Strain identifier
BacDive ID: 164350
Type strain:
Species: Flavobacterium nackdongense
Strain Designation: GS13
Strain history: H. Kim; NNIBR, South Korea; GS13.
NCBI tax ID(s): 2547394 (species)
General
@ref: 67770
BacDive-ID: 164350
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped, colony-forming
description: Flavobacterium nackdongense GS13 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from Sediment of a branch of the Nackdong River in Sangju.
NCBI tax id
- NCBI tax id: 2547394
- Matching level: species
strain history
- @ref: 67770
- history: H. Kim; NNIBR, South Korea; GS13.
doi: 10.13145/bacdive164350.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Flavobacteriaceae
- genus: Flavobacterium
- species: Flavobacterium nackdongense
- full scientific name: Flavobacterium nackdongense Kim and Yu 2020
@ref: 67770
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Flavobacterium
species: Flavobacterium nackdongense
full scientific name: Flavobacterium nackdongense Kim and Yu 2020
strain designation: GS13
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
68261 | negative | rod-shaped | no | |
69480 | negative | 99.996 | ||
69480 | no | 90.948 |
colony morphology
- @ref: 68261
- colony color: yellow
- colony shape: circular
- medium used: Reasoner's 2A agar (R2A)
pigmentation
- @ref: 68261
- production: no
- name: Flexirubin type pigments
Culture and growth conditions
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
67770 | positive | growth | 25 | mesophilic |
68261 | positive | growth | 10-30 | |
68261 | positive | optimum | 20 | psychrophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
68261 | positive | growth | 6.5-8 |
68261 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 68261
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69480 | no | 99.994 |
69481 | no | 100 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
68261 | NaCl | positive | growth | 0 %(w/v) |
68261 | NaCl | positive | optimum | 0 %(w/v) |
observation
- @ref: 67770
- observation: quinones: MK-6
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68261 | 17632 | nitrate | + | reduction |
68261 | 28017 | starch | + | hydrolysis |
68261 | 62968 | cellulose | + | hydrolysis |
68261 | casein | - | hydrolysis | |
68261 | 16991 | dna | - | hydrolysis |
68261 | 53424 | tween 20 | - | hydrolysis |
68261 | 53423 | tween 40 | - | hydrolysis |
68261 | 53425 | tween 60 | - | hydrolysis |
68261 | 53426 | tween 80 | - | hydrolysis |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68261 | cytochrome oxidase | + | 1.9.3.1 |
68261 | catalase | + | 1.11.1.6 |
68261 | alkaline phosphatase | + | 3.1.3.1 |
68261 | leucine arylamidase | + | 3.4.11.1 |
68261 | valine arylamidase | + | |
68261 | trypsin | + | 3.4.21.4 |
68261 | acid phosphatase | + | 3.1.3.2 |
68261 | naphthol-AS-BI-phosphohydrolase | + | |
68261 | esterase (C 4) | - | |
68261 | esterase Lipase (C 8) | - | |
68261 | lipase (C 14) | - | |
68261 | cystine arylamidase | - | 3.4.11.3 |
68261 | alpha-chymotrypsin | - | 3.4.21.1 |
68261 | alpha-galactosidase | - | 3.2.1.22 |
68261 | beta-galactosidase | - | 3.2.1.23 |
68261 | beta-glucuronidase | - | 3.2.1.31 |
68261 | alpha-glucosidase | - | 3.2.1.20 |
68261 | beta-glucosidase | - | 3.2.1.21 |
68261 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68261 | alpha-mannosidase | - | 3.2.1.24 |
68261 | alpha-fucosidase | - | 3.2.1.51 |
fatty acid profile
fatty acids
@ref fatty acid percentage 68261 C14:0 1.2 68261 C16:0 2.2 68261 C12:0 iso 1.1 68261 C13:0 iso 3.4 68261 C14:0 iso 2.9 68261 C15:0 iso 16 68261 C16:0 iso 6.7 68261 C15:1 iso G 4.3 68261 C16:1 iso H 3.7 68261 C13:0 anteiso 2.1 68261 C15:0 anteiso 6.7 68261 C15:1 anteiso A 1.5 68261 C17:1 anteiso w9c 1.7 68261 C15:1 w6c 1.7 68261 C17:1 w6c 1.6 68261 C16:0 3OH 2.1 68261 C15:0 iso 3OH 3.6 68261 C16:0 iso 3OH 7.8 68261 C17:0 iso 3OH 4.1 68261 C16:1 w7c/C16:1 w6c 19.1 68261 C17:1 iso w9c / C16:0 10-methyl 1.7 - type of FA analysis: whole cell analysis
- software version: Sherlock 6.1
- library/peak naming table: TSBA6
- system: MIS MIDI
- cutoff value:
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | geographic location | latitude | longitude | enrichment culture | enrichment culture duration | enrichment culture temperature |
---|---|---|---|---|---|---|---|---|---|---|
67770 | Sediment of a branch of the Nackdong River in Sangju | Republic of Korea | KOR | Asia | ||||||
68261 | sediment of a branch of the Nackdong River | Republic of Korea | KOR | Asia | Sangju | 36.471 | 128.154 | R2A agar | 7 days | 25 |
Sequence information
16S sequences
- @ref: 67770
- description: Flavobacterium nackdongense 16S ribosomal RNA gene, complete sequence
- accession: MH168565
- length: 1513
- database: ena
- NCBI tax ID: 2547394
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Flavobacterium nackdongense GS13 | GCA_004355225 | complete | ncbi | 2547394 |
66792 | Flavobacterium nackdongense GS13 | 2848968057 | complete | img | 2547394 |
GC content
- @ref: 67770
- GC-content: 36.2
- method: genome sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 93.238 | yes |
flagellated | no | 97.059 | yes |
gram-positive | no | 98.162 | no |
anaerobic | no | 98.528 | yes |
aerobic | yes | 83.082 | yes |
halophile | no | 98.252 | yes |
spore-forming | no | 95.175 | no |
glucose-util | yes | 90.272 | no |
thermophile | no | 98.859 | yes |
glucose-ferment | no | 87.217 | no |
External links
@ref: 67770
culture collection no.: JCM 32765, KCTC 62569
literature
- topic: Phylogeny
- Pubmed-ID: 31745602
- title: Flavobacterium nackdongense sp. nov., a cellulose-degrading bacterium isolated from sediment.
- authors: Kim H, Yu SM
- journal: Arch Microbiol
- DOI: 10.1007/s00203-019-01770-5
- year: 2019
- mesh: Bacterial Typing Techniques, Base Composition, Cellulose/*metabolism, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Flavobacterium/classification/genetics/*isolation & purification/*metabolism, Geologic Sediments/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rivers/microbiology, Sequence Analysis, DNA
- topic2: Metabolism
Reference
@id | authors | title | doi/url | journal |
---|---|---|---|---|
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 | |
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 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
68261 | Hyangmi Kim & Sang Mi Yu | Flavobacterium nackdongense sp. nov., a cellulose-degrading bacterium isolated from sediment | 10.1007/s00203-019-01770-5 | Arch Microbiol 202: 591-595 2020 |
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 |