Strain identifier
BacDive ID: 140959
Type strain:
Species: Daejeonia ginsenosidivorans
Strain Designation: NP5
NCBI tax ID(s): 1813881 (species)
General
@ref: 43859
BacDive-ID: 140959
keywords: 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming
description: Daejeonia ginsenosidivorans NP5 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from water of Kaist Duck Lake in Daejeon city, Korea.
NCBI tax id
- NCBI tax id: 1813881
- Matching level: species
doi: 10.13145/bacdive140959.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Flavobacteriaceae
- genus: Daejeonia
- species: Daejeonia ginsenosidivorans
- full scientific name: Daejeonia ginsenosidivorans Siddiqi et al. 2017
@ref: 43859
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Daejeonia
species: Daejeonia ginsenosidivorans
strain designation: NP5
type strain: yes
Morphology
cell morphology
- @ref: 43859
- gram stain: negative
- cell length: 1.2-3.0 µm
- cell width: 0.2-0.5 µm
- cell shape: rod-shaped
- motility: no
colony morphology
- @ref: 43859
- colony color: light-yellow
- colony shape: circular
- incubation period: 2-3 days
- medium used: Tryptic soy agar
pigmentation
- @ref: 43859
- production: no
- name: Flexirubin-type pigment
Culture and growth conditions
culture medium
@ref | name | growth |
---|---|---|
43859 | LB (Luria-Bertani) MEDIUM | no |
43859 | MacConkey agar | no |
43859 | Nutrient agar (NA) | yes |
43859 | Reasoner's 2A agar (R2A) | yes |
43859 | Tryptic soy agar | yes |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
43859 | positive | growth | 18-37 | |
43859 | positive | optimum | 30 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
43859 | positive | growth | 5.5-8.0 |
43859 | positive | optimum | 6.0-7.0 |
Physiology and metabolism
oxygen tolerance
- @ref: 43859
- oxygen tolerance: aerobe
spore formation
- @ref: 43859
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
43859 | NaCl | positive | growth | 0.5-3 %(w/v) |
43859 | NaCl | positive | optimum | 0-0.5 %(w/v) |
observation
- @ref: 43859
- observation: quinone MK-6
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43859 | 16808 | 2-dehydro-D-gluconate | - | builds acid from |
43859 | 16193 | 3-hydroxybenzoate | - | builds acid from |
43859 | 37054 | 3-hydroxybutyrate | - | builds acid from |
43859 | 17879 | 4-hydroxybenzoate | - | builds acid from |
43859 | 58143 | 5-dehydro-D-gluconate | - | builds acid from |
43859 | 17128 | adipate | - | builds acid from |
43859 | 27689 | decanoate | - | builds acid from |
43859 | 16947 | citrate | - | builds acid from |
43859 | 16899 | D-mannitol | - | builds acid from |
43859 | 16988 | D-ribose | - | builds acid from |
43859 | 17924 | D-sorbitol | - | builds acid from |
43859 | 24265 | gluconate | - | builds acid from |
43859 | 17268 | myo-inositol | - | builds acid from |
43859 | 17240 | itaconate | - | builds acid from |
43859 | 30849 | L-arabinose | - | builds acid from |
43859 | 18287 | L-fucose | - | builds acid from |
43859 | 15971 | L-histidine | - | builds acid from |
43859 | 62345 | L-rhamnose | - | builds acid from |
43859 | 25115 | malate | - | builds acid from |
43859 | 18401 | phenylacetate | - | builds acid from |
43859 | 17814 | salicin | - | builds acid from |
43859 | 9300 | suberic acid | - | builds acid from |
43859 | 17992 | sucrose | - | builds acid from |
43859 | 58143 | 5-dehydro-D-gluconate | - | carbon source |
43859 | 16947 | citrate | - | carbon source |
43859 | 24265 | gluconate | - | carbon source |
43859 | 25115 | malate | - | carbon source |
43859 | 17814 | salicin | - | carbon source |
43859 | 85146 | carboxymethylcellulose | - | hydrolysis |
43859 | 53424 | tween 20 | - | hydrolysis |
43859 | 17632 | nitrate | - | reduction |
43859 | 30089 | acetate | + | builds acid from |
43859 | 17634 | D-glucose | + | builds acid from |
43859 | 16024 | D-mannose | + | builds acid from |
43859 | 28087 | glycogen | + | builds acid from |
43859 | L-alanine 4-nitroanilide | + | builds acid from | |
43859 | 17203 | L-proline | + | builds acid from |
43859 | 17115 | L-serine | + | builds acid from |
43859 | 24996 | lactate | + | builds acid from |
43859 | 15792 | malonate | + | builds acid from |
43859 | 17306 | maltose | + | builds acid from |
43859 | 28053 | melibiose | + | builds acid from |
43859 | 506227 | N-acetylglucosamine | + | builds acid from |
43859 | 17272 | propionate | + | builds acid from |
43859 | 31011 | valerate | + | builds acid from |
43859 | 30089 | acetate | + | carbon source |
43859 | 17634 | D-glucose | + | carbon source |
43859 | 16024 | D-mannose | + | carbon source |
43859 | 28087 | glycogen | + | carbon source |
43859 | 16977 | L-alanine | + | carbon source |
43859 | 17203 | L-proline | + | carbon source |
43859 | 17115 | L-serine | + | carbon source |
43859 | 24996 | lactate | + | carbon source |
43859 | 15792 | malonate | + | carbon source |
43859 | 17306 | maltose | + | carbon source |
43859 | 28053 | melibiose | + | carbon source |
43859 | 506227 | N-acetylglucosamine | + | carbon source |
43859 | 17272 | propionate | + | carbon source |
43859 | 31011 | valerate | + | carbon source |
43859 | casein | + | hydrolysis | |
43859 | 16991 | dna | + | hydrolysis |
43859 | 4853 | esculin | + | hydrolysis |
43859 | 28017 | starch | + | hydrolysis |
43859 | 5291 | gelatin | +/- | hydrolysis |
metabolite production
- @ref: 43859
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
43859 | cytochrome oxidase | + | 1.9.3.1 |
43859 | catalase | + | 1.11.1.6 |
43859 | alkaline phosphatase | + | 3.1.3.1 |
43859 | esterase (C 4) | + | |
43859 | esterase Lipase (C 8) | + | |
43859 | lipase (C 14) | + | |
43859 | leucine arylamidase | + | 3.4.11.1 |
43859 | valine arylamidase | + | |
43859 | cystine arylamidase | + | 3.4.11.3 |
43859 | trypsin | + | 3.4.21.4 |
43859 | alpha-chymotrypsin | + | 3.4.21.1 |
43859 | acid phosphatase | + | 3.1.3.2 |
43859 | naphthol-AS-BI-phosphohydrolase | + | |
43859 | alpha-glucosidase | + | 3.2.1.20 |
43859 | beta-glucosidase | + | 3.2.1.21 |
43859 | alpha-galactosidase | - | 3.2.1.22 |
43859 | beta-galactosidase | - | 3.2.1.23 |
43859 | beta-glucuronidase | - | 3.2.1.31 |
43859 | alpha-mannosidase | - | 3.2.1.24 |
43859 | alpha-fucosidase | - | 3.2.1.51 |
43859 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
43859 | urease | - | 3.5.1.5 |
fatty acid profile
fatty acids
@ref fatty acid percentage 43859 C15:0 anteiso 7.5 43859 C15:0 2OH 0.5 43859 C16:0 1.1 43859 C16:0 3OH 0.6 43859 C16:1ω7c / C16:1ω6c 6.3 43859 C17:0 2OH 0.9 43859 C17:1ω6c 0.6 43859 C18:0 3OH 8.5 43859 C18:1ω5c 1 43859 C13:0 iso 3.4 43859 C14:0 iso 3.5 43859 C14:0 iso 3OH 0.5 43859 C15:0 iso 27.7 43859 C15:0 iso 3OH 2.9 43859 C16:0 iso 4.6 43859 C16:0 iso 3OH 11.1 43859 C16:1 iso H 2 43859 C17:0 iso 3OH 13.6 43859 C17:1 iso I /C17:1 anteiso B 1.2 43859 iso-C17:1ω9c/C16:0 10-methyl 2.8 - type of FA analysis: whole cell analysis
- incubation medium: R2A agar
- agar/liquid: agar
- software version: Sherlock 6.1
- library/peak naming table: TSBA6.1
- system: MIS MIDI
- instrument: Hewlett Packard 6890 gas chromatograph
- cutoff value:
Isolation, sampling and environmental information
isolation
- @ref: 43859
- sample type: water of Kaist Duck Lake in Daejeon city, Korea
- geographic location: Daejeon city
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
- enrichment culture: R2A agar
- enrichment culture duration: 7 days
- enrichment culture temperature: 30
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Lake (large)
Sequence information
16S sequences
- @ref: 43859
- description: 16S rRNA gene sequence
- accession: KT950745
- database: nuccore
GC content
- @ref: 43859
- GC-content: 44.8
- method: high performance liquid chromatography (HPLC)
External links
@ref: 43859
culture collection no.: KACC 18626, LMG 29198
literature
- topic: Phylogeny
- Pubmed-ID: 28809138
- title: Daejeonia ginsenosidivorans gen. nov., sp. nov., a ginsenoside-transforming bacterium isolated from lake water.
- authors: Siddiqi MZ, Choi GM, Kim MS, Im WT
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001994
- year: 2017
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Ginsenosides/*metabolism, Lakes/*microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Transcriptome
Reference
@id | authors | title | doi/url | 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 | ||
43859 | Muhammad Zubair Siddiqi, Gyu-Min Choi, Mi-Sun Kim, Wan-Taek Im | Daejeonia ginsenosidivorans gen. nov., sp. nov., a ginsenoside-transforming bacterium isolated from lake water | 10.1099/ijsem.0.001994 | IJSEM 67: 2665-2671 2017 | 28809138 |