Strain identifier

BacDive ID: 158459

Type strain: Yes

Species: Micromonospora craniellae

Strain Designation: LHW63014

Strain history: <- L. Li, Shanghai Jiao Tong Univ., China; LHW63014

NCBI tax ID(s): 2294034 (species)

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

@ref: 65135

BacDive-ID: 158459

DSM-Number: 106193

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

description: Micromonospora craniellae LHW63014 is an aerobe, spore-forming, mesophilic bacterium that was isolated from marine sponge.

NCBI tax id

  • NCBI tax id: 2294034
  • Matching level: species

strain history

  • @ref: 65135
  • history: <- L. Li, Shanghai Jiao Tong Univ., China; LHW63014

doi: 10.13145/bacdive158459.20230509.8.1

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 craniellae
  • full scientific name: Micromonospora craniellae Li et al. 2019

@ref: 65135

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Micromonospora

species: Micromonospora craniellae

full scientific name: Micromonospora craniellae Li et al. 2019

strain designation: LHW63014

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
67817positiveno
69480positive100

colony morphology

@refcolony colormedium used
69302Daffodil yellow (1007), pastel yellow (1034)ISP 4
69302Daffodil yellow (1007), pastel yellow (1034)suter with tyrosine
69302Daffodil yellow (1007), pastel yellow (1034)suter without tyrosine
69302Maize yellow (1006)ISP 7
69302Signal orange (2010)ISP 2

multicellular morphology

@refforms multicellular complexfurther descriptioncomplex namemedium name
67817yesforms well-developed branched substrate mycelium. Aerial hyphae is absent.
69302noAerial myceliumISP 2
69302noAerial myceliumISP 4
69302noAerial myceliumISP 7
69302noAerial myceliumsuter with tyrosine
69302noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
69302noMelanin
69302nosoluble pigment

multimedia

  • @ref: 65135
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_106193.jpg
  • caption: Medium 83 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
65135TRYPTICASE 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
65135CZAPEK PEPTONE AGAR (DSMZ Medium 83)yeshttps://mediadive.dsmz.de/medium/83Name: CZAPEK PEPTONE AGAR (DSMZ Medium 83) Composition: Sucrose 30.0 g/l Agar 20.0 g/l Peptone 5.0 g/l NaNO3 3.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.5 g/l KCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
65135positivegrowth28mesophilic
67817positivegrowth20-34

culture pH

  • @ref: 67817
  • ability: positive
  • type: growth
  • pH: 6-9
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 67817
  • oxygen tolerance: aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
67817Single or clustered spherical spores (0.7 µm in diameter) with smooth surface are observed.sporeyes
69480yes100
69481yes100

halophily

@refsaltgrowthtested relationconcentration
67817NaClpositivemaximum4 %
69302NaClpositivegrowth0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6930222599arabinose+growth
6781717632nitrate+reduction
6781785146carboxymethylcellulose+hydrolysis
678175291gelatin+hydrolysis
6781753423tween 40+hydrolysis
6781753425tween 60+hydrolysis
6781753424tween 20-hydrolysis
6781753426tween 80-hydrolysis
678174853esculin-hydrolysis
6781728017starch-hydrolysis
67817milk-assimilation
6781712936D-galactose+carbon source
6781717634D-glucose+carbon source
6781717716lactose+carbon source
6781716024D-mannose+carbon source
6781728053melibiose+carbon source
6781762345L-rhamnose+carbon source
6781717992sucrose+carbon source
6781727082trehalose+carbon source
6781750144sodium pyruvate+carbon source
6781717108D-arabinose-carbon source
6781717057cellobiose-carbon source
6781716813galactitol-carbon source
6781715824D-fructose-carbon source
6781717754glycerol-carbon source
6781717268myo-inositol-carbon source
6781717306maltose-carbon source
6781716899D-mannitol-carbon source
6781716634raffinose-carbon source
6781716988D-ribose-carbon source
6781717924D-sorbitol-carbon source
6781717151xylitol-carbon source
6781765327D-xylose-carbon source
6781732954sodium acetate-carbon source
6781753258sodium citrate-carbon source
6781716467L-arginine+nitrogen source
6781715971L-histidine+nitrogen source
6781724741hydroxyproline+nitrogen source
6781718019L-lysine+nitrogen source
6781716977L-alanine-nitrogen source
6781717196L-asparagine-nitrogen source
6781729991L-aspartate-nitrogen source
6781717561L-cysteine-nitrogen source
6781729988L-glutamate-nitrogen source
6781718050L-glutamine-nitrogen source
6781715428glycine-nitrogen source
6781715603L-leucine-nitrogen source
6781716643L-methionine-nitrogen source
6781717295L-phenylalanine-nitrogen source
6781717203L-proline-nitrogen source
6781717115L-serine-nitrogen source
6781716857L-threonine-nitrogen source
6781716828L-tryptophan-nitrogen source
6781717895L-tyrosine-nitrogen source
6781716414L-valine-nitrogen source
6781716708adenine-nitrogen source
6781717368hypoxanthine-nitrogen source
6781715318xanthine-nitrogen source
6930262968cellulose-growth
6930228757fructose-growth
6930217234glucose+growth
6930217268inositol+/-growth
6930237684mannose-growth
6930216634raffinose+/-growth
6930226546rhamnose+growth
6930217992sucrose+growth
6930218222xylose-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

metabolite production

@refChebi-IDmetaboliteproduction
6781789634melaninno
6781716136hydrogen sulfideno

enzymes

@refvalueactivityec
67817catalase+1.11.1.6
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
68382esterase (C 4)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
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

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    67817C16:04
    67817C17:06
    67817C18:03.8
    67817C19:00.7
    67817C15:0 iso15.7
    67817C16:0 iso26.5
    67817C17:0 iso5.2
    67817C18:0 iso0.6
    67817C15:0 anteiso1.3
    67817C17:0 anteiso4.6
    67817C17:1 w8c12.1
    67817C18:1 w9c11.7
    67817C17:1 anteiso w9c0.3
    67817C16:1 w7c / C16:1 w6c or C16:1 w6c / C16:1 w7c2.7
    67817C19:1 w9c / C19:1 w11c or C19:1 w9c / C19:1 w11c0.8
    6781710-methyl C16:0 or iso-C17:1w9c3
  • type of FA analysis: whole cell analysis
  • incubation medium: ISP2 broth
  • agar/liquid: liquid
  • incubation temperature: 28
  • incubation time: 7
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6.1
  • system: MIS MIDI

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69302-+-----+-----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69302+/-++/--+-+/-++-+/----+-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
65135marine spongeXisha Islands, Hainan Province (16° 45' N, 112° 21' E)ChinaCHNAsia16.75112.35
67817Craniella species sponge (coral reef at 20 m depth)Xisha IslandsChinaCHNAsia16.75112.35Streptomyces Isolation Medium3 % unrefined sea salt (w/v), 50 mg l-1 cycloheximide and 25 mg l-1 nalidixic acid4-12 weeks28Marine sponge samples were collected by surface-supplied diving and delivered in ice. After being washed in sterile artificial sea water three times, the sponge tissues were cut, ground and spread on Streptomyces Isolation Medium. The plates were incubated at 28°C for 4-12 weeks.

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Host#Invertebrates (Other)#Porifera (Sponges)

Sequence information

16S sequences

  • @ref: 65135
  • description: Jishengella sp. strain LHW63014 16S ribosomal RNA gene, partial sequence
  • accession: MG200153
  • length: 1479
  • database: ena
  • NCBI tax ID: 2294034

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Micromonospora craniellae LHW63014GCA_014764405completencbi2294034
66792Micromonospora craniellae strain LHW630142294034.4completepatric2294034
66792Micromonospora craniellae LHW630142866394982draftimg2294034
67817Micromonospora craniellae LHW63014GCA_003419945contigncbi2294034

GC content

@refGC-contentmethod
6513571.0
6781771genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno97.538yes
gram-positiveyes91.993yes
anaerobicno99.163yes
aerobicyes93.653no
halophileno94.13yes
spore-formingyes94.049no
glucose-utilyes87.537yes
thermophileno98.175yes
motileno92.276yes
glucose-fermentno92.889yes

External links

@ref: 65135

culture collection no.: DSM 106193, CCTCC AA 2018012

straininfo link

  • @ref: 111257
  • straininfo: 401557

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Genetics33160875Complete genome sequence of Micromonospora craniellae LHW63014(T), a potential metal ion-chelating agent producer.Yang X, Zhu ZH, Ji X, Liu ZM, Zhang H, Wei BMar Genomics10.1016/j.margen.2020.1008302020Chelating Agents/*analysis, *Genes, Bacterial, *Genome, Bacterial, Micromonospora/*genetics/metabolism, *Multigene Family, Pacific Ocean, Whole Genome SequencingMetabolism
Phylogeny34787539Micromonospora tarapacensis sp. nov., a bacterium isolated from a hypersaline lake.Villalobos AS, Wiese J, Borchert E, Rahn T, Slaby BM, Steiner LX, Kunzel S, Dorador C, Imhoff JFInt J Syst Evol Microbiol10.1099/ijsem.0.0051092021Bacterial Typing Techniques, Base Composition, Chile, DNA, Bacterial/genetics, Desert Climate, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Lakes/*microbiology, *Micromonospora/classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Saline Waters, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournal
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
65135Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-106193Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 106193)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67817Lei Li, Hong-rui Zhu, Qi-hang Xu, Hou-wen Lin, Yan-hua LuMicromonospora craniellae sp. nov., isolated from a marine sponge, and reclassification of Jishengella endophytica as Micromonospora endophytica comb. nov.10.1099/ijsem.0.003209IJSEM 69: 715-720 2019
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69302Wink, J.Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweighttps://cdn.dsmz.de/wink/DSM%20106193.pdf
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
111257Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID401557.1