Strain identifier

BacDive ID: 134134

Type strain: Yes

Species: Pedobacter himalayensis

Strain history: CIP <- 2005, JCM <- 2003, S. Shivaji: strain HHS22

NCBI tax ID(s): 246796 (species)

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General

@ref: 31433

BacDive-ID: 134134

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped

description: Pedobacter himalayensis JCM 12171 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from Water collected from the Hamta Glacier.

NCBI tax id

  • NCBI tax id: 246796
  • Matching level: species

strain history

@refhistory
67770S. Shivaji HHS 22.
119902CIP <- 2005, JCM <- 2003, S. Shivaji: strain HHS22

doi: 10.13145/bacdive134134.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Pedobacter
  • species: Pedobacter himalayensis
  • full scientific name: Pedobacter himalayensis Shivaji et al. 2005

@ref: 31433

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Pedobacter

species: Pedobacter himalayensis

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31433negativerod-shapedno
69480yes97.033
69480negative99.97
119902negativerod-shapedno

pigmentation

@refproductionname
31433no
119902noFlexirubin

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
42245MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119902CIP Medium 368yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=368
119902CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
31433positivegrowth04-25
31433positiveoptimum22psychrophilic
42245positivegrowth22psychrophilic
67770positivegrowth22psychrophilic
119902positivegrowth5-25psychrophilic
119902nogrowth30mesophilic
119902nogrowth37mesophilic
119902nogrowth41thermophilic

culture pH

@refabilitytypepHPH range
31433positivegrowth06-10alkaliphile
31433positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31433aerobe
119902obligate aerobe

spore formation

@refspore formationconfidence
31433no
69481no100
69480no99.978

halophily

@refsaltgrowthtested relationconcentration
31433NaClpositiveoptimum5.8 %
119902NaClpositivegrowth0-10 %

observation

  • @ref: 67770
  • observation: quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3143315963ribitol+carbon source
3143316449alanine+carbon source
3143322599arabinose+carbon source
3143329016arginine+carbon source
3143335391aspartate+carbon source
3143317057cellobiose+carbon source
3143315740formate+carbon source
3143328757fructose+carbon source
3143333984fucose+carbon source
3143328260galactose+carbon source
3143317234glucose+carbon source
3143329987glutamate+carbon source
3143317754glycerol+carbon source
3143317306maltose+carbon source
3143329864mannitol+carbon source
3143337684mannose+carbon source
3143328053melibiose+carbon source
3143317268myo-inositol+carbon source
3143326271proline+carbon source
3143315361pyruvate+carbon source
3143316634raffinose+carbon source
3143326546rhamnose+carbon source
3143333942ribose+carbon source
3143317814salicin+carbon source
3143317822serine+carbon source
3143330911sorbitol+carbon source
3143330031succinate+carbon source
3143317992sucrose+carbon source
3143326986threonine+carbon source
3143327082trehalose+carbon source
3143318222xylose+carbon source
314334853esculin+hydrolysis
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837117151xylitol-builds acid from
683716731melezitose-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837117113erythritol-builds acid from
11990216947citrate+carbon source
1199024853esculin+hydrolysis
11990217632nitrate-reduction
11990216301nitrite-reduction
11990217632nitrate-respiration

metabolite production

  • @ref: 119902
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31433catalase+1.11.1.6
31433gelatinase+
31433cytochrome oxidase+1.9.3.1
119902oxidase+
119902beta-galactosidase+3.2.1.23
119902alcohol dehydrogenase+1.1.1.1
119902gelatinase+
119902amylase+
119902DNase+
119902caseinase+3.4.21.50
119902catalase+1.11.1.6
119902tween esterase-
119902lecithinase+
119902lipase-
119902lysine decarboxylase-4.1.1.18
119902ornithine decarboxylase-4.1.1.17
119902phenylalanine ammonia-lyase+4.3.1.24
119902protease+
119902tryptophan deaminase-
119902urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
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

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119902-+++-++---++++-+++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119902+/--+/-+/-+/-+/----+/-+/-+/-+/-------+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/--+/-+/-+/--+/-+/----+/-----+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119902++-++-+++++++++++++-+-+-----------++-----+-------------+---+--------------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
67770Water collected from the Hamta GlacierHimalayan mountainIndiaINDAsia
119902Environment, Glacial waterIndiaINDAsia

Safety information

risk assessment

  • @ref: 119902
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31433
  • description: Pedobacter sp. HHS22 partial 16S rRNA gene, type strain HHS22
  • accession: AJ583425
  • length: 1452
  • database: nuccore
  • NCBI tax ID: 246796

Genome sequences

  • @ref: 66792
  • description: Pedobacter himalayensis strain HHS 22
  • accession: 246796.4
  • assembly level: wgs
  • database: patric
  • NCBI tax ID: 246796

GC content

@refGC-content
3143341
6777041.25

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes87.891yes
gram-positiveno97.984yes
anaerobicno96.357yes
aerobicyes81.52no
halophileno85.768no
spore-formingno93.352yes
glucose-utilyes95.072yes
flagellatedno67.971yes
thermophileno99.253yes
glucose-fermentyes92.858no

External links

@ref: 31433

culture collection no.: JCM 12171, MTCC 6384, HHS 22, CIP 108787

straininfo link

  • @ref: 91735
  • straininfo: 139001

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15879237Pedobacter himalayensis sp. nov., from the Hamta glacier located in the Himalayan mountain ranges of India.Shivaji S, Chaturvedi P, Reddy GSN, Suresh KInt J Syst Evol Microbiol10.1099/ijs.0.63532-02005Bacterial Typing Techniques, Bacteroidetes/*classification/cytology/*isolation & purification/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Ice Cover/*microbiology, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny28109203Pedobacter lusitanus sp. nov., isolated from sludge of a deactivated uranium mine.Covas C, Caetano T, Cruz A, Santos T, Dias L, Klein G, Abdulmawjood A, Rodriguez-Alcala LM, Pimentel LL, Gomes A, Freitas AC, Garcia-Serrano A, Fontecha J, Mendo SInt J Syst Evol Microbiol10.1099/ijsem.0.0018142017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Fatty Acids/chemistry, Genes, Bacterial, *Mining, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Portugal, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Sphingolipids, *Uranium, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
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
31433Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172773928776041
42245Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6454
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
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
91735Reimer, 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-ID139001.1
119902Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108787Collection of Institut Pasteur (CIP 108787)