Strain identifier

BacDive ID: 135725

Type strain: Yes

Species: Dolosigranulum pigrum

Strain Designation: R-91/1468, R91/1468

Strain history: CIP <- 1997, NCFB <- PHLS: strain R91/1468

NCBI tax ID(s): 883103 (strain), 29394 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.2:
version 9.1:
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 9.3 (current version)

General

@ref: 34923

BacDive-ID: 135725

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive

description: Dolosigranulum pigrum R-91/1468 is an anaerobe, mesophilic, Gram-positive bacterium of the family Carnobacteriaceae.

NCBI tax id

NCBI tax idMatching level
29394species
883103strain

strain history

@refhistory
67771<- CIP <- NCFB 2975 <- Public Health Labs, Colindale, UK <- FW Gay, R91/1468
34923CIP <- 1997, NCFB <- PHLS: strain R91/1468

doi: 10.13145/bacdive135725.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Carnobacteriaceae
  • genus: Dolosigranulum
  • species: Dolosigranulum pigrum
  • full scientific name: Dolosigranulum pigrum Aguirre et al. 1994

@ref: 34923

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Carnobacteriaceae

genus: Dolosigranulum

species: Dolosigranulum pigrum

strain designation: R-91/1468, R91/1468

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
67771positive
34923positivecoccus-shapedno

colony morphology

  • @ref: 34923

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
34923MEDIUM 74 - for Dolosigranulum pigrumyesDistilled water make up to (1000.000 ml);Todd hewitt broth (30.000 g)
34923CIP Medium 90yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=90

culture temp

@refgrowthtypetemperature
34923positivegrowth37
51495positivegrowth37
34923positivegrowth25-30
34923nogrowth10
34923nogrowth37
34923nogrowth41
34923nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
51495anaerobe
51495microaerophile
67771anaerobe
34923facultative anaerobe
125439facultative anaerobe97.6

halophily

  • @ref: 34923
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: 6.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
349234853esculin-hydrolysis
34923606565hippurate-hydrolysis
3492317632nitrate-reduction
3492316301nitrite-reduction

metabolite production

  • @ref: 34923
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 34923
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
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
34923oxidase-
34923beta-galactosidase+3.2.1.23
34923alcohol dehydrogenase-1.1.1.1
34923catalase-1.11.1.6
34923gamma-glutamyltransferase-2.3.2.2
34923lysine decarboxylase-4.1.1.18
34923urease-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
34923--++-+---+++-----+--

Isolation, sampling and environmental information

isolation

@refcountryorigin.countrycontinentsample typegeographic locationisolation date
34923United KingdomGBREurope
51495United KingdomGBREuropeHuman spinal cord,removed at autopsyColchester
67771United KingdomGBREuropeFrom human spinal cord, removed at autopsyColchester
34923United KingdomGBREuropeHuman, Acute multiple sclerosisColchester General Hospital1988

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Organ#Spinal Cord
#Host#Human

taxonmaps

  • @ref: 69479
  • File name: preview.99_1916.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_27;96_1072;97_1252;98_1504;99_1916&stattab=map
  • Last taxonomy: Dolosigranulum pigrum subclade
  • 16S sequence: GU395995
  • Sequence Identity:
  • Total samples: 33246
  • soil counts: 1684
  • aquatic counts: 2385
  • animal counts: 28449
  • plant counts: 728

Safety information

risk assessment

  • @ref: 34923
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
67771Dolosigranulum pigrum strain 33929-06 16S ribosomal RNA gene, partial sequenceGU3959951375nuccore29394
124043Dolosigranulum pigrum gene for 16S rRNA, partial sequence, strain: NBRC 15550.AB6809001472nuccore29394
124043Dolosigranulum pigrum NBRC 15550 gene for 16S rRNA, partial sequence.LC752391588nuccore29394
124043D.pigrum 16S rRNA gene (partial)X709071523nuccore29394

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dolosigranulum pigrum ATCC 51524GCA_000245815scaffoldncbi883103
66792Dolosigranulum pigrum ATCC 51524883103.3wgspatric883103
66792Dolosigranulum pigrum ATCC 515242513237341draftimg883103

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes89.299no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no87.121no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no91.507yes
125438spore-formingspore-formingAbility to form endo- or exosporesno81.565no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno92.453yes
125438motile2+flagellatedAbility to perform flagellated movementno86.5no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes87.6
125439BacteriaNetmotilityAbility to perform movementyes60.1
125439BacteriaNetgram_stainReaction to gram-stainingvariable72.4
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthfacultative anaerobe97.6

External links

@ref: 34923

culture collection no.: CIP 104051, ATCC 51524, IFO 15550, NCFB 2975, LMG 19521, KCTC 15002, CCUG 33392, LMG 15126, NBRC 15550, NCIMB 702975

straininfo link

  • @ref: 93023
  • straininfo: 8240

literature

  • topic: Phylogeny
  • Pubmed-ID: 8294309
  • title: Phenotypic and phylogenetic characterization of some Gemella-like organisms from human infections: description of Dolosigranulum pigrum gen. nov., sp. nov.
  • authors: Aguirre M, Morrison D, Cookson BD, Gay FW, Collins MD
  • journal: J Appl Bacteriol
  • DOI: 10.1111/j.1365-2672.1993.tb01602.x
  • year: 1993
  • mesh: Base Sequence, DNA Primers, DNA, Bacterial/analysis, Gram-Positive Bacteria/*classification/genetics/isolation & purification, Gram-Positive Bacterial Infections/*microbiology, Humans, Molecular Sequence Data, Phenotype, *Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/*genetics
  • topic2: Pathogenicity

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
34923Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104051Collection of Institut Pasteur (CIP 104051)
51495Curators of the CCUGhttps://www.ccug.se/strain?id=33392Culture Collection University of Gothenburg (CCUG) (CCUG 33392)
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
93023Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID8240.1
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG