Strain identifier
BacDive ID: 11862
Type strain:
Species: Aminobacter carboxidus
Strain history: CIP <- 2005, P. Kämpfer, Giessen Univ., Giessen, Germany <- I. Mc Donald, Waikato Univ., Hamilton, New-Zealand: strain CC495
NCBI tax ID(s): 305698 (species)
General
@ref: 6994
BacDive-ID: 11862
DSM-Number: 17454
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Aminobacter carboxidus DSM 17454 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil of beech woodland.
NCBI tax id
- NCBI tax id: 305698
- Matching level: species
strain history
@ref | history |
---|---|
6994 | <- P. Kämpfer <- I. R. McDonald; CC495 |
120627 | CIP <- 2005, P. Kämpfer, Giessen Univ., Giessen, Germany <- I. Mc Donald, Waikato Univ., Hamilton, New-Zealand: strain CC495 |
doi: 10.13145/bacdive11862.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Phyllobacteriaceae
- genus: Aminobacter
- species: Aminobacter carboxidus
- full scientific name: Aminobacter carboxidus (Meyer et al. 1994 ex Nozhevnikova and Zavarzin 1974) Hördt et al. 2020
synonyms
@ref synonym 20215 Aminobacter lissarensis 20215 Carbophilus carboxidus
@ref: 6994
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhizobiales
family: Phyllobacteriaceae
genus: Aminobacter
species: Aminobacter lissarensis
full scientific name: Aminobacter lissarensis McDonald et al. 2005
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31512 | negative | 1.4 µm | 0.55 µm | rod-shaped | yes | |
69480 | negative | 99.972 | ||||
120627 | negative | rod-shaped | yes |
pigmentation
@ref | production | name |
---|---|---|
31512 | yes | |
120627 | no | Pyocyanin |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6994 | R2A MEDIUM (DSMZ Medium 830) | yes | https://mediadive.dsmz.de/medium/830 | Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water |
34007 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
120627 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 | |
120627 | CIP Medium 566 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6994 | positive | growth | 28 | mesophilic |
31512 | positive | growth | 25 | mesophilic |
31512 | positive | optimum | 25 | mesophilic |
34007 | positive | growth | 25 | mesophilic |
58909 | positive | growth | 26-37 | mesophilic |
120627 | positive | growth | 25-30 | mesophilic |
120627 | no | growth | 5 | psychrophilic |
120627 | no | growth | 10 | psychrophilic |
120627 | no | growth | 37 | mesophilic |
120627 | no | growth | 41 | thermophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
31512 | positive | growth | 6.7-7.2 |
31512 | positive | optimum | 6.95 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
6994 | aerobe |
31512 | aerobe |
58909 | aerobe |
120627 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.982 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
120627 | NaCl | positive | growth | 0-2 % |
120627 | NaCl | no | growth | 4 % |
120627 | NaCl | no | growth | 6 % |
120627 | NaCl | no | growth | 8 % |
120627 | NaCl | no | growth | 10 % |
observation
- @ref: 31512
- observation: aggregates in clumps
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31512 | 37054 | 3-hydroxybutyrate | + | carbon source |
31512 | 30089 | acetate | + | carbon source |
31512 | 16449 | alanine | + | carbon source |
31512 | 22599 | arabinose | + | carbon source |
31512 | 35391 | aspartate | + | carbon source |
31512 | 17057 | cellobiose | + | carbon source |
31512 | 28757 | fructose | + | carbon source |
31512 | 28260 | galactose | + | carbon source |
31512 | 17234 | glucose | + | carbon source |
31512 | 27570 | histidine | + | carbon source |
31512 | 24996 | lactate | + | carbon source |
31512 | 25017 | leucine | + | carbon source |
31512 | 17306 | maltose | + | carbon source |
31512 | 29864 | mannitol | + | carbon source |
31512 | 37684 | mannose | + | carbon source |
31512 | 506227 | N-acetylglucosamine | + | carbon source |
31512 | 18257 | ornithine | + | carbon source |
31512 | 26271 | proline | + | carbon source |
31512 | 17272 | propionate | + | carbon source |
31512 | 15361 | pyruvate | + | carbon source |
31512 | 26546 | rhamnose | + | carbon source |
31512 | 33942 | ribose | + | carbon source |
31512 | 17822 | serine | + | carbon source |
31512 | 30911 | sorbitol | + | carbon source |
31512 | 17992 | sucrose | + | carbon source |
31512 | 27082 | trehalose | + | carbon source |
31512 | 16296 | D-tryptophan | + | carbon source |
31512 | 18222 | xylose | + | carbon source |
120627 | 16947 | citrate | - | carbon source |
120627 | 4853 | esculin | - | hydrolysis |
120627 | 17632 | nitrate | + | reduction |
120627 | 16301 | nitrite | + | reduction |
120627 | 17632 | nitrate | - | respiration |
antibiotic resistance
- @ref: 120627
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
- @ref: 120627
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
120627 | oxidase | + | |
120627 | beta-galactosidase | - | 3.2.1.23 |
120627 | alcohol dehydrogenase | - | 1.1.1.1 |
120627 | gelatinase | - | |
120627 | amylase | - | |
120627 | DNase | - | |
120627 | caseinase | - | 3.4.21.50 |
120627 | catalase | + | 1.11.1.6 |
120627 | tween esterase | - | |
120627 | lecithinase | - | |
120627 | lipase | - | |
120627 | lysine decarboxylase | - | 4.1.1.18 |
120627 | ornithine decarboxylase | - | 4.1.1.17 |
120627 | protease | - | |
120627 | tryptophan deaminase | - | |
120627 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120627 | - | - | + | - | - | + | - | - | + | - | + | - | - | - | - | + | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120627 | + | + | + | + | + | - | - | + | - | - | + | - | - | + | + | + | + | - | + | + | - | + | - | + | + | - | + | - | - | - | - | + | + | + | - | + | + | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | + | - | - | + | - | + | - | - | - | - | - | - | + | - | + | - | + | - | - | - | - | - | - | - | + | - | - | + | - | + | + | + | + | - | + | + | - | - | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | continent | country | origin.country |
---|---|---|---|---|---|
6994 | soil of beech woodland | County Down | Europe | ||
58909 | Soil,unpolluted beech woodland soil | Northern Ireland,County Down | Europe | United Kingdom | GBR |
120627 | Environment, Soil, Beech woodland | Lissara House, county Down | Europe | United Kingdom | GBR |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Forest |
#Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_1038.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_220;97_697;98_812;99_1038&stattab=map
- Last taxonomy: Mesorhizobium
- 16S sequence: AF107722
- Sequence Identity:
- Total samples: 1264
- soil counts: 780
- aquatic counts: 308
- animal counts: 145
- plant counts: 31
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
6994 | 1 | Risk group (German classification) |
120627 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 6994
- description: Aminobacter lissarensis strain CC495 16S ribosomal RNA gene, complete sequence
- accession: AF107722
- length: 1435
- database: ena
- NCBI tax ID: 305698
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Aminobacter lissarensis DSM 17454 | GCA_014207495 | scaffold | ncbi | 305698 |
66792 | Aminobacter lissarensis strain DSM 17454 | 305698.3 | wgs | patric | 305698 |
66792 | Aminobacter lissarensis DSM 17454 | 2861412741 | draft | img | 305698 |
GC content
- @ref: 31512
- GC-content: 62.5
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
flagellated | no | 70.554 | no |
gram-positive | no | 97.676 | yes |
anaerobic | no | 98.917 | no |
aerobic | yes | 94.708 | yes |
halophile | no | 89.358 | no |
spore-forming | no | 94.666 | no |
glucose-util | yes | 93.72 | yes |
thermophile | no | 99.003 | no |
motile | yes | 89.953 | yes |
glucose-ferment | no | 89.97 | no |
External links
@ref: 6994
culture collection no.: DSM 17454, CCUG 50579, CIP 108661, NCIMB 13798, CC 495
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Metabolism | 16102909 | Analysis of genes involved in methyl halide degradation in Aminobacter lissarensis CC495. | Warner KL, Larkin MJ, Harper DB, Murrell JC, McDonald IR | FEMS Microbiol Lett | 10.1016/j.femsle.2005.07.021 | 2005 | Alphaproteobacteria/enzymology/*genetics/*metabolism, Amino Acid Sequence, Bacterial Proteins/chemistry/*genetics, Biodegradation, Environmental, Cloning, Molecular, Conserved Sequence, DNA, Bacterial/chemistry/genetics, Gene Order, *Genes, Bacterial, Hydrocarbons, Brominated/*metabolism, Hyphomicrobium/genetics, Methyl Chloride/*metabolism, Molecular Sequence Data, Multigene Family, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Synteny | Enzymology |
Phylogeny | 16166673 | Aminobacter ciceronei sp. nov. and Aminobacter lissarensis sp. nov., isolated from various terrestrial environments. | McDonald IR, Kampfer P, Topp E, Warner KL, Cox MJ, Hancock TLC, Miller LG, Larkin MJ, Ducrocq V, Coulter C, Harper DB, Murrell JC, Oremland RS | Int J Syst Evol Microbiol | 10.1099/ijs.0.63716-0 | 2005 | *Agriculture, Alphaproteobacteria/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Biodegradation, Environmental, California, Canada, Carbamates/metabolism, Culture Media, DNA, Bacterial/analysis, Fagus, Genes, rRNA, Herbicides/metabolism, Hydrocarbons, Brominated/metabolism, Methyl Chloride/metabolism, Molecular Sequence Data, Northern Ireland, Pesticides/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, *Trees, Triazines/metabolism | Metabolism |
Phylogeny | 33848814 | Phylogenomic analysis and characterization of carbon monoxide utilization genes in the family Phyllobacteriaceae with reclassification of Aminobacter carboxidus (Meyer et al. 1993, Hordt et al. 2020) as Aminobacter lissarensis comb. nov. (McDonald et al. 2005). | Artuso I, Turrini P, Pirolo M, Lucidi M, Tescari M, Visaggio D, Mansi A, Lugli GA, Ventura M, Visca P | Syst Appl Microbiol | 10.1016/j.syapm.2021.126199 | 2021 | Bacterial Typing Techniques, *Carbon Monoxide, DNA, Bacterial, Multilocus Sequence Typing, Phyllobacteriaceae/*classification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizobiaceae, Sequence Analysis, DNA | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
6994 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17454) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17454 | |||
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 | |||
31512 | 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 | 27808 | 28776041 | |
34007 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6314 | ||||
58909 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 50579) | https://www.ccug.se/strain?id=50579 | |||
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) | |||
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 | |||
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 | |||
120627 | Curators of the CIP | Collection of Institut Pasteur (CIP 108661) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108661 |