Strain identifier

BacDive ID: 229

Type strain: Yes

Species: Dolosicoccus paucivorans

Strain Designation: 2991-95

Strain history: CIP <- 1999, CCUG <- 1998, M.D. Collins, IFR, Reading, UK: strain Collins 2992-95 <- R.R. Facklam, CDC, Atlanta, USA <- Cleveland Clinical Micro. Ref. Lab.

NCBI tax ID(s): 84521 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6094

BacDive-ID: 229

DSM-Number: 15742

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

description: Dolosicoccus paucivorans 2991-95 is a microaerophile, mesophilic, Gram-positive human pathogen that was isolated from human blood, 78-yr-old male, pneumonia.

NCBI tax id

  • NCBI tax id: 84521
  • Matching level: species

strain history

@refhistory
6094<- CCUG <- M. D. Collins, IFR Reading <- R. R. Facklam, CDC <- Cleveland Clinical Micro. Ref. lab.
121635CIP <- 1999, CCUG <- 1998, M.D. Collins, IFR, Reading, UK: strain Collins 2992-95 <- R.R. Facklam, CDC, Atlanta, USA <- Cleveland Clinical Micro. Ref. Lab.

doi: 10.13145/bacdive229.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Aerococcaceae
  • genus: Dolosicoccus
  • species: Dolosicoccus paucivorans
  • full scientific name: Dolosicoccus paucivorans Collins et al. 1999

@ref: 6094

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Aerococcaceae

genus: Dolosicoccus

species: Dolosicoccus paucivorans

full scientific name: Dolosicoccus paucivorans Collins et al. 1999

strain designation: 2991-95

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
23251positiveovoid-shapedno
121635positivecoccus-shapedno

colony morphology

@reftype of hemolysishemolysis ability
23251alpha1
121635

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6094TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
6094COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
39491MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
121635CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
6094positivegrowth37mesophilic
23251nogrowth10psychrophilic
23251nogrowth45thermophilic
39491positivegrowth37mesophilic
54739positivegrowth37mesophilic
121635positivegrowth25-41
121635nogrowth10psychrophilic
121635nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6094microaerophile
23251facultative anaerobe
54739obligate aerobe
121635facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
23251NaClnomaximum6.5 %
121635NaClnogrowth6.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2325115361pyruvate-assimilation
2325123456cyclodextrin-builds acid from
2325116634raffinose-builds acid from
2325116443D-tagatose-builds acid from
2325117754glycerol-builds acid from
2325128087glycogen-builds acid from
2325115443inulin-builds acid from
2325130849L-arabinose-builds acid from
2325118403L-arabitol-builds acid from
2325117266L-sorbose-builds acid from
2325117306maltose-builds acid from
232516731melezitose-builds acid from
2325128053melibiose-builds acid from
23251320055methyl beta-D-glucopyranoside-builds acid from
23251506227N-acetylglucosamine-builds acid from
2325127941pullulan-builds acid from
2325133942ribose-builds acid from
2325130911sorbitol-builds acid from
2325117992sucrose-builds acid from
2325127082trehalose-builds acid from
232514853esculin-hydrolysis
23251606565hippurate-hydrolysis
2325128017starch-hydrolysis
2325116634raffinose+builds acid from
2325133942ribose+builds acid from
2325117992sucrose+builds acid from
2325117716lactose+/-builds acid from
2325117306maltose+/-builds acid from
2325129864mannitol+/-builds acid from
1216354853esculin-hydrolysis
121635606565hippurate-hydrolysis
12163517632nitrate-reduction
12163516301nitrite-reduction
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose+fermentation
6837965327D-xylose+fermentation
6837916899D-mannitol+fermentation
6837917306maltose+fermentation
6837917716lactose+fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation
6837516199urea-hydrolysis
6837529016arginine-hydrolysis
6837518257ornithine-degradation
683754853esculin-hydrolysis
6837517634D-glucose-fermentation
6837515824D-fructose-fermentation
6837516024D-mannose-fermentation
6837517306maltose-fermentation
6837517716lactose-fermentation
6837527082trehalose-fermentation
6837516899D-mannitol-fermentation
6837516634raffinose-fermentation
6837516988D-ribose-fermentation
6837517057cellobiose-fermentation
6837517632nitrate-reduction
6837517992sucrose-fermentation
6837559640N-acetylglucosamine-fermentation
6837532528turanose-fermentation
6837522599arabinose-fermentation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.
2325128001vancomycinyesyes
6837528368novobiocinyesyes1.8 µg

metabolite production

@refChebi-IDmetaboliteproduction
2325152071dextranno
2325115688acetoinno
6837515688acetoinno
12163535581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-test
6837515688acetoin-
12163515688acetoin-

enzymes

@refvalueactivityec
23251acid phosphatase+3.1.3.2
23251alkaline phosphatase-3.1.3.1
23251alpha-fucosidase-3.2.1.51
23251alpha-galactosidase-3.2.1.22
23251alpha-glucosidase-3.2.1.20
23251alpha-mannosidase-3.2.1.24
23251arginine dihydrolase-3.5.3.6
23251beta-glucuronidase-3.2.1.31
23251beta-mannosidase-3.2.1.25
23251catalase-1.11.1.6
23251chymotrypsin-3.4.4.5
23251cystine arylamidase-3.4.11.3
23251cytochrome oxidase-1.9.3.1
23251esterase (C 4)+/-
23251esterase lipase (C 8)+/-
23251glycyl tryptophan arylamidase-
23251leucine arylamidase-3.4.11.1
23251lipase (C 14)-
23251N-acetyl-beta-glucosaminidase-3.2.1.52
23251pyroglutamic acid arylamidase+
23251tripeptide aminopeptidase-3.4.11.4
23251trypsin-3.4.21.4
23251urease-3.5.1.5
23251valine arylamidase-
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
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
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)+
68382alkaline phosphatase+3.1.3.1
68375beta-glucuronidase-3.2.1.31
68375pyrrolidonyl arylamidase+3.4.19.3
68375alkaline phosphatase-3.1.3.1
68375L-arginine arylamidase-
68375beta-galactosidase-3.2.1.23
68375beta-glucosidase-3.2.1.21
68375ornithine decarboxylase-4.1.1.17
68375arginine dihydrolase-3.5.3.6
68375urease-3.5.1.5
68379catalase-1.11.1.6
68379gelatinase-
68379urease-3.5.1.5
68379beta-glucosidase-3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase-3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase+3.5.1.B15
121635oxidase-
121635beta-galactosidase-3.2.1.23
121635alcohol dehydrogenase-1.1.1.1
121635catalase+1.11.1.6
121635gamma-glutamyltransferase-2.3.2.2
121635lysine decarboxylase-4.1.1.18
121635ornithine decarboxylase-4.1.1.17
121635urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYGCAT
54739-+++--------+++++++--

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
54739-+++------+---------
121635-+-+------++---+----

API ID32STA

@refUREADH ArgODCESCGLUFRUMNEMALLACTREMANRAFRIBCELNITVPbeta GALArgAPALPyrANOVOSACNAGTURARAbeta GUR
54739-------------------+------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic locationisolation date
6094human blood, 78-yr-old male, pneumoniaUSAUSANorth America
54739Human blood,78-yr-old male,pneumoniaUSAUSANorth America1995Cleveland
121635Human, BloodUnited States of AmericaUSANorth AmericaCleveland, Ohio1995

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host#Human#Male
#Host Body-Site#Oral cavity and airways#Lung
#Host Body Product#Fluids#Blood

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
6094yes, in single cases1Risk group (German classification)
1216351Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6094
  • description: Streptococcus sp. 16S rRNA gene, isolate 2992-95
  • accession: AJ012666
  • length: 1510
  • database: ena
  • NCBI tax ID: 84521

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dolosicoccus paucivorans DSM 15742GCA_900100125contigncbi84521
66792Dolosicoccus paucivorans strain DSM 1574284521.3wgspatric84521
66792Dolosicoccus paucivorans DSM 157422622736585draftimg84521

GC content

  • @ref: 23251
  • GC-content: 40.5
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno97.13yes
flagellatedno98.774yes
gram-positiveyes93.57yes
anaerobicno95.504yes
halophileyes91.992no
spore-formingno96.162no
thermophileno94.303no
glucose-utilyes88.118no
aerobicno95.575no
glucose-fermentyes89.469no

External links

@ref: 6094

culture collection no.: DSM 15742, ATCC BAA 56, CCM 4936, CIP 106314, CCUG 39307

straininfo link

  • @ref: 69912
  • straininfo: 44275

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10555324Dolosicoccus paucivorans gen. nov., sp. nov., isolated from human blood.Collins MD, Rodriguez Jovita M, Hutson RA, Falsen E, Sjoden B, Facklam RRInt J Syst Bacteriol10.1099/00207713-49-4-14391999Bacteremia/microbiology, Bacterial Typing Techniques, Blood/*microbiology, Catalase/metabolism, Genes, rRNA, Gram-Positive Bacterial Infections/*microbiology, Gram-Positive Cocci/*classification/*genetics/isolation & purification/physiology, Humans, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Phylogeny34181136Reclassification of Facklamia ignava, Facklamia sourekii and Facklamia tabacinasalis as Falseniella ignava gen. nov., comb. nov., Hutsoniella sourekii gen. nov., comb. nov., and Ruoffia tabacinasalis gen. nov., comb. nov., and description of Ruoffia halotolerans sp. nov., isolated from hypersaline Inland Sea of Qatar.Fotedar R, Sankaranarayanan K, Caldwell ME, Zeyara A, Al Malki A, Kaul R, Al Shamari H, Ali M, Al Marri M, Lawson PAAntonie Van Leeuwenhoek10.1007/s10482-021-01587-72021*Aerococcaceae, Bacterial Typing Techniques, DNA, Bacterial/genetics, Phospholipids/analysis, Phylogeny, Qatar, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6094Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15742)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15742
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
23251Matthew D. Collins, Mar Rodriguez Jovita, Roger A. Hutson, Enevold Falsen, Berit Sjödén, Richard R. Facklam10.1099/00207713-49-4-1439Dolosicoccus paucivorans gen. nov., sp. nov., isolated from human bloodIJSEM 49: 1439-1442 199910555324
39491Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18431
54739Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 39307)https://www.ccug.se/strain?id=39307
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
68375Automatically annotated from API ID32STA
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
69912Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44275.1StrainInfo: A central database for resolving microbial strain identifiers
121635Curators of the CIPCollection of Institut Pasteur (CIP 106314)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106314