Strain identifier

BacDive ID: 159669

Type strain: Yes

Species: Amycolatopsis panacis

Strain history: CCTCC AA 2017044 <-- L.-X. Zhao; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM PH21725.

NCBI tax ID(s): 2340917 (species)

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General

@ref: 66520

BacDive-ID: 159669

DSM-Number: 105902

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

description: Amycolatopsis panacis DSM 105902 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from red clay.

NCBI tax id

  • NCBI tax id: 2340917
  • Matching level: species

strain history

@refhistory
66520<- L.-C. Li, Yunnan Institute of Microbiology, Yunnan University, P.R. China; YIM PH21725
67771<- Lin-Chao Li, Yunnan Institute of Microbiology
67770CCTCC AA 2017044 <-- L.-X. Zhao; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM PH21725.

doi: 10.13145/bacdive159669.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Amycolatopsis
  • species: Amycolatopsis panacis
  • full scientific name: Amycolatopsis panacis Peng et al. 2019

@ref: 66520

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Pseudonocardiales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis panacis

full scientific name: Amycolatopsis panacis Peng et al. 2019

type strain: yes

Morphology

cell morphology

  • @ref: 67811
  • gram stain: positive

colony morphology

@refcolony colormedium used
69293Beige (1001)ISP 2
69293Light ivory (1015)ISP 5
69293Light ivory (1015)ISP 7
69293Light ivory (1015)suter with tyrosine
69293Light ivory (1015)suter without tyrosine
69293Oyster white (1013)ISP 3
69293Oyster white (1013)ISP 4
69293Sand yellow (1002)ISP 6

multicellular morphology

@refforms multicellular complexcomplex colorfurther descriptioncomplex namemedium name
67811yesyellowish-white, yellowish-pink or yellowCells form well-developed aerial and substrate mycelia. Substrate mycelia are fragmented into long, rod-like elements (0.4-1.5 to 0.6-2.5 µm in size). Aerial and substrate mycelia present as yellowish-white, yellowish-pink or yellow, depending on the medium tested.
69293yesCream (9001)Aerial myceliumISP 2
69293yesSignal white (9003)Aerial myceliumISP 3
69293noAerial myceliumISP 4
69293yesSignal white (9003)Aerial myceliumISP 5
69293noAerial myceliumISP 6
69293yesSignal white (9003)Aerial myceliumISP 7
69293noAerial myceliumsuter with tyrosine
69293noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
69293noMelanin
69293nosoluble pigment

Culture and growth conditions

culture medium

  • @ref: 66520
  • name: N-Z-AMINE-MEDIUM (DSMZ Medium 554)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/554
  • composition: Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water

culture temp

@refgrowthtypetemperature
66520positivegrowth28
67770positivegrowth28
67771positivegrowth28
67811positivegrowth15-40
67811positiveoptimum28

culture pH

@refabilitytypepHPH range
67811positivegrowth5-13alkaliphile
67811positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
67771aerobe
67811aerobe
69480aerobe90.798

spore formation

  • @ref: 69481
  • spore formation: yes
  • confidence: 100

halophily

@refsaltgrowthtested relationconcentration
67811NaClpositivegrowth0-3.5 %(w/v)
67811NaClpositiveoptimum0.5 %(w/v)
69293NaClpositivegrowth0-7.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-9 (H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6929322599arabinose-growth
6781128017starch+hydrolysis
6781118186tyrosine+hydrolysis
6781117368hypoxanthine+hydrolysis
678115291gelatin-hydrolysis
67811milk-assimilation
6781117634D-glucose+builds acid from
6781117306maltose+builds acid from
6781115824D-fructose+builds acid from
6781117057cellobiose+builds acid from
6781116024D-mannose+builds acid from
6781162345L-rhamnose+builds acid from
6781116988D-ribose-builds acid from
6781116899D-mannitol-builds acid from
6781117268myo-inositol-builds acid from
6781123652dextrin+assimilation
6781117306maltose+carbon source
6781116551D-trehalose+carbon source
6781117057cellobiose+carbon source
6781117992sucrose+carbon source
6781116634raffinose+carbon source
6781136219alpha-lactose+carbon source
6781128053melibiose+carbon source
6781117814salicin+carbon source
6781117925alpha-D-glucose+carbon source
6781116024D-mannose+carbon source
6781115824D-fructose+carbon source
6781112936D-galactose+carbon source
6781162345L-rhamnose+carbon source
6781117924D-sorbitol+carbon source
6781116899D-mannitol+carbon source
6781117268myo-inositol+carbon source
6781118222xylose+carbon source
6781153258sodium citrate+carbon source
6781184997sodium gluconate+carbon source
6781191260disodium malate+carbon source
6781116988D-ribose-carbon source
6781117347testosterone-carbon source
6781116414L-valine+nitrogen source
6781128300glutamine+nitrogen source
6781116643L-methionine+nitrogen source
6781117561L-cysteine+nitrogen source
6781117191L-isoleucine+nitrogen source
6781117295L-phenylalanine+nitrogen source
6781135391aspartate+nitrogen source
6781116977L-alanine+nitrogen source
6781127897tryptophan+nitrogen source
6781116467L-arginine+nitrogen source
6929362968cellulose-growth
6929328757fructose+growth
6929317234glucose+growth
6929317268inositol-growth
6929337684mannose+growth
6929316634raffinose-growth
6929326546rhamnose-growth
6929317992sucrose-growth
6929318222xylose-growth
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 67811
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
67811catalase+1.11.1.6
67811cytochrome oxidase+1.9.3.1
67811urease+3.5.1.5
67811alkaline phosphatase+3.1.3.1
67811acid phosphatase+3.1.3.2
67811esterase (C 4)+
67811esterase Lipase (C 8)+
67811leucine arylamidase+3.4.11.1
67811proline-arylamidase+3.4.11.5
67811cystine arylamidase+3.4.11.3
67811naphthol-AS-BI-phosphohydrolase+
67811alpha-glucosidase+3.2.1.20
67811N-acetyl-beta-glucosaminidase+3.2.1.52
67811alpha-mannosidase+3.2.1.24
67811trypsin-3.4.21.4
67811chymotrypsin-3.4.4.5
67811alpha-galactosidase-3.2.1.22
67811beta-galactosidase-3.2.1.23
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382lipase (C 14)+
68382leucine arylamidase+3.4.11.1
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
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    67811C15:0 anteiso2.4
    67811C17:0 anteiso4.8
    67811C14:0 iso2.9
    67811C15:0 iso16.5
    67811C16:0 iso15.6
    67811C17:0 iso7.3
    67811C16:011.7
    67811C17:023.9
    67811C17:1 w6c3.2
    67811C18:03.1
    67811Sum In Feature 35.8
    67811Summed Feature 35.8
  • type of FA analysis: whole cell analysis
  • incubation medium: PSB
  • incubation temperature: 25
  • incubation time: 3
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69293---+---------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69293+++/-+++/-+/---++---+/--++/--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudehost speciesenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
66520red clayXiaohouchong, Anning, Yunnan (24º 42' N, 102º 19' E)ChinaCHNAsia24.7102.317
67770Rhizospheric soil from a Panax notoginseng plantation in AnningYunnan ProvinceChinaCHNAsiaPanax notoginseng
67771From soilKumming city, Yunnan provinceChinaCHNAsia
67811notoginseng rhizospheric soil samplePanax notoginseng plantation in Anning, Yunnan ProvinceChinaCHNAsiaGauze's medium no. 1supplemented with 25 mg l-1 nalidixic acid and 50 mg l-1 nystatin15 days28The air-dried sample was serially diluted

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
66520Amycolatopsis sp. strain YIMPH21725 16S ribosomal RNA gene, partial sequenceMH2660431336nuccore37632
66520Amycolatopsis panacis strain YIM PH21725 16S ribosomal RNA gene, partial sequenceMK0322641510nuccore2340917

Genome sequences

  • @ref: 67811
  • description: Amycolatopsis panacis YIM PH21725
  • accession: GCA_003600245
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 2340917

GC content

@refGC-contentmethod
6652069.43sequence analysis
6781169.43genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes89.237yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.58yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.798yes
69480spore-formingspore-formingAbility to form endo- or exosporesyes76.597no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.5yes
69480flagellatedmotile2+Ability to perform flagellated movementno89no

External links

@ref: 66520

culture collection no.: DSM 105902, CCTCC AA 2017044, KCTC 49031, YIM PH21725, JCM 33574

straininfo link

  • @ref: 112141
  • straininfo: 398881

literature

  • topic: Phylogeny
  • Pubmed-ID: 30605074
  • title: Amycolatopsis panacis sp. nov., isolated from Panax notoginseng rhizospheric soil.
  • authors: Peng G, Xiong DS, Li LC, Hu JY, Bao S, Chen YW, Li YQ, Xu LH, Miao CP, Zhao LX
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003202
  • year: 2019
  • mesh: Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Panax notoginseng/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournal
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
66520Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-105902Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 105902)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
67811Guang Peng, Deng-Sen Xiong, Lin-Chao Li, Jia-Yun Hu, Sheng Bao, You-Wei Chen, Yi-Qing Li, Li-Hua Xu, Cui-Ping Miao, Li-Xing ZhaoAmycolatopsis panacis sp. nov., isolated from Panax notoginseng rhizospheric soil10.1099/ijsem.0.003202IJSEM 69: 567-571 2019
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69293Wink, J.Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweighttps://cdn.dsmz.de/wink/DSM%20105902.pdf
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
112141Reimer, 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-ID398881.1