Strain identifier

BacDive ID: 3041

Type strain: Yes

Species: Lancefieldella rimae

Strain Designation: D140H-11A

Strain history: CIP <- 2008, JCM <- I. Olsen, Oslo Univ, Norway <- DSM <- ATCC <- VPI D140H-11A: strain 10299

NCBI tax ID(s): 553184 (strain), 1383 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 2980

BacDive-ID: 3041

DSM-Number: 7090

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

description: Lancefieldella rimae D140H-11A is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from human gingival crevice.

NCBI tax id

NCBI tax idMatching level
553184strain
1383species

strain history

@refhistory
2980<- ATCC <- VPI, D140H-11A
67770DSM 7090 <-- ATCC 49626 <-- VPI D140H-11A.
122239CIP <- 2008, JCM <- I. Olsen, Oslo Univ, Norway <- DSM <- ATCC <- VPI D140H-11A: strain 10299

doi: 10.13145/bacdive3041.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Coriobacteriia
  • order: Coriobacteriales
  • family: Atopobiaceae
  • genus: Lancefieldella
  • species: Lancefieldella rimae
  • full scientific name: Lancefieldella rimae (Olsen et al. 1991) Nouioui et al. 2018

  • synonyms

    @refsynonym
    20215Lactobacillus rimae
    20215Atopobium rimae

@ref: 2980

domain: Bacteria

phylum: Actinobacteria

class: Coriobacteriia

order: Coriobacteriales

family: Atopobiaceae

genus: Lancefieldella

species: Lancefieldella rimae

full scientific name: Lancefieldella rimae (Olsen et al. 1991) Nouioui et al. 2018

strain designation: D140H-11A

type strain: yes

Morphology

cell morphology

  • @ref: 122239
  • gram stain: positive
  • cell shape: oval-shaped
  • motility: yes

colony morphology

  • @ref: 50459
  • incubation period: 2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2980PYG 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
37299MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
122239CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6
122239CIP Medium 10yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=10

culture temp

@refgrowthtypetemperaturerange
2980positivegrowth37mesophilic
37299positivegrowth37mesophilic
50459positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
2980anaerobe
50459anaerobe
122239anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12223917632nitrate-reduction
12223916301nitrite-reduction
6838016199urea-hydrolysis
6838029016arginine+hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
12223935581indoleno
6838035581indoleno

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole 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
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
122239oxidase-
122239catalase-1.11.1.6
122239urease-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
122239--++------++---+----

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
2980-+---++---------------+------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
2980human gingival crevice
50459Human gingival crevice
67770Human gingival crevices
122239Human, Gingival creviceOsloNorwayNOREurope1991

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Oral cavity and airways#Gingiva
#Host Body-Site#Oral cavity and airways#Tooth

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
29802Risk group (German classification)
1222391Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Atopobium rimae 16S ribosomal RNA gene, partial sequenceAF2923711445ena1383
2980A.rimae 16S rRNAX671491349ena1383
67770Atopobium rimae gene for 16S ribosomal RNA, partial sequence, strain: JCM 10299AB5409861474ena1383

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lancefieldella rimae ATCC 49626 SRR9217479-mag-bin.11GCA_905373575contigncbi553184
66792Atopobium rimae ATCC 49626553184.4wgspatric553184
66792Atopobium rimae ATCC 49626 strain SRR9217479-mag-bin.11553184.9wgspatric553184
66792Atopobium rimae strain DSM 70901383.3wgspatric1383
66792Atopobium rimae DSM 70902834436906draftimg1383
66792Atopobium rimae ATCC 49626643886019completeimg553184
67770Lancefieldella rimae ATCC 49626GCA_000174015contigncbi553184
67770Lancefieldella rimae DSM 7090GCA_001438885scaffoldncbi1383

GC content

@refGC-contentmethod
298045.0thermal denaturation, midpoint method (Tm)
6777045thermal denaturation, midpoint method (Tm)

External links

@ref: 2980

culture collection no.: DSM 7090, ATCC 49626, CCUG 31168, VPI D140H-11A, JCM 10299, CIP 109880, IFO 15546, LMG 11476, NBRC 15546, NCFB 2896

straininfo link

  • @ref: 72561
  • straininfo: 92323

literature

  • topic: Phylogeny
  • Pubmed-ID: 1854640
  • title: Lactobacillus uli sp. nov. and Lactobacillus rimae sp. nov. from the human gingival crevice and emended descriptions of lactobacillus minutus and Streptococcus parvulus.
  • authors: Olsen I, Johnson JL, Moore LV, Moore WE
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-41-2-261
  • year: 1991
  • mesh: Base Composition, DNA, Bacterial, Electrophoresis, Polyacrylamide Gel, Fatty Acids/metabolism, Gingival Pocket/*microbiology, Humans, Lactobacillus/*classification/genetics/isolation & purification/metabolism, Microbial Sensitivity Tests, Sequence Homology, Nucleic Acid, Streptococcus/*classification
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2980Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7090)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7090
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
37299Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7674
50459Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 31168)https://www.ccug.se/strain?id=31168
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
68382Automatically annotated from API zym
72561Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92323.1StrainInfo: A central database for resolving microbial strain identifiers
122239Curators of the CIPCollection of Institut Pasteur (CIP 109880)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109880