Strain identifier
BacDive ID: 5382
Type strain:
Species: Qipengyuania citrea
Strain Designation: RE35F/1
Strain history: CIP <- 2001, E.B.M. Denner, Inst. Mikrobiol. Genetik, Vienna, Austria: strain RE35F/1 <- D. Vybiral
NCBI tax ID(s): 225971 (species)
General
@ref: 5351
BacDive-ID: 5382
DSM-Number: 14432
keywords: genome sequence, 16S sequence, Bacteria, psychrophilic, Gram-negative
description: Qipengyuania citrea RE35F/1 is a psychrophilic, Gram-negative bacterium that was isolated from seawater.
NCBI tax id
- NCBI tax id: 225971
- Matching level: species
strain history
@ref | history |
---|---|
5351 | <- E. B. M. Denner; RE35F/1 <- D. Vybiral |
67770 | IAM 15372 <-- KCTC 12214 <-- CIP 107092 <-- E. B. M. Denner RE35F/1 <-- D. Vybiral. |
118302 | CIP <- 2001, E.B.M. Denner, Inst. Mikrobiol. Genetik, Vienna, Austria: strain RE35F/1 <- D. Vybiral |
doi: 10.13145/bacdive5382.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Sphingomonadales
- family: Erythrobacteraceae
- genus: Qipengyuania
- species: Qipengyuania citrea
- full scientific name: Qipengyuania citrea (Denner et al. 2002) Xu et al. 2020
synonyms
- @ref: 20215
- synonym: Erythrobacter citreus
@ref: 5351
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Sphingomonadales
family: Erythrobacteraceae
genus: Erythrobacter
species: Erythrobacter citreus
full scientific name: Erythrobacter citreus Denner et al. 2002
strain designation: RE35F/1
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | negative | 99.992 | ||
118302 | negative | oval-shaped | no |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
5351 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | 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 |
38663 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
118302 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
5351 | positive | growth | 20 | psychrophilic |
38663 | positive | growth | 25 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
118302 | positive | growth | 25-37 | mesophilic |
118302 | no | growth | 5 | psychrophilic |
118302 | no | growth | 15 | psychrophilic |
118302 | no | growth | 41 | thermophilic |
118302 | no | growth | 45 | thermophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.984 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
118302 | NaCl | no | growth | 0 % |
118302 | NaCl | no | growth | 2 % |
118302 | NaCl | no | growth | 4 % |
118302 | NaCl | no | growth | 6 % |
118302 | NaCl | no | growth | 8 % |
118302 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: Q-10
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
118302 | 16947 | citrate | - | carbon source |
118302 | 4853 | esculin | - | hydrolysis |
118302 | 606565 | hippurate | + | hydrolysis |
118302 | 17632 | nitrate | - | builds gas from |
118302 | 17632 | nitrate | - | reduction |
118302 | 16301 | nitrite | - | builds gas from |
118302 | 16301 | nitrite | - | reduction |
118302 | 15792 | malonate | - | assimilation |
118302 | 17234 | glucose | - | degradation |
118302 | 17632 | nitrate | - | respiration |
metabolite production
- @ref: 118302
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
118302 | 15688 | acetoin | - | |
118302 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | + | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
118302 | oxidase | + | |
118302 | beta-galactosidase | - | 3.2.1.23 |
118302 | alcohol dehydrogenase | - | 1.1.1.1 |
118302 | gelatinase | - | |
118302 | amylase | - | |
118302 | caseinase | - | 3.4.21.50 |
118302 | catalase | + | 1.11.1.6 |
118302 | tween esterase | + | |
118302 | gamma-glutamyltransferase | + | 2.3.2.2 |
118302 | lecithinase | - | |
118302 | lipase | - | |
118302 | lysine decarboxylase | - | 4.1.1.18 |
118302 | ornithine decarboxylase | - | 4.1.1.17 |
118302 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
118302 | protease | - | |
118302 | tryptophan deaminase | - | |
118302 | urease | - | 3.5.1.5 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
118302 | - | + | + | + | - | + | + | + | - | - | + | + | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
5351 | seawater | Corsica, Bay of Calvi | France | FRA | Europe | |
67770 | Western Mediterranean Sea | |||||
118302 | Environment, Seawater | Corsica | France | FRA | Europe | 1994 |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_361.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_251;97_274;98_305;99_361&stattab=map
- Last taxonomy: Qipengyuania
- 16S sequence: AF118020
- Sequence Identity:
- Total samples: 563
- soil counts: 28
- aquatic counts: 489
- animal counts: 32
- plant counts: 14
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
5351 | 1 | Risk group (German classification) |
118302 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
5351 | Erythrobacter citreus strain RE35F/1 16S ribosomal RNA gene, partial sequence | AF118020 | 1444 | ena | 225971 |
67770 | Erythrobacter citreus 16S ribosomal RNA gene, partial sequence | AF227259 | 1359 | ena | 225971 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Erythrobacter citreus strain CGMCC 1.8703 | 225971.7 | wgs | patric | 225971 |
66792 | Erythrobacter citreus DSM 14432 | 2928592673 | draft | img | 225971 |
67770 | Qipengyuania citrea CGMCC 1.8703 | GCA_009828015 | contig | ncbi | 225971 |
GC content
@ref | GC-content | method |
---|---|---|
5351 | 62.0-62.4 | high performance liquid chromatography (HPLC) |
67770 | 64.2 | genome sequence analysis |
67770 | 62 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 87.261 | no |
gram-positive | no | 96.467 | no |
anaerobic | no | 99.198 | no |
aerobic | yes | 95.583 | no |
halophile | no | 82.897 | no |
spore-forming | no | 92.858 | no |
glucose-util | yes | 83.585 | no |
flagellated | no | 96.969 | no |
thermophile | no | 97.567 | no |
glucose-ferment | no | 92.654 | no |
External links
@ref: 5351
culture collection no.: DSM 14432, CIP 107092, JCM 21816, CGMCC 1.8703, CGMCC 1.8709, IAM 15372, KCTC 12214
straininfo link
- @ref: 74872
- straininfo: 100645
literature
- topic: Phylogeny
- Pubmed-ID: 34047831
- title: Qipengyuania soli sp. nov., Isolated from Mangrove Soil.
- authors: Liu Y, Pei T, Deng MR, Zhu H
- journal: Curr Microbiol
- DOI: 10.1007/s00284-021-02538-1
- year: 2021
- mesh: Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids, *Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil
- topic2: Transcriptome
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
5351 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14432) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14432 | |
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 | |
38663 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/19294 | ||
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 | |
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 | |
74872 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID100645.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
118302 | Curators of the CIP | Collection of Institut Pasteur (CIP 107092) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107092 |