Strain identifier
BacDive ID: 130647
Type strain:
Species: Cribrihabitans marinus
Strain Designation: CZ-AM5
Strain history: Z.-P. Liu CZ-AM5.
NCBI tax ID(s): 1227549 (species)
General
@ref: 22102
BacDive-ID: 130647
DSM-Number: 29340
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Cribrihabitans marinus CZ-AM5 is a mesophilic bacterium that was isolated from biofilm formed in an aerated biological filter in a recirculating marine aquaculture system.
NCBI tax id
- NCBI tax id: 1227549
- Matching level: species
strain history
@ref | history |
---|---|
22102 | <- JCM <- Z.-P. Liu; CZ-AM5 |
67770 | Z.-P. Liu CZ-AM5. |
doi: 10.13145/bacdive130647.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Cribrihabitans
- species: Cribrihabitans marinus
- full scientific name: Cribrihabitans marinus Chen et al. 2014
@ref: 22102
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Cribrihabitans
species: Cribrihabitans marinus
full scientific name: Cribrihabitans marinus Chen et al. 2014
strain designation: CZ-AM5
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | no | 92.883 | |
69480 | 99.998 | negative |
colony morphology
- @ref: 22102
- incubation period: 2-3 days
Culture and growth conditions
culture medium
- @ref: 22102
- name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
- growth: yes
- link: https://mediadive.dsmz.de/medium/514
- composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
22102 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.998 |
observation
- @ref: 67770
- observation: quinones: Q-10
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 | 16899 | D-mannitol | + | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | - | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
22102 | catalase | + | 1.11.1.6 |
68369 | gelatinase | - | |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
22102 | - | - | - | - | - | +/- | - | - | - | - | - | + | +/- | +/- | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
22102 | biofilm formed in an aerated biological filter in a recirculating marine aquaculture system | Tianjin | China | CHN | Asia |
67770 | Biofilm formed in an aerated biological filter in a recirculating marine aquaculture system | Tianjin | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Built environment | #Water reservoir (Aquarium/pool) |
#Engineered | #Laboratory | #Lab enrichment |
#Environmental | #Biofilm |
taxonmaps
- @ref: 69479
- File name: preview.99_156553.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_42219;97_76483;98_103198;99_156553&stattab=map
- Last taxonomy: Cribrihabitans marinus subclade
- 16S sequence: JX306766
- Sequence Identity:
- Total samples: 416
- soil counts: 6
- aquatic counts: 356
- animal counts: 53
- plant counts: 1
Safety information
risk assessment
- @ref: 22102
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22102
- description: Cribrihabitans marinus strain CZ-AM5 16S ribosomal RNA gene, complete sequence
- accession: JX306766
- length: 1425
- database: ena
- NCBI tax ID: 1227549
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Cribrihabitans marinus CGMCC 1.13219 | GCA_014640375 | contig | ncbi | 1227549 |
66792 | Cribrihabitans marinus strain CGMCC 1.13219 | 1227549.4 | wgs | patric | 1227549 |
66792 | Cribrihabitans marinus strain DSM 29340 | 1227549.3 | wgs | patric | 1227549 |
66792 | Cribrihabitans marinus DSM 29340 | 2693429871 | draft | img | 1227549 |
67770 | Cribrihabitans marinus DSM 29340 | GCA_900109035 | contig | ncbi | 1227549 |
GC content
@ref | GC-content | method |
---|---|---|
22102 | 60.4 | high performance liquid chromatography (HPLC) |
67770 | 60.4 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 65.191 | no |
gram-positive | no | 97.802 | no |
anaerobic | no | 98.788 | no |
aerobic | yes | 91.603 | no |
halophile | yes | 75.993 | no |
spore-forming | no | 96.905 | no |
thermophile | no | 87.307 | no |
glucose-util | yes | 58.423 | yes |
flagellated | no | 88.071 | no |
glucose-ferment | no | 91.936 | yes |
External links
@ref: 22102
culture collection no.: DSM 29340, CGMCC 1.13219, JCM 19401
straininfo link
- @ref: 89158
- straininfo: 402099
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 24425741 | Cribrihabitans marinus gen. nov., sp. nov., isolated from a biological filter in a marine recirculating aquaculture system. | Chen Z, Liu Y, Liu LZ, Zhong ZP, Liu ZP, Liu Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.059576-0 | 2014 | *Aquaculture, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry, *Water Microbiology | Genetics |
Phylogeny | 25180090 | Cribrihabitans neustonicus sp. nov., isolated from coastal surface seawater, and emended description of the genus Cribrihabitans Chen et al. 2014. | Hameed A, Shahina M, Lin SY, Lai WA, Liu YC, Hsu YH, Young CC | Int J Syst Evol Microbiol | 10.1099/ijs.0.066142-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistry | Genetics |
Phylogeny | 27334981 | Lutimaribacter marinistellae sp. nov., isolated from a starfish. | Zhang Y, Tang P, Xu Y, Fang W, Wang X, Fang Z, Xiao Y | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001251 | 2016 | Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Starfish/*microbiology, Ubiquinone/chemistry | Transcriptome |
Reference
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
22102 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29340 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29340) | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | 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 | |||||
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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
89158 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID402099.1 |