Strain identifier

BacDive ID: 17743

Type strain: Yes

Species: Chitinophaga sancti

Strain Designation: BA-3

Strain history: CIP <- 2002, NCIMB <- H. Reichenbach <- ATCC <- R.A. Lewin: strain BA-3 <- A. Cataldi

NCBI tax ID(s): 1121282 (strain), 1004 (species)

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General

@ref: 442

BacDive-ID: 17743

DSM-Number: 784

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

description: Chitinophaga sancti BA-3 is an obligate aerobe, Gram-negative, motile bacterium of the family Chitinophagaceae.

NCBI tax id

NCBI tax idMatching level
1004species
1121282strain

strain history

@refhistory
442<- H. Reichenbach <- ATCC <- R.A. Lewin, BA-3 <- A. Cataldi
122411CIP <- 2002, NCIMB <- H. Reichenbach <- ATCC <- R.A. Lewin: strain BA-3 <- A. Cataldi

doi: 10.13145/bacdive17743.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Chitinophagia
  • order: Chitinophagales
  • family: Chitinophagaceae
  • genus: Chitinophaga
  • species: Chitinophaga sancti
  • full scientific name: Chitinophaga sancti (Lewin 1969) Kämpfer et al. 2006

  • synonyms

    • @ref: 20215
    • synonym: Flexibacter sancti

@ref: 442

domain: Bacteria

phylum: Bacteroidetes

class: Chitinophagia

order: Sphingobacteriales

family: Chitinophagaceae

genus: Chitinophaga

species: Chitinophaga sancti

full scientific name: Chitinophaga sancti (Lewin 1969) Kämpfer et al. 2006 emend. Hahnke et al. 2016

strain designation: BA-3

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
122411negativerod-shapedyes
69480negative92.386

colony morphology

  • @ref: 122411

pigmentation

  • @ref: 122411
  • production: yes
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
442CY-AGAR (DSMZ Medium 67)yeshttps://mediadive.dsmz.de/medium/67Name: CY-AGAR (DSMZ Medium 67) Composition: Agar 15.0 g/l Casitone 3.0 g/l CaCl2 x 2 H2O 1.36 g/l Yeast extract 1.0 g/l Distilled water
34946MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
442R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
122411CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
122411CIP Medium 35yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=35

culture temp

@refgrowthtypetemperature
442positivegrowth30
34946positivegrowth30
122411positivegrowth15-30
122411nogrowth5
122411nogrowth37
122411nogrowth41
122411nogrowth45

Physiology and metabolism

oxygen tolerance

  • @ref: 122411
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

halophily

@refsaltgrowthtested relationconcentration
122411NaClpositivegrowth0 %
122411NaClnogrowth2 %
122411NaClnogrowth4 %
122411NaClnogrowth6 %
122411NaClnogrowth8 %
122411NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1224114853esculin+hydrolysis
122411606565hippurate-hydrolysis
12241117632nitrate+reduction
12241116301nitrite-reduction
12241115792malonate-assimilation
12241117632nitrate-respiration

antibiotic resistance

  • @ref: 122411
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 122411
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12241115688acetoin+
12241117234glucose+

enzymes

@refvalueactivityec
122411oxidase+
122411beta-galactosidase+3.2.1.23
122411alcohol dehydrogenase-1.1.1.1
122411gelatinase-
122411amylase+
122411DNase-
122411caseinase-3.4.21.50
122411catalase-1.11.1.6
122411tween esterase-
122411gamma-glutamyltransferase+2.3.2.2
122411lecithinase-
122411lipase-
122411lysine decarboxylase-4.1.1.18
122411ornithine decarboxylase-4.1.1.17
122411protease-
122411tryptophan deaminase-
122411urease-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
122411-++--++-+-++----++--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122411+++++-++++++++-++++-++++----------++-----+------------++---+-------------------+------+------------

Isolation, sampling and environmental information

taxonmaps

  • @ref: 69479
  • File name: preview.99_19306.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_334;96_3567;97_4382;98_5611;99_19306&stattab=map
  • Last taxonomy: Chitinophaga sancti
  • 16S sequence: NR_040917
  • Sequence Identity:
  • Total samples: 157
  • soil counts: 64
  • aquatic counts: 51
  • animal counts: 40
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
4421Risk group (German classification)
1224111Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218F.sancti 16S ribosomal RNAM627951478nuccore1004
20218Flexibacter sancti gene for 16S rRNA, strain:IFO 15057AB0780661481nuccore1004
20218Chitinophaga sancti gene for 16S rRNA, partial sequence, strain: NBRC 15057AB6807621451nuccore1004
442Chitinophaga sancti strain IFO 15057 16S ribosomal RNA, partial sequenceNR_0409171481nuccore1004
124043Chitinophaga sancti partial 16S rRNA gene, strain HAMBI 1988LT8999721501nuccore1004

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chitinophaga sancti DSM 784GCA_900119105scaffoldncbi1004
66792Chitinophaga sancti strain DSM 7841004.4wgspatric1004
66792Chitinophaga sancti DSM 7842595699005draftimg1004
66792Chitinophaga sancti DSM 7842563366652draftimg1004

GC content

@refGC-contentmethod
44245.9
44244.2sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno92.386no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no93.952yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes73.82no
69480spore-formingspore-formingAbility to form endo- or exosporesno72.27no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno96.972yes
69480flagellatedmotile2+Ability to perform flagellated movementno89.75no

External links

@ref: 442

culture collection no.: DSM 784, ATCC 23092, IFO 15057, NBRC 15057, CCUG 56030, LMG 8377, HAMBI 1988, VKM B-1428, CIP 107780, NCIMB 1379

straininfo link

@refstraininfo
8673310281
86734409474

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22307507Chitinophaga oryziterrae sp. nov., isolated from the rhizosphere soil of rice (Oryza sativa L.).Chung EJ, Park TS, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.036442-02012Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Oryza/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analysis, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny30608225Chitinophaga silvisoli sp. nov., isolated from forest soil.Wang C, Lv Y, Li A, Feng G, Bao G, Zhu H, Tan ZInt J Syst Evol Microbiol10.1099/ijsem.0.0032122019Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32501195Chitinophaga tropicalis sp. nov., isolated from forest soil.Zhang XJ, Feng GD, Yao Q, Zhang J, Phuong LTB, Zhu HInt J Syst Evol Microbiol10.1099/ijsem.0.0042482020Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vietnam, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
442Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 784)https://www.dsmz.de/collection/catalogue/details/culture/DSM-784
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
34946Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5253
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
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
86733Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10281.1StrainInfo: A central database for resolving microbial strain identifiers
86734Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID409474.1StrainInfo: A central database for resolving microbial strain identifiers
122411Curators of the CIPCollection of Institut Pasteur (CIP 107780)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107780
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy