Strain identifier

BacDive ID: 8052

Type strain: Yes

Species: Micromonospora endophytica

Strain Designation: 202201

Strain history: CGMCC 4.5597 <-- Q.-Y. Xie et al. 202201.

NCBI tax ID(s): 515350 (species)

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General

@ref: 16790

BacDive-ID: 8052

DSM-Number: 45430

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive

description: Micromonospora endophytica 202201 is an aerobe, spore-forming, mesophilic bacterium that was isolated from surface-sterilized roots of Acanthus illicifolius.

NCBI tax id

  • NCBI tax id: 515350
  • Matching level: species

strain history

@refhistory
16790<- K. Hong, Inst. of Tropical Bioscience & Biotech., Haikou City; 202201 <- R. Wang
67770CGMCC 4.5597 <-- Q.-Y. Xie et al. 202201.

doi: 10.13145/bacdive8052.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micromonosporales
  • family: Micromonosporaceae
  • genus: Micromonospora
  • species: Micromonospora endophytica
  • full scientific name: Micromonospora endophytica (Xie et al. 2011) Li et al. 2019

  • synonyms

    • @ref: 20215
    • synonym: Jishengella endophytica

@ref: 16790

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora endophytica

full scientific name: Micromonospora endophytica (Xie et al. 2011) Li et al. 2019

strain designation: 202201

type strain: yes

Morphology

cell morphology

@refgram stainconfidence
29900positive
69480positive100

colony morphology

@refcolony colormedium used
69394Daffodil yellow (10007), Maize yellow (1006)suter without tyrosine
69394Bright red orange (2008)ISP 2
69394Pastel yellow (1034), Pastel orange (2003)ISP 4
69394Yellow orange (2000), Bright red orange (2008), Copper brown (8004)ISP 3
69394Yellow orange (2000), Daffodil yellow (1007)ISP 6
69394Yellow orange (2000), Daffodil yellow (1007)suter with tyrosine
69394Yellow orange (2000), Pastel yellow (1034), Bright red orange (2008)ISP 5
69394Yellow orange (2000), Red orange (2001)ISP 7

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69394noAerial myceliumISP 2
69394noAerial myceliumISP 3
69394noAerial myceliumISP 4
69394noAerial myceliumISP 5
69394noAerial myceliumISP 6
69394noAerial myceliumISP 7
69394noAerial myceliumsuter with tyrosine
69394noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
29900yes
69394noMelanin
69394nosoluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
69394DSM_45430_image3.jpegPlates (553, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69394DSM_45430_image4.jpegPlates (553, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16790GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
16790N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium554.pdf
16790GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium65.pdf

culture temp

@refgrowthtypetemperaturerange
16790positivegrowth28mesophilic
29900positivegrowth04-45
29900positiveoptimum31.5mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
29900positivegrowth04-11alkaliphile
29900positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29900
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29900yes
69481yes100
69480yes99.999

halophily

@refsaltgrowthtested relationconcentration
29900NaClpositivegrowth<3 %
29900NaClpositiveoptimum1 %
69394NaClpositivegrowth0-5 %

observation

@refobservation
29900aggregates in clumps
67770quinones: MK-9(H4), MK-9(H6), MK-9(H8), MK-10(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
299005291gelatin+carbon source
6939422599arabinose+growth
6939462968cellulose-growth
6939428757fructose+growth
6939417234glucose+growth
6939417268inositol+/-growth
6939437684mannose+/-growth
6939416634raffinose+/-growth
6939426546rhamnose-growth
6939417992sucrose+growth
6939418222xylose+growth
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
29900gelatinase+
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
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69394---+-++---+--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69394++/-+/--++/-+/-++++/--+-+++--

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
16790surface-sterilized roots of Acanthus illicifoliusAcanthus ilicifoliusHainan Province, Wenchang, mangrove reserve zoneChinaCHNAsia
67770Surface-sterilized roots of Acanthus illicifolius from the mangrove reserve zoneAcanthus illicifoliusHainan ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host#Plants#Shrub (Scrub)
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part

Safety information

risk assessment

  • @ref: 16790
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16790
  • description: Jishengella endophytica strain 202201 16S ribosomal RNA gene, partial sequence
  • accession: EU560726
  • length: 1508
  • database: ena
  • NCBI tax ID: 515350

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora endophytica NBRC 109090GCA_018326245completencbi515350
66792Jishengella endophytica strain DSM 45430515350.6wgspatric515350
66792Jishengella endophytica strain JCM 18317515350.9wgspatric515350
66792Micromonospora endophytica (Xie et al. 2001) Li et al. 2019 strain NBRC 109090515350.10completepatric515350
66792Micromonospora endophytica JCM 183172832004796draftimg515350
66792Micromonospora endophytica DSM 454302866065130draftimg515350
67770Micromonospora endophytica DSM 45430GCA_003236305contigncbi515350
67770Micromonospora endophytica JCM 18317GCA_003581605contigncbi515350

GC content

@refGC-contentmethod
1679072.3high performance liquid chromatography (HPLC)
2990072.3
6777073genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.124no
gram-positiveyes89.99yes
anaerobicno99.337yes
aerobicyes93.305yes
halophileno93.352yes
spore-formingyes93.427yes
thermophileno96.499yes
glucose-utilyes87.809yes
motileno95.045no
glucose-fermentno91.61yes

External links

@ref: 16790

culture collection no.: DSM 45430, BCC 72028, CGMCC 4.5597, NBRC 109090, JCM 18317

straininfo link

  • @ref: 77480
  • straininfo: 403645

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20543149Jishengella endophytica gen. nov., sp. nov., a new member of the family Micromonosporaceae.Xie QY, Wang C, Wang R, Qu Z, Lin HP, Goodfellow M, Hong KInt J Syst Evol Microbiol10.1099/ijs.0.025288-02010Acanthaceae/*microbiology, DNA, Bacterial/genetics, Fatty Acids/metabolism, Micromonosporaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny27707427Verrucosispora sonchi sp. nov., a novel endophytic actinobacterium isolated from the leaves of common sowthistle (Sonchus oleraceus L.).Ma Z, Zhao S, Cao T, Liu C, Huang Y, Gao Y, Yan K, Xiang W, Wang XInt J Syst Evol Microbiol10.1099/ijsem.0.0015372016Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonosporaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Plant Leaves/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sonchus/*microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny30168792Jishengella zingiberis sp. nov., isolated from root tissue of Zingiber montanum.Thawai C, He YW, Tadtong SInt J Syst Evol Microbiol10.1099/ijsem.0.0029982018Actinobacteria/genetics, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonosporaceae/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistry, Zingiberaceae/*microbiologyTranscriptome
Phylogeny30605079Micromonospora craniellae sp. nov., isolated from a marine sponge, and reclassification of Jishengella endophytica as Micromonospora endophytica comb. nov.Li L, Zhu HR, Xu QH, Lin HW, Lu YHInt J Syst Evol Microbiol10.1099/ijsem.0.0032092019Animals, Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Genes, Bacterial, Micromonospora/*classification/isolation & purification, Micromonosporaceae/classification, Nucleic Acid Hybridization, *Phylogeny, Porifera/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Phylogeny31310194Micromonospora radicis sp. nov., isolated from roots of Azadirachta indica var. siamensis Valenton, and reclassification of Jishengella zingiberis as Micromonospora zingiberis comb. nov.Kuncharoen N, Kudo T, Yuki M, Okuma M, Pittayakhajonwut P, Tanasupawat SInt J Syst Evol Microbiol10.1099/ijsem.0.0035742019Azadirachta/*microbiology, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonospora/*classification/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thailand, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32223833Micromonospora pelagivivens sp. nov., a new species of the genus Micromonospora isolated from deep-sea sediment in Japan.Intra B, Panbangred W, Inahashi Y, Take A, Mori M, Omura S, Matsumoto AInt J Syst Evol Microbiol10.1099/ijsem.0.0041362020Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Japan, Micromonospora/*classification/isolation & purification, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivativesTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16790Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45430)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45430
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
29900Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2627228776041
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69394Wink, J.https://cdn.dsmz.de/wink/DSM%2045430.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
77480Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403645.1StrainInfo: A central database for resolving microbial strain identifiers