Strain identifier

BacDive ID: 133551

Type strain: Yes

Species: Flavobacterium glycines

Strain Designation: Gm-149

Strain history: CIP <- 2010, NBRC

NCBI tax ID(s): 551990 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 29482

BacDive-ID: 133551

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-negative, motile, rod-shaped

description: Flavobacterium glycines Gm-149 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from Environment, Rhizosphere of field-grown soybean.

NCBI tax id

  • NCBI tax id: 551990
  • Matching level: species

strain history

@refhistory
422522010, NBRC
119699CIP <- 2010, NBRC

doi: 10.13145/bacdive133551.20230509.8.1

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 glycines
  • full scientific name: Flavobacterium glycines Madhaiyan et al. 2010

@ref: 29482

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium glycines

strain designation: Gm-149

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
29482negative0.8-1 µm0.2-0.3 µmrod-shapedyesgliding
69480negative99.998
119699negativerod-shapedno

pigmentation

  • @ref: 29482
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
42252MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119699CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566
119699CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
29482positivegrowth10-35
29482positiveoptimum28mesophilic
42252positivegrowth30mesophilic

culture pH

@refabilitytypepH
29482positivegrowth06-08
29482positiveoptimum06-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29482facultative anaerobe
119699obligate aerobe

spore formation

@refspore formationconfidence
29482no
69481no100
69480no99.999

observation

  • @ref: 29482
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2948222599arabinose+carbon source
2948217306maltose+carbon source
2948237684mannose+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
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-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
6837117306maltose+builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-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
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
11969917632nitrate+reduction
11969916301nitrite-reduction

metabolite production

  • @ref: 119699
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29482catalase+1.11.1.6
29482cytochrome oxidase+1.9.3.1
119699oxidase+
119699catalase+1.11.1.6
119699urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119699-++--++--+++++-+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119699--++-----++++-+/-------------++/-+-+-+++---+/----+/------

Isolation, sampling and environmental information

isolation

  • @ref: 119699
  • sample type: Environment, Rhizosphere of field-grown soybean
  • geographic location: Tamilnadu
  • country: India
  • origin.country: IND
  • continent: Asia

Safety information

risk assessment

  • @ref: 119699
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 29482
  • description: Flavobacterium glycines strain Gm-149 16S ribosomal RNA gene, partial sequence
  • accession: EU672803
  • length: 1403
  • database: nuccore
  • NCBI tax ID: 551990

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium glycines Gm-149GCA_900100165scaffoldncbi551990
66792Flavobacterium glycines NBRC 105008GCA_007989005contigncbi551990
66792Flavobacterium glycines NBRC 105008GCA_001686935contigncbi551990
66792Flavobacterium glycines strain NBRC 105008551990.7wgspatric551990
66792Flavobacterium glycines strain NBRC 105008551990.4wgspatric551990
66792Flavobacterium glycines NBRC 1050082772190675draftimg551990
66792Flavobacterium glycines Gm-1492660237900draftimg551990

GC content

  • @ref: 29482
  • GC-content: 35.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno88.82no
flagellatedno93.8yes
gram-positiveno98.005yes
anaerobicno99.588no
aerobicyes87.812no
halophileno97.423no
spore-formingno94.121yes
glucose-fermentno88.815no
thermophileno98.923no
glucose-utilyes86.637no

External links

@ref: 29482

culture collection no.: ICMP 17618, NBRC 105008, CIP 110235

straininfo link

  • @ref: 91499
  • straininfo: 370653

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19897620Flavobacterium glycines sp. nov., a facultative methylotroph isolated from the rhizosphere of soybean.Madhaiyan M, Poonguzhali S, Lee JS, Lee KC, Sundaram SInt J Syst Evol Microbiol10.1099/ijs.0.014019-02009Autotrophic Processes, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Flavobacterium/*classification/genetics/*isolation & purification/metabolism, Methanol/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Soybeans/*microbiologyMetabolism
Phylogeny27902211Flavobacterium eburneum sp. nov., isolated from reclaimed saline land soil.Hwang WM, Kim D, Kang K, Ahn TYInt J Syst Evol Microbiol10.1099/ijsem.0.0015682017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Salinity, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny27902216Flavobacterium gilvum sp. nov., isolated from stream water.Shin SK, Ha Y, Cho YJ, Kwon S, Yong D, Yi HInt J Syst Evol Microbiol10.1099/ijsem.0.0015942017
Phylogeny30047082Flavobacterium parvum sp. nov., isolated from soil polluted by sewer water.Lee HS, Hwang WM, Kang K, Ahn TYJ Microbiol10.1007/s12275-018-8145-92018Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Korea, Locomotion, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Sodium Chloride/metabolism, *Soil Microbiology, Temperature, Vitamin K 2/analysisTranscriptome
Phylogeny30320544Flavobacterium riviphilum sp. nov., isolated from a freshwater creek.Sheu SY, Su CL, Chen WMInt J Syst Evol Microbiol10.1099/ijsem.0.0030702018Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Taiwan, Vitamin K 2/analogs & derivatives/chemistry, Water MicrobiologyTranscriptome

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
29482Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172588228776041
42252Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8072
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91499Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID370653.1
119699Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110235Collection of Institut Pasteur (CIP 110235)