Strain identifier
BacDive ID: 17420
Type strain:
Species: Xanthobacter autotrophicus
Strain Designation: 7C
Strain history: CIP <- 1998, JCM <- DSM <- IMG <- D. Siebert: strain 7C, Corynebacterium autotrophicum
NCBI tax ID(s): 280 (species)
General
@ref: 201
BacDive-ID: 17420
DSM-Number: 432
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, rod-shaped
description: Xanthobacter autotrophicus 7C is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from black pool sludge.
NCBI tax id
- NCBI tax id: 280
- Matching level: species
strain history
@ref | history |
---|---|
201 | <- IMG (Corynebacterium autotrophicum) <- D. Siebert, 7C |
67770 | DSM 432 <-- IMG <-- D. Siebert 7C. |
116654 | CIP <- 1998, JCM <- DSM <- IMG <- D. Siebert: strain 7C, Corynebacterium autotrophicum |
doi: 10.13145/bacdive17420.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Xanthobacteraceae
- genus: Xanthobacter
- species: Xanthobacter autotrophicus
- full scientific name: Xanthobacter autotrophicus (Baumgarten et al. 1974) Wiegel et al. 1978 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Corynebacterium autotrophicum
@ref: 201
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Xanthobacteraceae
genus: Xanthobacter
species: Xanthobacter autotrophicus
full scientific name: Xanthobacter autotrophicus (Baumgarten et al. 1974) Wiegel et al. 1978
strain designation: 7C
type strain: yes
Morphology
cell morphology
- @ref: 116654
- gram stain: negative
- cell shape: rod-shaped
- motility: no
colony morphology
- @ref: 116654
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
201 | HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428) | yes | https://mediadive.dsmz.de/medium/428 | Name: HETEROTROPHIC MEDIUM H3P (DSMZ Medium 428) Composition: Agar 19.802 g/l Na2HPO4 x 2 H2O 2.87129 g/l KH2PO4 2.27723 g/l D-Glucose 1.9802 g/l Na-lactate 0.990099 g/l Na-pyruvate 0.990099 g/l D-Mannitol 0.990099 g/l DL-Malate 0.990098 g/l Na-acetate 0.990098 g/l Yeast extract 0.990098 g/l NH4Cl 0.990098 g/l Disodium succinate 0.990098 g/l MgSO4 x 7 H2O 0.495049 g/l Ferric ammonium citrate 0.049505 g/l CaCl2 x 2 H2O 0.00990098 g/l NaVO3 x H2O 0.00495049 g/l Thiamine-HCl x 2 H2O 0.00247525 g/l Nicotinic acid 0.00247525 g/l Pyridoxine hydrochloride 0.00247525 g/l Calcium pantothenate 0.00247525 g/l H3BO3 0.00148515 g/l CoCl2 x 6 H2O 0.000990099 g/l Riboflavin 0.00049505 g/l ZnSO4 x 7 H2O 0.00049505 g/l MnCl2 x 4 H2O 0.000148515 g/l Na2MoO4 x 2 H2O 0.000148515 g/l NiCl2 x 6 H2O 9.90099e-05 g/l CuCl2 x 2 H2O 4.95049e-05 g/l Vitamin B12 4.95049e-05 g/l Folic acid 9.90099e-06 g/l Biotin 4.9505e-06 g/l Distilled water |
201 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
40407 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
116654 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
201 | positive | growth | 30 | mesophilic |
40407 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
116654 | positive | growth | 25-37 | mesophilic |
116654 | no | growth | 5 | psychrophilic |
116654 | no | growth | 10 | psychrophilic |
116654 | no | growth | 41 | thermophilic |
116654 | no | growth | 45 | thermophilic |
Physiology and metabolism
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
116654 | NaCl | positive | growth | 0 % |
116654 | NaCl | no | growth | 2 % |
116654 | NaCl | no | growth | 4 % |
116654 | NaCl | no | growth | 6 % |
116654 | NaCl | no | growth | 8 % |
116654 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: Q-10
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
116654 | 16947 | citrate | + | carbon source |
116654 | 4853 | esculin | - | hydrolysis |
116654 | 606565 | hippurate | + | hydrolysis |
116654 | 17632 | nitrate | + | reduction |
116654 | 16301 | nitrite | - | reduction |
116654 | 17632 | nitrate | - | respiration |
metabolite production
- @ref: 116654
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
116654 | 15688 | acetoin | - | |
116654 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
116654 | oxidase | + | |
116654 | beta-galactosidase | + | 3.2.1.23 |
116654 | alcohol dehydrogenase | - | 1.1.1.1 |
116654 | gelatinase | - | |
116654 | amylase | - | |
116654 | DNase | - | |
116654 | caseinase | - | 3.4.21.50 |
116654 | catalase | + | 1.11.1.6 |
116654 | tween esterase | - | |
116654 | gamma-glutamyltransferase | - | 2.3.2.2 |
116654 | lecithinase | - | |
116654 | lipase | - | |
116654 | lysine decarboxylase | - | 4.1.1.18 |
116654 | ornithine decarboxylase | - | 4.1.1.17 |
116654 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
116654 | tryptophan deaminase | - | |
116654 | 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 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116654 | - | - | + | - | - | + | - | - | + | - | + | + | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116654 | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | + | - | - | - | + | - | - | - | - | - | - | + | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | + | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
201 | black pool sludge | Göttingen | Germany | DEU | Europe |
67770 | Black pool sludge | ||||
116654 | Environment, Black pool sludge |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Built environment | #Water reservoir (Aquarium/pool) |
#Engineered | #Waste | #Activated sludge |
taxonmaps
- @ref: 69479
- File name: preview.99_4714.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_355;96_1529;97_2844;98_3536;99_4714&stattab=map
- Last taxonomy: Xanthobacter
- 16S sequence: X94201
- Sequence Identity:
- Total samples: 208
- soil counts: 34
- aquatic counts: 110
- animal counts: 32
- plant counts: 32
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
201 | 1 | Risk group (German classification) |
116654 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | X.autotrophicus 16S ribosomal RNA (strain 7c) | X94201 | 1412 | ena | 280 |
20218 | Xanthobacter autotrophicus gene for 16S rRNA, partial sequence, strain: NBRC 102463 | AB681805 | 1410 | ena | 280 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Xanthobacter autotrophicus DSM 432 | GCA_005871085 | scaffold | ncbi | 280 |
66792 | Xanthobacter autotrophicus strain DSM 432 | 280.16 | wgs | patric | 280 |
66792 | Xanthobacter autotrophicus DSM 432 | 2596583657 | draft | img | 280 |
GC content
@ref | GC-content | method |
---|---|---|
201 | 69.7 | |
201 | 67.3 | |
67770 | 69.7 | thermal denaturation, midpoint method (Tm) |
67770 | 67 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 76.406 | no |
flagellated | no | 94.025 | no |
gram-positive | no | 98.586 | no |
anaerobic | no | 97.126 | no |
aerobic | yes | 89.762 | no |
halophile | no | 85.949 | no |
spore-forming | no | 95.3 | no |
thermophile | no | 97.033 | yes |
glucose-util | yes | 78.583 | no |
glucose-ferment | no | 91.109 | no |
External links
@ref: 201
culture collection no.: DSM 432, ATCC 35674, JCM 1202, BCRC 12235, CIP 105431, IAM 12579, IAM 12636, LMG 7043, NBRC 102463, NCAIM B.01945, NCIMB 10809, NRRL B-14836, CCRC 12235
straininfo link
- @ref: 86416
- straininfo: 5136
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
201 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 432) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-432 | |||
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 | |
40407 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/17450 | ||||
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 | |||
86416 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID5136.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
116654 | Curators of the CIP | Collection of Institut Pasteur (CIP 105431) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105431 |