Strain identifier
BacDive ID: 14151
Type strain:
Species: Caenibius tardaugens
Strain Designation: ARi-1
Strain history: CIP <- 2003, JCM <- K. Fujii: strain ARI-1
NCBI tax ID(s): 1219035 (strain), 169176 (species)
General
@ref: 6574
BacDive-ID: 14151
DSM-Number: 16702
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative
description: Caenibius tardaugens ARi-1 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge of sewage treatment plant.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1219035 | strain |
169176 | species |
strain history
@ref | history |
---|---|
6574 | <- K. Fujii, Muroran; ARi-1 |
67770 | K. Fujii ARI-1. |
123430 | CIP <- 2003, JCM <- K. Fujii: strain ARI-1 |
doi: 10.13145/bacdive14151.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Erythrobacteraceae
- genus: Caenibius
- species: Caenibius tardaugens
- full scientific name: Caenibius tardaugens (Fujii et al. 2003) Hördt et al. 2020
synonyms
- @ref: 20215
- synonym: Novosphingobium tardaugens
@ref: 6574
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Hyphomicrobiaceae
genus: Caenibius
species: Caenibius tardaugens
full scientific name: Caenibius tardaugens (Fujii et al. 2003) Hördt et al. 2020
strain designation: ARi-1
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | negative | 99.998 | ||
123430 | negative | rod-shaped | no |
colony morphology
@ref | incubation period |
---|---|
6574 | 3-7 days |
60910 | 3 days |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6574 | REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) | yes | https://mediadive.dsmz.de/medium/1a | Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
39969 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
123430 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 | |
123430 | CIP Medium 35 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=35 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6574 | positive | growth | 28 | mesophilic |
39969 | positive | growth | 25 | mesophilic |
60910 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
123430 | positive | growth | 25-37 | mesophilic |
123430 | no | growth | 5 | psychrophilic |
123430 | no | growth | 10 | psychrophilic |
123430 | no | growth | 41 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
60910 | aerobe |
123430 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 95 |
69480 | no | 99.972 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
123430 | NaCl | positive | growth | 0 % |
123430 | NaCl | no | growth | 2 % |
123430 | NaCl | no | growth | 4 % |
123430 | NaCl | no | growth | 6 % |
123430 | NaCl | no | growth | 8 % |
123430 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: Q-10
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | - | builds acid from | 32528 |
68371 | gentiobiose | - | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | - | builds acid from | 27082 |
68371 | sucrose | - | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | maltose | - | builds acid from | 17306 |
68371 | cellobiose | - | builds acid from | 17057 |
68371 | salicin | - | builds acid from | 17814 |
68371 | esculin | - | builds acid from | 4853 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | N-acetylglucosamine | + | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | + | builds acid from | 16024 |
68371 | D-fructose | + | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | D-galactose | + | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-ribose | - | builds acid from | 16988 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
123430 | citrate | - | carbon source | 16947 |
123430 | esculin | - | hydrolysis | 4853 |
123430 | nitrate | + | reduction | 17632 |
123430 | nitrite | - | reduction | 16301 |
123430 | nitrate | - | respiration | 17632 |
metabolite production
- @ref: 123430
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
123430 | oxidase | + | |
123430 | beta-galactosidase | - | 3.2.1.23 |
123430 | alcohol dehydrogenase | - | 1.1.1.1 |
123430 | gelatinase | - | |
123430 | amylase | - | |
123430 | DNase | - | |
123430 | caseinase | - | 3.4.21.50 |
123430 | catalase | + | 1.11.1.6 |
123430 | tween esterase | - | |
123430 | lecithinase | - | |
123430 | lipase | - | |
123430 | lysine decarboxylase | - | 4.1.1.18 |
123430 | ornithine decarboxylase | - | 4.1.1.17 |
123430 | protease | - | |
123430 | tryptophan deaminase | - | |
123430 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123430 | - | + | + | + | - | + | - | - | + | - | + | + | - | - | - | - | - | - | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123430 | - | - | - | - | - | - | - | - | - | + | + | + | + | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
6574 | activated sludge of sewage treatment plant | Tokyo | Japan | JPN | Asia |
60910 | Activated sludge of sewage treatment plant | Japan | JPN | Asia | |
67770 | Activated sludge of sewage treatment plant in Tokyo | ||||
123430 | Environment, Activated sludge of a sewage treatment plant | Tokyo | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Waste | #Activated sludge |
#Engineered | #Waste | #Water treatment plant |
taxonmaps
- @ref: 69479
- File name: preview.99_1545.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_883;97_1031;98_1220;99_1545&stattab=map
- Last taxonomy: Novosphingobium tardaugens subclade
- 16S sequence: AB681118
- Sequence Identity:
- Total samples: 2030
- soil counts: 462
- aquatic counts: 1092
- animal counts: 373
- plant counts: 103
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
6574 | 1 | Risk group (German classification) |
123430 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Novosphingobium tardaugens gene for 16S rRNA, partial sequence, strain: NBRC 16725 | AB681118 | 1410 | ena | 169176 |
6574 | Novosphingomonas sp. ARI-1 gene for 16S rRNA | AB070237 | 1418 | ena | 169176 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Caenibius tardaugens NBRC 16725 | GCA_003860345 | complete | ncbi | 1219035 |
66792 | Novosphingobium tardaugens NBRC 16725 | 1219035.3 | wgs | patric | 1219035 |
66792 | Novosphingobium tardaugens NBRC 16725 | 1219035.9 | complete | patric | 1219035 |
66792 | Novosphingobium tardaugens NBRC 16725 | 2600255065 | draft | img | 1219035 |
67770 | Caenibius tardaugens NBRC 16725 | GCA_000466945 | contig | ncbi | 1219035 |
GC content
- @ref: 6574
- GC-content: 61
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 95 | no |
motile | no | 79.778 | no |
flagellated | no | 96.67 | no |
gram-positive | no | 96.986 | no |
anaerobic | no | 98.944 | no |
aerobic | yes | 91.302 | yes |
halophile | no | 95.632 | no |
spore-forming | no | 93.013 | no |
thermophile | no | 97.886 | no |
glucose-util | yes | 67.92 | no |
glucose-ferment | no | 93.129 | no |
External links
@ref: 6574
culture collection no.: DSM 16702, ATCC BAA 531, IFO 16725, JCM 11434, NBRC 16725, CCUG 56307, CIP 107959, KCTC 12110
straininfo link
- @ref: 83317
- straininfo: 100829
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 12656151 | Novosphingobium tardaugens sp. nov., an oestradiol-degrading bacterium isolated from activated sludge of a sewage treatment plant in Tokyo. | Fujii K, Satomi M, Morita N, Motomura T, Tanaka T, Kikuchi S | Int J Syst Evol Microbiol | 10.1099/ijs.0.02301-0 | 2003 | Alphaproteobacteria/classification/genetics/*isolation & purification/*metabolism, Base Composition, Biodegradation, Environmental, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Estradiol/*metabolism, Fatty Acids/analysis, Lipids/analysis, Microscopy, Electron, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sewage/*microbiology, Tokyo | Metabolism |
Phylogeny | 24737793 | Novosphingobium kunmingense sp. nov., isolated from a phosphate mine. | Xie F, Quan S, Liu D, He W, Wang Y, Ma H, Chen G, Chao Y, Qian S | Int J Syst Evol Microbiol | 10.1099/ijs.0.057273-0 | 2014 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Mining, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphates/*chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistry | Genetics |
29997609 | A Virus Infecting Marine Photoheterotrophic Alphaproteobacteria (Citromicrobium spp.) Defines a New Lineage of ssDNA Viruses. | Zheng Q, Chen Q, Xu Y, Suttle CA, Jiao N | Front Microbiol | 10.3389/fmicb.2018.01418 | 2018 | |||
Genetics | 30938330 | High-Quality Whole-Genome Sequence of an Estradiol-Degrading Strain, Novosphingobium tardaugens NBRC 16725. | Ibero J, Sanz D, Galan B, Diaz E, Garcia JL | Microbiol Resour Announc | 10.1128/MRA.01715-18 | 2019 | ||
Metabolism | 31683600 | Testosterone Degradative Pathway of Novosphingobium tardaugens. | Ibero J, Galan B, Diaz E, Garcia JL | Genes (Basel) | 10.3390/genes10110871 | 2019 | Androgens/*metabolism, Bacterial Proteins/genetics/*metabolism, Biotransformation, Hydroxysteroid Dehydrogenases/genetics/*metabolism, Sphingomonadaceae/*enzymology/genetics, Testosterone/*metabolism | Enzymology |
Metabolism | 33424788 | Unraveling the 17beta-Estradiol Degradation Pathway in Novosphingobium tardaugens NBRC 16725. | Ibero J, Galan B, Rivero-Buceta V, Garcia JL | Front Microbiol | 10.3389/fmicb.2020.588300 | 2020 | ||
Genetics | 34946795 | Identification of the EdcR Estrogen-Dependent Repressor in Caenibius tardaugens NBRC 16725: Construction of a Cellular Estradiol Biosensor. | Ibero J, Galan B, Garcia JL | Genes (Basel) | 10.3390/genes12121846 | 2021 | Bacterial Proteins/*genetics, Biosensing Techniques/methods, Estradiol/*genetics, Estrogens/*genetics, Estrone/*genetics, Promoter Regions, Genetic/genetics, Sphingomonadaceae/*genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
6574 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16702) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16702 | |||
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 | |
39969 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5527 | ||||
60910 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 56307) | https://www.ccug.se/strain?id=56307 | |||
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) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68371 | Automatically annotated from API 50CH acid | |||||
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 | |||
83317 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID100829.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
123430 | Curators of the CIP | Collection of Institut Pasteur (CIP 107959) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107959 |