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Strain identifier

BacDive ID: 7410

Type strain: Yes

Species: Microbacterium foliorum

Strain Designation: P 333/02

Strain history: LMG 19580 <-- DSM 12966 <-- U. Behrendt P 333/02.

NCBI tax ID(s): 104336 (species)

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

@ref: 4869

BacDive-ID: 7410

DSM-Number: 12966

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Microbacterium foliorum P 333/02 is a mesophilic bacterium that was isolated from phyllosphere of grasses.

NCBI tax id

  • NCBI tax id: 104336
  • Matching level: species

strain history

doi: 10.13145/bacdive7410.20221219.7.1

Name and taxonomic classification

LPSN

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

@ref: 4869

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium foliorum

full scientific name: Microbacterium foliorum Behrendt et al. 2001 emend. Nouioui et al. 2018

strain designation: P 333/02

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 89.539

colony morphology

@refcolony colorincubation periodmedium used
18373Lemon yellow (1012)10-14 daysISP 2
18373Lemon yellow (1012)10-14 daysISP 3
18373Lemon yellow (1012)10-14 daysISP 4
18373Lemon yellow (1012)10-14 daysISP 5
18373Lemon yellow (1012)10-14 daysISP 6
18373Lemon yellow (1012)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18373noISP 2
18373noISP 3
18373noISP 4
18373noISP 5
18373noISP 6
18373noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4869TRYPTICASE 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
18373ISP 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
18373ISP 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:
18373ISP 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
18373ISP 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
18373ISP 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
18373ISP 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
38188MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)

culture temp

@refgrowthtypetemperaturerange
18373positiveoptimum28mesophilic
4869positivegrowth28mesophilic
38188positivegrowth25mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 97.416

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 96.324

murein

  • @ref: 4869
  • 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
6837917716lactose-fermentation
6837917306maltose-fermentation
6837916899D-mannitol-fermentation
6837965327D-xylose-fermentation
6837916988D-ribose-fermentation
6837917634D-glucose-fermentation
683795291gelatin+hydrolysis
6837916199urea+hydrolysis
683794853esculin+hydrolysis
6837917632nitrate-reduction

enzymes

@refvalueactivityec
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
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18373-----++-+++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18373-++-+------++-++-+-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
4869phyllosphere of grassesGermanyDEUEurope
67770Phyllosphere of grasses

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: AJ249780
  • Sequence Identity:
  • Total samples: 11128
  • soil counts: 2516
  • aquatic counts: 1834
  • animal counts: 5498
  • plant counts: 1280

Safety information

risk assessment

  • @ref: 4869
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 4869
  • description: Microbacterium foliorum partial 16S rRNA gene, strain DSM 12966
  • accession: AJ249780
  • length: 1480
  • database: ena
  • NCBI tax ID: 104336

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium foliorum strain DSM 12966104336.4wgspatric104336
66792Microbacterium foliorum DSM 129662867847951draftimg104336
66792Microbacterium foliorum DSM 129662751185893draftimg104336
67770Microbacterium foliorum strain NRRL B-24224 chromosome, complete genomeCP031425ena104336
67770Microbacterium foliorum DSM 12966GCA_000956415contigncbi104336
66792Microbacterium foliorum DSM 12966GCA_024168445contigncbi104336
66792Pseudomonas viridiflava p21.E10GCA_900584765contigpatric33069
66792uncultured Prevotella sp. HGM04885GCA_900770495contigpatric159272

GC content

@refGC-contentmethod
486967high performance liquid chromatography (HPLC)
6777068.7genome sequence analysis

External links

@ref: 4869

culture collection no.: DSM 12966, LMG 19580, NRRL B-24224, JCM 11569, CIP 107137, IAM 15188, KCTC 19915, NBRC 103072, NCIMB 14329

straininfo link

@refpassport
20218http://www.straininfo.net/strains/58406
20218http://www.straininfo.net/strains/58404
20218http://www.straininfo.net/strains/684864

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
Phylogeny16166712Microbacterium xylanilyticum sp. nov., a xylan-degrading bacterium isolated from a biofilm.Kim KK, Park HY, Park W, Kim IS, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.63706-02005Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Biodegradation, Environmental, Biofilms/*growth & development, *Bioreactors, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Waste Disposal, Fluid/*methods, Xylans/*metabolismGenetics
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
Genetics29650566Genome Sequences of Ilzat and Eleri, Two Phages Isolated Using Microbacterium foliorum NRRL B-24224.Ali I, Jones AE, Mohamed A, Sivanathan VGenome Announc10.1128/genomeA.00144-182018Phylogeny
Genetics30637400Genome Sequences of Three Microbacterium Phages Isolated from Flowers.Iles KS, Zack KM, Betsko AJ, Garlena RA, Russell DA, Fetters A, Jacobs-Sera D, Ashman TL, Hatfull GFMicrobiol Resour Announc10.1128/MRA.01468-182019Phylogeny
Genetics30714032Complete Genome Sequence of Microbacterium foliorum NRRL B-24224, a Host for Bacteriophage Discovery.Russell DA, Garlena RA, Hatfull GFMicrobiol Resour Announc10.1128/MRA.01467-182019Pathogenicity
Genetics33184160Genome Sequences of Bacteriophages ClearAsMud and Kauala, Isolated from Microbacterium foliorum.Lin H, Reeves M, Acevedo M, Bass K, Chau E, Ching B, Enriquez E, Evans S, Mamora K, Pang C, Santos M, Tafoya C, Vaca M, Van Iderstein W, Velasco L, Williams V, Yonemoto G, Yonemoto T, Choi J, Dean N, Diaz AMicrobiol Resour Announc10.1128/MRA.01026-202020Phylogeny
Genetics33479002Complete Genome Sequence of Microbacterium Bacteriophage Erla.Milhaven M, Hastings E, Brister D, Cevallos L, Chilukuri S, Diyya A, Garg A, Hernandez R, Kelly D, Lazo K, Le J, Maag G, Marfatia PD, Mehta R, Nejad A, Porche J, Queiroz A, Sackett D, Santos Molina P, Slade T, So M, Thakur K, Urquidez Negrete A, Wackett S, Weiss S, McCarthy L, Wheaton K, Rudner AD, McCutcheon JP, Pfeifer SPMicrobiol Resour Announc10.1128/MRA.01354-202021
Genetics34264121Genome Sequences of Akoni, Ashton, and Truong, Podoviridae Bacteriophages Isolated from Microbacterium foliorum.Fakhre F, Gonzalez RM, Howells EK, Otero L, Pegoraro KN, Robichaux KC, Rodier A, Sadowski CL, Carter VP, Gray AD, Klein GC, Lebosada C, Miklaszewski CM, Sutton SN, Chase MA, Coleman CN, Corbett B, Cunha MO, Daffner M, Deam CJ, Deloso LJ, DeSomma AM, Pinera Gallardo J, Horne ME, Kanahan O, Lam V, Morgan RT, Mustor EM, Ricardo-Iglesias M, Sartorio CJ, Sciacchitano AR, Tvenstrup AW, Wood AR, Pollenz RSMicrobiol Resour Announc10.1128/MRA.00516-212021Phylogeny
Genetics34913713Complete Genome Sequence of Bacteriophage IndyLu, Isolated from a Microbacterium foliorum Culture.Suris A, Alvarado S, Butler T, Canales C, Castro M, Gaston J, Goppert M, Huckaby R, Laposky J, Lee J, Mullins E, Ustundag D, Zuniga J, Cox F, Edwards DMicrobiol Resour Announc10.1128/MRA.01079-212021Phylogeny
Genetics35743053Characterization of Phages YuuY, KaiHaiDragon, and OneinaGillian Isolated from Microbacterium foliorum.Kim U, Paul ES, Diaz AInt J Mol Sci10.3390/ijms231266092022*Actinomycetales, *Bacteriophages/genetics, Genome, Viral, Genomics, Host Specificity, MicrobacteriumPhylogeny
Genetics36121218Annotation of the Complete Genome Sequences of Bacteriophages Sara and Birdfeeder.Adams BM, Adams JB, Brewster RL, Cutler MS, Davis AE, Gallegos AH, Hernandez JS, May LH, Montoya EG, Reagan AT, Shurley JF, Grinath AS, Thomas MAMicrobiol Resour Announc10.1128/mra.00780-222022
Genetics36154145Complete Genome Sequence of Bacteriophage Eula, Isolated on Microbacterium foliorum.Cook T, Raffan S, Born T, Breece C, Chandler I, DiLeo H, Eudy A, Lyon K, Nicholson C, Serrano A, Sigmon M, Stevenson S, Townsell K, Van Patten G, Leonard JE, Collins DPMicrobiol Resour Announc10.1128/mra.00728-222022Phylogeny
Genetics36197284Genome Sequence and Characteristics of the Microbacterium foliorum Cluster EE Bacteriophage Burgy.Van Roekel HF, Georgen JJ, Kock RA, Coleman STMicrobiol Resour Announc10.1128/mra.00912-222022
Genetics36227095Genome Sequences of Microbacterium foliorum Phages Anseraureola, Pondwater, and Yasuo.Bamgbowu D, Bsoumai J, Butura J, Cady E, Cholod G, Collibee I, Dompreh L, Eisner S, Elmaleh M, Fitzgerald K, Gillis E, Horgan A, Judd D, Keefe J, Kovalski E, LaBianca K, Lee P, Lin F, Maiuri H, McDonald C, McKnight A, Meseerole M, Mizra F, Monger E, Moore E, Nguyen N, Noel B, O'Connor D, Pagani R, Palmgren M, Pan K, Pech B, Qian J, Rastegar S, Simas B, Southard A, Tracy M, Vuong H, Whelan S, Zou A, Punska E, Pause R, Zhang F, Ribbe A, Chien P, Rocheleau JMicrobiol Resour Announc10.1128/mra.00849-222022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4869Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12966)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12966
18373Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM12966.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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
38188Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4540
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
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)