Strain identifier

BacDive ID: 133103

Type strain: Yes

Species: Subtercola lobariae

Strain Designation: 9583b

Strain history: CGMCC 1.12976 <-- Z.-T. Zhao; Shandong Normal Univ., China; 9583b.

NCBI tax ID(s): 1588641 (species)

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General

@ref: 64131

BacDive-ID: 133103

DSM-Number: 103962

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-positive, rod-shaped, colony-forming

description: Subtercola lobariae 9583b is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from specimens of the lichen Lobaria retigera collected from Jiaozi Snow Mountain, Yunnan Province.

NCBI tax id

  • NCBI tax id: 1588641
  • Matching level: species

strain history

@refhistory
64131<- H.-L. Si, Shandong Univ., Jinan, China; 9583b
67770CGMCC 1.12976 <-- Z.-T. Zhao; Shandong Normal Univ., China; 9583b.

doi: 10.13145/bacdive133103.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Subtercola
  • species: Subtercola lobariae
  • full scientific name: Subtercola lobariae Si et al. 2017

@ref: 64131

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Subtercola

species: Subtercola lobariae

full scientific name: Subtercola lobariae Si et al. 2017

strain designation: 9583b

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25307positive0.7-1.0 µm0.5-0.6 µmrod-shapedno
69480positive100
69480no92.844

colony morphology

  • @ref: 25307
  • colony size: 3-5 mm
  • colony color: white
  • colony shape: circular
  • incubation period: 3 days
  • medium used: ISP2

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25307ISP2yes
64131R2A 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
64131GYM 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

culture temp

@refgrowthtypetemperaturerange
25307positivegrowth4-28
25307positiveoptimum20psychrophilic
64131positivegrowth20psychrophilic
67770positivegrowth20psychrophilic

culture pH

@refabilitytypepHPH range
25307positivegrowth4.0-8.0acidophile
25307positiveoptimum6

Physiology and metabolism

oxygen tolerance

  • @ref: 25307
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.986

observation

  • @ref: 67770
  • observation: quinones: MK-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2530717128adipate-assimilation
2530717968butyrate-assimilation
2530785146carboxymethylcellulose-hydrolysis
25307casein-hydrolysis
2530716947citrate-assimilation
2530718333D-arabitol-respiration
253078391D-gluconate-respiration
2530716991dna-hydrolysis
2530724265gluconate-assimilation
2530725115malate-assimilation
2530717306maltose-assimilation
2530729864mannitol-assimilation
25307506227N-acetylglucosamine-assimilation
2530717632nitrate-reduction
2530728017starch-hydrolysis
2530727082trehalose-respiration
2530717925alpha-D-glucose+respiration
2530722599arabinose+assimilation
2530717057cellobiose+respiration
2530712936D-galactose+respiration
2530716024D-mannose+respiration
2530723652dextrin+respiration
253074853esculin+hydrolysis
2530728066gentiobiose+respiration
2530717234glucose+builds acid from
2530717234glucose+assimilation
2530717754glycerol+respiration
2530717268myo-inositol+respiration
2530737684mannose+assimilation
2530728053melibiose+respiration
2530718401phenylacetate+assimilation
2530717814salicin+respiration
2530753426tween 80+/-hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis resistantis sensitive
25307100147nalidixic acidyesyes
25307161680aztreonamyesyes
2530775248potassium telluriteyesyes
253071 % sodium lactateyesyes
2530771321fusidateyesyes
2530716523d-serineyesyes
2530729673rifamycin svyesyes
2530750694minocyclineyesyes
253076472lincomycinyesyes
2530728001vancomycinyesyes
2530732735guanidinium chlorideyesyes
2530775273niaproofyesyes
2530775193tetrazolium violetyesyes
2530748607lithium chlorideyesyes
2530764103sodium butyrateyesyes
2530775229sodium bromateyesyes

metabolite production

  • @ref: 25307
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
25307acid phosphatase+3.1.3.2
25307alpha-galactosidase-3.2.1.22
25307alpha-glucosidase+3.2.1.20
25307alpha-mannosidase+3.2.1.24
25307arginine dihydrolase-3.5.3.6
25307beta-galactosidase+3.2.1.23
25307beta-glucosidase+3.2.1.21
25307catalase+1.11.1.6
25307cystine arylamidase+/-3.4.11.3
25307cytochrome oxidase-1.9.3.1
25307esterase Lipase (C 8)+/-
25307gelatinase-
25307leucine arylamidase+3.4.11.1
25307N-acetyl-beta-glucosaminidase-3.2.1.52
25307naphthol-AS-BI-phosphohydrolase+
25307trypsin+3.4.21.4
25307urease-3.5.1.5
25307valine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25307C15:0 anteiso68.8
    25307C17:0 anteiso4.2
    25307C14:0 2OH10.3
    25307C17:1ω9c3.5
    25307C14:0 iso 3OH2.3
    25307C15:0 iso1.4
    25307C16:0 iso6.7
  • type of FA analysis: whole cell analysis
  • incubation medium: ISP2
  • agar/liquid: liquid
  • incubation temperature: 25
  • incubation time: 2
  • software version: Sherlock 4.5
  • library/peak naming table: TSBA 40
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation datehost species
25307specimens of the lichen Lobaria retigera collected from Jiaozi Snow Mountain, Yunnan ProvinceJiaozi Snow Mountain, Yunnan ProvinceChinaCHNAsia251022012-11
64131lichen Lobaria retigeraYunnan Province, Jiaozi Snow Mountain (25.86° N 102.81°E)ChinaCHNAsia26.86102.81
67770Lichen (Lobaria retigera) from Jiaozi Snow MountainYunnan ProvinceChinaCHNAsiaLobaria retigera

isolation source categories

  • Cat1: #Host
  • Cat2: #Other
  • Cat3: #Lichen

Safety information

risk assessment

  • @ref: 64131
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64131
  • description: Subtercola lobariae strain 9583b 16S ribosomal RNA gene, partial sequence
  • accession: KM924549
  • length: 1460
  • database: ena
  • NCBI tax ID: 1588641

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Subtercola lobariae 9583bGCA_016881145contigncbi1588641
66792Subtercola lobariae CGMCC 1.12976GCA_014640255contigncbi1588641
66792Subtercola lobariae strain CGMCC 1.129761588641.3wgspatric1588641

GC content

  • @ref: 64131
  • GC-content: 66.8
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno78no
motileno91.404yes
gram-positiveyes93.052no
anaerobicno99.705yes
aerobicyes94.211yes
halophileno92.014no
spore-formingno94.791no
thermophileno99.466yes
glucose-utilyes86.354yes
flagellatedno98.776yes
glucose-fermentno94.048no

External links

@ref: 64131

culture collection no.: DSM 103962, CGMCC 1.12976, KCTC 33586, JCM 33410

straininfo link

  • @ref: 91365
  • straininfo: 400288

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28005519Subtercola lobariae sp. nov., an actinobacterium of the family Microbacteriaceae isolated from the lichen Lobaria retigera.Si HL, Shi FX, Zhang LL, Yue HS, Wang HY, Zhao ZTInt J Syst Evol Microbiol10.1099/ijsem.0.0017532017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Lichens/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistryTranscriptome
Phylogeny29214367Subtercola vilae sp. nov., a novel actinobacterium from an extremely high-altitude cold volcano lake in Chile.Villalobos AS, Wiese J, Aguilar P, Dorador C, Imhoff JFAntonie Van Leeuwenhoek10.1007/s10482-017-0994-42017Actinomycetales/*genetics/physiology, Altitude, Chile, Lakes, Phylogeny, RNA, Ribosomal, 16S/*genetics, Sequence Analysis, DNA/methodsTranscriptome
Phylogeny35840645Subtercola endophyticus sp. nov., a cold-adapted bacterium isolated from Abies koreana.Jiang L, Peng Y, Seo J, Jeon D, Jo MG, Lee JH, Jeong JC, Kim CY, Park HC, Lee JSci Rep10.1038/s41598-022-16116-32022*Abies/genetics, *Actinomycetales/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorstitledoi/urljournalpubmedcatalogue
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
25307H. L. S. Si, F. X.,Zhang, L. L.,Yue, H. S.,Wang, H. Y.,Zhao, Z. T.Subtercola lobariae sp. nov., an actinobacterium of the family Microbacteriaceae isolated from the lichen Lobaria retigera10.1099/ijsem.0.001753IJSEM 67: 1516-1521 201728005519
64131Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103962Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103962)
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
91365Reimer, 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-ID400288.1