Strain identifier

BacDive ID: 3934

Type strain: Yes

Species: Calidifontibacter indicus

Strain Designation: PC IW-02, PC IW02

Strain history: A. Ruckmani and S. Mayilraj PC IW02.

NCBI tax ID(s): 419650 (species)

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General

@ref: 16563

BacDive-ID: 3934

DSM-Number: 22967

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

description: Calidifontibacter indicus PC IW-02 is a mesophilic bacterium that has a Sand yellow pigmentation and was isolated from warm spring water.

NCBI tax id

  • NCBI tax id: 419650
  • Matching level: species

strain history

@refhistory
16563<- S. Mayilraj, MTCC; PC IW-02 <- A. Ruckmani
67770A. Ruckmani and S. Mayilraj PC IW02.

doi: 10.13145/bacdive3934.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Dermacoccaceae
  • genus: Calidifontibacter
  • species: Calidifontibacter indicus
  • full scientific name: Calidifontibacter indicus Ruckmani et al. 2011

@ref: 16563

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dermacoccaceae

genus: Calidifontibacter

species: Calidifontibacter indicus

full scientific name: Calidifontibacter indicus Ruckmani et al. 2011

strain designation: PC IW-02, PC IW02

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480no94.719
69480100positive

colony morphology

@refcolony colormedium used
69216Ivory (1014)ISP 4
69216Ivory (1014)ISP 5
69216Ivory (1014)suter without tyrosine
69216Ivory (1014), sand yellow (1002)ISP 2
69216Light ivory (1015), sand yellow (1002)ISP 7
69216Sand yellow (1002)ISP 3
69216Sand yellow (1002)ISP 6
69216Sand yellow (1002)suter with tyrosine

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69216noAerial myceliumsuter without tyrosine
69216noAerial myceliumsuter with tyrosine
69216noAerial myceliumISP 4
69216noAerial myceliumISP 3
69216noAerial myceliumISP 2
69216noAerial myceliumISP 7
69216noAerial myceliumISP 6
69216noAerial myceliumISP 5

pigmentation

  • @ref: 69216
  • production: yes
  • color: Sand yellow (1002)
  • name: soluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
69216DSM_22967_image5.jpeg(ISP6, SSM+T, SSM-T)Helmholtz-Zentrum für Infektionsforschung GmbH
69216DSM_22967_image6.jpeg(ISP6, SSM+T, SSM-T)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture temp

  • @ref: 67770
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.983

halophily

  • @ref: 69216
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-7.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6921622599arabinose-growth
6921662968cellulose-growth
6921628757fructose+growth
6921617234glucose+growth
6921617268inositol+/-growth
6921637684mannose-growth
6921616634raffinose-growth
6921626546rhamnose-growth
6921617992sucrose+growth
6921618222xylose-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

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
69216---+-----+---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69216+++/--++/----++/---------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
16563warm spring waterWestern Ghats (N 12.77° E 75.22°)IndiaINDAsia12.7775.22
67770Warm spring of Western GhatsIndiaINDAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Thermal spring

taxonmaps

  • @ref: 69479
  • File name: preview.99_17460.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_8956;97_10766;98_13207;99_17460&stattab=map
  • Last taxonomy: Calidifontibacter indicus subclade
  • 16S sequence: EF187228
  • Sequence Identity:
  • Total samples: 1089
  • soil counts: 138
  • aquatic counts: 118
  • animal counts: 797
  • plant counts: 36

Safety information

risk assessment

  • @ref: 16563
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16563
  • description: Calidifontibacter indicus strain PC IW02 16S ribosomal RNA gene, partial sequence
  • accession: EF187228
  • length: 1400
  • database: ena
  • NCBI tax ID: 419650

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Calidifontibacter indicus strain DSM 22967419650.3wgspatric419650
66792Calidifontibacter indicus DSM 229672778260926draftimg419650
67770Calidifontibacter indicus DSM 22967GCA_003386865contigncbi419650

GC content

  • @ref: 16563
  • GC-content: 77

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes91.666no
anaerobicno97.853no
halophileno96.917no
spore-formingno85.792no
glucose-utilyes90.408yes
aerobicyes85.128no
flagellatedno97.861no
thermophileno97.967no
motileno96.796no
glucose-fermentno89.737yes

External links

@ref: 16563

culture collection no.: DSM 22967, JCM 16038, MTCC 8338, NBRC 109629

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21075908Calidifontibacter indicus gen. nov., sp. nov., a member of the family Dermacoccaceae isolated from a hot spring, and emended description of the family Dermacoccaceae.Ruckmani A, Kaur I, Schumann P, Klenk HP, Mayilraj SInt J Syst Evol Microbiol10.1099/ijs.0.025593-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Amino Acids/analysis, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hot Springs/*microbiology, India, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Phylogeny28629492Calidifontibacter terrae sp. nov., an actinomycete isolated from soil, with potential applications in cosmetics.Dahal RH, Shim DS, Kim JY, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0018932017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny28920829Allobranchiibius huperziae gen. nov., sp. nov., a member of Dermacoccaceae isolated from the root of a medicinal plant Huperzia serrata (Thunb.).Ai MJ, Sun Y, Sun HM, Liu HY, Yu LY, Zhang YQInt J Syst Evol Microbiol10.1099/ijsem.0.0022842017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Huperzia/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, Plants, Medicinal/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16563Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22967)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22967
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69216Wink, J.https://cdn.dsmz.de/wink/DSM%2022967.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1