Strain identifier

BacDive ID: 141046

Type strain: Yes

Species: Propioniciclava sinopodophylli

Strain Designation: TEYR-7

Strain history: <- Lei Zhang, Northwest A&F Univ., Yangling, Shannxi

NCBI tax ID(s): 1837344 (species)

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

@ref: 43926

BacDive-ID: 141046

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

description: Propioniciclava sinopodophylli TEYR-7 is a facultative anaerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from surface-sterilized leaves of Sinopodophyllum hexandrum collected from the Qinling Mountains in Shaanxi Province, northwest China.

NCBI tax id

  • NCBI tax id: 1837344
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Lei Zhang, Northwest A&F Univ., Yangling, Shannxi

doi: 10.13145/bacdive141046.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Propionibacteriaceae
  • genus: Propioniciclava
  • species: Propioniciclava sinopodophylli
  • full scientific name: Propioniciclava sinopodophylli Zhang et al. 2017
  • synonyms

    @refsynonym
    20215Brevilactibacter sinopodophylli
    20215Propioniciclava sinopodophylli

@ref: 43926

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Propionibacteriales

family: Propionibacteriaceae

genus: Propioniciclava

species: Propioniciclava sinopodophylli

strain designation: TEYR-7

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43926positive1.1-1.5 µm0.6-0.7 µmrod-shapedno
69480no92.481
69480positive100

colony morphology

  • @ref: 43926
  • colony size: 2-3 mm
  • colony color: pale yellow
  • colony shape: circular
  • incubation period: 2 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

@refnamegrowth
43926MacConkey agarno
43926Reasoner's 2A agar (R2A)yes
43926Tryptic soy agaryes

culture temp

@refgrowthtypetemperaturerange
43926positivegrowth15-37
43926positiveoptimum28-30mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
43926positivegrowth6.0-9.0alkaliphile
43926positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43926facultative anaerobe
67771facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
43926NaClpositivegrowth0-3 %(w/v)
43926NaClpositiveoptimum0-1 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4392617128adipate-assimilation
4392627689decanoate-assimilation
4392617634D-glucose-assimilation
4392616899D-mannitol-assimilation
4392616024D-mannose-assimilation
4392630849L-arabinose-assimilation
4392617306maltose-assimilation
43926506227N-acetylglucosamine-assimilation
4392618401phenylacetate-assimilation
4392632032potassium gluconate-assimilation
4392653258sodium citrate-assimilation
4392627613amygdalin-builds acid from
4392615963ribitol-builds acid from
4392617108D-arabinose-builds acid from
4392618333D-arabitol-builds acid from
4392628847D-fucose-builds acid from
4392612936D-galactose-builds acid from
4392662318D-lyxose-builds acid from
4392616899D-mannitol-builds acid from
439266731melezitose-builds acid from
4392628053melibiose-builds acid from
4392616634raffinose-builds acid from
4392616988D-ribose-builds acid from
4392617924D-sorbitol-builds acid from
4392616443D-tagatose-builds acid from
4392616551D-trehalose-builds acid from
4392632528turanose-builds acid from
4392665327D-xylose-builds acid from
4392616813galactitol-builds acid from
4392617113erythritol-builds acid from
4392628066gentiobiose-builds acid from
4392617268myo-inositol-builds acid from
4392615443inulin-builds acid from
4392630849L-arabinose-builds acid from
4392618403L-arabitol-builds acid from
4392618287L-fucose-builds acid from
4392662345L-rhamnose-builds acid from
4392617266L-sorbose-builds acid from
4392665328L-xylose-builds acid from
43926320061methyl alpha-D-glucopyranoside-builds acid from
4392643943methyl alpha-D-mannoside-builds acid from
4392674863methyl beta-D-xylopyranoside-builds acid from
43926506227N-acetylglucosamine-builds acid from
43926potassium 2-dehydro-D-gluconate-builds acid from
43926potassium 5-dehydro-D-gluconate-builds acid from
4392632032potassium gluconate-builds acid from
4392617151xylitol-builds acid from
4392685146carboxymethylcellulose-hydrolysis
43926casein-hydrolysis
4392617895L-tyrosine-hydrolysis
4392625115malate+assimilation
4392617057cellobiose+builds acid from
4392615824D-fructose+builds acid from
4392617634D-glucose+builds acid from
4392617306maltose+builds acid from
4392616024D-mannose+builds acid from
439264853esculin+builds acid from
4392615978glycerol 3-phosphate+builds acid from
4392617992sucrose+builds acid from
439264853esculin+hydrolysis
439265291gelatin+hydrolysis
43926O-nitrophenyl-beta-D-galactopyranosid+hydrolysis
4392628017starch+hydrolysis
4392617632nitrate+reduction
4392616004(R)-lactate+/-builds acid from
4392618305arbutin+/-builds acid from
4392628087glycogen+/-builds acid from
4392617814salicin+/-builds acid from
4392628017starch+/-builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
4392616136hydrogen sulfideno
4392635581indoleno
4392630089acetateyes
4392617272propionateyes

enzymes

@refvalueactivityec
43926cytochrome oxidase+1.9.3.1
43926catalase+1.11.1.6
43926urease+3.5.1.5
43926arginine dihydrolase-3.5.3.6
43926lysine decarboxylase-4.1.1.18
43926ornithine decarboxylase-4.1.1.17
43926acid phosphatase+3.1.3.2
43926esterase (C 4)+
43926esterase Lipase (C 8)+
43926alpha-glucosidase+3.2.1.20
43926beta-galactosidase+3.2.1.23
43926beta-glucosidase+3.2.1.21
43926leucine arylamidase+3.4.11.1
43926naphthol-AS-BI-phosphohydrolase+
43926alpha-chymotrypsin+/-3.4.21.1
43926alpha-galactosidase+/-3.2.1.22
43926valine arylamidase+/-
43926N-acetyl-beta-glucosaminidase-3.2.1.52
43926alkaline phosphatase-3.1.3.1
43926cystine arylamidase-3.4.11.3
43926alpha-fucosidase-3.2.1.51
43926beta-glucuronidase-3.2.1.31
43926lipase (C 14)-
43926alpha-mannosidase-3.2.1.24
43926trypsin-3.4.21.4

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43926C15:0 anteiso33.8
    43926C17:0 anteiso1.5
    43926anteiso-C17:1B / iso-C17:1 I7.6
    43926anteiso-C17:1ω9c1c0.8
    43926C12:0 aldehyde / unknown 10.928 / iso-C16:1 I / C12.1
    43926C14:03.1
    43926C16:013.9
    43926C16:1ω7c / C16:1ω6c6.1
    43926C16:1ω9c1.3
    43926C17:02.6
    43926C17:1ω6c1c1
    43926C17:1ω8c1c1.2
    43926C18:01.5
    43926C18:1ω6c1c1.7
    43926C18:1ω7c1c / C18:1ω6c1c2
    43926C18:1ω9c1c2.5
    43926C18:2ω6c, ω9c and/or anteiso-C 18 : 02
    43926C14:0 iso9
    43926C15:0 iso1.4
    43926C16:0 iso4.1
    43926C18:1 iso H0.8
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A agar
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 2
  • software version: Sherlock 6.0
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890 N gas chromatograph
  • method/protocol: Sasser, 1990

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
43926surface-sterilized leaves of Sinopodophyllum hexandrum collected from the Qinling Mountains in Shaanxi Province, northwest ChinaQinling Mountains in Shaanxi ProvinceChinaCHNAsia33.95107.75R2A agarsupplemented with 50 µg/mL cycloheximide2 weeks25
67771From the root of Sinopodophyllum hexandrum (Royle) YingTaibai MountainChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_37125.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_282;96_5377;97_21761;98_27318;99_37125&stattab=map
  • Last taxonomy: Brevilactibacter sinopodophylli subclade
  • 16S sequence: KX009027
  • Sequence Identity:
  • Total samples: 2340
  • soil counts: 52
  • aquatic counts: 1769
  • animal counts: 502
  • plant counts: 17

Sequence information

16S sequences

  • @ref: 43926
  • description: 16S rRNA gene sequence
  • accession: KX009027
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Propioniciclava sinopodophylli KCTC 33808GCA_004324755contigncbi1837344
66792Propioniciclava sinopodophylli strain KCTC 338081837344.3wgspatric1837344
66792Propioniciclava sinopodophylli KCTC 338082867481428draftimg1837344

GC content

  • @ref: 43926
  • GC-content: 71.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno95.299no
gram-positiveyes88.331yes
anaerobicno97.278yes
aerobicyes67.651no
halophileno96.922yes
spore-formingno93.196no
glucose-utilyes90.492no
flagellatedno97.695no
glucose-fermentno66.073no
thermophileno96.746yes

External links

@ref: 43926

culture collection no.: CCTCC AB 2015257, KCTC 33808

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28901898Propioniciclava sinopodophylli sp. nov., isolated from leaves of Sinopodophyllum hexandrum (Royle) Ying.Zhang L, Li Q, Chen C, Li X, Li M, Hu J, Shen XInt J Syst Evol Microbiol10.1099/ijsem.0.0022652017Bacterial Typing Techniques, Base Composition, Berberidaceae/*microbiology, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Leaves/*microbiology, Propionibacteriaceae/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny34020025Genomic description and characterization of Nigeribacterium massiliense gen. nov., sp. nov., isolated from the human gut.Khare M, Sinha D, Zgheib R, Traore SI, Lagier JC, Raoult D, Fournier PEMicrobes Infect10.1016/j.micinf.2021.1048422021Base Composition, Child, Preschool, DNA, Bacterial/genetics, *Genomics, Humans, Male, Phylogeny, RNA, Ribosomal, 16S/geneticsGenetics

Reference

@idauthorstitledoi/urljournalpubmed
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
43926Lei Zhang, Qiqi Li, Chaoqiong Chen, Xin Li, Muhang Li, Jingjiang Hu, Xihui ShenPropioniciclava sinopodophylli sp. nov., isolated from leaves of Sinopodophyllum hexandrum (Royle) Ying10.1099/ijsem.0.002265IJSEM 67: 4111-4115 201728901898
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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