Strain identifier

BacDive ID: 5826

Type strain: Yes

Species: Modestobacter roseus

Strain Designation: 5NBRC 108673

Strain history: <- S Qin, Xuzhou Normal Univ., China

NCBI tax ID(s): 1181884 (species)

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

@ref: 18182

BacDive-ID: 5826

DSM-Number: 45764

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

description: Modestobacter roseus 5NBRC 108673 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from surface-sterilized roots of the coastal halophyte Salicornia europaea L., healthy plant tissue.

NCBI tax id

  • NCBI tax id: 1181884
  • Matching level: species

strain history

@refhistory
18182<- S. Qin, Jiangsu Normal University, China; KLBMP 1279
67771<- S Qin, Xuzhou Normal Univ., China

doi: 10.13145/bacdive5826.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Geodermatophilales
  • family: Geodermatophilaceae
  • genus: Modestobacter
  • species: Modestobacter roseus
  • full scientific name: Modestobacter roseus Qin et al. 2013

@ref: 18182

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Geodermatophilaceae

genus: Modestobacter

species: Modestobacter roseus

full scientific name: Modestobacter roseus Qin et al. 2013

strain designation: 5NBRC 108673

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
30790positiverod-shapedyes
67771positive
69480positive100

colony morphology

@refcolony colormedium used
69428ColorlessISP 4
69428Oyster white (1013)ISP 7
69428Oyster white (1013)suter with tyrosine
69428Oyster white (1013)suter without tyrosine
69428Pastel yellow (1034)ISP 2
69428Pastel yellow (1034)ISP 3
69428Yellow orange (2000)ISP 6

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69428noAerial myceliumISP 2
69428noAerial myceliumISP 3
69428noAerial myceliumISP 4
69428noAerial myceliumISP 6
69428noAerial myceliumISP 7
69428noAerial myceliumsuter with tyrosine
69428noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
30790yes
69428noMelanin
69428nosoluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
18182https://www.dsmz.de/microorganisms/photos/DSM_45764.jpgMedium 830 28°C© Leibniz-Institut DSMZ
69428DSM_45764_image3.jpegPlates (830, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69428DSM_45764_image4.jpegPlates (830, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18182GYM 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
18182R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
18182ISP2 MEDIUM (DSMZ Medium 987)yeshttps://mediadive.dsmz.de/medium/987Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water
18182TRYPTICASE 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
18182positivegrowth28mesophilic
30790positivegrowth10-37
30790positiveoptimum28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
30790positivegrowth06-11alkaliphile
30790positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30790aerobe
67771aerobe

spore formation

@refspore formationconfidence
30790no
69481no95
69480no93.568

halophily

@refsaltgrowthtested relationconcentration
30790NaClpositivegrowth0-10 %
69428NaClpositivegrowth0-5 %

observation

  • @ref: 67771
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6942822599arabinose+growth
3079022599arabinose+carbon source
3079024265gluconate+carbon source
3079017234glucose+carbon source
3079025115malate+carbon source
3079017306maltose+carbon source
3079029864mannitol+carbon source
3079037684mannose+carbon source
30790506227N-acetylglucosamine+carbon source
307904853esculin+hydrolysis
6942862968cellulose+growth
6942828757fructose+growth
6942817234glucose+growth
6942817268inositol+/-growth
6942837684mannose+growth
6942816634raffinose+/-growth
6942826546rhamnose+growth
6942817992sucrose+growth
6942818222xylose+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
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
68382alpha-chymotrypsin+3.4.21.1
68382trypsin-3.4.21.4
68382leucine arylamidase+3.4.11.1
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
69428------+------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69428-+++/-++/-+/--++/-+/----++---

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitude
18182surface-sterilized roots of the coastal halophyte Salicornia europaea L., healthy plant tissueSalicornia europaeaJiangsu Province, Nantong coast (121° 0' 38.96'' E 32° 34' 24.91'' N)ChinaCHNAsia32.5736121.011
67771Fromfrom surface-sterilized roots of a coastal halophyteSalicornia europaea Linn., collected from JiangsuChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1976.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_1096;97_1284;98_1546;99_1976&stattab=map
  • Last taxonomy: Modestobacter
  • 16S sequence: JQ819258
  • Sequence Identity:
  • Total samples: 31692
  • soil counts: 18491
  • aquatic counts: 2890
  • animal counts: 5702
  • plant counts: 4609

Safety information

risk assessment

  • @ref: 18182
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 18182
  • description: Modestobacter roseus strain KLBMP 1279 16S ribosomal RNA gene, partial sequence
  • accession: JQ819258
  • length: 1451
  • database: ena
  • NCBI tax ID: 1181884

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Modestobacter roseus DSM 45764GCA_007994135contigncbi1181884
66792Modestobacter roseus strain DSM 457641181884.3wgspatric1181884
66792Modestobacter roseus DSM 457642585427561draftimg1181884

GC content

@refGC-contentmethod
1818271.7high performance liquid chromatography (HPLC)
3079071.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno95no
motileyes78.715yes
gram-positiveyes91.381yes
anaerobicno98.768yes
aerobicyes87.738yes
halophileno89.028no
spore-formingno81.386yes
flagellatedno93.572no
thermophileno99.123yes
glucose-utilyes87.909yes
glucose-fermentno89.47yes

External links

@ref: 18182

culture collection no.: DSM 45764, KCTC 19887, NBRC 108673, KLBMP 1279

straininfo link

  • @ref: 75308
  • straininfo: 405268

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23148095Modestobacter roseus sp. nov., an endophytic actinomycete isolated from the coastal halophyte Salicornia europaea Linn., and emended description of the genus Modestobacter.Qin S, Bian GK, Zhang YJ, Xing K, Cao CL, Liu CH, Dai CC, Li WJ, Jiang JHInt J Syst Evol Microbiol10.1099/ijs.0.044412-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Chenopodiaceae/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Salt-Tolerant Plants/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny27537546Modestobacter lacusdianchii sp. nov., a Phosphate-Solubilizing Actinobacterium with Ability to Promote Microcystis Growth.Zhang BH, Salam N, Cheng J, Li HQ, Yang JY, Zha DM, Zhang YQ, Ai MJ, Hozzein WN, Li WJPLoS One10.1371/journal.pone.01610692016Actinobacteria/genetics/*metabolism, Culture Media, DNA, Bacterial/genetics, Microcystis/genetics/*growth & development, Phosphates/metabolism, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny28809149Cumulibacter manganitolerans gen. nov., sp. nov., isolated from sludge of a manganese mine.Huang J, Li J, Cao M, Liao S, Wang GInt J Syst Evol Microbiol10.1099/ijsem.0.0020042017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Manganese, *Mining, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
18182Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45764)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45764
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
30790Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2712128776041
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69428Wink, J.https://cdn.dsmz.de/wink/DSM%2045764.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
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
75308Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405268.1StrainInfo: A central database for resolving microbial strain identifiers