Strain identifier
BacDive ID: 7619
Type strain:
Species: Paenarthrobacter ilicis
Strain Designation: Cr-2
Strain history: CIP <- 2001, CCUG <- 1989, LMG <- 1981, NCPPB <- 1962, Mandel: strain Cr-2
NCBI tax ID(s): 43665 (species)
General
@ref: 8563
BacDive-ID: 7619
DSM-Number: 20138
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive
description: Paenarthrobacter ilicis Cr-2 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from american holly .
NCBI tax id
- NCBI tax id: 43665
- Matching level: species
strain history
@ref | history |
---|---|
8563 | <- ATCC <- M. Mandel; (Corynebacterium ilicis) |
67770 | CECT 4207 <-- NCPPB 1228 <-- M. Mandel CR2 <-- M. Mandel and E. F. Guba. |
120047 | CIP <- 2001, CCUG <- 1989, LMG <- 1981, NCPPB <- 1962, Mandel: strain Cr-2 |
doi: 10.13145/bacdive7619.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Micrococcaceae
- genus: Paenarthrobacter
- species: Paenarthrobacter ilicis
- full scientific name: Paenarthrobacter ilicis (Collins et al. 1982) Busse 2016
synonyms
- @ref: 20215
- synonym: Arthrobacter ilicis
@ref: 8563
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Micrococcaceae
genus: Paenarthrobacter
species: Paenarthrobacter ilicis
full scientific name: Paenarthrobacter ilicis (Collins et al. 1982) Busse 2016
strain designation: Cr-2
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | positive | 100 | ||
120047 | positive | rod-shaped | yes |
colony morphology
@ref | colony color | incubation period | medium used | hemolysis ability |
---|---|---|---|---|
18628 | Sand yellow (1002) | 10-14 days | ISP 2 | |
18628 | Zinc yellow (1016) | 10-14 days | ISP 3 | |
18628 | Colorless | 10-14 days | ISP 6 | |
18628 | Colorless | 10-14 days | ISP 7 | |
120047 | 1 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
18628 | no | ISP 2 |
18628 | no | ISP 3 |
18628 | no | ISP 6 |
18628 | no | ISP 7 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
8563 | CORYNEBACTERIUM AGAR (DSMZ Medium 53) | yes | https://mediadive.dsmz.de/medium/53 | Name: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled water |
18628 | ISP 2 | yes | Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes | |
18628 | ISP 3 | yes | Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms: | |
18628 | ISP 6 | yes | Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes | |
18628 | ISP 7 | yes | Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes | |
41900 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
120047 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8563 | positive | growth | 30 | mesophilic |
18628 | positive | optimum | 28 | mesophilic |
41900 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
120047 | positive | growth | 10-37 | |
120047 | no | growth | 41 | thermophilic |
120047 | no | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 120047
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.718 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
18628 | NaCl | positive | maximum | 5 % |
120047 | NaCl | positive | growth | 0-4 % |
120047 | NaCl | no | growth | 6 % |
120047 | NaCl | no | growth | 8 % |
120047 | NaCl | no | growth | 10 % |
murein
- @ref: 8563
- murein short key: A11.17
- type: A3alpha L-Lys-L-Ala-L-Thr-L-Ala
observation
- @ref: 67770
- observation: quinones: MK-9(H2)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68368 | 5291 | gelatin | - | hydrolysis |
68368 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | + | hydrolysis |
68368 | 16947 | citrate | + | assimilation |
68368 | 18257 | ornithine | - | degradation |
68368 | 25094 | lysine | + | degradation |
68368 | 29016 | arginine | + | hydrolysis |
120047 | 16947 | citrate | - | carbon source |
120047 | 4853 | esculin | + | hydrolysis |
120047 | 606565 | hippurate | + | hydrolysis |
120047 | 17632 | nitrate | - | reduction |
120047 | 16301 | nitrite | - | reduction |
120047 | 17632 | nitrate | - | respiration |
68379 | 17632 | nitrate | + | reduction |
68379 | 4853 | esculin | + | hydrolysis |
68379 | 16199 | urea | + | hydrolysis |
68379 | 5291 | gelatin | + | hydrolysis |
68379 | 17634 | D-glucose | + | fermentation |
68379 | 16988 | D-ribose | + | fermentation |
68379 | 65327 | D-xylose | - | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 17306 | maltose | + | fermentation |
68379 | 17716 | lactose | + | fermentation |
68379 | 17992 | sucrose | + | fermentation |
68379 | 28087 | glycogen | - | fermentation |
antibiotic resistance
- @ref: 120047
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: yes
- is resistant: no
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | no |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | yes |
120047 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test | methylred-test |
---|---|---|---|---|---|
68368 | 15688 | acetoin | - | ||
68368 | 35581 | indole | - | ||
120047 | 15688 | acetoin | - | ||
120047 | 17234 | glucose | - |
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 | 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 | 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 |
68379 | gelatinase | + | |
68379 | urease | + | 3.5.1.5 |
68379 | beta-glucosidase | + | 3.2.1.21 |
68379 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68379 | alpha-glucosidase | + | 3.2.1.20 |
68379 | beta-galactosidase | + | 3.2.1.23 |
68379 | beta-glucuronidase | + | 3.2.1.31 |
68379 | alkaline phosphatase | - | 3.1.3.1 |
68379 | pyrrolidonyl arylamidase | + | 3.4.19.3 |
68379 | pyrazinamidase | + | 3.5.1.B15 |
68368 | gelatinase | - | |
68368 | tryptophan deaminase | + | 4.1.99.1 |
68368 | urease | + | 3.5.1.5 |
68368 | ornithine decarboxylase | - | 4.1.1.17 |
68368 | lysine decarboxylase | + | 4.1.1.18 |
68368 | arginine dihydrolase | + | 3.5.3.6 |
68368 | beta-galactosidase | + | 3.2.1.23 |
120047 | oxidase | - | |
120047 | beta-galactosidase | + | 3.2.1.23 |
120047 | alcohol dehydrogenase | - | 1.1.1.1 |
120047 | gelatinase | + | |
120047 | amylase | - | |
120047 | DNase | + | |
120047 | caseinase | + | 3.4.21.50 |
120047 | catalase | + | 1.11.1.6 |
120047 | tween esterase | - | |
120047 | gamma-glutamyltransferase | + | 2.3.2.2 |
120047 | lecithinase | - | |
120047 | lipase | - | |
120047 | lysine decarboxylase | - | 4.1.1.18 |
120047 | ornithine decarboxylase | - | 4.1.1.17 |
120047 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
120047 | protease | + | |
120047 | tryptophan deaminase | - | |
120047 | urease | - | 3.5.1.5 |
API coryne
@ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18628 | + | + | + | - | + | + | + | + | + | + | + | + | + | - | - | + | + | + | - |
API zym
@ref | 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 | Control |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
18628 | + | + | + | - | + | + | + | + | - | + | + | + | + | - | - | + | + | + | - | |
120047 | + | + | + | - | + | - | - | + | - | + | + | + | + | + | + | + | + | + | - | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL |
---|---|---|---|---|---|---|---|---|---|---|---|
18628 | + | + | + | - | + | + | + | + | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120047 | + | + | + | + | + | - | + | + | + | + | + | + | + | + | + | + | + | + | + | - | + | + | + | - | - | + | - | - | + | - | - | + | + | + | + | + | - | - | - | - | - | + | - | - | - | - | - | - | - | + | + | + | - | + | + | - | + | - | - | + | + | + | + | + | + | - | + | - | - | + | - | + | + | + | - | + | - | - | - | + | + | - | - | - | - | - | + | - | + | + | + | + | + | + | + | - | + | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
8563 | american holly (Ilex opaca) | Ilex opaca | ||||
47870 | Ilex poaca | USA | USA | North America | ||
67770 | American holly (Ilex opaca) | Ilex opaca | ||||
120047 | American holly, Ilex opaca | United States of America | USA | North America | 1989 |
isolation source categories
- Cat1: #Host
- Cat2: #Plants
- Cat3: #Tree
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
8563 | 1 | Risk group (German classification) |
18628 | 1 | Hazard group |
120047 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 8563
- description: A.ilicis 16S rRNA gene
- accession: X83407
- length: 1486
- database: ena
- NCBI tax ID: 43665
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Paenarthrobacter ilicis DSM 20138 | GCA_016907545 | contig | ncbi | 43665 |
66792 | Paenarthrobacter ilicis strain CECT 4207 | 43665.5 | wgs | patric | 43665 |
66792 | Paenarthrobacter ilicis strain DSM 20138 | 43665.6 | wgs | patric | 43665 |
66792 | Arthrobacter ilicis CECT 4207 | 2824339274 | draft | img | 43665 |
66792 | Paenarthrobacter ilicis DSM 20138 | 2893582668 | draft | img | 43665 |
67770 | Paenarthrobacter ilicis CECT 4207 | GCA_011761315 | scaffold | ncbi | 43665 |
GC content
@ref | GC-content | method |
---|---|---|
8563 | 61.5 | |
67770 | 61.5 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | yes | 91.229 | no |
anaerobic | no | 99.469 | no |
halophile | no | 94.03 | no |
spore-forming | no | 88.014 | no |
glucose-util | yes | 85.788 | no |
aerobic | yes | 95.745 | no |
flagellated | no | 90.64 | no |
thermophile | no | 99.302 | no |
motile | yes | 50.583 | no |
glucose-ferment | no | 80.234 | yes |
External links
@ref: 8563
culture collection no.: DSM 20138, ATCC 14264, NCPPB 1228, CCUG 23889, LMG 3659, LMG 7254, CIP 107004, CCM 4967, JCM 12267, CECT 4207, CFBP 1380, HAMBI 1849, IAM 14586, ICMP 2607, IFO 15514, NBRC 15514, VKM Ac-1987, PDDCC 2607
straininfo link
- @ref: 77063
- straininfo: 1002
literature
- topic: Phylogeny
- Pubmed-ID: 18676493
- title: Corynebacterium ilicis is typified by ICMP 2608 =ICPB CI144, Arthrobacter ilicis is typified by DSM 20138 =ATCC 14264 =NCPPB 1228 and the two are not homotypic synonyms, and clarification of the authorship of these two species. Opinion 87.
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.2008/006221-0
- year: 2008
- mesh: Arthrobacter/*classification, Corynebacterium/*classification, Species Specificity, *Terminology as Topic
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
8563 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20138) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-20138 | |
18628 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM20138.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |
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 | |
41900 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/19196 | ||
47870 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 23889) | https://www.ccug.se/strain?id=23889 | |
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) | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
68368 | Automatically annotated from API 20E | |||
68379 | Automatically annotated from API Coryne | |||
68382 | Automatically annotated from API zym | |||
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 | |
77063 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID1002.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
120047 | Curators of the CIP | Collection of Institut Pasteur (CIP 107004) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107004 |