Strain identifier
BacDive ID: 2092
Type strain:
Species: Arcobacter nitrofigilis
Strain Designation: CI
Strain history: CIP <- 1994, LMG <- 1986, CCUG, Campylobacter nitrofragilis <- S. Neill <- 1984, McClung, Canada
NCBI tax ID(s): 572480 (strain), 28199 (species)
General
@ref: 3103
BacDive-ID: 2092
DSM-Number: 7299
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, motile
description: Arcobacter nitrofigilis CI is a microaerophile, mesophilic, motile bacterium that was isolated from roots of Spartina alterniflora .
NCBI tax id
NCBI tax id | Matching level |
---|---|
28199 | species |
572480 | strain |
strain history
@ref | history |
---|---|
3103 | <- CCUG <- C.R. McClung |
67770 | LMG 7604 <-- CCUG 15892 <-- C. R. McClung; Beltsville Agric. Res. Center, USA; CI. |
121311 | CIP <- 1994, LMG <- 1986, CCUG, Campylobacter nitrofragilis <- S. Neill <- 1984, McClung, Canada |
doi: 10.13145/bacdive2092.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Epsilonproteobacteria
- order: Campylobacterales
- family: Arcobacteraceae
- genus: Arcobacter
- species: Arcobacter nitrofigilis
- full scientific name: Arcobacter nitrofigilis (McClung et al. 1983) Vandamme et al. 1991
synonyms
- @ref: 20215
- synonym: Campylobacter nitrofigilis
@ref: 3103
domain: Bacteria
phylum: Proteobacteria
class: Epsilonproteobacteria
order: Campylobacterales
family: Arcobacteraceae
genus: Arcobacter
species: Arcobacter nitrofigilis
full scientific name: Arcobacter nitrofigilis (McClung et al. 1983) Vandamme et al. 1991
strain designation: CI
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 92.172 | ||
69480 | 100 | negative | ||
121311 | yes | negative | rod-shaped |
colony morphology
@ref | type of hemolysis | incubation period |
---|---|---|
3103 | gamma | 1-2 days |
46369 | 3 days | |
121311 |
multimedia
- @ref: 66793
- multimedia content: EM_DSM_7299_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
3103 | VIBRIO NATRIEGENS MEDIUM (DSMZ Medium 115) | yes | https://mediadive.dsmz.de/medium/115 | Name: VIBRIO NATRIEGENS MEDIUM (DSMZ Medium 115) Composition: NaCl 15.0 g/l Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water |
3103 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
38144 | MEDIUM 25 - for Arcobacter nitrofigilis | yes | Distilled water make up to (1000.000 ml);Sodium chloride (15.000 g);Magnesium chloride hexahydrate (1.000 g);Agar (15.000 g);Yeast extract (5.000 g);Horse blood(50.000 ml);Succinic acid (2.000 g);Beef extract (5.000 g);Sodium glutamate (2.000 g);Special p | |
121311 | CIP Medium 25 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=25 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
3103 | positive | growth | 25 | mesophilic |
38144 | positive | growth | 37 | mesophilic |
46369 | positive | growth | 25 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
121311 | positive | growth | 22 | psychrophilic |
121311 | no | growth | 10 | psychrophilic |
121311 | no | growth | 41 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
3103 | microaerophile |
46369 | microaerophile |
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.865
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
121311 | NaCl | positive | growth | 2 % |
121311 | NaCl | no | growth | 4 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68369 | 25115 | malate | + | assimilation |
68369 | 17128 | adipate | + | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | - | assimilation |
68369 | 17306 | maltose | + | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | - | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | + | reduction |
121311 | 606565 | hippurate | - | hydrolysis |
121311 | 17632 | nitrate | + | reduction |
121311 | 16301 | nitrite | - | reduction |
121311 | 132112 | sodium thiosulfate | - | builds gas from |
68373 | 606565 | hippurate | - | hydrolysis |
68373 | 17634 | D-glucose | - | assimilation |
68373 | 30031 | succinate | + | assimilation |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is sensitive | sensitivity conc. |
---|---|---|---|---|---|
68373 | 48923 | erythromycin | yes | yes | 14 µg |
68373 | 474053 | cefazolin | yes | yes | 224 µg |
68373 | 100147 | nalidixic acid | yes | yes | 84 µg |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68373 | 16136 | hydrogen sulfide | no |
68369 | 35581 | indole | no |
121311 | 35581 | indole | no |
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
3103 | catalase | + | 1.11.1.6 |
3103 | cytochrome-c oxidase | + | 1.9.3.1 |
68373 | catalase | + | 1.11.1.6 |
68373 | L-aspartate arylamidase | - | 3.4.11.21 |
68373 | L-arginine arylamidase | - | |
68373 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68373 | gamma-glutamyltransferase | - | 2.3.2.2 |
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | - | |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
121311 | oxidase | + | |
121311 | gelatinase | - | |
121311 | DNase | - | |
121311 | catalase | + | 1.11.1.6 |
121311 | lecithinase | - | |
121311 | urease | + | 3.5.1.5 |
fatty acid profile
fatty acids
@ref fatty acid percentage ECL 46369 C12:0 6.4 12 46369 C14:0 3.3 14 46369 C16:0 31.5 16 46369 C18:0 0.6 18 46369 C12:0 3OH 2.7 13.455 46369 C12:0 ALDE ? 1.2 10.915 46369 C13:0 ISO 2OH 0.4 13.814 46369 C14:0 3OH/C16:1 ISO I 2.3 15.485 46369 C16:1 ω7c 31.5 15.819 46369 C18:1 ω7c /12t/9t 18.2 17.824 46369 C18:2 ω6,9c/C18:0 ANTE 0.7 17.724 46369 Unidentified 0.6 46369 unknown 12.486 0.5 12.486 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3103 | + | - | - | - | - | - | - | - | + | +/- | +/- | +/- | +/- | + | - | - | + | + | - | - | + |
API CAM
@ref | URE | NIT | EST | HIP | GGT | TTC | PYRA | ArgA | AspA | PAL | H2S | GLU | SUT | NAL | CFZ | ACE | PROP | MLT | CIT | ERO | CAT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3103 | - | + | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | + |
3103 | - | + | + | - | - | + | - | - | - | + | - | - | + | - | - | + | + | - | - | - | |
3103 | + | + | + | - | - | + | - | - | - | + | - | - | + | - | - | - | +/- | - | - | - | + |
3103 | - | + | + | - | - | + | - | - | - | + | - | - | + | - | - | +/- | + | - | +/- | - | |
46369 | + | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | + | - | - | + |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121311 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|---|
3103 | roots of Spartina alterniflora (marshland) | Spartina alterniflora | Nova Scotia | Canada | CAN | North America | |
46369 | Roots of short Spartina alterniflora | Halifax,Nova Scotia | Canada | CAN | North America | ||
67770 | Roots of short Spartina. alternijlora | Spartina. alternijlora | Halifax, Nova Scotia | Canada | CAN | North America | |
121311 | Plant, Roots, Spartina alterniflora | Canada | CAN | North America | 1984 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Wetland (Swamp) |
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
#Host Body-Site | #Plant | #Root (Rhizome) |
taxonmaps
- @ref: 69479
- File name: preview.99_15309.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_53;96_1229;97_1456;98_1776;99_15309&stattab=map
- Last taxonomy: Arcobacter nitrofigilis subclade
- 16S sequence: L14627
- Sequence Identity:
- Total samples: 12
- aquatic counts: 11
- animal counts: 1
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
3103 | 1 | Risk group (German classification) |
121311 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 3103
- description: Arcobacter nitrofigilis 16S ribosomal RNA
- accession: L14627
- length: 1461
- database: ena
- NCBI tax ID: 28199
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Arcobacter nitrofigilis DSM 7299 | GCA_000092245 | complete | ncbi | 572480 |
66792 | Arcobacter nitrofigilis DSM 7299 | 572480.3 | complete | patric | 572480 |
66792 | Arcobacter nitrofigilis DSM 7299 | 646564506 | complete | img | 572480 |
GC content
- @ref: 3103
- GC-content: 29.0
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 77 | no |
motile | yes | 88.29 | no |
flagellated | yes | 82.424 | no |
gram-positive | no | 98.279 | no |
anaerobic | no | 79.026 | no |
aerobic | no | 88.359 | no |
halophile | no | 72.467 | no |
spore-forming | no | 92.871 | no |
thermophile | no | 99.627 | yes |
glucose-util | no | 58.571 | no |
glucose-ferment | no | 89.346 | no |
External links
@ref: 3103
culture collection no.: CCUG 15892, CECT 7204, DSM 7299, ATCC 33309, CCUG 15893, LMG 7604, NCTC 12251, JCM 33357, CIP 103745
straininfo link
- @ref: 71739
- straininfo: 978
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
3103 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7299) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-7299 | |||
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 | |||
38144 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/15576 | ||||
46369 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 15893) | https://www.ccug.se/strain?id=15893 | |||
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) | |||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
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/ | ||||
68369 | Automatically annotated from API 20NE | |||||
68373 | Automatically annotated from API CAM | |||||
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) | |||
71739 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID978.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121311 | Curators of the CIP | Collection of Institut Pasteur (CIP 103745) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103745 |