Strain identifier
BacDive ID: 7477
Type strain:
Species: Zimmermannella alba
Strain Designation: A59836
Strain history: CIP <- 2004, IAM <- IFO <- D.A. de Briel, Strasbourg Hosp., Strasbourg, France: strain A59836
NCBI tax ID(s): 1915061 (species)
General
@ref: 6990
BacDive-ID: 7477
DSM-Number: 17449
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped
description: Zimmermannella alba A59836 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from human urine.
NCBI tax id
- NCBI tax id: 1915061
- Matching level: species
strain history
@ref | history |
---|---|
6990 | <- IAM <- TISTR (Zimmermannella alba) <- D. A. De Briel; A59836 |
67770 | NBRC 15616 (Microbacterium sp.) <-- IFO 15616 <-- D. A. de Briel A59836. |
116181 | CIP <- 2004, IAM <- IFO <- D.A. de Briel, Strasbourg Hosp., Strasbourg, France: strain A59836 |
doi: 10.13145/bacdive7477.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Micrococcales
- family: Microbacteriaceae
- genus: Zimmermannella
- species: Zimmermannella alba
- full scientific name: Zimmermannella alba Lin et al. 2004
synonyms
- @ref: 20215
- synonym: Pseudoclavibacter albus
@ref: 6990
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Microbacteriaceae
genus: Pseudoclavibacter
species: Pseudoclavibacter sp.
full scientific name: Pseudoclavibacter sp.
strain designation: A59836
type strain: no
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility |
---|---|---|---|---|---|
29956 | positive | 0.8 µm | 0.35 µm | rod-shaped | no |
116181 | positive | rod-shaped | no |
colony morphology
- @ref: 116181
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6990 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water |
33251 | 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) | |
116181 | CIP Medium 6 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6990 | positive | growth | 28 | mesophilic |
29956 | positive | optimum | 30 | mesophilic |
33251 | positive | growth | 30 | mesophilic |
58790 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
116181 | positive | growth | 25-41 | |
116181 | no | growth | 10 | psychrophilic |
116181 | no | growth | 15 | psychrophilic |
116181 | no | growth | 45 | thermophilic |
culture pH
- @ref: 29956
- ability: positive
- type: optimum
- pH: 7
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
29956 | aerobe |
58790 | microaerophile |
116181 | obligate aerobe |
spore formation
- @ref: 29956
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29956 | NaCl | positive | growth | 0.2-0.3 % |
29956 | NaCl | positive | optimum | 0.25 % |
116181 | NaCl | positive | growth | 0-4 % |
116181 | NaCl | no | growth | 6 % |
116181 | NaCl | no | growth | 8 % |
116181 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: MK-10, MK-9, MK-7, MK-8
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
116181 | 16947 | citrate | - | carbon source |
116181 | 4853 | esculin | - | hydrolysis |
116181 | 606565 | hippurate | + | hydrolysis |
116181 | 17632 | nitrate | - | reduction |
116181 | 16301 | nitrite | - | reduction |
116181 | 17632 | nitrate | - | respiration |
antibiotic resistance
- @ref: 116181
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
- @ref: 116181
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
116181 | 15688 | acetoin | - | |
116181 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
29956 | alkaline phosphatase | + | 3.1.3.1 |
29956 | catalase | + | 1.11.1.6 |
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 |
116181 | oxidase | - | |
116181 | beta-galactosidase | - | 3.2.1.23 |
116181 | alcohol dehydrogenase | + | 1.1.1.1 |
116181 | gelatinase | - | |
116181 | amylase | + | |
116181 | DNase | - | |
116181 | caseinase | - | 3.4.21.50 |
116181 | catalase | + | 1.11.1.6 |
116181 | tween esterase | + | |
116181 | gamma-glutamyltransferase | + | 2.3.2.2 |
116181 | lecithinase | + | |
116181 | lipase | - | |
116181 | lysine decarboxylase | - | 4.1.1.18 |
116181 | ornithine decarboxylase | - | 4.1.1.17 |
116181 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
116181 | protease | - | |
116181 | tryptophan deaminase | - | |
116181 | urease | - | 3.5.1.5 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116181 | - | - | + | - | - | + | - | - | + | - | - | + | + | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116181 | - | + | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | geographic location |
---|---|---|---|---|---|
6990 | human urine | France | FRA | Europe | |
58790 | Human urine | France | FRA | Europe | Strasbourg |
67770 | Urine | France | FRA | Europe | |
116181 | Urine | France | FRA | Europe | Strasbourg |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Human | |
#Host Body Product | #Fluids | #Urine |
taxonmaps
- @ref: 69479
- File name: preview.99_757.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_459;97_526;98_604;99_757&stattab=map
- Last taxonomy: Pseudoclavibacter alba subclade
- 16S sequence: AB012590
- Sequence Identity:
- Total samples: 8250
- soil counts: 1422
- aquatic counts: 1777
- animal counts: 4134
- plant counts: 917
Safety information
risk assessment
- @ref: 116181
- biosafety level: 1
- biosafety level comment: Risk group (French classification)
Sequence information
16S sequences
- @ref: 6990
- description: Zimmermannella alba gene for 16S rRNA, partial sequence, strain: IFO 15616
- accession: AB012590
- length: 1481
- database: ena
- NCBI tax ID: 272241
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Zimmermannella alba NBRC 15616 | 1349786.3 | wgs | patric | 1349786 |
66792 | Pseudoclavibacter alba NBRC 15616 | 2731957610 | draft | img | 1349786 |
67770 | [Zimmermannella] alba NBRC 15616 | GCA_001570905 | contig | ncbi | 1349786 |
GC content
@ref | GC-content | method |
---|---|---|
6990 | 68 | |
67770 | 64.7 | genome sequence analysis |
67770 | 68 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 93.909 | no |
gram-positive | yes | 94.457 | no |
anaerobic | no | 98.609 | no |
halophile | no | 88.46 | yes |
spore-forming | no | 93.535 | no |
glucose-util | yes | 81.467 | no |
flagellated | no | 97.557 | no |
aerobic | yes | 68.645 | no |
glucose-ferment | no | 80.521 | no |
thermophile | no | 99.323 | yes |
External links
@ref: 6990
culture collection no.: DSM 17449, IAM 14724, NBRC 15616, TISTR 1510, CCUG 50212, IFO 15616, JCM 12865, CIP 108566
straininfo link
- @ref: 76922
- straininfo: 62503
literature
- topic: Phylogeny
- Pubmed-ID: 15388726
- title: Zimmermannella helvola gen. nov., sp. nov., Zimmermannella alba sp. nov., Zimmermannella bifida sp. nov., Zimmermannella faecalis sp. nov. and Leucobacter albus sp. nov., novel members of the family Microbacteriaceae.
- authors: Lin YC, Uemori K, de Briel DA, Arunpairojana V, Yokota A
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.02741-0
- year: 2004
- mesh: Actinomycetales/*classification/*isolation & purification/physiology/ultrastructure, Actinomycetales Infections/microbiology, Amino Acids, Diamino/analysis, Animals, Bacterial Typing Techniques, Base Composition, Blood/microbiology, Butter/microbiology, Cattle, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis, Feces/microbiology, Genes, rRNA, Humans, Microscopy, Electron, Scanning, Molecular Sequence Data, Muramic Acids/chemistry, Peptidoglycan/chemistry, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Urine/microbiology, Vitamin K 2/analysis, Wounds and Injuries/microbiology
- topic2: Enzymology
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
6990 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17449) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17449 | |||
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 | |||
29956 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26325 | 28776041 | |
33251 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6202 | ||||
58790 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 50212) | https://www.ccug.se/strain?id=50212 | |||
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/ | ||||
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 | |||
76922 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID62503.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
116181 | Curators of the CIP | Collection of Institut Pasteur (CIP 108566) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108566 |