Strain identifier

BacDive ID: 5561

Type strain: Yes

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)

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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

@refhistory
8275<- JCM/RIKEN <- J. Chun, Seoul Nat. Univ.; AT1048
67770J. Chun AT1048.
122547CIP <- 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

@refgram staincell lengthcell widthcell shapemotilityconfidence
31740negative1.1-2.3 µm0.2-0.3 µmrod-shapedno
69480negative99.995
122547negativerod-shapedno

pigmentation

  • @ref: 31740
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8275R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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
42075MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122547CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
122547CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
8275positivegrowth15psychrophilic
31740positivegrowth5-21.8psychrophilic
31740positiveoptimum14.3-18.9psychrophilic
42075positivegrowth7psychrophilic
67770positivegrowth15psychrophilic

culture pH

@refabilitytypepHPH range
31740positivegrowth06-11alkaliphile
31740positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31740aerobe
122547obligate aerobe

spore formation

@refspore formationconfidence
31740no
69481no100
69480no99.997

halophily

  • @ref: 31740
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-3 %

observation

@refobservation
31740aggregates in chains
67770quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3174017234glucose+carbon source
3174017306maltose+carbon source
3174037684mannose+carbon source
31740506227N-acetylglucosamine+carbon source
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12254717632nitrate-reduction
12254716301nitrite-reduction

metabolite production

  • @ref: 122547
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31740catalase+1.11.1.6
31740cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
122547oxidase+
122547catalase+1.11.1.6
122547urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122547-+---++---++---+-+--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122547------------------------+/-------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentcountryorigin.country
8275soil sample of a penguin habitatKing Sejong Station on King George IslandAustralia and Oceania
67770Soil sample of a penguin habitat near the King Sejong StationKing George IslandAntarcticaAntarcticaATA
122547Terrestrial samplesAntarcticaAntarcticaATA

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Birds

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
82751Risk group (German classification)
1225471Risk 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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium segetis strain DSM 19741271157.3wgspatric271157
66792Flavobacterium segetis DSM 197412695420957draftimg271157
67770Flavobacterium segetis DSM 19741GCA_900129575scaffoldncbi271157

GC content

@refGC-contentmethod
827535.0
3174035
6777035high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.573yes
gram-positiveno98.164yes
anaerobicno99.585yes
halophileno87.956no
spore-formingno94.243yes
glucose-utilyes86.931yes
aerobicyes93.824no
flagellatedno94.431no
thermophileno99.729no
glucose-fermentno92.432no

External links

@ref: 8275

culture collection no.: DSM 19741, CIP 109332, IMSNU 14050, JCM 12385, KCTC 12224

straininfo link

  • @ref: 75043
  • straininfo: 131136

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16738098Flavobacterium weaverense sp. nov. and Flavobacterium segetis sp. nov., novel psychrophiles isolated from the Antarctic.Yi H, Chun JInt J Syst Evol Microbiol10.1099/ijs.0.64164-02006Antarctic 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, ThermodynamicsGenetics
Phylogeny28742006Flavobacterium soyangense sp. nov., a psychrotolerant bacterium, isolated from an oligotrophic freshwater lake.Nam GG, Joung Y, Park M, Kim S, Jeon HT, Cho JCInt J Syst Evol Microbiol10.1099/ijsem.0.0019872017Bacterial 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/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8275Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19741)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19741
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31740Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2801528776041
42075Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7062
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
75043Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID131136.1StrainInfo: A central database for resolving microbial strain identifiers
122547Curators of the CIPCollection of Institut Pasteur (CIP 109332)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109332