Strain identifier
BacDive ID: 3040
Type strain:
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)
General
@ref: 8840
BacDive-ID: 3040
DSM-Number: 20469
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic
description: Lancefieldella parvula 1246 is an anaerobe, mesophilic bacterium that was isolated from Human gingival crevices.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1382 | species |
521095 | strain |
strain history
@ref | history |
---|---|
8840 | <- VPI, 0546 <- A.R. Prévot, 1246 |
67770 | DSM 20469 <-- VPI 0546 <-- A. R. Prévot 1246. |
121601 | 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 |
doi: 10.13145/bacdive3040.20230509.8.1
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 parvula
- full scientific name: Lancefieldella parvula (Weinberg et al. 1937) Nouioui et al. 2018
synonyms
@ref synonym 20215 Peptostreptococcus parvulus 20215 Streptococcus parvulus 20215 Atopobium parvulum
@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
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | no | 90.383 | ||
69480 | 99.719 | positive | ||
121601 | no | positive | oval-shaped |
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
@ref | name | growth | link | composition |
---|---|---|---|---|
8840 | PYG MEDIUM (MODIFIED) (DSMZ Medium 104) | yes | https://mediadive.dsmz.de/medium/104 | Name: 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 |
36589 | MEDIUM 6 - Columbia agar with 10 % horse blood | yes | Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml) | |
121601 | CIP Medium 6 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6 | |
121601 | CIP Medium 31 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=31 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8840 | positive | growth | 37 | mesophilic |
36589 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
121601 | positive | growth | 30-37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
8840 | anaerobe | |
69480 | anaerobe | 99.413 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.999 |
murein
- @ref: 8840
- murein short key: A11.31
- type: A4alpha L-Lys-D-Asp
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
121601 | 17632 | nitrate | - | reduction |
121601 | 16301 | nitrite | - | reduction |
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16634 | raffinose | - | fermentation |
68380 | 29985 | L-glutamate | - | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | - | energy source |
metabolite production
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | indole test | voges-proskauer-test |
---|---|---|---|---|
68380 | 35581 | indole | - | |
121601 | 15688 | acetoin | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68380 | glutamyl-glutamate arylamidase | - | |
68380 | leucyl glycin arylamidase | - | 3.4.11.1 |
68380 | proline-arylamidase | - | 3.4.11.5 |
68380 | alkaline phosphatase | - | 3.1.3.1 |
68380 | tryptophan deaminase | - | 4.1.99.1 |
68380 | alpha-fucosidase | - | 3.2.1.51 |
68380 | glutamate decarboxylase | - | 4.1.1.15 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-arabinosidase | - | 3.2.1.55 |
68380 | beta-Galactosidase 6-phosphate | - | |
68380 | beta-galactosidase | + | 3.2.1.23 |
68380 | alpha-galactosidase | - | 3.2.1.22 |
68380 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
121601 | oxidase | - | |
121601 | alcohol dehydrogenase | - | 1.1.1.1 |
121601 | catalase | - | 1.11.1.6 |
121601 | lysine decarboxylase | - | 4.1.1.18 |
121601 | ornithine decarboxylase | - | 4.1.1.17 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121601 | - | - | + | + | - | + | - | - | - | - | + | + | - | - | - | + | - | - | - | - |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
8840 | - | - | - | + | - | - | - | - | - | +/- | - | - | - | - | - | - | - | + | - | - | +/- | +/- | +/- | + | +/- | +/- | +/- | - | +/- |
8840 | - | - | - | + | - | + | + | - | - | - | + | - | - | - | - | - | - | +/- | - | - | +/- | +/- | - | +/- | - | - | +/- | - | +/- |
Isolation, sampling and environmental information
isolation
@ref | sample type | isolation date |
---|---|---|
67770 | Human gingival crevices | |
121601 | Human, Gingival crevices | 1992 |
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
@ref | biosafety level | biosafety level comment |
---|---|---|
8840 | 2 | Risk group (German classification) |
121601 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Atopobium parvulum 16S ribosomal RNA gene, partial sequence | AF292372 | 1425 | ena | 521095 |
8840 | A.parvulum 16S rRNA | X67150 | 1348 | ena | 1382 |
67770 | Atopobium parvulum gene for 16S ribosomal RNA, partial sequence, strain: JCM 10300 | AB558168 | 1473 | ena | 521095 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Lancefieldella parvula DSM 20469 | GCA_000024225 | complete | ncbi | 521095 |
66792 | Lancefieldella parvulum DSM 20469 SRR9217392-mag-bin.20 | GCA_905371835 | contig | ncbi | 521095 |
66792 | Atopobium parvulum DSM 20469 | 521095.6 | complete | patric | 521095 |
66792 | Atopobium parvulum DSM 20469 strain SRR9217392-mag-bin.20 | 521095.16 | wgs | patric | 521095 |
66792 | Lancefieldella parvulum DSM 20469 | 644736327 | complete | img | 521095 |
GC content
@ref | GC-content | method |
---|---|---|
8840 | 44.0 | |
67770 | 53 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 93.024 | no |
flagellated | no | 97.953 | no |
gram-positive | yes | 87.009 | no |
anaerobic | yes | 98.64 | yes |
aerobic | no | 97.931 | no |
halophile | no | 75.65 | no |
spore-forming | no | 96.335 | no |
thermophile | no | 77.471 | yes |
glucose-util | yes | 87.674 | no |
glucose-ferment | yes | 78.687 | no |
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
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
8840 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20469) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20469 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
36589 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/14715 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68380 | Automatically annotated from API rID32A | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
72560 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID92324.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121601 | Curators of the CIP | Collection of Institut Pasteur (CIP 102970) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102970 |