Strain identifier

BacDive ID: 7473

Type strain: Yes

Species: Plantibacter flavus

Strain Designation: P 297/02, P297/02

Strain history: CIP <- 2004, JCM <- 2003, LMG <- U. Behrendt: strain P297/02

NCBI tax ID(s): 150123 (species)

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General

@ref: 5217

BacDive-ID: 7473

DSM-Number: 14012

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive, oval-shaped

description: Plantibacter flavus P 297/02 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from phylloshere of grasses.

NCBI tax id

  • NCBI tax id: 150123
  • Matching level: species

strain history

@refhistory
5217<- U. Behrendt; P 297/02
67770LMG 19919 <-- U. Behrendt P 297/02.
119388CIP <- 2004, JCM <- 2003, LMG <- U. Behrendt: strain P297/02

doi: 10.13145/bacdive7473.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Plantibacter
  • species: Plantibacter flavus
  • full scientific name: Plantibacter flavus Behrendt et al. 2002

@ref: 5217

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Plantibacter

species: Plantibacter flavus

full scientific name: Plantibacter flavus Behrendt et al. 2002

strain designation: P 297/02, P297/02

type strain: yes

Morphology

cell morphology

  • @ref: 119388
  • gram stain: positive
  • cell shape: oval-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18509Saffron yellow (1017)10-14 daysISP 2
18509Saffron yellow (1017)10-14 daysISP 3
18509Saffron yellow (1017)10-14 daysISP 4
18509Beige (1001)10-14 daysISP 5
18509Saffron yellow (1017)10-14 daysISP 6
18509Saffron yellow (1017)10-14 daysISP 7
119388

multicellular morphology

@refforms multicellular complexmedium name
18509noISP 2
18509noISP 3
18509noISP 4
18509noISP 5
18509noISP 6
18509noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5217TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
18509ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18509ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18509ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18509ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18509ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18509ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
33921MEDIUM 112 - for JanibacteryesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (1.000 g);Agar (20.000 g);Yeast extract (5.000 g);Peptone (10.000 g);Tween 80 (50.000 mg);Glycerol (2.000 g);Malt extract (5.000 g);Beef extract (2.000 g);Casamino acids (5.000 g);Ca
119388CIP Medium 112yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=112

culture temp

@refgrowthtypetemperaturerange
18509positiveoptimum28mesophilic
5217positivegrowth28mesophilic
33921positivegrowth30mesophilic
67770positivegrowth28mesophilic
119388positivegrowth10-30
119388nogrowth37mesophilic
119388nogrowth41thermophilic
119388nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119388
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
119388NaClpositivegrowth0-6 %
119388NaClnogrowth8 %
119388NaClnogrowth10 %

murein

  • @ref: 5217
  • murein short key: B07
  • type: B2gamma {Gly} [L-Dab] D-Glu-D-Dab

observation

  • @ref: 67770
  • observation: quinones: MK-10, MK-11

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371D-fucose-builds acid from28847
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
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
119388citrate-carbon source16947
119388esculin+hydrolysis4853
119388hippurate+hydrolysis606565
119388nitrate-reduction17632
119388nitrite-reduction16301
119388nitrate-respiration17632
68379nitrate-reduction17632
68379esculin+hydrolysis4853
68379urea-hydrolysis16199
68379gelatin-hydrolysis5291
68379D-glucose-fermentation17634
68379D-ribose-fermentation16988
68379D-xylose-fermentation65327
68379D-mannitol-fermentation16899
68379maltose-fermentation17306
68379lactose-fermentation17716
68379sucrose-fermentation17992
68379glycogen-fermentation28087

antibiotic resistance

  • @ref: 119388
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 119388
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11938815688acetoin-
11938817234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase+3.2.1.51
68382alpha-mannosidase-3.2.1.24
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
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase+3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
119388oxidase-
119388beta-galactosidase+3.2.1.23
119388alcohol dehydrogenase-1.1.1.1
119388gelatinase-
119388amylase+
119388DNase+
119388caseinase-3.4.21.50
119388catalase+1.11.1.6
119388tween esterase+
119388gamma-glutamyltransferase-2.3.2.2
119388lecithinase-
119388lipase-
119388lysine decarboxylase-4.1.1.18
119388ornithine decarboxylase-4.1.1.17
119388phenylalanine ammonia-lyase-4.3.1.24
119388protease-
119388tryptophan deaminase-
119388urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18509---++++-+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18509+++-++---+-++-++--+
119388+++-++++-++++-+++-+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119388---++/-+--+++++-+--+----+++++++-++-+----++++/--+/---+/--+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119388+++++--+-+++-+-++++-++++++-----+-+++---+-----------------+--+-------------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5217phylloshere of grassesPaulinenaueGermanyDEUEurope
67770Phyllosphere of grassesGermanyDEUEurope
119388Phyllosphere of grassesGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Leaf (Phyllosphere)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3079.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_895;97_1924;98_2366;99_3079&stattab=map
  • Last taxonomy: Plantibacter flavus
  • 16S sequence: AJ310417
  • Sequence Identity:
  • Total samples: 6679
  • soil counts: 1178
  • aquatic counts: 981
  • animal counts: 3384
  • plant counts: 1136

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
52171Risk group (German classification)
185091German classification
1193881Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5217
  • description: Plantibacter flavus partial 16S rRNA gene, strain DSM 14012T
  • accession: AJ310417
  • length: 1511
  • database: ena
  • NCBI tax ID: 150123

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Plantibacter flavus strain DSM 14012150123.11wgspatric150123
66792Plantibacter flavus DSM 140122781126045draftimg150123
67770Plantibacter flavus VKM Ac-2504GCA_900177615scaffoldncbi150123
67770Plantibacter flavus DSM 14012GCA_003755125contigncbi150123

GC content

  • @ref: 5217
  • GC-content: 70
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno91.129no
gram-positiveyes90no
anaerobicno99.463no
aerobicyes89.083no
halophileno90.46no
spore-formingno93.996no
thermophileno99.762yes
glucose-utilyes83.622no
flagellatedno97.839no
glucose-fermentno87.958yes

External links

@ref: 5217

culture collection no.: DSM 14012, LMG 19919, JCM 12144, CIP 108227, IAM 15049, NBRC 103081, VKM Ac-2504

straininfo link

  • @ref: 76918
  • straininfo: 84588

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12361245Diversity of grass-associated Microbacteriaceae isolated from the phyllosphere and litter layer after mulching the sward; polyphasic characterization of Subtercola pratensis sp. nov., Curtobacterium herbarum sp. nov. and Plantibacter flavus gen. nov., sp. nov.Behrendt U, Ulrich A, Schumann P, Naumann D, Suzuki KIInt J Syst Evol Microbiol10.1099/00207713-52-5-14412002Actinomycetales/*classification/genetics/isolation & purification/pathogenicity, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, Poaceae/*microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, Spectroscopy, Fourier Transform Infrared, Terminology as Topic, VirulenceGenetics
Phylogeny17012557Plantibacter auratus sp. nov., in the family Microbacteriaceae.Lin YC, Yokota AInt J Syst Evol Microbiol10.1099/ijs.0.64366-02006Actinomycetales/chemistry/*classification/genetics/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny25566956Okibacterium endophyticum sp. nov., a novel endophytic actinobacterium isolated from roots of Salsola affinis C. A. Mey.Wang HF, Zhang YG, Li L, Liu WH, Hozzein WN, Chen JY, Guo JW, Zhang YM, Li WJAntonie Van Leeuwenhoek10.1007/s10482-014-0376-02015Actinobacteria/*classification/genetics/*isolation & purification, Aerobiosis, Base Composition, Catalase/analysis, Cell Wall/chemistry, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Endophytes/*classification/genetics/*isolation & purification, Fatty Acids/analysis, Glutamic Acid/analysis, Glycolipids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/analysis, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Salsola/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Vitamin K 2/analysisEnzymology

Reference

@idauthorscataloguedoi/urltitle
5217Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14012)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14012
18509Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM14012.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
33921Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5826
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
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
76918Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID84588.1StrainInfo: A central database for resolving microbial strain identifiers
119388Curators of the CIPCollection of Institut Pasteur (CIP 108227)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108227