Strain identifier

BacDive ID: 3829

Type strain: Yes

Species: Pontibacter roseus

Strain Designation: SRC-1

Strain history: CIP <- 2008, DSMZ <- MTCC <- K. Suresh, Chandigarh, India: strain SRC-1

NCBI tax ID(s): 1122967 (strain), 336989 (species)

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General

@ref: 7040

BacDive-ID: 3829

DSM-Number: 17521

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

description: Pontibacter roseus SRC-1 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from muddy water from an occasional drainage system.

NCBI tax id

NCBI tax idMatching level
1122967strain
336989species

strain history

@refhistory
7040<- T. Chakrabarti, MTCC; SRC-1 <- K. Suresh
122264CIP <- 2008, DSMZ <- MTCC <- K. Suresh, Chandigarh, India: strain SRC-1

doi: 10.13145/bacdive3829.20230509.8.1

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 roseus
  • full scientific name: Pontibacter roseus (Suresh et al. 2006) Wang et al. 2010

  • synonyms

    • @ref: 20215
    • synonym: Effluviibacter roseus

@ref: 7040

domain: Bacteria

phylum: Bacteroidetes

class: Cytophagia

order: Cytophagales

family: Hymenobacteraceae

genus: Pontibacter

species: Pontibacter roseus

full scientific name: Pontibacter roseus (Suresh et al. 2006) Wang et al. 2010 emend. Zhang et al. 2013

strain designation: SRC-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31733negative01-03 µm0.3-0.5 µmrod-shapedno
69480negative99.995
122264negativerod-shapedno

pigmentation

  • @ref: 31733
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
33336MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
122264CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
31733positivegrowth04-37
31733positiveoptimum30-37mesophilic
33336positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
31733positivegrowth06-10alkaliphile
31733positiveoptimum08-10

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31733aerobe
122264obligate aerobe

spore formation

@refspore formationconfidence
31733no
69481no100
69480no99.918

halophily

@refsaltgrowthtested relationconcentration
31733NaClpositivegrowth0-8 %
31733NaClpositiveoptimum0-8 %

observation

  • @ref: 31733
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3173328757fructose+carbon source
3173328260galactose+carbon source
3173317234glucose+carbon source
3173317716lactose+carbon source
3173316634raffinose+carbon source
3173317992sucrose+carbon source
12226417632nitrate-reduction
12226416301nitrite-reduction

enzymes

@refvalueactivityec
31733catalase+1.11.1.6
31733cytochrome oxidase+1.9.3.1
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
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
122264oxidase+
122264catalase+1.11.1.6
122264urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122264-+---++++--+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7040muddy water from an occasional drainage systemChandigarhIndiaINDAsia
122264Environment, Muddy water, drainage systemChandigarhIndiaINDAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic
#Environmental#Terrestrial#Mud (Sludge)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3958.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_60;96_2013;97_2424;98_2998;99_3958&stattab=map
  • Last taxonomy: Pontibacter roseus subclade
  • 16S sequence: AM049256
  • Sequence Identity:
  • Total samples: 390
  • soil counts: 261
  • aquatic counts: 52
  • animal counts: 53
  • plant counts: 24

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
70401Risk group (German classification)
1222641Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7040
  • description: Effluviibacter roseus partial 16S rRNA gene, type strain SRC-1T
  • accession: AM049256
  • length: 1401
  • database: ena
  • NCBI tax ID: 336989

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pontibacter roseus DSM 17521GCA_000373265scaffoldncbi1122967
66792Pontibacter roseus DSM 175211122967.3wgspatric1122967
66792Pontibacter roseus DSM 175212515154084draftimg1122967

GC content

  • @ref: 7040
  • GC-content: 59.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno89.119no
flagellatedno96.314yes
gram-positiveno98.091yes
anaerobicno99.11no
aerobicyes90.214yes
halophileno78.545no
spore-formingno93.928no
thermophileno96.314yes
glucose-utilyes90.465no
glucose-fermentno83.721no

External links

@ref: 7040

culture collection no.: DSM 17521, CCTCC AB 207222, CIP 109903, MTCC 7260

straininfo link

  • @ref: 73340
  • straininfo: 297177

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16825654Effluviibacter roseus gen. nov., sp. nov., isolated from muddy water, belonging to the family "Flexibacteraceae".Suresh K, Mayilraj S, Chakrabarti TInt J Syst Evol Microbiol10.1099/ijs.0.64144-02006Aerobiosis, Amino Acids/metabolism, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Cytophagaceae/*classification/cytology/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA, Gentian Violet, Molecular Sequence Data, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Water MicrobiologyMetabolism
Phylogeny19648348Pontibacter xinjiangensis sp. nov., in the phylum 'Bacteroidetes', and reclassification of [Effluviibacter] roseus as Pontibacter roseus comb. nov.Wang Y, Zhang K, Cai F, Zhang L, Tang Y, Dai J, Fang CInt J Syst Evol Microbiol10.1099/ijs.0.011395-02009Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification/metabolism, Base Composition, Cytophagaceae/*classification/genetics/isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism
Phylogeny24748437Pontibacter humi sp. nov., isolated from mountain soil.Srinivasan S, Lee JJ, Lee SS, Kim MKCurr Microbiol10.1007/s00284-014-0580-12014Aerobiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytophagaceae/*classification/genetics/*isolation & purification/physiology, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Korea, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyGenetics
Genetics26203325High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1(T) (DSM 17521(T)) isolated from muddy waters of a drainage system in Chandigarh, India.Mukherjee S, Lapidus A, Shapiro N, Cheng JF, Han J, Reddy T, Huntemann M, Ivanova N, Mikhailova N, Chen A, Palaniappan K, Spring S, Goker M, Markowitz V, Woyke T, Tindall BJ, Klenk HP, Kyrpides NC, Pati AStand Genomic Sci10.1186/1944-3277-10-82015Transcriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7040Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17521)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17521
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
31733Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2800928776041
33336Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7699
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)
68382Automatically annotated from API zym
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
73340Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297177.1StrainInfo: A central database for resolving microbial strain identifiers
122264Curators of the CIPCollection of Institut Pasteur (CIP 109903)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109903