Strain identifier
BacDive ID: 158690
Type strain:
Species: Flavobacterium sediminilitoris
Strain Designation: YSM-43
Strain history: <- Jung-Hoon Yoon, Sungkyunkwan Univ.
NCBI tax ID(s): 2024526 (species)
General
@ref: 65427
BacDive-ID: 158690
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped, colony-forming
description: Flavobacterium sediminilitoris YSM-43 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from a tidal flat.
NCBI tax id
- NCBI tax id: 2024526
- Matching level: species
strain history
- @ref: 67771
- history: <- Jung-Hoon Yoon, Sungkyunkwan Univ.
doi: 10.13145/bacdive158690.20230509.8.1
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 sediminilitoris
- full scientific name: Flavobacterium sediminilitoris Park et al. 2018
@ref: 65427
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Flavobacterium
species: Flavobacterium sediminilitoris
strain designation: YSM-43
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement |
---|---|---|---|---|---|---|
65427 | negative | 0.8-4.0 µm | 0.2-0.5 µm | rod-shaped | yes | gliding |
67771 | rod-shaped | yes | gliding | |||
67771 | negative |
colony morphology
- @ref: 65427
- colony size: 0.5-1.0 mm
- colony color: moderate yellow
- colony shape: circular
- incubation period: 3 days
- medium used: marine agar
pigmentation
- @ref: 65427
- production: no
- name: Flexirubin-type pigments
Culture and growth conditions
culture medium
- @ref: 65427
- name: Marine agar (MA)
- growth: yes
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
65427 | positive | optimum | 30 | mesophilic |
65427 | positive | growth | 10 | psychrophilic |
65427 | positive | growth | 37 | mesophilic |
65427 | no | growth | 4 | psychrophilic |
65427 | no | growth | 40 | thermophilic |
67771 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
65427 | positive | optimum | 7-8 |
65427 | positive | growth | 5.5 |
65427 | no | growth | 5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
65427 | aerobe |
67771 | facultative anaerobe |
spore formation
- @ref: 65427
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
65427 | NaCl | positive | growth | 0-6 %(w/v) |
65427 | NaCl | positive | optimum | 1-2 %(w/v) |
observation
@ref | observation |
---|---|
65427 | Mg2+ Ions are not required for growth |
65427 | the predominant menaquinone is MK-6 |
65427 | the major polar lipids are phosphatidylethanolamine and one unidentified lipid |
67771 | quinones: MK-6 |
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
65427 | casein | + | hydrolysis | |
65427 | cellobiose | - | builds acid from | 17057 |
65427 | D-fructose | - | builds acid from | 15824 |
65427 | D-galactose | - | builds acid from | 12936 |
65427 | D-glucose | + | builds acid from | 17634 |
65427 | D-mannitol | - | builds acid from | 16899 |
65427 | D-mannose | + | builds acid from | 16024 |
65427 | D-ribose | - | builds acid from | 16988 |
65427 | D-sorbitol | - | builds acid from | 17924 |
65427 | D-xylose | - | builds acid from | 65327 |
65427 | esculin | - | hydrolysis | 4853 |
65427 | gelatin | + | hydrolysis | 5291 |
65427 | hypoxanthine | - | hydrolysis | 17368 |
65427 | L-arabinose | - | builds acid from | 30849 |
65427 | L-rhamnose | - | builds acid from | 62345 |
65427 | L-tyrosine | + | hydrolysis | 17895 |
65427 | lactose | - | builds acid from | 17716 |
65427 | maltose | + | builds acid from | 17306 |
65427 | melezitose | - | builds acid from | 6731 |
65427 | melibiose | - | builds acid from | 28053 |
65427 | myo-inositol | - | builds acid from | 17268 |
65427 | nitrate | + | reduction | 17632 |
65427 | raffinose | - | builds acid from | 16634 |
65427 | starch | + | hydrolysis | 28017 |
65427 | sucrose | - | builds acid from | 17992 |
65427 | trehalose | - | builds acid from | 27082 |
65427 | tween 80 | + | hydrolysis | 53426 |
65427 | urea | - | hydrolysis | 16199 |
65427 | xanthine | - | hydrolysis | 15318 |
metabolite production
- @ref: 65427
- Chebi-ID: 15138
- metabolite: sulfide
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
65427 | catalase | + | 1.11.1.6 |
65427 | cytochrome oxidase | + | 1.9.3.1 |
65427 | alkaline phosphatase | + | 3.1.3.1 |
65427 | esterase Lipase (C 8) | + | |
65427 | leucine arylamidase | + | 3.4.11.1 |
65427 | valine arylamidase | + | |
65427 | cystine arylamidase | + | 3.4.11.3 |
65427 | trypsin | + | 3.4.21.4 |
65427 | acid phosphatase | + | 3.1.3.2 |
65427 | naphthol-AS-BI-phosphohydrolase | + | |
65427 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
65427 | lipase (C 14) | - | |
65427 | alpha-chymotrypsin | - | 3.4.21.1 |
65427 | alpha-galactosidase | - | 3.2.1.22 |
65427 | beta-galactosidase | - | 3.2.1.23 |
65427 | beta-glucuronidase | - | 3.2.1.31 |
65427 | alpha-glucosidase | - | 3.2.1.20 |
65427 | beta-glucosidase | - | 3.2.1.21 |
65427 | alpha-mannosidase | - | 3.2.1.24 |
65427 | alpha-fucosidase | - | 3.2.1.51 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | enrichment culture | enrichment culture temperature |
---|---|---|---|---|---|---|---|
65427 | a tidal flat | South Sea | Republic of Korea | KOR | Asia | marine agar 2216 (MA; BD Difco) | 30 |
67771 | From tidal flat | Yeosu on the South Sea | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Tidal flat
taxonmaps
- @ref: 69479
- File name: preview.99_5065.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_2469;97_3013;98_3780;99_5065&stattab=map
- Last taxonomy: Flavobacterium
- 16S sequence: MF595513
- Sequence Identity:
- Total samples: 1349
- soil counts: 81
- aquatic counts: 989
- animal counts: 266
- plant counts: 13
Sequence information
16S sequences
- @ref: 65427
- description: 16S rRNA gene sequence
- accession: MF595513
- database: nuccore
Genome sequences
- @ref: 66792
- description: Flavobacterium sediminilitoris YSM-43
- accession: GCA_023008245
- assembly level: complete
- database: ncbi
- NCBI tax ID: 2024526
GC content
- @ref: 67771
- GC-content: 29.8
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
flagellated | no | 94.035 | yes |
gram-positive | no | 98.613 | yes |
anaerobic | no | 99.459 | yes |
aerobic | yes | 87.468 | no |
halophile | no | 89.218 | no |
spore-forming | no | 93.354 | yes |
motile | no | 86.848 | no |
glucose-ferment | no | 90.616 | no |
thermophile | no | 99.591 | no |
glucose-util | yes | 76.608 | no |
External links
@ref: 65427
culture collection no.: KACC 19435, KCTC 62142, NBRC 113020
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 29303697 | Flavobacterium sediminilitoris sp. nov., isolated from a tidal flat. | Park S, Choi J, Choi SJ, Yoon JH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002555 | 2018 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Geologic Sediments/*microbiology, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Genetics | 35993777 | Complete Genome Sequence of Flavobacterium sediminilitoris YSM-43(T), Isolated from Tidal Sediment in Yeosu. | Lee PA, Cha IT, Lee KE, Son YK, Yu J, Kim JN, Seol D | Microbiol Resour Announc | 10.1128/mra.00054-22 | 2022 | Phylogeny |
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 | ||
65427 | Sooyeon Park, Jeehyun Choi, Su Jung Choi, Jung-Hoon Yoon | Flavobacterium sediminilitoris sp. nov., isolated from a tidal flat | 10.1099/ijsem.0.002555 | IJSEM 68: 630-635 2018 | 29303697 |
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 | ||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||
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/ |