Strain identifier

BacDive ID: 133108

Type strain: Yes

Species: Actinophytocola xanthii

Strain Designation: 11-183

Strain history: <- J.-S. Lee, KCTC; KCTC 39690 <- L. Yuan and W. Wang, North China University of Science and Technology; 11-183

NCBI tax ID(s): 1912961 (species)

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General

@ref: 64845

BacDive-ID: 133108

DSM-Number: 109075

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

description: Actinophytocola xanthii 11-183 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from soil sample that was collected from the rhizosphere of Xanthium sibiricum.

NCBI tax id

  • NCBI tax id: 1912961
  • Matching level: species

strain history

  • @ref: 64845
  • history: <- J.-S. Lee, KCTC; KCTC 39690 <- L. Yuan and W. Wang, North China University of Science and Technology; 11-183

doi: 10.13145/bacdive133108.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Actinophytocola
  • species: Actinophytocola xanthii
  • full scientific name: Actinophytocola xanthii Wang et al. 2017

@ref: 64845

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Actinophytocola

species: Actinophytocola xanthii

full scientific name: Actinophytocola xanthii Wang et al. 2017

strain designation: 11-183

type strain: yes

Morphology

cell morphology

  • @ref: 25309
  • gram stain: positive
  • motility: no

colony morphology

  • @ref: 25309
  • colony color: brown-black
  • medium used: ISP2

multicellular morphology

@refforms multicellular complexfurther descriptioncomplex namecomplex colormedium name
25309yescompact, branched substrate mycelium during aerobic cultivation
25309aerial myceliumwhiteISP2

pigmentation

@refproductionname
25309yesdiffusible pigment
25309noMelanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
25309ISP2yes
25309glucose-asparaine agaryes
25309potato extract agaryes
25309Czapek's agarno
25309ISP9no
64845ISP2 MEDIUM (DSMZ Medium 987)yeshttps://mediadive.dsmz.de/medium/987Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
25309positivegrowth15-37
25309positiveoptimum28mesophilic
64845positivegrowth28mesophilic

culture pH

@refabilitytypepH
25309positivegrowth6.5-8.0
25309positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 25309
  • oxygen tolerance: aerobe

spore formation

  • @ref: 25309
  • spore description: cylindrical
  • type of spore: spore
  • spore formation: yes

halophily

@refsalttested relationconcentrationgrowth
25309NaCloptimum0-1 %
25309NaClgrowth0-2.0 %(w/v)positive

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2530915428glycine-nitrogen source
2530917368hypoxanthine-nitrogen source
2530917561L-cysteine-nitrogen source
2530917895L-tyrosine-nitrogen source
2530917632nitrate-reduction
2530916199urea-hydrolysis
2530916449alanine+nitrogen source
2530917057cellobiose+carbon source
2530962968cellulose+hydrolysis
2530915824D-fructose+carbon source
2530917924D-sorbitol+carbon source
2530965327D-xylose+carbon source
253095291gelatin+hydrolysis
2530917234glucose+carbon source
2530916977L-alanine+nitrogen source
2530930849L-arabinose+carbon source
2530929985L-glutamate+nitrogen source
2530915971L-histidine+nitrogen source
2530918019L-lysine+nitrogen source
2530916643L-methionine+nitrogen source
2530917295L-phenylalanine+nitrogen source
2530962345L-rhamnose+carbon source
2530990603L-serine 2-naphthylamide+nitrogen source
2530916857L-threonine+nitrogen source
2530916828L-tryptophan+nitrogen source
2530917716lactose+carbon source
2530917306maltose+carbon source
2530928017starch+hydrolysis
2530917992sucrose+carbon source
6836925115malate+assimilation
6836917128adipate+assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin+hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

@refChebi-IDmetaboliteproduction
2530916136hydrogen sulfideno
6836935581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
25309amylase+
25309catalase+1.11.1.6
25309cellulase+3.2.1.4
25309cytochrome oxidase-1.9.3.1
25309urease-3.5.1.5
68369gelatinase+
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382alkaline phosphatase+3.1.3.1
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
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
    25309C17:1ω6c14.5
    25309C16:0 iso28.55
    25309C16:1 iso H15.58
  • type of FA analysis: whole cell analysis
  • incubation medium: TSB (Tryptic Soy broth)
  • agar/liquid: liquid
  • incubation temperature: 28
  • incubation time: 14
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA 6
  • system: MIS MIDI
  • method/protocol: Sasser 1990

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
64845-++/-+/--++-+-+--+-+-+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
64845------++-----+--++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
25309soil sample that was collected from the rhizosphere of Xanthium sibiricumTangshan, Hebei, ChinaChinaCHNAsia
64845rhizosphere soil of Xanthium sibiricumHebei province, TangshanChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_7713.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_770;97_898;98_1053;99_7713&stattab=map
  • Last taxonomy: Actinophytocola xanthii
  • 16S sequence: KX083521
  • Sequence Identity:
  • Total samples: 412
  • soil counts: 333
  • aquatic counts: 17
  • animal counts: 32
  • plant counts: 30

Safety information

risk assessment

  • @ref: 64845
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64845
  • description: Actinophytocola xanthii strain KCTC 39690 16S ribosomal RNA gene, partial sequence
  • accession: KX083521
  • length: 1515
  • database: ena
  • NCBI tax ID: 1912961

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Actinophytocola xanthii 11-183GCA_001921205contigncbi1912961
66792Actinophytocola xanthii 11-1832791354901draftimg1912961

GC content

  • @ref: 25309
  • GC-content: 71.7

External links

@ref: 64845

culture collection no.: KCTC 39690, MCCC 1K02062, DSM 109075

straininfo link

  • @ref: 91369
  • straininfo: 406834

literature

  • topic: Phylogeny
  • Pubmed-ID: 28073395
  • title: Actinophytocola xanthii sp. nov., an actinomycete isolated from rhizosphere soil of the plant Xanthium sibiricum.
  • authors: Wang W, Wang B, Meng H, Xing Z, Lai Q, Yuan L
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001781
  • year: 2017
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry, Xanthium/*microbiology
  • 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
25309W. W. Wang, B.,Meng, H.,Xing, Z.,Lai, Q.,Yuan, L.Actinophytocola xanthii sp. nov., an actinomycete isolated from rhizosphere soil of the plant Xanthium sibiricum10.1099/ijsem.0.001781IJSEM 67: 1152-1157 201728073395
64845Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-109075Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 109075)
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
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
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/
91369Reimer, 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-ID406834.1