Strain identifier

BacDive ID: 140370

Type strain: No

Species: Conexibacter stalactiti

Strain Designation: YC2-25

Strain history: <- Soon Dong Lee, Jeju National Univ.

NCBI tax ID(s): 1940611 (species)

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General

@ref: 42977

BacDive-ID: 140370

DSM-Number: 103719

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

description: Conexibacter stalactiti YC2-25 is an aerobe, Gram-positive, motile bacterium that forms circular colonies and was isolated from pieces of stalactites from a lava cave.

NCBI tax id

  • NCBI tax id: 1940611
  • Matching level: species

strain history

@refhistory
42977<- S. D. Lee, Jeju National Univ., Rep. of Korea; YC2-25
67770KCTC 39840 <-- S. D. Lee; Jeju Natl. Univ., South Korea; YC2-25.
67771<- Soon Dong Lee, Jeju National Univ.

doi: 10.13145/bacdive140370.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Thermoleophilia
  • order: Solirubrobacterales
  • family: Conexibacteraceae
  • genus: Conexibacter
  • species: Conexibacter stalactiti
  • full scientific name: Conexibacter stalactiti Lee 2017

@ref: 42977

domain: Bacteria

phylum: Actinobacteria

class: Thermoleophilia

order: Solirubrobacterales

family: Conexibacteraceae

genus: Conexibacter

species: Conexibacter stalactiti

full scientific name: Conexibacter stalactiti Lee 2017

strain designation: YC2-25

type strain: no

Morphology

cell morphology

  • @ref: 43891
  • gram stain: positive
  • cell length: 0.8-0.9 µm
  • cell width: 0.5 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 43891
  • colony size: 0.3-1.0 mm
  • colony color: cream to light yellow
  • colony shape: circular
  • incubation period: 14 days
  • medium used: Trypicase soy agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43891ISP2 agaryes
43891Nutrient agar (NA)yes
43891Reasoner's 2A agar (R2A)yes
43891Trypicase soy agaryes
42977TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43891positivegrowth10-30
43891positiveoptimum30mesophilic
43891nogrowth37mesophilic
42977positivegrowth28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
43891positivegrowth4.0-9.0alkaliphile
43891positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43891aerobe
67771aerobe

spore formation

  • @ref: 43891
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
43891NaClpositivegrowth1 %(w/v)
43891NaClnogrowth2 %(w/v)

observation

@refobservation
43891Mycolic acids
43891quinone MK-7
67770quinones: MK-7(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4389165327D-xylose-builds acid from
4389117268myo-inositol-builds acid from
4389165328L-xylose-builds acid from
4389129864mannitol-builds acid from
4389117632nitrate-reduction
43891581435-dehydro-D-gluconate+builds acid from
4389117057cellobiose+builds acid from
4389117108D-arabinose+builds acid from
4389115824D-fructose+builds acid from
4389117234glucose+builds acid from
4389137684mannose+builds acid from
4389126546rhamnose+builds acid from
4389127082trehalose+builds acid from
438914853esculin+degradation
438915291gelatin+hydrolysis
4389127613amygdalin+/-builds acid from
4389128260galactose+/-builds acid from
4389128066gentiobiose+/-builds acid from
4389117754glycerol+/-builds acid from
4389133942ribose+/-builds acid from

enzymes

@refvalueactivityec
43891cytochrome oxidase+1.9.3.1
43891catalase+1.11.1.6
43891esterase Lipase (C 8)+
43891esterase (C 4)+/-
43891leucine arylamidase+/-3.4.11.1
43891naphthol-AS-BI-phosphohydrolase+/-
43891beta-glucuronidase+/-3.2.1.31
43891acid phosphatase+3.1.3.2
43891beta-glucosidase+3.2.1.21
43891alkaline phosphatase+/-3.1.3.1
43891lipase (C 14)-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43891C15:0 anteiso1.4
    43891C17:0 anteiso3.7
    43891C17:1 anteiso ω9c1.7
    43891C12:06.5
    43891C14:01.1
    43891C15:1ω5c1
    43891C16:011.3
    43891C16:1ω7c / C16:1ω6c1.1
    43891C17:1ω8c2
    43891C18:011.1
    43891C18:1ω7c1.5
    43891C18:1ω9c35.3
    43891C19:0ω10c cyclo / C19:1ω6c1.2
    43891C10:0 iso1.5
    43891C16:0 iso2.8
    43891C17:0 iso1
    43891C17:1 iso ω5c3.3
    43891C19:0 iso4.2
  • type of FA analysis: whole cell analysis
  • incubation medium: Tryptic soy agar
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 14
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
42977pieces of stalactites from a lava caveJeju, Yong-cheon Cave (33° 32' 55.2'' N, 126° 46' 42.4'' E)Republic of KoreaKORAsia33.5487126.778
43891pieces of stalactites collected from Yongcheon lava cave, Jeju, Republic of KoreaJeju islandRepublic of KoreaKORAsia33.5487126.778Starch-casein agar1% soluble starch, 0.03% casein, 0.2 % KNO3, 0.2% NaCl, 0.2 % KH2PO4, 0.002% CaCO3, 0.005% MgSO4.7H2O, 0.001% FeSO4.7H2O, 1.8% agar, pH 7.24 weeks30
67770Pieces of stalactites from Yongcheon Cave in JejuRepublic of KoreaKORAsia
67771From a piece of stalactities inside caveJejuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Geologic
#Environmental#Terrestrial#Volcanic

Safety information

risk assessment

  • @ref: 42977
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42977
  • description: Conexibacter sp. YC2-25 partial 16S rRNA gene, strain YC2-25
  • accession: LT719154
  • length: 1443
  • database: ena
  • NCBI tax ID: 1940611

GC content

  • @ref: 42977
  • GC-content: 70.3
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 42977

culture collection no.: DSM 103719, KCTC 39840, JCM 32753

straininfo link

  • @ref: 96668
  • straininfo: 397988

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28868998Conexibacter stalactiti sp. nov., isolated from stalactites in a lava cave and emended description of the genus Conexibacter.Lee SDInt J Syst Evol Microbiol10.1099/ijsem.0.0020832017Actinobacteria/genetics, Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny36018778Capillimicrobium parvum gen. nov., sp. nov., a novel representative of Capillimicrobiaceae fam. nov. within the order Solirubrobacterales, isolated from a grassland soil.Vieira S, Huber KJ, Geppert A, Wolf J, Neumann-Schaal M, Luckner M, Wanner G, Musken M, Overmann JInt J Syst Evol Microbiol10.1099/ijsem.0.0055082022Bacteria, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Grassland, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *SoilTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
42977Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103719Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103719)
43891Soon Dong LeeConexibacter stalactiti sp. nov., isolated from stalactites in a lava cave and emended description of the genus Conexibacter10.1099/ijsem.0.002083IJSEM 67: 3214-3218 201728868998
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
96668Reimer, 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-ID397988.1