Strain identifier

BacDive ID: 133131

Type strain: Yes

Species: Amycolatopsis albispora

Strain Designation: WP1

Strain history: <- Gaiyun Zhang

NCBI tax ID(s): 1804986 (species)

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General

@ref: 24893

BacDive-ID: 133131

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

description: Amycolatopsis albispora WP1 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from deep-sea sediment.

NCBI tax id

  • NCBI tax id: 1804986
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Gaiyun Zhang

doi: 10.13145/bacdive133131.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Amycolatopsis
  • species: Amycolatopsis albispora
  • full scientific name: Amycolatopsis albispora Zhang et al. 2016

@ref: 24893

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Pseudonocardiales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis albispora

strain designation: WP1

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
24893positiveno
69480positive100
69480no91.936

Culture and growth conditions

culture medium

  • @ref: 24893
  • name: MZ2 medium
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
24893positivegrowth4.0-45.0
24893positiveoptimum30.0-35.0mesophilic
67771positivegrowth30-35mesophilic

culture pH

@refabilitytypepHPH range
24893positivegrowth5.0-11.0alkaliphile
24893positiveoptimum8.0-9.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
24893aerobe
67771aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
24893white sporessporeyes
69481yes100
69480yes100

halophily

@refsaltgrowthtested relationconcentration
24893NaClpositivegrowth0.0-8.0 %(w/v)
24893NaCloptimum0.0-3.0 %(w/v)

murein

  • @ref: 24893
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2489327613amygdalin-builds acid from
2489317108D-arabinose-builds acid from
2489317234glucose-fermentation
2489317234glucose-builds acid from
2489317268myo-inositol-builds acid from
2489329864mannitol-builds acid from
2489328053melibiose-builds acid from
2489326546rhamnose-builds acid from
2489330911sorbitol-builds acid from
2489317992sucrose-builds acid from
2489327897tryptophan-energy source
24893casein+hydrolysis
2489362968cellulose+hydrolysis
2489317632nitrate+reduction
2489328017starch+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
2489316136hydrogen sulfideno
2489335581indoleno
2489389634melaninno
2489315688acetoinyes

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-testindole test
2489317234glucose-
2489315688acetoin+
2489335581indole-

enzymes

@refvalueactivityec
24893acid phosphatase+3.1.3.2
24893alkaline phosphatase+3.1.3.1
24893alpha-chymotrypsin-3.4.21.1
24893alpha-fucosidase-3.2.1.51
24893alpha-galactosidase-3.2.1.22
24893alpha-glucosidase+3.2.1.20
24893alpha-mannosidase-3.2.1.24
24893arginine dihydrolase+3.5.3.6
24893beta-galactosidase+3.2.1.23
24893beta-glucosidase+3.2.1.21
24893beta-glucuronidase-3.2.1.31
24893catalase+1.11.1.6
24893cystine arylamidase+3.4.11.3
24893cytochrome oxidase-1.9.3.1
24893esterase (C 4)+
24893esterase lipase (C 8)+
24893gelatinase+
24893leucine arylamidase+3.4.11.1
24893lipase (C 14)-
24893lysine decarboxylase-4.1.1.18
24893N-acetyl-beta-glucosaminidase+3.2.1.52
24893naphthol-AS-BI-phosphohydrolase+
24893ornithine decarboxylase-4.1.1.17
24893trypsin-3.4.21.4
24893tryptophan deaminase-4.1.99.1
24893urease+3.5.1.5
24893valine arylamidase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperaturecountryorigin.countrycontinent
24893deep-sea sedimentIndian Ocean at site TVG1 (-2945 m)-2763modified Zobell 2216E agarMZ2; 1.0 g yeast extract, 5.0 g tryptone, 34 g NaCl, 15 g agar and 1 l distilled water, pH 7.4–7.621 days28
67771Marine sediment of Indian OceanChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

Sequence information

16S sequences

  • @ref: 24893
  • description: Amycolatopsis sp. WP1 16S ribosomal RNA gene, partial sequence
  • accession: KT751086
  • length: 1481
  • database: nuccore
  • NCBI tax ID: 1804986

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amycolatopsis albispora WP1GCA_003312875completencbi1804986
66792Amycolatopsis albispora WP12856864784completeimg1804986

GC content

  • @ref: 24893
  • GC-content: 72.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.925yes
flagellatedno97.264yes
gram-positiveyes89.69yes
anaerobicno99.393yes
aerobicyes94.731yes
halophileno79.445no
spore-formingyes93.294yes
glucose-utilyes89.494no
thermophileno97.911yes
glucose-fermentno92.312yes

External links

@ref: 24893

culture collection no.: KCTC 39642, MCCC 1A10745

literature

  • topic: Phylogeny
  • Pubmed-ID: 27380629
  • title: Amycolatopsis albispora sp. nov., isolated from deep-sea sediment.
  • authors: Zhang G, Wang L, Li J, Zhou Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001277
  • year: 2016
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Glycolipids/chemistry, Indian Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

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
24893G. W. Zhang, Lina,Li, Jinglong,Zhou, YuanAmycolatopsis albispora sp. nov., isolated from deep-sea sediment10.1099/ijsem.0.001277IJSEM 66: 3860-3864 201627380629
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
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