-arabinose | - | assimilation |
43809 | 17634 | D-glucose | - | assimilation |
43809 | 16899 | D-mannitol | - | assimilation |
43809 | 16024 | D-mannose | - | assimilation |
43809 | 25115 | malate | - | assimilation |
43809 | 24265 | gluconate | - | assimilation |
43809 | 17306 | maltose | - | assimilation |
43809 | 506227 | N-acetylglucosamine | - | assimilation |
43809 | 18401 | phenylacetate | - | assimilation |
43809 | 16808 | 2-dehydro-D-gluconate | - | builds acid from |
43809 | 15963 | ribitol | - | builds acid from |
43809 | 27613 | amygdalin | - | builds acid from |
43809 | 18305 | arbutin | - | builds acid from |
43809 | 17108 | D-arabinose | - | builds acid from |
43809 | 18333 | D-arabitol | - | builds acid from |
43809 | 17057 | cellobiose | - | builds acid from |
43809 | 15824 | D-fructose | - | builds acid from |
43809 | 28847 | D-fucose | - | builds acid from |
43809 | 12936 | D-galactose | - | builds acid from |
43809 | 17634 | D-glucose | - | builds acid from |
43809 | 62318 | D-lyxose | - | builds acid from |
43809 | 16899 | D-mannitol | - | builds acid from |
43809 | 16024 | D-mannose | - | builds acid from |
43809 | 16988 | D-ribose | - | builds acid from |
43809 | 16443 | D-tagatose | - | builds acid from |
43809 | 65327 | D-xylose | - | builds acid from |
43809 | 16813 | galactitol | - | builds acid from |
43809 | 17113 | erythritol | - | builds acid from |
43809 | 4853 | esculin | - | builds acid from |
43809 | 24265 | gluconate | - | builds acid from |
43809 | 17754 | glycerol | - | builds acid from |
43809 | 28087 | glycogen | - | builds acid from |
43809 | 17268 | myo-inositol | - | builds acid from |
43809 | 15443 | inulin | - | builds acid from |
43809 | 30849 | L-arabinose | - | builds acid from |
43809 | 18403 | L-arabitol | - | builds acid from |
43809 | 18287 | L-fucose | - | builds acid from |
43809 | 17266 | L-sorbose | - | builds acid from |
43809 | 65328 | L-xylose | - | builds acid from |
43809 | 17716 | lactose | - | builds acid from |
43809 | 6731 | melezitose | - | builds acid from |
43809 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
43809 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
43809 | 37657 | methyl D-glucoside | - | builds acid from |
43809 | 506227 | N-acetylglucosamine | - | builds acid from |
43809 | 16634 | raffinose | - | builds acid from |
43809 | 26546 | rhamnose | - | builds acid from |
43809 | 17814 | salicin | - | builds acid from |
43809 | 30911 | sorbitol | - | builds acid from |
43809 | 28017 | starch | - | builds acid from |
43809 | 17151 | xylitol | - | builds acid from |
43809 | 17234 | glucose | - | fermentation |
43809 | casein | - | hydrolysis | |
43809 | 5291 | gelatin | - | hydrolysis |
43809 | 28017 | starch | - | hydrolysis |
43809 | 17632 | nitrate | - | reduction |
43809 | 58143 | 5-dehydro-D-gluconate | + | builds acid from |
43809 | 28066 | gentiobiose | + | builds acid from |
43809 | 17306 | maltose | + | builds acid from |
43809 | 28053 | melibiose | + | builds acid from |
43809 | 17992 | sucrose | + | builds acid from |
43809 | 27082 | trehalose | + | builds acid from |
43809 | 32528 | turanose | + | builds acid from |
43809 | 16991 | dna | + | hydrolysis |
43809 | 4853 | esculin | +/- | degradation |
metabolite production
- @ref: 43809
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
43809 | cytochrome oxidase | + | 1.9.3.1 |
43809 | catalase | + | 1.11.1.6 |
43809 | beta-galactosidase | + | 3.2.1.23 |
43809 | arginine dihydrolase | - | 3.5.3.6 |
43809 | urease | - | 3.5.1.5 |
fatty acid profile
fatty acids
@ref fatty acid percentage 43809 C15:0 anteiso 44.7 43809 C17:0 anteiso 5.4 43809 C14:0 1.08 43809 C16:0 14.16 43809 C18:0 6.39 43809 C14:0 iso 1.69 43809 C15:0 iso 5.48 43809 C16:0 iso 15.83 43809 C17:0 iso 1.4 - type of FA analysis: whole cell analysis
- incubation medium: TSA
- agar/liquid: agar
- incubation temperature: 30
- incubation time: 3
- incubation_oxygen: aerobic
- software version: Sherlock 6.0
- library/peak naming table: TSBA6
- system: MIS MIDI
- cutoff value:
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
24173 | soil inside a natural cave | Jeju | Republic of Korea | KOR | Asia |
43809 | A soil sample of a natural cave in Jeju; collected at a distance of 3 mm from the entrance of the cave | Jeju Island | Republic of Korea | KOR | Asia |
67771 | From soil inside a natural cave in Jeju | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Geologic |
#Environmental | #Terrestrial | #Soil |
Safety information
risk assessment
- @ref: 24173
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24173
- description: Paenibacillus sp. C4-5 partial 16S rRNA gene, strain C4-5
- accession: LN852381
- length: 1431
- database: ena
- NCBI tax ID: 1660197
GC content
@ref | GC-content | method |
---|---|---|
24173 | 54.8 | high performance liquid chromatography (HPLC) |
67771 | 54.8 |
External links
@ref: 24173
culture collection no.: DSM 100100, KCTC 33652
straininfo link
- @ref: 90727
- straininfo: 399288
literature
topic | Pubmed-ID | title | authors | journal | DOI | year |
---|---|---|---|---|---|---|
Phylogeny | 26558840 | Paenibacillus cavernae sp. nov., isolated from soil of a natural cave. | Dong Lee S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000762 | 2015 |
Phylogeny | 33666545 | Paenibacillus cymbidii sp. nov., isolated from Cymbidium goeringii roots. | Sun L, Wang P, Zhao D, Wang J, Wu Q, Liu L, Lyu Z | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004731 | 2021 |
Reference
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
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 | |||
24173 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100100 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100100) | |||
43809 | Soon Dong Lee | Paenibacillus cavernae sp. nov., isolated from soil of a natural cave | 10.1099/ijsem.0.000762 | IJSEM 66: 598-603 2016 | 26558840 | |
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
90727 | 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-ID399288.1 |