Strain identifier
BacDive ID: 12663
Type strain:
Species: Propionimicrobium lymphophilum
Strain history: CIP <- 2003, JCM <- ATCC <- W.E.C. Moore, Blacksburg, USA: strain VPI 7625B
NCBI tax ID(s): 1123001 (strain), 33012 (species)
General
@ref: 1870
BacDive-ID: 12663
DSM-Number: 4903
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, rod-shaped
description: Propionimicrobium lymphophilum CCUG 27816 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from submaxillary tissue.
NCBI tax id
NCBI tax id | Matching level |
---|---|
33012 | species |
1123001 | strain |
strain history
@ref | history |
---|---|
1870 | <- ATCC <- W.E.C. Moore, VPI 7625B |
67770 | ATCC 27520 <-- W. E. C. Moore VPI 7625 B. |
120724 | CIP <- 2003, JCM <- ATCC <- W.E.C. Moore, Blacksburg, USA: strain VPI 7625B |
doi: 10.13145/bacdive12663.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Propionibacteriales
- family: Propionibacteriaceae
- genus: Propionimicrobium
- species: Propionimicrobium lymphophilum
- full scientific name: Propionimicrobium lymphophilum (Torrey 1916) Stackebrandt et al. 2002
synonyms
@ref synonym 20215 Propionibacterium lymphophilum 20215 Bacillus lymphophilus
@ref: 1870
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Propionibacteriaceae
genus: Propionimicrobium
species: Propionimicrobium lymphophilum
full scientific name: Propionimicrobium lymphophilum (Torrey 1916) Stackebrandt et al. 2002
type strain: yes
Morphology
cell morphology
- @ref: 120724
- gram stain: positive
- cell shape: rod-shaped
- motility: no
colony morphology
- @ref: 120724
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
66793 | EM_DSM_4903_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_4903_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_4903_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_4903_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_4903_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
1870 | 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 |
37134 | MEDIUM 26 - for Gardnerella and Propionibacterium lymphophilum | yes | Distilled water make up to (1000.000 ml);Horse serum (200.000 ml);Brainheart infusion (37.000 g);Maltose 10 % solution - M0173 (200.000 ml) | |
120724 | CIP Medium 26 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=26 | |
120724 | CIP Medium 433 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=433 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
1870 | positive | growth | 37 | mesophilic |
37134 | positive | growth | 37 | mesophilic |
48963 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
1870 | anaerobe |
48963 | anaerobe |
120724 | anaerobe |
murein
- @ref: 1870
- murein short key: A11.31
- type: A4alpha L-Lys-D-Asp
observation
- @ref: 67770
- observation: quinones: MK-9(H4)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
120724 | 17108 | D-arabinose | - | degradation |
120724 | 15824 | D-fructose | + | degradation |
120724 | 17634 | D-glucose | + | degradation |
120724 | 65327 | D-xylose | - | degradation |
120724 | 17057 | cellobiose | - | degradation |
120724 | 17716 | lactose | - | degradation |
120724 | 17306 | maltose | + | degradation |
120724 | 17814 | salicin | - | degradation |
120724 | 17992 | sucrose | - | degradation |
120724 | 4853 | esculin | - | hydrolysis |
120724 | 17632 | nitrate | - | reduction |
120724 | 16301 | nitrite | - | reduction |
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
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 |
---|---|---|---|
120724 | 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 | glycin arylamidase | - | |
68380 | alanine arylamidase | - | 3.4.11.2 |
68380 | tyrosine arylamidase | - | |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | leucine arylamidase | - | 3.4.11.1 |
68380 | phenylalanine arylamidase | - | |
68380 | leucyl glycin arylamidase | - | 3.4.11.1 |
68380 | proline-arylamidase | - | 3.4.11.5 |
68380 | L-arginine arylamidase | - | |
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 | alpha-glucosidase | - | 3.2.1.20 |
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 |
120724 | oxidase | - | |
120724 | beta-galactosidase | - | 3.2.1.23 |
120724 | gelatinase | - | |
120724 | amylase | - | |
120724 | DNase | - | |
120724 | caseinase | - | 3.4.21.50 |
120724 | catalase | - | 1.11.1.6 |
120724 | tween esterase | - | |
120724 | lecithinase | - | |
120724 | lipase | - | |
120724 | protease | - | |
120724 | urease | - | 3.5.1.5 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1870 | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
1870 | submaxillary tissue |
48963 | Human submaxillary tissue |
67770 | Submaxillary tissue |
120724 | Human, Submaxillary tissue |
isolation source categories
- Cat1: #Host Body-Site
- Cat2: #Oral cavity and airways
- Cat3: #Mouth
taxonmaps
- @ref: 69479
- File name: preview.99_2335.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15360;96_1261;97_1496;98_1822;99_2335&stattab=map
- Last taxonomy: Propionimicrobium lymphophilum subclade
- 16S sequence: AJ003056
- Sequence Identity:
- Total samples: 9509
- soil counts: 283
- aquatic counts: 1384
- animal counts: 7765
- plant counts: 77
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
1870 | 2 | Risk group (German classification) |
120724 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Propionibacterium lymphophilum ATCC 27520 16S rRNA gene, partial sequence | U02907 | 388 | ena | 33012 |
20218 | Propionibacterium lymphophilum DSM 4903 16S rRNA gene | AJ003056 | 1502 | ena | 33012 |
20218 | Propionimicrobium lymphophilum gene for 16S ribosomal RNA, partial sequence, strain: JCM 5829 | AB729070 | 1482 | ena | 33012 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Propionimicrobium lymphophilum DSM 4903 | 1123001.3 | wgs | patric | 1123001 |
66792 | Propionimicrobium lymphophilum DSM 4903 | 2523533555 | draft | img | 1123001 |
67770 | Propionimicrobium lymphophilum DSM 4903 | GCA_000423485 | scaffold | ncbi | 1123001 |
GC content
@ref | GC-content | method |
---|---|---|
1870 | 54.0 | |
67770 | 56 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 92.858 | no |
flagellated | no | 97.516 | no |
gram-positive | yes | 90.089 | no |
anaerobic | yes | 90.534 | yes |
aerobic | no | 93.677 | yes |
halophile | no | 78.275 | no |
spore-forming | no | 93.85 | no |
glucose-util | yes | 84.281 | no |
thermophile | no | 92.036 | yes |
glucose-ferment | yes | 70.598 | no |
External links
@ref: 1870
culture collection no.: CCUG 27816, NCTC 11866, LMG 16728, DSM 4903, ATCC 27520, JCM 5829, VPI 7625B, CIP 103263, NCIMB 702587, NCDO 2587
straininfo link
- @ref: 81875
- straininfo: 8646
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
1870 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4903) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-4903 | |||
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 | |
37134 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/15041 | ||||
48963 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 27816) | https://www.ccug.se/strain?id=27816 | |||
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 | |||||
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 | |||
81875 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID8646.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
120724 | Curators of the CIP | Collection of Institut Pasteur (CIP 103263) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103263 |