Strain identifier

BacDive ID: 12607

Type strain: Yes

Species: Promicromonospora xylanilytica

Strain history: DSM 21603 <-- S.-K. Tang and W.-J. Li YIM 61515 <-- S. Qin.

NCBI tax ID(s): 566022 (species)

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General

@ref: 15839

BacDive-ID: 12607

DSM-Number: 21603

keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, ovoid-shaped

description: Promicromonospora xylanilytica DSM 21603 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from healthy surface-sterilized leaves of a traditional Chinese medicinal plant, Maytenus austroyunnanensis.

NCBI tax id

  • NCBI tax id: 566022
  • Matching level: species

strain history

@refhistory
15839<- S.-K. Tang and W.-J. Li, Yunnan Univ., Kunming; YIM 61515 <- S. Qin
67770DSM 21603 <-- S.-K. Tang and W.-J. Li YIM 61515 <-- S. Qin.

doi: 10.13145/bacdive12607.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Promicromonosporaceae
  • genus: Promicromonospora
  • species: Promicromonospora xylanilytica
  • full scientific name: Promicromonospora xylanilytica Qin et al. 2012

@ref: 15839

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Promicromonosporaceae

genus: Promicromonospora

species: Promicromonospora xylanilytica

full scientific name: Promicromonospora xylanilytica Qin et al. 2012

type strain: yes

Morphology

cell morphology

  • @ref: 30272
  • gram stain: positive
  • cell shape: ovoid-shaped
  • motility: no

colony morphology

@refcolony colormedium used
69291Ivory (1014)ISP 5
69291Light ivory (1015)ISP 3
69291Light ivory (1015)suter with tyrosine
69291Nut brown (8011), Fawn brown (8007), Sand yellow (1002)ISP 4
69291Sand yellow (1002)ISP 6
69291Sand yellow (1002), Clay brown (8003)suter without tyrosine
69291Sand yellow (1002), Ivory (1014)ISP 7
69291Sand yellow (1002), Light ivory (1015)ISP 2

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69291noAerial myceliumISP 2
69291noAerial myceliumISP 3
69291noAerial myceliumISP 4
69291noAerial myceliumISP 5
69291noAerial myceliumISP 6
69291noAerial myceliumISP 7
69291noAerial myceliumsuter with tyrosine
69291noAerial myceliumsuter without tyrosine

pigmentation

@refproductionnamecolor
30272yes
69291noMelanin
69291yessoluble pigmentSand yellow (1002), ochre brown (8001)

multimedia

@refmultimedia contentcaptionintellectual property rights
69291DSM_21603_image3.jpegPlates (535, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69291DSM_21603_image4.jpegPlates (535, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69291DSM_21603_image5.jpeg(ISP6, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69291DSM_21603_image6.jpeg(ISP6, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15839GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
15839TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15839positivegrowth28mesophilic
30272positivegrowth10-37
30272positiveoptimum28mesophilic
67770positivegrowth28mesophilic

culture pH

  • @ref: 30272
  • ability: positive
  • type: growth
  • pH: 6.0-9.0
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 30272
  • oxygen tolerance: aerobe

spore formation

  • @ref: 30272
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
30272NaClpositivegrowth0-9 %
69291NaClpositivegrowth0-7.5 %

murein

  • @ref: 15839
  • murein short key: A11.59
  • type: A4alpha L-Lys-L-Ala-D-Glu

observation

  • @ref: 67770
  • observation: quinones: MK-9(H6), MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3027228757fructose+carbon source
3027217234glucose+carbon source
3027217754glycerol+carbon source
3027217716lactose+carbon source
3027217306maltose+carbon source
3027237684mannose+carbon source
3027216634raffinose+carbon source
3027217814salicin+carbon source
3027217992sucrose+carbon source
3027217632nitrate+reduction
6929122599arabinose+growth
6929162968cellulose-growth
6929128757fructose+growth
6929117234glucose+growth
6929117268inositol-growth
6929137684mannose+/-growth
6929116634raffinose-growth
6929126546rhamnose+growth
6929117992sucrose+growth
6929118222xylose+growth
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917716lactose-fermentation

enzymes

@refvalueactivityec
30272acid phosphatase+3.1.3.2
30272catalase+1.11.1.6
30272cytochrome oxidase+1.9.3.1
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
68382alkaline phosphatase+3.1.3.1
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase+3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69291-+++-++++-++/----+/--+/-+/-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69291++/-+/-+/-++/-+--++/-+/-+-++++-

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
15839healthy surface-sterilized leaves of a traditional Chinese medicinal plant, Maytenus austroyunnanensisMaytenus austroyunnanensisXishuangbanna, Yunnan ProvinceChinaCHNAsia
67770Surface-sterilized leaves of Maytenus austroyunnanensis from the tropical rainforest in XishuangbannaMaytenus austroyunnanensisYunnan Province, south-west ChinaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#Host Body-Site#Plant#Leaf (Phyllosphere)
#Host Body-Site#Plant#Sterilized plant part

taxonmaps

  • @ref: 69479
  • File name: preview.99_5455.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1939;97_2331;98_2876;99_5455&stattab=map
  • Last taxonomy: Promicromonospora
  • 16S sequence: FJ214352
  • Sequence Identity:
  • Total samples: 1384
  • soil counts: 788
  • aquatic counts: 29
  • animal counts: 66
  • plant counts: 501

Safety information

risk assessment

  • @ref: 15839
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15839
  • description: Promicromonospora xylanilytica strain YIM 61515 16S ribosomal RNA gene, partial sequence
  • accession: FJ214352
  • length: 1437
  • database: ena
  • NCBI tax ID: 566022

GC content

@refGC-contentmethod
1583970.4high performance liquid chromatography (HPLC)
3027270.4

External links

@ref: 15839

culture collection no.: DSM 21603, CCTCC AA 208046, JCM 19561, YIM 61515

straininfo link

  • @ref: 81821
  • straininfo: 396839

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21335503Promicromonospora xylanilytica sp. nov., an endophytic actinomycete isolated from surface-sterilized leaves of the medicinal plant Maytenus austroyunnanensis.Qin S, Jiang JH, Klenk HP, Zhu WY, Zhao GZ, Zhao LX, Tang SK, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.032185-02011Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Endophytes/*classification/genetics/*isolation & purification/physiology, Fatty Acids/analysis, Maytenus/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, Plant Leaves/*microbiology, Plants, Medicinal/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysis, Xylans/metabolismEnzymology
Phylogeny21890721Promicromonospora endophytica sp. nov., an endophytic actinobacterium isolated from the root of an Australian native Grey Box tree.Kaewkla O, Franco CMMInt J Syst Evol Microbiol10.1099/ijs.0.033258-02011Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Eucalyptus/*microbiology, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
29441465Xylanilyticolides A-C, Three New Compounds from Cultures of the Actinomycete Promicromonospora xylanilytica YIM 61515.Wang ZX, Qin S, Xu LH, Chen HP, Sun H, Huang R, Li ZH, Feng T, Liu JKNat Prod Bioprospect10.1007/s13659-018-0154-12018
Phylogeny31532356Antribacter gilvus gen. nov., sp. nov., a new member of the family Promicromonosporaceae from a karstic cavern.Zhang LY, Fang BZ, Jiao JY, Zhang XT, Liu L, Meng XL, Ming H, Nie GX, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0036822019Actinobacteria/*classification/isolation & purification, Actinomycetales/classification, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15839Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21603)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21603
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
30272Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2661328776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69291Wink, J.https://cdn.dsmz.de/wink/DSM%2021603.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
81821Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID396839.1StrainInfo: A central database for resolving microbial strain identifiers