Strain identifier

BacDive ID: 130401

Type strain: Yes

Species: Microvirga flocculans

Strain Designation: TFB

Variant: Isotype of BacDive ID 131143

Strain history: CIP <- 2004, JCM <- 2003, M. Takeda: strain TFB

NCBI tax ID(s): 217168 (species)

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General

@ref: 21678

BacDive-ID: 130401

DSM-Number: 28869

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

description: Microvirga flocculans TFB is a thermophilic, Gram-negative, motile bacterium that was isolated from run-off of a bathhouse, Koyokan, located at the Kazawa hot spring.

NCBI tax id

  • NCBI tax id: 217168
  • Matching level: species

strain history

@refhistory
21678<- CIP; CIP 108443 <- JCM; JCM 11936 <- M. Takeda, Division of Materials Science and Chemical Engineering, Faculty of Engineering, Yokohama National University; TFB
67770M. Takeda TFB.
119400CIP <- 2004, JCM <- 2003, M. Takeda: strain TFB

doi: 10.13145/bacdive130401.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Methylobacteriaceae
  • genus: Microvirga
  • species: Microvirga flocculans
  • full scientific name: Microvirga flocculans (Takeda et al. 2004) Weon et al. 2010

  • synonyms

    @refsynonym
    20215Balneimonas flocculans
    20215Balneomonas flocculans

@ref: 21678

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Methylobacteriaceae

genus: Microvirga

species: Microvirga flocculans

full scientific name: Microvirga flocculans (Takeda et al. 2004) Weon et al. 2010

strain designation: TFB

variant: Isotype of BacDive ID 131143

type strain: yes

Morphology

cell morphology

  • @ref: 119400
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 119400
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
21678MICROVIRGA FLOCULATUS MEDIUM (DSMZ Medium 1553)yeshttps://mediadive.dsmz.de/medium/1553Name: MICROVIRGA FLOCULATUS MEDIUM (DSMZ Medium 1553) Composition: Agar 15.0 g/l Yeast extract 0.25 g/l Peptone 0.25 g/l K2HPO4 0.1 g/l NaH2PO4 0.05 g/l MgSO4 x 7 H2O 0.02 g/l Distilled water
37432MEDIUM 586 - for Balneimonas flocculansyesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.020 g);Agar (15.000 g);Yeast extract (0.250 g);Peptone (0.250 g);Di Potassium monohydrogenophosphate (0.100 g);Sodium dihydrogen phosphate (0.050 g)
119400CIP Medium 586yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=586

culture temp

@refgrowthtypetemperaturerange
21678positivegrowth45thermophilic
37432positivegrowth45thermophilic
67770positivegrowth43thermophilic
119400positivegrowth25-45
119400nogrowth5psychrophilic
119400nogrowth10psychrophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
119400NaClpositivegrowth0-2 %
119400NaClnogrowth4 %
119400NaClnogrowth6 %
119400NaClnogrowth8 %
119400NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose+builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
119400citrate-carbon source16947
119400esculin-hydrolysis4853
119400nitrate-reduction17632
119400nitrite-reduction16301

antibiotic resistance

  • @ref: 119400
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6777062968celluloseyes
11940035581indoleno

enzymes

@refvalueactivityec
119400oxidase+
119400beta-galactosidase-3.2.1.23
119400alcohol dehydrogenase-1.1.1.1
119400catalase+1.11.1.6
119400lysine decarboxylase-4.1.1.18
119400ornithine decarboxylase-4.1.1.17
119400tryptophan deaminase-
119400urease-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
119400--++-+--+-++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119400----+------------------------------------+------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
21678run-off of a bathhouse, Koyokan, located at the Kazawa hot springGunma PrefectureJapanJPNAsia
67770Kazawa hot springGunma Pref.JapanJPNAsia
119400Environment, BathwaterJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#House
#Environmental#Aquatic#Thermal spring
#Condition#Thermophilic (>45°C)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
216781Risk group (German classification)
1194001Risk group (French classification)

Sequence information

16S sequences

  • @ref: 21678
  • description: Balneimonas flocculans gene for 16S rRNA
  • accession: AB098515
  • length: 1439
  • database: ena
  • NCBI tax ID: 1336243

Genome sequences

  • @ref: 67770
  • description: Microvirga flocculans ATCC BAA-817
  • accession: GCA_000518665
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 1336243

GC content

  • @ref: 67770
  • GC-content: 64
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes65.733no
flagellatedno72.26no
gram-positiveno97.946no
anaerobicno97.949no
halophileno89.361no
spore-formingno94.861no
glucose-utilyes87.988no
aerobicyes90.046no
thermophileno50yes
glucose-fermentno90.788no

External links

@ref: 21678

culture collection no.: DSM 28869, ATCC BAA 817, CIP 108443, IAM 15034, JCM 11936, KCTC 12101

straininfo link

  • @ref: 88933
  • straininfo: 107098

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15046301Balneomonas flocculans gen. nov., sp. nov., a new cellulose-producing member of the alpha-2 subclass of Proteobacteria.Takeda M, Suzuki I, Koizumi JSyst Appl Microbiol10.1078/0723202043228817452004Alphaproteobacteria/*classification/genetics/*metabolism/ultrastructure, Base Composition, Base Sequence, Cellulose/chemistry/*metabolism, DNA, Bacterial/chemistry/genetics, Microscopy, Electron, Scanning, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/chemistry/genetics, Water MicrobiologyMetabolism
Phylogeny20023055Description of Microvirga aerophila sp. nov. and Microvirga aerilata sp. nov., isolated from air, reclassification of Balneimonas flocculans Takeda et al. 2004 as Microvirga flocculans comb. nov. and emended description of the genus Microvirga.Weon HY, Kwon SW, Son JA, Jo EH, Kim SJ, Kim YS, Kim BY, Ka JOInt J Syst Evol Microbiol10.1099/ijs.0.018770-02009*Air Microbiology, Base Composition, Bradyrhizobiaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, Fatty Acids/metabolism, Methylobacteriaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism

Reference

@idauthorstitledoi/urlcatalogue
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
21678Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28869Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28869)
37432Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6066
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
88933Reimer, 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-ID107098.1
119400Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108443Collection of Institut Pasteur (CIP 108443)