Strain identifier

BacDive ID: 140785

Type strain: Yes

Species: Nocardioides kandeliae

Strain history: <- Chenghai Gao, Guangxi Academy of Sciences, China

NCBI tax ID(s): 1972704 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 8.1 (current version)

General

@ref: 64898

BacDive-ID: 140785

DSM-Number: 104480

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

description: Nocardioides kandeliae KCTC 39886 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from leafs of Kandelia candel located in Beihai City.

NCBI tax id

  • NCBI tax id: 1972704
  • Matching level: species

strain history

@refhistory
64898<- C. Gao; Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nangning Guangxi; BGMRC2075 <- C. Gao
67771<- Chenghai Gao, Guangxi Academy of Sciences, China

doi: 10.13145/bacdive140785.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Nocardioides
  • species: Nocardioides kandeliae
  • full scientific name: Nocardioides kandeliae Liu et al. 2017

@ref: 64898

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides kandeliae

full scientific name: Nocardioides kandeliae Liu et al. 2017

type strain: yes

Morphology

cell morphology

  • @ref: 43563
  • gram stain: positive
  • cell length: 0.8-3.1 µm
  • cell width: 0.3-0.7 µm
  • cell shape: rod-shaped

colony morphology

  • @ref: 43563
  • colony size: 1-2 mm
  • colony color: Cream
  • colony shape: circular
  • incubation period: 3 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43563Reasoner's 2A agar (R2A)yes
64898TRYPTICASE 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
43563positivegrowth10-35
43563positiveoptimum28-30mesophilic
64898positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
43563positivegrowth7-11alkaliphile
43563positiveoptimum6.5-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43563aerobe
67771aerobe

spore formation

  • @ref: 43563
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
43563NaClpositivegrowth0-10 %(w/v)
43563NaClpositiveoptimum2 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4356362968cellulose-hydrolysis
435635291gelatin-hydrolysis
4356328017starch-hydrolysis
4356353424tween 20-hydrolysis
4356353423tween 40-hydrolysis
4356353426tween 80-hydrolysis
43563167632-oxobutanoate-respiration
4356313705acetoacetate-respiration
43563161680aztreonam-respiration
4356373706bromosuccinate-respiration
4356316947citrate-respiration
4356315570D-alanine-respiration
4356333801D-saccharate-respiration
4356315740formate-respiration
4356371321fusidate-respiration
435635291gelatin-respiration
4356332735guanidinium chloride-respiration
4356317596inosine-respiration
4356318183L-pyroglutamic acid-respiration
4356317716lactose-respiration
435636472lincomycin-respiration
4356348607lithium chloride-respiration
4356337657methyl D-glucoside-respiration
4356351850methyl pyruvate-respiration
4356350694minocycline-respiration
4356328037N-acetylgalactosamine-respiration
4356335418n-acetylneuraminate-respiration
43563100147nalidixic acid-respiration
4356375273niaproof-respiration
4356375248potassium tellurite-respiration
4356375229sodium bromate-respiration
4356364103sodium butyrate-respiration
4356317164stachyose-respiration
4356345735troleandomycin-respiration
4356328001vancomycin-respiration
43563581435-dehydro-D-gluconate+carbon source
4356317057cellobiose+carbon source
4356315824D-fructose+carbon source
4356328847D-fucose+carbon source
4356312936D-galactose+carbon source
4356317634D-glucose+carbon source
4356316899D-mannitol+carbon source
4356316024D-mannose+carbon source
4356316988D-ribose+carbon source
4356317924D-sorbitol+carbon source
4356317151xylitol+carbon source
4356316813galactitol+carbon source
435634853esculin+carbon source
4356328066gentiobiose+carbon source
4356317754glycerol+carbon source
4356315443inulin+carbon source
4356316467L-arginine+carbon source
4356329991L-aspartate+carbon source
4356318287L-fucose+carbon source
4356362345L-rhamnose+carbon source
4356317306maltose+carbon source
4356328053melibiose+carbon source
4356317268myo-inositol+carbon source
4356316634raffinose+carbon source
4356327082trehalose+carbon source
4356315588D-malate+respiration
4356316651(S)-lactate+respiration
4356315589L-malate+respiration
43563645522-hydroxybutyrate+respiration
43563309162-oxoglutarate+respiration
43563370543-hydroxybutyrate+respiration
43563739183-O-methyl-D-glucose+respiration
43563181014-hydroxyphenylacetic acid+respiration
4356330089acetate+respiration
4356318333D-arabitol+respiration
4356329990D-aspartate+respiration
4356312936D-galactose+respiration
435638391D-gluconate+respiration
4356314314D-glucose 6-phosphate+respiration
4356315748D-glucuronate+respiration
4356316024D-mannose+respiration
4356316523D-serine+respiration
4356323652dextrin+respiration
4356316537galactarate+respiration
4356324175galacturonate+respiration
4356316865gamma-aminobutyric acid+respiration
4356332323glucuronamide+respiration
4356324741hydroxyproline+respiration
4356329985L-glutamate+respiration
4356315971L-histidine+respiration
4356317115L-serine+respiration
4356374611methyl (R)-lactate+respiration
4356317309pectin+respiration
4356317272propionate+respiration
4356326490quinate+respiration

metabolite production

  • @ref: 43563
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
43563urease+3.5.1.5
43563alpha-glucosidase+3.2.1.20
43563alkaline phosphatase+3.1.3.1
43563lipase (C 14)+
43563valine arylamidase+
43563cystine arylamidase+3.4.11.3
43563trypsin+3.4.21.4
43563beta-glucuronidase+3.2.1.31
43563beta-glucosidase+3.2.1.21
43563leucine arylamidase+/-3.4.11.1
43563esterase (C 4)+/-
43563esterase Lipase (C 8)+/-
43563N-acetyl-beta-glucosaminidase+/-3.2.1.52
43563acid phosphatase+/-3.1.3.2
43563naphthol-AS-BI-phosphohydrolase+/-
43563chymotrypsin+/-3.4.4.5
43563alpha-galactosidase-3.2.1.22
43563alpha-mannosidase-3.2.1.24
43563beta-D-fucosidase-3.2.1.38
43563beta-galactosidase-3.2.1.23

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
43563leafs of Kandelia candel located in Beihai CityBeihai City, Guangxi ProvinceChinaCHNAsia21.411109.162
64898Kandelia candel (Linn.) DruceGuangxi province, Beihai city (21° 24' 42'' N 109° 09' 46'' E)ChinaCHNAsia21.4117109.163
67771From Kandelia candelBeihaiChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#Host#Plants#Tree
#Host Body-Site#Plant#Leaf (Phyllosphere)

taxonmaps

  • @ref: 69479
  • File name: preview.99_157846.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_30563;97_77061;98_104011;99_157846&stattab=map
  • Last taxonomy: Nocardioides kandeliae subclade
  • 16S sequence: KY270876
  • Sequence Identity:
  • Total samples: 695
  • soil counts: 214
  • aquatic counts: 86
  • animal counts: 369
  • plant counts: 26

Safety information

risk assessment

  • @ref: 64898
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64898
  • description: Nocardioides kandeliae strain BGMRC 2075 16S ribosomal RNA gene, partial sequence
  • accession: KY270876
  • length: 1490
  • database: ena
  • NCBI tax ID: 1972704

GC content

  • @ref: 64898
  • GC-content: 70.8
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 64898

culture collection no.: KCTC 39886, DSM 104480, BGMRC 2075

straininfo link

  • @ref: 96790
  • straininfo: 404754

literature

  • topic: Phylogeny
  • Pubmed-ID: 28895524
  • title: Nocardioides kandeliae sp. nov., an endophytic actinomycete isolated from leaves of Kandelia candel.
  • authors: Liu J, Li F, Gao CH, Han Y, Hao H, Yi XX, Huang RM
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002218
  • year: 2017
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Leaves/*microbiology, RNA, Ribosomal, 16S/genetics, Rhizophoraceae/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

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
43563Jun Liu, Fei Li, Cheng-Hai Gao, Yu Han, Huili Hao, Xiang-Xi Yi, Ri-Ming HuangNocardioides kandeliae sp. nov., an endophytic actinomycete isolated from leaves of Kandelia candel10.1099/ijsem.0.002218IJSEM 67: 3888-3893 201728895524
64898Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104480Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104480)
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/
96790Reimer, 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-ID404754.1