Strain identifier
BacDive ID: 5561
Type strain:
Species: Flavobacterium segetis
Strain Designation: AT1048
Strain history: CIP <- 2006, JCM <- 2004, J. Chun, Seoul Univ., Seoul, Korea: strain AT1048
NCBI tax ID(s): 271157 (species)
General
@ref: 8275
BacDive-ID: 5561
DSM-Number: 19741
keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative, rod-shaped
description: Flavobacterium segetis AT1048 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from soil sample of a penguin habitat.
NCBI tax id
- NCBI tax id: 271157
- Matching level: species
strain history
@ref | history |
---|---|
8275 | <- JCM/RIKEN <- J. Chun, Seoul Nat. Univ.; AT1048 |
67770 | J. Chun AT1048. |
122547 | CIP <- 2006, JCM <- 2004, J. Chun, Seoul Univ., Seoul, Korea: strain AT1048 |
doi: 10.13145/bacdive5561.20230509.8.1
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 segetis
- full scientific name: Flavobacterium segetis Yi and Chun 2006
@ref: 8275
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Flavobacterium
species: Flavobacterium segetis
full scientific name: Flavobacterium segetis Yi and Chun 2006
strain designation: AT1048
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31740 | negative | 1.1-2.3 µm | 0.2-0.3 µm | rod-shaped | no | |
69480 | negative | 99.995 | ||||
122547 | negative | rod-shaped | no |
pigmentation
- @ref: 31740
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
8275 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water |
42075 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
122547 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 | |
122547 | CIP Medium 566 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8275 | positive | growth | 15 | psychrophilic |
31740 | positive | growth | 5-21.8 | psychrophilic |
31740 | positive | optimum | 14.3-18.9 | psychrophilic |
42075 | positive | growth | 7 | psychrophilic |
67770 | positive | growth | 15 | psychrophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31740 | positive | growth | 06-11 | alkaliphile |
31740 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31740 | aerobe |
122547 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
31740 | no | |
69481 | no | 100 |
69480 | no | 99.997 |
halophily
- @ref: 31740
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-3 %
observation
@ref | observation |
---|---|
31740 | aggregates in chains |
67770 | quinones: MK-6 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31740 | 17234 | glucose | + | carbon source |
31740 | 17306 | maltose | + | carbon source |
31740 | 37684 | mannose | + | carbon source |
31740 | 506227 | N-acetylglucosamine | + | carbon source |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | - | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 18287 | L-fucose | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 32528 | turanose | - | builds acid from |
68371 | 28066 | gentiobiose | - | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28087 | glycogen | - | builds acid from |
68371 | 28017 | starch | - | builds acid from |
68371 | 16634 | raffinose | - | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 27082 | trehalose | - | builds acid from |
68371 | 17992 | sucrose | - | builds acid from |
68371 | 28053 | melibiose | - | builds acid from |
68371 | 17716 | lactose | - | builds acid from |
68371 | 17306 | maltose | - | builds acid from |
68371 | 17057 | cellobiose | - | builds acid from |
68371 | 17814 | salicin | - | builds acid from |
68371 | 18305 | arbutin | - | builds acid from |
68371 | 27613 | amygdalin | - | builds acid from |
68371 | 59640 | N-acetylglucosamine | - | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 16899 | D-mannitol | - | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 16024 | D-mannose | - | builds acid from |
68371 | 15824 | D-fructose | - | builds acid from |
68371 | 17634 | D-glucose | - | builds acid from |
68371 | 12936 | D-galactose | - | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 65327 | D-xylose | - | builds acid from |
68371 | 16988 | D-ribose | - | builds acid from |
68371 | 30849 | L-arabinose | - | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | - | builds acid from |
122547 | 17632 | nitrate | - | reduction |
122547 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 122547
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
31740 | catalase | + | 1.11.1.6 |
31740 | cytochrome oxidase | + | 1.9.3.1 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | esterase (C 4) | - | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
122547 | oxidase | + | |
122547 | catalase | + | 1.11.1.6 |
122547 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122547 | - | + | - | - | - | + | + | - | - | - | + | + | - | - | - | + | - | + | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122547 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | +/- | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | continent | country | origin.country |
---|---|---|---|---|---|
8275 | soil sample of a penguin habitat | King Sejong Station on King George Island | Australia and Oceania | ||
67770 | Soil sample of a penguin habitat near the King Sejong Station | King George Island | Antarctica | Antarctica | ATA |
122547 | Terrestrial samples | Antarctica | Antarctica | ATA |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Soil |
#Host | #Birds |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
8275 | 1 | Risk group (German classification) |
122547 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 8275
- description: Flavobacterium segetis strain AT1048 16S ribosomal RNA gene, partial sequence
- accession: AY581115
- length: 1436
- database: ena
- NCBI tax ID: 271157
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Flavobacterium segetis strain DSM 19741 | 271157.3 | wgs | patric | 271157 |
66792 | Flavobacterium segetis DSM 19741 | 2695420957 | draft | img | 271157 |
67770 | Flavobacterium segetis DSM 19741 | GCA_900129575 | scaffold | ncbi | 271157 |
GC content
@ref | GC-content | method |
---|---|---|
8275 | 35.0 | |
31740 | 35 | |
67770 | 35 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 91.573 | yes |
gram-positive | no | 98.164 | yes |
anaerobic | no | 99.585 | yes |
halophile | no | 87.956 | no |
spore-forming | no | 94.243 | yes |
glucose-util | yes | 86.931 | yes |
aerobic | yes | 93.824 | no |
flagellated | no | 94.431 | no |
thermophile | no | 99.729 | no |
glucose-ferment | no | 92.432 | no |
External links
@ref: 8275
culture collection no.: DSM 19741, CIP 109332, IMSNU 14050, JCM 12385, KCTC 12224
straininfo link
- @ref: 75043
- straininfo: 131136
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16738098 | Flavobacterium weaverense sp. nov. and Flavobacterium segetis sp. nov., novel psychrophiles isolated from the Antarctic. | Yi H, Chun J | Int J Syst Evol Microbiol | 10.1099/ijs.0.64164-0 | 2006 | Antarctic Regions, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Flavobacterium/*classification/genetics/growth & development/isolation & purification, Freezing, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, Thermodynamics | Genetics |
Phylogeny | 28742006 | Flavobacterium soyangense sp. nov., a psychrotolerant bacterium, isolated from an oligotrophic freshwater lake. | Nam GG, Joung Y, Park M, Kim S, Jeon HT, Cho JC | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001987 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Lakes/*microbiology, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
8275 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19741) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19741 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
31740 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28015 | 28776041 | |
42075 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7062 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68371 | Automatically annotated from API 50CH acid | |||||
68382 | Automatically annotated from API zym | |||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
75043 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID131136.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
122547 | Curators of the CIP | Collection of Institut Pasteur (CIP 109332) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109332 |