Strain identifier

BacDive ID: 6360

Type strain: Yes

Species: Oribacterium sinus

Strain history: CIP <- 2003, J.P. Carlier, Inst. Pasteur, Paris, France: strain AIP 354-02 <- Nancy Hosp., Nancy, France

NCBI tax ID(s): 237576 (species)

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General

@ref: 6852

BacDive-ID: 6360

DSM-Number: 17245

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, motile, ovoid-shaped, human pathogen

description: Oribacterium sinus DSM 17245 is an anaerobe, mesophilic, Gram-positive human pathogen that was isolated from human, maxillary sinus.

NCBI tax id

  • NCBI tax id: 237576
  • Matching level: species

strain history

@refhistory
6852<- CCUG <- J.-P.Carlier AIP 354-02 <- University Hospital of Nancy
122636CIP <- 2003, J.P. Carlier, Inst. Pasteur, Paris, France: strain AIP 354-02 <- Nancy Hosp., Nancy, France

doi: 10.13145/bacdive6360.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Lachnospiraceae
  • genus: Oribacterium
  • species: Oribacterium sinus
  • full scientific name: Oribacterium sinus Carlier et al. 2004

@ref: 6852

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Lachnospiraceae

genus: Oribacterium

species: Oribacterium sinus

full scientific name: Oribacterium sinus Carlier et al. 2004

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31215positiveovoid-shapedyes
69480positive99.719
122636rod-shapedyes

colony morphology

@refincubation period
579774 days
122636

pigmentation

  • @ref: 31215
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6852PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
6852WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339)yeshttps://mediadive.dsmz.de/medium/339Name: WILKINS-CHALGREN ANAEROBE BROTH (DSMZ Medium 339) Composition: dehydrated Wilkins-Chalgren medium 33.0 g/l L-Cysteine HCl 0.3 g/l Sodium resazurin 0.0005 g/l Distilled water
38250MEDIUM 20 - for Anaerobic bacteriayesAgar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
122636CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
6852positivegrowth37mesophilic
38250positivegrowth37mesophilic
57977positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
6852anaerobe
31215anaerobe
57977anaerobe
69480anaerobe99.486
122636anaerobe

spore formation

@refspore formationconfidence
31215no
69480no99.997

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3121528260galactose+carbon source
3121517234glucose+carbon source
3121516634raffinose+carbon source
3121517992sucrose+carbon source
12263617108D-arabinose-degradation
12263615824D-fructose+degradation
12263617634D-glucose+degradation
12263665327D-xylose-degradation
12263617057cellobiose-degradation
12263617716lactose-degradation
12263617306maltose-degradation
12263617814salicin-degradation
12263617992sucrose+degradation
1226364853esculin-hydrolysis
12263617632nitrate+reduction
12263616301nitrite-reduction
12263617632nitrate+respiration
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
3121535581indoleyes
12263635581indoleyes
6838035581indoleno

metabolite tests

@refChebi-IDmetaboliteindole test
3121535581indole+
6838035581indole-

enzymes

@refvalueactivityec
31215alpha-galactosidase+3.2.1.22
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
68380serine arylamidase+
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase+
68380glycin arylamidase+
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase+3.4.11.1
68380proline-arylamidase+3.4.11.5
68380L-arginine arylamidase+
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
122636oxidase-
122636beta-galactosidase+3.2.1.23
122636gelatinase-
122636amylase-
122636DNase-
122636caseinase-3.4.21.50
122636catalase-1.11.1.6
122636tween esterase-
122636lecithinase-
122636lipase-
122636protease-
122636urease-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
122636-----+-----+++-+----

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
6852--++-+-----------+++----+++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6852human, maxillary sinusNancyFranceFRAEurope
57977Human maxillary sinusNancyFranceFRAEurope
122636Human, Maxillary sinusNancyFranceFRAEurope

isolation source categories

Cat1Cat2
#Host#Human
#Host Body-Site#Oral cavity and airways

taxonmaps

  • @ref: 69479
  • File name: preview.99_1828.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_112;96_314;97_350;98_395;99_1828&stattab=map
  • Last taxonomy: Oribacterium
  • 16S sequence: AY323228
  • Sequence Identity:
  • Total samples: 48126
  • soil counts: 511
  • aquatic counts: 598
  • animal counts: 46753
  • plant counts: 264

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
6852yes, in single cases1Risk group (German classification)
1226361Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6852
  • description: Oribacterium sinus 16S ribosomal RNA gene, partial sequence
  • accession: AY323228
  • length: 1374
  • database: ena
  • NCBI tax ID: 237576

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Oribacterium sinus DSM 17245GCA_014202695scaffoldncbi237576
66792Oribacterium sinus strain DSM 17245237576.163wgspatric237576
66792Oribacterium sinus DSM 172452861591105draftimg237576

GC content

  • @ref: 6852
  • GC-content: 42.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes78no
flagellatedno69.623no
gram-positiveyes66.217no
anaerobicyes98.496no
aerobicno98.482no
halophileno74.356no
spore-formingno82.865no
glucose-utilyes85.412yes
thermophileno98.316no
motileyes81.784no
glucose-fermentyes74.913no

External links

@ref: 6852

culture collection no.: DSM 17245, CCUG 48084, CIP 107991, AIP 354-02

straininfo link

  • @ref: 75833
  • straininfo: 134303

literature

  • topic: Phylogeny
  • Pubmed-ID: 15388717
  • title: Oribacterium sinus gen. nov., sp. nov., within the family 'Lachnospiraceae' (phylum Firmicutes).
  • authors: Carlier JP, K'ouas G, Bonne I, Lozniewski A, Mory F
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63060-0
  • year: 2004
  • mesh: Bacterial Typing Techniques, Base Composition, Child, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA/genetics, Gram-Positive Bacteria/*classification/*isolation & purification/physiology/ultrastructure, Gram-Positive Bacterial Infections/*microbiology, Humans, Molecular Sequence Data, Movement, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sinusitis/*microbiology, Spores, Bacterial, Suppuration/*microbiology
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6852Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17245)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17245
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
31215Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2754128776041
38250Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5563
57977Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48084)https://www.ccug.se/strain?id=48084
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)
68380Automatically annotated from API rID32A
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)
75833Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134303.1StrainInfo: A central database for resolving microbial strain identifiers
122636Curators of the CIPCollection of Institut Pasteur (CIP 107991)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107991