Strain identifier

BacDive ID: 3040

Type strain: Yes

Species: Lancefieldella parvula

Strain Designation: 1246

Strain history: CIP <- 2008, JCM <- M.D. Collins: strain JCM 10300, 1987, ATCC <- E.P. Cato: strain VPI 0546 <- A.R. Prévot, Inst. Pasteur, Paris, France: strain 1246, Streptococcus parvulus

NCBI tax ID(s): 521095 (strain), 1382 (species)

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General

@ref: 8840

BacDive-ID: 3040

DSM-Number: 20469

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

description: Lancefieldella parvula 1246 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from Human gingival crevices.

NCBI tax id

NCBI tax idMatching level
1382species
521095strain

strain history

@refhistory
8840<- VPI, 0546 <- A.R. Prévot, 1246
67770DSM 20469 <-- VPI 0546 <-- A. R. Prévot 1246.
121601CIP <- 2008, JCM <- M.D. Collins: strain JCM 10300, 1987, ATCC <- E.P. Cato: strain VPI 0546 <- A.R. Prévot, Inst. Pasteur, Paris, France: strain 1246, Streptococcus parvulus

doi: 10.13145/bacdive3040.20250331.9.3

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 parvula
  • full scientific name: Lancefieldella parvula (Weinberg et al. 1937) Nouioui et al. 2018

  • synonyms

    @refsynonym
    20215Streptococcus parvulus
    20215Atopobium parvulum
    20215Peptostreptococcus parvulus

@ref: 8840

domain: Bacteria

phylum: Actinobacteria

class: Coriobacteriia

order: Coriobacteriales

family: Atopobiaceae

genus: Lancefieldella

species: Lancefieldella parvula

full scientific name: Lancefieldella parvula (Weinberg et al. 1937) Nouioui et al. 2018

strain designation: 1246

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
121601positiveoval-shapedno
125439negative99.9
125438no95

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_20469_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8840PYG 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
36589MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
121601CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6
121601CIP Medium 31yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=31

culture temp

@refgrowthtypetemperature
8840positivegrowth37
36589positivegrowth37
67770positivegrowth37
121601positivegrowth30-37

Physiology and metabolism

oxygen tolerance

  • @ref: 8840
  • oxygen tolerance: anaerobe

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 99.9

murein

  • @ref: 8840
  • murein short key: A11.31
  • type: A4alpha L-Lys-D-Asp

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838027897tryptophan-energy source
6838017632nitrate-reduction
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
12160117632nitrate-reduction
12160116301nitrite-reduction
6838029016arginine-hydrolysis
6838016199urea-hydrolysis

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6838035581indole-
12160115688acetoin-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
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
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382lipase (C 14)-
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382alkaline phosphatase-3.1.3.1
121601oxidase-
121601alcohol dehydrogenase-1.1.1.1
121601catalase-1.11.1.6
121601lysine decarboxylase-4.1.1.18
121601ornithine decarboxylase-4.1.1.17
68380glutamyl-glutamate arylamidase-
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
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

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121601--++-+----++---+----

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8840---+-----+/--------+--+/-+/-+/-++/-+/-+/--+/-
8840---+-++---+------+/---+/-+/--+/---+/--+/-

Isolation, sampling and environmental information

isolation

@refsample typeisolation date
67770Human gingival crevices
121601Human, Gingival crevices1992

taxonmaps

  • @ref: 69479
  • File name: preview.99_4091.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_150;96_2076;97_2501;98_3094;99_4091&stattab=map
  • Last taxonomy: Lancefieldella parvula subclade
  • 16S sequence: X67150
  • Sequence Identity:
  • Total samples: 161047
  • soil counts: 2274
  • aquatic counts: 2818
  • animal counts: 154946
  • plant counts: 1009

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
88402Risk group (German classification)
1216011Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Atopobium parvulum 16S ribosomal RNA gene, partial sequenceAF2923721425nuccore521095
8840A.parvulum 16S rRNAX671501348nuccore1382
67770Atopobium parvulum gene for 16S ribosomal RNA, partial sequence, strain: JCM 10300AB5581681473nuccore521095

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Lancefieldella parvula DSM 20469GCA_000024225completencbi521095
66792Lancefieldella parvulum DSM 20469 SRR9217392-mag-bin.20GCA_905371835contigncbi521095
66792Atopobium parvulum DSM 20469521095.6completepatric521095
66792Atopobium parvulum DSM 20469 strain SRR9217392-mag-bin.20521095.16wgspatric521095
66792Lancefieldella parvulum DSM 20469644736327completeimg521095

GC content

@refGC-contentmethod
884044.0
6777053thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes85.441no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes87.192yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no96.933yes
125438spore-formingspore-formingAbility to form endo- or exosporesno80.883no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno91.06yes
125438motile2+flagellatedAbility to perform flagellated movementno95no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.9
125439BacteriaNetmotilityAbility to perform movementyes82.2
125439BacteriaNetgram_stainReaction to gram-stainingnegative99.9
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe65.6

External links

@ref: 8840

culture collection no.: CCUG 32760, CIP 102970, DSM 20469, ATCC 33793, VPI 0546, JCM 10300, KCTC 3663

straininfo link

  • @ref: 72560
  • straininfo: 92324

literature

  • topic: Enzymology
  • Pubmed-ID: 22405584
  • title: Antimicrobial activity of Streptococcus salivarius K12 on bacteria involved in oral malodour.
  • authors: Masdea L, Kulik EM, Hauser-Gerspach I, Ramseier AM, Filippi A, Waltimo T
  • journal: Arch Oral Biol
  • DOI: 10.1016/j.archoralbio.2012.02.011
  • year: 2012
  • mesh: Actinobacteria/*growth & development/isolation & purification, Administration, Oral, Bacterial Proteins/pharmacology, Bacteriocins/pharmacology, Eubacterium/growth & development/isolation & purification, Gram-Positive Bacteria/growth & development/isolation & purification, Halitosis/*microbiology/*prevention & control, Humans, In Vitro Techniques, Linear Models, Microbial Sensitivity Tests, Probiotics/*pharmacology, Streptococcus/*physiology
  • topic2: Phylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8840Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20469)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20469
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
36589Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14715
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
72560Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92324.1StrainInfo: A central database for resolving microbial strain identifiers
121601Curators of the CIPCollection of Institut Pasteur (CIP 102970)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102970
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1