Strain identifier

BacDive ID: 141006

Type strain: Yes

Species: Amycolatopsis acidiphila

Strain Designation: 2-5

Strain history: <- SB Kim, CNU

NCBI tax ID(s): 715473 (species)

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General

@ref: 43897

BacDive-ID: 141006

keywords: genome sequence, 16S sequence, Bacteria, aerobe, pigmented

description: Amycolatopsis acidiphila 2-5 is an aerobe bacterium that has a light brown diffusible pigments pigmentation and was isolated from coal mine soil from coal mine site, Nalaikh Province, Ulaanbataar, Mongolia.

NCBI tax id

  • NCBI tax id: 715473
  • Matching level: species

strain history

@refhistory
67770S. B. Kim; Chungnam Natl. Univ., South Korea; 2-5.
67771<- SB Kim, CNU

doi: 10.13145/bacdive141006.20230509.8.1

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 acidiphila
  • full scientific name: Amycolatopsis acidiphila Oyuntsetseg et al. 2017

@ref: 43897

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Pseudonocardiales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis acidiphila

strain designation: 2-5

type strain: yes

Morphology

colony morphology

@refcolony colormedium used
43897light yellowStarch casein agar
43897light yellowmodified Benett's agar
43897light yellowISP 2 agar
43897light yellowISP 3 agar

pigmentation

  • @ref: 43897
  • production: yes
  • name: light brown diffusible pigments

Culture and growth conditions

culture medium

@refnamegrowthcomposition
43897ISP 2 agaryes
43897ISP 3 agaryes
43897modified Bennett's agaryesglucose 10 g/L, casitone 2 g/L, yeast extract 1 g/L, Lab-Lemco powder 0.8 g/L and agar 15 /L, pH 5.5
43897Starch casein agaryessoluble starch 10 g/L, casein 0.3 g/L, KNO3 2 g/L, NaCl2 g/L, K2HPO4 2 g/L, MgSO4.7H2O 0.05 g/L, CaCO3 0.02 g/L, FeSO4.7H2O 0.01 g/L, agar 15 g/L, pH 4.5, supplemented with cycloheximide and nystatin (50 µg/mL)

culture temp

@refgrowthtypetemperaturerange
43897positivegrowth15-40
43897positiveoptimum30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
43897positivegrowth4.5-7.5
43897positiveoptimum5.5-6.0

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
43897NaClpositiveoptimum0 %(w/v)
43897NaClpositivegrowth0-6 %(w/v)

observation

@refobservation
43897quinone MK-9
67770quinones: MK-9(H4)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
43897L-alanine 4-nitroanilide-carbon source
43897L-lysine-carbon source18019
43897carboxymethylcellulose-degradation85146
43897dna-degradation16991
43897starch-degradation28017
43897tributyrin-degradation35020
43897nitrate-reduction17632
43897D-fructose+carbon source15824
43897D-galactose+carbon source12936
43897D-glucose+carbon source17634
43897D-mannitol+carbon source16899
43897D-sorbitol+carbon source17924
43897D-xylose+carbon source65327
43897L-arabinose+carbon source30849
43897L-arginine+carbon source16467
43897L-asparagine+carbon source17196
43897L-glutamine+carbon source18050
43897L-histidine+carbon source15971
43897L-isoleucine+carbon source17191
43897L-rhamnose+carbon source62345
43897melibiose+carbon source28053
43897myo-inositol+carbon source17268
43897raffinose+carbon source16634
43897salicin+carbon source17814
43897sarcosine+carbon source15611
43897casein+degradation
43897gelatin+degradation5291
43897tween 20+degradation53424
43897tween 40+degradation53423
43897tween 60+degradation53425
43897tween 80+degradation53426
43897xanthine+degradation15318

enzymes

@refvalueactivityec
43897N-acetyl-beta-glucosaminidase+3.2.1.52
43897acid phosphatase+3.1.3.2
43897alpha-chymotrypsin+3.4.21.1
43897esterase (C 4)+
43897esterase Lipase (C 8)+
43897alpha-glucosidase+3.2.1.20
43897leucine arylamidase+3.4.11.1
43897naphthol-AS-BI-phosphohydrolase+
43897cystine arylamidase+/-3.4.11.3
43897beta-galactosidase+/-3.2.1.23
43897lipase (C 14)+/-
43897alpha-mannosidase+/-3.2.1.24
43897valine arylamidase+/-
43897alkaline phosphatase-3.1.3.1
43897alpha-fucosidase-3.2.1.51
43897alpha-galactosidase-3.2.1.22
43897beta-glucuronidase-3.2.1.31
43897trypsin-3.4.21.4
43897beta-glucosidase+3.2.1.21

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43897C15:0 anteiso11.1
    43897C17:0 anteiso2
    43897C16:09.3
    43897C17:1ω6c18.9
    43897C14:0 iso1.7
    43897C15:0 iso13.5
    43897C16:0 iso35
    43897C16:1 iso H2.8
    43897C17:0 iso2.1
  • type of FA analysis: whole cell analysis
  • incubation medium: modified Benett´s agar (acidified)
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation pH: 5.5
  • software version: Sherlock 6.1
  • library/peak naming table: RTSBA6
  • system: MIS MIDI
  • instrument: Hewlett Packard 7890 gas chromatograph

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
43897coal mine soil (pH 5.9) from coal mine site, Nalaikh Province, Ulaanbataar, MongoliaNalaikh Province, UlaanbataarMongoliaMNGAsiaacidified starch casein agarsoluble starch 10 g/L, casein 0.3 g/L, KNO3 2 g/L, NaCl2 g/L, K2HPO4 2 g/L, MgSO4.7H2O 0.05 g/L, CaCO3 0.02 g/L, FeSO4.7H2O 0.01 g/L, agar 15 g/L, pH 4.5, supplemented with cycloheximide and nystatin (50 µg/mL)1 week30
67770Soil at Nalaikh coal mining siteNalaikh ProvinceMongoliaMNGAsia
67771Mongolian Coal mining soilMongoliaMNGAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_97344.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_13899;97_16937;98_66693;99_97344&stattab=map
  • Last taxonomy: Amycolatopsis
  • 16S sequence: GU132436
  • Sequence Identity:
  • Total samples: 119
  • soil counts: 97
  • aquatic counts: 7
  • animal counts: 14
  • plant counts: 1

Sequence information

16S sequences

  • @ref: 43897
  • description: 16S rRNA gene sequence
  • accession: GU132436
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Amycolatopsis acidiphila JCM 30562GCA_007713745contigncbi715473
66792Amycolatopsis acidiphila strain JCM 30562715473.3wgspatric715473
66792Amycolatopsis acidiphila JCM 305622899342247draftimg715473
66792Amycolatopsis acidiphila KCTC 39523GCA_021391495completencbi715473

GC content

  • @ref: 43897
  • GC-content: 72
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno97.868no
gram-positiveyes87.838no
anaerobicno99.076no
aerobicyes89.772yes
halophileno90.694no
spore-formingyes85.254no
motileno92.915no
glucose-fermentno90.294no
thermophileno94.911no
glucose-utilyes89.67yes

External links

@ref: 43897

culture collection no.: KCTC 39523, JCM 30562

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28857027Amycolatopsis acidiphila sp. nov., a moderately acidophilic species isolated from coal mine soil.Oyuntsetseg B, Cho SH, Jeon SJ, Lee HB, Shin KS, Kim IS, Kim SBInt J Syst Evol Microbiol10.1099/ijsem.0.0021262017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, *Coal Mining, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Mongolia, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31851605Amycolatopsis acidicola sp. nov., isolated from peat swamp forest soil.Teo WFA, Srisuk N, Duangmal KInt J Syst Evol Microbiol10.1099/ijsem.0.0039332020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Forests, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/chemistry, *WetlandsTranscriptome
Phylogeny33128034Amycolatopsis acididurans sp. nov., isolated from peat swamp forest soil in Thailand.Teo WFA, Lipun K, Srisuk N, Duangmal KJ Antibiot (Tokyo)10.1038/s41429-020-00382-22020Amycolatopsis/classification/genetics/*isolation & purification, Base Composition, Fatty Acids/*chemistry, Lipids/*chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil, *Soil Microbiology, Thailand, WetlandsEnzymology

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
43897Bilguun Oyuntsetseg, Sung-Heun Cho, Sun Jeong Jeon, Hyang Burm Lee, Kee-Sun Shin, In-Seop Kim, Seung Bum KimAmycolatopsis acidiphila sp. nov., a moderately acidophilic species isolated from coal mine soil10.1099/ijsem.0.002126IJSEM 67: 3387-3392 201728857027
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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/