Strain identifier

BacDive ID: 133007

Type strain: Yes

Species: Pontibacter virosus

Strain Designation: W14

Strain history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; W14 <- P. Kohli

NCBI tax ID(s): 1765052 (species)

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General

@ref: 24795

BacDive-ID: 133007

DSM-Number: 100231

keywords: genome sequence, 16S sequence, Bacteria, aerobe, heterotroph, mesophilic, Gram-negative, motile, rod-shaped, colony-forming, pigmented

description: Pontibacter virosus W14 is an aerobe, heterotroph, mesophilic bacterium that forms circular colonies and has a red pigmentation.

NCBI tax id

  • NCBI tax id: 1765052
  • Matching level: species

strain history

  • @ref: 24795
  • history: <- R. Lal, Univ. Delhi, Dept. Zoology, India; W14 <- P. Kohli

doi: 10.13145/bacdive133007.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Cytophagia
  • order: Cytophagales
  • family: Hymenobacteraceae
  • genus: Pontibacter
  • species: Pontibacter virosus
  • full scientific name: Pontibacter virosus Kohli et al. 2016

@ref: 24795

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Hymenobacteraceae

genus: Pontibacter

species: Pontibacter virosus

full scientific name: Pontibacter virosus Kohli et al. 2016

strain designation: W14

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
24987negative1.0-1.6 µm0.4-0.6 µmrod-shapedyes
69480negative99.997

colony morphology

  • @ref: 24987
  • colony color: red
  • colony shape: circular
  • incubation period: 2 days
  • medium used: LB (lysogeny broth) agar

pigmentation

  • @ref: 24987
  • production: yes
  • color: red

Culture and growth conditions

culture medium

@refnamegrowth
24987LB (lysogeny broth) agaryes
24987NA (Nutrient Agar)yes
24987Marine agar (MA)yes
24987TSA (Trypticase soy agar)yes
24987yeast agaryes
24987brain heart infusion agaryes

culture temp

@refgrowthtypetemperaturerange
24987positiveoptimum28mesophilic
24987positivegrowth20.0-40.0

culture pH

@refabilitytypepH
24987positiveoptimum7
24987positivegrowth6.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 24987
  • oxygen tolerance: aerobe

nutrition type

  • @ref: 24987
  • type: heterotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.974

halophily

@refsalttested relationconcentrationgrowth
24987NaCloptimum1 %
24987NaClgrowth0.0-5.0 %positive

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2498716947citrate-hydrolysis
2498717268myo-inositol-carbon source
2498726546rhamnose-carbon source
2498733942ribose-carbon source
2498730911sorbitol-carbon source
24987casein+hydrolysis
2498717108D-arabinose+carbon source
2498717108D-arabinose+builds acid from
2498715824D-fructose+carbon source
2498712936D-galactose+carbon source
2498717634D-glucose+carbon source
2498717634D-glucose+builds acid from
2498716899D-mannitol+carbon source
2498716899D-mannitol+builds acid from
2498716024D-mannose+carbon source
2498716024D-mannose+builds acid from
249874853esculin+hydrolysis
2498728757fructose+builds acid from
249875291gelatin+hydrolysis
2498717368hypoxanthine+hydrolysis
2498717716lactose+carbon source
2498717306maltose+carbon source
2498717306maltose+builds acid from
2498730911sorbitol+builds acid from
2498728017starch+hydrolysis
2498717992sucrose+carbon source
2498717992sucrose+builds acid from
2498753424tween 20+hydrolysis
2498753426tween 80+hydrolysis
2498715318xanthine+hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitiveis resistant
2498717698chloramphenicolyesyes
24987100241ciprofloxacinyesyes
24987100147nalidixic acidyesyes
2498727701oxytetracyclineyesyes
2498728001vancomycinyesyes
249878309polymyxin byesyes
2498728077rifampicinyesyes
2498727902tetracyclineyesyes
2498728971ampicillinyesyes
249876104kanamycinyesyes
249872637amikacinyesyes
2498717334penicillinyesyes
2498717833gentamicinyesyes

metabolite production

@refChebi-IDmetaboliteproduction
2498716136hydrogen sulfideno
2498735581indoleno

enzymes

@refvalueactivityec
24987catalase+1.11.1.6
24987cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperature
24795hexachlorocyclohexane-contaminated dumpsite soilUttar Pradesh, Lucknow, Ummari VillageIndiaINDAsia
24987LB (lysogeny broth) agar2 days28

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment
#Engineered#Contamination
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_129386.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_60;96_1869;97_2246;98_37800;99_129386&stattab=map
  • Last taxonomy: Pontibacter virosus subclade
  • 16S sequence: KT719408
  • Sequence Identity:
  • Total samples: 1
  • aquatic counts: 1

Sequence information

16S sequences

  • @ref: 24795
  • description: Pontibacter virosus strain W14 16S ribosomal RNA gene, partial sequence
  • accession: KT719408
  • length: 1430
  • database: ena
  • NCBI tax ID: 1765052

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pontibacter virosus DSM 100231GCA_003096355scaffoldncbi1765052
66792Pontibacter virosus strain DSM 1002311765052.3wgspatric1765052
66792Pontibacter virosus DSM 1002312756170242draftimg1765052

GC content

@refGC-contentmethod
2498751.3Thermal denaturation, fluorometry
2479551.3fluorimetric

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno95.745no
gram-positiveno98.4yes
anaerobicno99.097yes
halophileno84.182no
spore-formingno94.012no
glucose-utilyes87.015no
aerobicyes89.806no
thermophileno97.105no
motileno88.803yes
glucose-fermentno85.91no

External links

@ref: 24795

culture collection no.: DSM 100231, KCTC 42941, MCC 2932

literature

  • topic: Phylogeny
  • Pubmed-ID: 27488455
  • title: Pontibacter virosus sp. nov., isolated from a hexachlorocyclohexane-contaminated dumpsite.
  • authors: Kohli P, Nayyar N, Sharma A, Singh AK, Lal R
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001363
  • year: 2016
  • mesh: Bacterial Typing Techniques, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Hexachlorocyclohexane, India, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24795Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100231Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100231)
24987P. N. Kohli, Namita,Sharma, Anukriti,Singh, Amit Kumar,Lal, RupPontibacter virosus sp. nov., isolated from a hexachlorocyclohexane-contaminated dumpsite10.1099/ijsem.0.001363IJSEM 66: 4395-4400 201627488455
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
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/
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