Strain identifier

BacDive ID: 7413

Type strain: Yes

Species: Microbacterium phyllosphaerae

Strain Designation: P 369/106, P369/06

Strain history: CIP <- 2001, U. Behrendt, ZALF, Müncheberg, Germany: strain P369/06

NCBI tax ID(s): 124798 (species)

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General

@ref: 5053

BacDive-ID: 7413

DSM-Number: 13468

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

description: Microbacterium phyllosphaerae P 369/106 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from phyllosphere of grasses.

NCBI tax id

  • NCBI tax id: 124798
  • Matching level: species

strain history

@refhistory
5053<- U. Behrendt; P 369/06
330862001, U. Behrendt, Center for Agricultural Landscape and Land Use Research Müncheberg, Germany: strain P369/06
67770LMG 19581 <-- DSM 13468 <-- U. Behrendt P 369/06.
121813CIP <- 2001, U. Behrendt, ZALF, Müncheberg, Germany: strain P369/06

doi: 10.13145/bacdive7413.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Microbacterium
  • species: Microbacterium phyllosphaerae
  • full scientific name: Microbacterium phyllosphaerae Behrendt et al. 2001

@ref: 5053

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium phyllosphaerae

full scientific name: Microbacterium phyllosphaerae Behrendt et al. 2001

strain designation: P 369/106, P369/06

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
121813positiverod-shapedyes
125439positive95.5
125438positive90.114

colony morphology

@refcolony colorincubation periodmedium used
18376Colorless10-14 daysISP 2
18376Zinc yellow (1018)10-14 daysISP 3
18376Zinc yellow (1018)10-14 daysISP 4
18376Beige (1001)10-14 daysISP 5
18376Colorless10-14 daysISP 6
18376Colorless10-14 daysISP 7
121813

multicellular morphology

@refforms multicellular complexmedium name
18376noISP 2
18376noISP 3
18376noISP 4
18376noISP 5
18376noISP 6
18376noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5053TRYPTICASE 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
18376ISP 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
18376ISP 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:
18376ISP 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
18376ISP 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
18376ISP 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
18376ISP 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
33086MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121813CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperature
18376positiveoptimum28
5053positivegrowth28
33086positivegrowth25
67770positivegrowth28
121813positivegrowth10-37
121813nogrowth41
121813nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
121813facultative anaerobe
125439obligate aerobe95.9

halophily

@refsaltgrowthtested relationconcentration
121813NaClpositivegrowth0-4 %
121813NaClnogrowth6 %
121813NaClnogrowth8 %
121813NaClnogrowth10 %

murein

  • @ref: 5053
  • murein short key: B06
  • type: B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

observation

  • @ref: 67770
  • observation: quinones: MK-12, MK-11

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837928087glycogen-fermentation
6837917992sucrose-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837916899D-mannitol-fermentation
6837965327D-xylose-fermentation
6837916988D-ribose-fermentation
683795291gelatin-hydrolysis
6837916199urea+hydrolysis
683794853esculin+hydrolysis
6837917632nitrate-reduction
12181316947citrate-carbon source
1218134853esculin+hydrolysis
121813606565hippurate-hydrolysis
12181317632nitrate-reduction
12181316301nitrite-reduction
12181317632nitrate+respiration
68371Potassium 5-ketogluconate-builds acid from
6837118305arbutin+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837917634D-glucose-fermentation
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
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
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837159640N-acetylglucosamine+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

antibiotic resistance

  • @ref: 121813
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 121813
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12181315688acetoin+
12181317234glucose+

enzymes

@refvalueactivityec
68382beta-glucosidase+3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382alkaline phosphatase-3.1.3.1
68382lipase (C 14)-
121813oxidase-
121813beta-galactosidase+3.2.1.23
121813alcohol dehydrogenase-1.1.1.1
121813gelatinase+/-
121813amylase-
121813DNase+
121813caseinase+3.4.21.50
121813catalase+1.11.1.6
121813tween esterase+
121813gamma-glutamyltransferase-2.3.2.2
121813lecithinase-
121813lipase-
121813lysine decarboxylase-4.1.1.18
121813ornithine decarboxylase-4.1.1.17
121813phenylalanine ammonia-lyase-4.3.1.24
121813tryptophan deaminase-
121813urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68382alpha-fucosidase-3.2.1.51
68379gelatinase-
68379urease+3.5.1.5
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18376-----++-++---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18376-++-+------++-++---
121813----+--+-++++-++++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121813+--+++---++++----+---++/-+++++-+/-++-+++--++/-+/---+/---+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121813+++++--+++-----++++------------+-+-------------------------++-+--+-------+------------+------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
5053phyllosphere of grassesGermanyDEUEurope
67770Phyllosphere of grasses
121813Phyllosphere of grassesGermanyDEUEuropePaulinenaue1993

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_791.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_137;97_148;98_165;99_791&stattab=map
  • Last taxonomy: Microbacterium
  • 16S sequence: AJ277840
  • Sequence Identity:
  • Total samples: 11128
  • soil counts: 2516
  • aquatic counts: 1834
  • animal counts: 5498
  • plant counts: 1280

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
50531Risk group (German classification)
1218131Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
5053Microbacterium phyllosphaerae partial 16S rRNA gene, strain DSM 13468AJ2778401478nuccore124798
124043Microbacterium phyllosphaerae strain DSM 13468 16S ribosomal RNA gene, partial sequence.OQ8766611418nuccore124798

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium phyllosphaerae DSM 13468GCA_017876435contigncbi124798
66792Microbacterium phyllosphaerae strain DSM 13468124798.17wgspatric124798
66792Microbacterium phyllosphaerae DSM 134682918350604draftimg124798

GC content

  • @ref: 5053
  • GC-content: 64
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes90.114no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.922yes
125438spore-formingspore-formingAbility to form endo- or exosporesno73.066no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes84.117no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.467no
125438motile2+flagellatedAbility to perform flagellated movementno76.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno71.2
125439BacteriaNetmotilityAbility to perform movementno62.2
125439BacteriaNetgram_stainReaction to gram-stainingpositive95.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe95.9

External links

@ref: 5053

culture collection no.: DSM 13468, LMG 19581, NRRL B-24227, JCM 11571, CIP 107138, IAM 15191, KCTC 19917, NBRC 103077, NCIMB 14330, VTT E-072687

straininfo link

  • @ref: 76862
  • straininfo: 14967

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11491322Description of Microbacterium foliorum sp. nov. and Microbacterium phyllosphaerae sp. nov., isolated from the phyllosphere of grasses and the surface litter after mulching the sward, and reclassification of Aureobacterium resistens (Funke et al. 1998) as Microbacterium resistens comb. nov..Behrendt U, Ulrich A, Schumann PInt J Syst Evol Microbiol10.1099/00207713-51-4-12672001Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Base Composition, Cell Wall/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Molecular Sequence Data, Phylogeny, Poaceae/microbiology, Species SpecificityMetabolism
Phylogeny19060085Microbacterium profundi sp. nov., isolated from deep-sea sediment of polymetallic nodule environments.Wu YH, Wu M, Wang CS, Wang XG, Yang JY, Oren A, Xu XWInt J Syst Evol Microbiol10.1099/ijs.0.2008/000455-02008Actinomycetales/*classification/genetics/*physiology/ultrastructure, *Environment, Geologic Sediments/*microbiology, *Metals, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Species SpecificityGenetics
Phylogeny22199224Microbacterium murale sp. nov., isolated from an indoor wall.Kampfer P, Schafer J, Lodders N, Martin KInt J Syst Evol Microbiol10.1099/ijs.0.037705-02011Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Environmental Microbiology, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny25563915Microbacterium panaciterrae sp. nov., isolated from the rhizosphere of ginseng.Nguyen NL, Kim YJ, Hoang VA, Min JW, Hwang KH, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.0000412015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Panax/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitle
5053Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13468)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13468
18376Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM13468.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
33086Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4541
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
76862Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14967.1StrainInfo: A central database for resolving microbial strain identifiers
121813Curators of the CIPCollection of Institut Pasteur (CIP 107138)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107138
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1