Strain identifier
BacDive ID: 12643
Type strain:
Species: Propionibacterium freudenreichii
Strain Designation: E11.1
Strain history: CIP <- 1987, NCIB <- 1950, ATCC <- R. J. Williams: strain E11.1, Propionibacterium shermanii <- C. B. van Niel: strain VPI 0405
NCBI tax ID(s): 1752 (subspecies)
General
@ref: 1869
BacDive-ID: 12643
DSM-Number: 4902
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, rod-shaped
description: Propionibacterium freudenreichii E11.1 is an anaerobe, mesophilic, Gram-positive bacterium of the family Propionibacteriaceae.
NCBI tax id
- NCBI tax id: 1752
- Matching level: subspecies
strain history
@ref | history |
---|---|
1869 | <- ATCC <- R.J. Williams, E11.1 (Propionibacterium shermanii) <- C.B. Van Niel |
119456 | CIP <- 1987, NCIB <- 1950, ATCC <- R. J. Williams: strain E11.1, Propionibacterium shermanii <- C. B. van Niel: strain VPI 0405 |
doi: 10.13145/bacdive12643.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Propionibacteriales
- family: Propionibacteriaceae
- genus: Propionibacterium
- species: Propionibacterium freudenreichii
- full scientific name: Propionibacterium freudenreichii van Niel 1928 (Approved Lists 1980)
synonyms
@ref synonym 20215 Propionibacterium shermanii 20215 Propionibacterium freudenreichii subsp. shermanii
@ref: 1869
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Propionibacteriaceae
genus: Propionibacterium
species: Propionibacterium freudenreichii
full scientific name: Propionibacterium freudenreichii van Niel 1928 emend. Nouioui et al. 2018
strain designation: E11.1
type strain: no
Morphology
cell morphology
- @ref: 119456
- gram stain: positive
- cell shape: rod-shaped
- motility: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
1869 | 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 |
41657 | MEDIUM 20 - for Anaerobic bacteria | yes | Agar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml) | |
119456 | CIP Medium 20 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
1869 | positive | growth | 30 | mesophilic |
41657 | positive | growth | 37 | mesophilic |
53417 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
1869 | anaerobe |
53417 | anaerobe |
119456 | anaerobe |
murein
- @ref: 1869
- murein short key: A31
- type: A1gamma m-Dpm-direct
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
119456 | 17632 | nitrate | - | reduction |
119456 | 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 | Chebi-ID | metabolite | production |
---|---|---|---|
119456 | 35581 | indole | no |
68380 | 35581 | indole | no |
metabolite tests
- @ref: 68380
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68380 | serine arylamidase | + | |
68380 | glutamyl-glutamate arylamidase | - | |
68380 | histidine arylamidase | + | |
68380 | tyrosine arylamidase | + | |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | leucine arylamidase | + | 3.4.11.1 |
68380 | phenylalanine arylamidase | + | |
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 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-arabinosidase | - | 3.2.1.55 |
68380 | beta-glucosidase | - | 3.2.1.21 |
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 |
119456 | oxidase | - | |
119456 | catalase | + | 1.11.1.6 |
119456 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | - | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
fatty acid profile
fatty acids
@ref fatty acid percentage ECL 53417 C14:0 0.7 14 53417 C15:0 3.8 15 53417 C16:0 5.8 16 53417 C17:0 5.4 17 53417 C18:0 0.7 18 53417 C13:0 3OH/C15:1 i I/H 0.3 14.469 53417 C14:0 2OH 2.1 15.205 53417 C14:0 3OH/C16:1 ISO I 1.2 15.485 53417 C14:0 ISO 0.4 13.618 53417 C14:0 ISO 3OH 0.4 15.117 53417 C15:0 ANTEISO 44.9 14.711 53417 C15:0 ISO 3.3 14.621 53417 C16:0 iso 1.3 15.626 53417 C17:0 anteiso 9.6 16.722 53417 C17:0 ANTEISO DMA 4.8 17.195 53417 C17:0 iso 1.1 16.629 53417 C17:1 ISO I/C16:0 DMA 4.8 16.481 53417 C18:1 ISO H 2.7 17.46 53417 C18:1 ω9c 1.2 17.769 53417 C18:2 ω6,9c/C18:0 ANTE 2.5 17.724 53417 Unidentified 0.8 14.953 53417 Unidentified 0.9 15.683 53417 Unidentified 0.4 16.108 53417 Unidentified 0.8 17.105 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119456 | - | - | + | - | - | + | - | - | - | - | - | - | - | + | - | + | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1869 | - | - | - | + | - | +/- | - | - | - | - | - | - | - | - | - | - | - | + | + | - | + | + | - | + | +/- | + | + | - | + |
1869 | - | - | - | + | - | +/- | - | - | - | - | - | - | - | - | - | - | - | + | + | + | + | + | - | + | + | + | + | - | + |
1869 | - | - | - | + | - | + | - | - | - | - | +/- | - | - | - | - | - | - | +/- | + | - | + | + | - | + | - | - | + | - | + |
1869 | - | - | - | + | - | + | - | - | - | - | +/- | - | - | - | - | - | - | +/- | + | - | + | + | - | + | - | +/- | + | - | + |
Isolation, sampling and environmental information
taxonmaps
- @ref: 69479
- File name: preview.99_271.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15360;96_190;97_206;98_230;99_271&stattab=map
- Last taxonomy: Propionibacterium freudenreichii subclade
- 16S sequence: Y10819
- Sequence Identity:
- Total samples: 21525
- soil counts: 2003
- aquatic counts: 4110
- animal counts: 15016
- plant counts: 396
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
1869 | 1 | Risk group (German classification) |
119456 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Propionibacterium freudenreichii subsp. shermanii 16S-23S ribosomal RNA intergenic spacer region, complete sequence | AF218434 | 338 | ena | 1752 |
1869 | P. freudenreichii subsp. shermanii partial 16S rRNA, 23S rRNA and 5S rRNA genes plus ITS | Y10819 | 5116 | ena | 1744 |
1869 | Propionibacterium freudenreichii subsp. shermanii strain CIP 103027 16S ribosomal RNA gene, partial sequence | AY883041 | 459 | ena | 1752 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Propionibacterium freudenreichii strain PFRJS-23 | 1744.122 | complete | patric | 1744 |
66792 | Propionibacterium freudenreichii strain PFRJS11 | 1744.109 | complete | patric | 1744 |
66792 | Propionibacterium freudenreichii strain PFRJS12 | 1744.108 | complete | patric | 1744 |
66792 | Propionibacterium freudenreichii strain PFRJS12-1 | 1744.105 | complete | patric | 1744 |
66792 | Propionibacterium freudenreichii strain PFRJS12-3 | 1744.142 | complete | patric | 1744 |
66792 | Propionibacterium freudenreichii strain PFRJS13 | 1744.117 | complete | patric | 1744 |
66792 | Propionibacterium freudenreichii strain PFRJS14 | 1744.107 | complete | patric | 1744 |
66792 | Propionibacterium freudenreichii strain PFRJS15 | 1744.120 | complete | patric | 1744 |
66792 | Propionibacterium freudenreichii strain PFRJS17 | 1744.121 | complete | patric | 1744 |
66792 | Propionibacterium freudenreichii strain PFRJS18 | 1744.113 | complete | patric | 1744 |
66792 | Propionibacterium freudenreichii strain PFRJS2 | 1744.112 | complete | patric | 1744 |
66792 | Propionibacterium freudenreichii strain PFRJS20 | 1744.118 | complete | patric | 1744 |
66792 | Propionibacterium freudenreichii strain PFRJS21 | 1744.119 | complete | patric | 1744 |
66792 | Propionibacterium freudenreichii strain PFRJS22 | 1744.141 | complete | patric | 1744 |
66792 | Propionibacterium freudenreichii strain PFRJS22-genome | 1744.106 | complete | patric | 1744 |
66792 | Propionibacterium freudenreichii strain PFRJS25 | 1744.104 | complete | patric | 1744 |
66792 | Propionibacterium freudenreichii strain PFRJS4 | 1744.111 | complete | patric | 1744 |
66792 | Propionibacterium freudenreichii strain PFRJS7 | 1744.116 | complete | patric | 1744 |
66792 | Propionibacterium freudenreichii strain PFRJS8 | 1744.110 | complete | patric | 1744 |
66792 | Propionibacterium freudenreichii strain PFRJS9 | 1744.123 | complete | patric | 1744 |
GC content
- @ref: 1869
- GC-content: 65.0
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 93.486 | no |
gram-positive | yes | 91.337 | no |
anaerobic | yes | 68.906 | yes |
aerobic | no | 91.789 | yes |
halophile | no | 87.115 | no |
spore-forming | no | 91.923 | no |
thermophile | no | 70.707 | yes |
glucose-util | yes | 88.875 | no |
flagellated | no | 98.074 | no |
glucose-ferment | yes | 76.45 | no |
External links
@ref: 1869
culture collection no.: DSM 4902, ATCC 9614, NCDO 853, NCIB 8099, CCUG 36819, VPI 0405, CIP 103027, NCIMB 8099
straininfo link
- @ref: 81856
- straininfo: 8663
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 9097423 | Identification and quantification of Bifidobacterium species isolated from food with genus-specific 16S rRNA-targeted probes by colony hybridization and PCR. | Kaufmann P, Pfefferkorn A, Teuber M, Meile L | Appl Environ Microbiol | 10.1128/aem.63.4.1268-1273.1997 | 1997 | Bacterial Typing Techniques, Bifidobacterium/classification/genetics/*isolation & purification, DNA Probes, *Food Microbiology, Molecular Probe Techniques, Molecular Sequence Data, Polymerase Chain Reaction, RNA, Bacterial/*analysis/genetics, RNA, Ribosomal, 16S/*analysis/genetics | Biotechnology |
Enzymology | 10795576 | Isolation and characterization of proline iminopeptidase from Propionibacterium freudenreichii ATCC 9614. | Stepaniak L | Nahrung | 10.1002/(SICI)1521-3803(20000301)44:2<102::AID-FOOD102>3.0.CO;2-Z | 2000 | Aminopeptidases/chemistry/*isolation & purification/metabolism, Bacterial Proteins/analysis, Chromatography, High Pressure Liquid, Cytoplasm/enzymology, Electrophoresis, Polyacrylamide Gel, Hydrogen-Ion Concentration, Indicators and Reagents, Isoelectric Point, Molecular Weight, Propionibacterium/*enzymology, Substrate Specificity, Temperature | Phylogeny |
Genetics | 15507000 | In silico exploration of the fructose-6-phosphate phosphorylation step in glycolysis: genomic evidence of the coexistence of an atypical ATP-dependent along with a PPi-dependent phosphofructokinase in Propionibacterium freudenreichii subsp. shermanii. | Meurice G, Deborde C, Jacob D, Falentin H, Boyaval P, Dimova D | In Silico Biol | 2004040043 | 2004 | Adenosine Triphosphate/metabolism, Amino Acid Sequence, Computational Biology, Evolution, Molecular, Fructosephosphates/*metabolism, Genome, Bacterial, Genomics, Glycolysis/genetics, Molecular Sequence Data, Phosphorylation, Phosphotransferases/*genetics/*metabolism, Phosphotransferases (Alcohol Group Acceptor)/classification/genetics, Phylogeny, Propionibacterium/*enzymology/genetics/metabolism, Sequence Alignment, Sequence Homology, Amino Acid | Metabolism |
16347134 | Utilization of Lactate Isomers by Propionibacterium freudenreichii subsp. shermanii: Regulatory Role for Intracellular Pyruvate. | Crow VL | Appl Environ Microbiol | 10.1128/aem.52.2.352-358.1986 | 1986 | |||
Enzymology | 16347414 | Properties of Alanine Dehydrogenase and Aspartase from Propionibacterium freudenreichii subsp. shermanii. | Crow VL | Appl Environ Microbiol | 10.1128/aem.53.8.1885-1892.1987 | 1987 | ||
Metabolism | 19118369 | Mechanism of conjugated linoleic acid and vaccenic acid formation in human faecal suspensions and pure cultures of intestinal bacteria. | McIntosh FM, Shingfield KJ, Devillard E, Russell WR, Wallace RJ | Microbiology (Reading) | 10.1099/mic.0.022921-0 | 2009 | Adult, Butyrivibrio/*growth & development/isolation & purification/metabolism, Culture Media/metabolism, Feces/chemistry/*microbiology, Gram-Positive Bacteria/*growth & development/isolation & purification/metabolism, Humans, Intestines/*microbiology, Isomerism, Linoleic Acids, Conjugated/chemistry/*metabolism, Middle Aged, Oleic Acids/chemistry/*metabolism | Enzymology |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1869 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4902) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-4902 | |||
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 | |
41657 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/14779 | ||||
53417 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 36819) | https://www.ccug.se/strain?id=36819 | |||
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) | |||
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 | |||
81856 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID8663.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
119456 | Curators of the CIP | Collection of Institut Pasteur (CIP 103027) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103027 |