Strain identifier
BacDive ID: 5706
Type strain:
Species: Chryseobacterium palustre
Strain Designation: 3A10
Strain history: CIP <- 2010, DSMZ <- C. Pires, UCP, Porto, Portugal: strain 3A10
NCBI tax ID(s): 1121288 (strain), 493376 (species)
General
@ref: 15821
BacDive-ID: 5706
DSM-Number: 21579
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Chryseobacterium palustre 3A10 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rhizosphere sediment sample from a polluted site.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1121288 | strain |
493376 | species |
strain history
@ref | history |
---|---|
15821 | <- C. Pires, Escola Superior Biotecnol. (UCP), Porto, Portugal; 3A10 |
121516 | CIP <- 2010, DSMZ <- C. Pires, UCP, Porto, Portugal: strain 3A10 |
doi: 10.13145/bacdive5706.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Weeksellaceae
- genus: Chryseobacterium
- species: Chryseobacterium palustre
- full scientific name: Chryseobacterium palustre Pires et al. 2010
synonyms
- @ref: 20215
- synonym: Kaistella palustris
@ref: 15821
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Weeksellaceae
genus: Chryseobacterium
species: Chryseobacterium palustre
full scientific name: Chryseobacterium palustre Pires et al. 2010 emend. Hahnke et al. 2016
strain designation: 3A10
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29291 | negative | 1.8 µm | 0.6 µm | rod-shaped | no | |
69480 | no | 92.171 | ||||
69480 | negative | 99.994 | ||||
121516 | negative | rod-shaped | yes |
pigmentation
- @ref: 29291
- production: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
15821 | TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) | yes | https://mediadive.dsmz.de/medium/545 | Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water |
40741 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
121516 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
15821 | positive | growth | 28 | mesophilic |
29291 | positive | growth | 10-37 | |
29291 | positive | optimum | 30 | mesophilic |
40741 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29291 | positive | growth | 06-09 | alkaliphile |
29291 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
29291 | aerobe |
121516 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.99 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29291 | NaCl | positive | growth | 0-6 % |
29291 | NaCl | positive | optimum | 2.5 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29291 | 17128 | adipate | + | carbon source |
29291 | 22599 | arabinose | + | carbon source |
29291 | 28757 | fructose | + | carbon source |
29291 | 17234 | glucose | + | carbon source |
29291 | 28087 | glycogen | + | carbon source |
29291 | 17716 | lactose | + | carbon source |
29291 | 25115 | malate | + | carbon source |
29291 | 17306 | maltose | + | carbon source |
29291 | 29864 | mannitol | + | carbon source |
29291 | 37684 | mannose | + | carbon source |
29291 | 506227 | N-acetylglucosamine | + | carbon source |
29291 | 26546 | rhamnose | + | carbon source |
29291 | 30911 | sorbitol | + | carbon source |
29291 | 17992 | sucrose | + | carbon source |
29291 | 18222 | xylose | + | carbon source |
29291 | 4853 | esculin | + | hydrolysis |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | - | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 18287 | L-fucose | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 32528 | turanose | - | builds acid from |
68371 | 28066 | gentiobiose | - | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28087 | glycogen | - | builds acid from |
68371 | 16634 | raffinose | - | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 27082 | trehalose | - | builds acid from |
68371 | 17992 | sucrose | - | builds acid from |
68371 | 28053 | melibiose | - | builds acid from |
68371 | 17716 | lactose | - | builds acid from |
68371 | 17057 | cellobiose | - | builds acid from |
68371 | 17814 | salicin | - | builds acid from |
68371 | 4853 | esculin | - | builds acid from |
68371 | 18305 | arbutin | - | builds acid from |
68371 | 27613 | amygdalin | - | builds acid from |
68371 | 59640 | N-acetylglucosamine | - | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 16899 | D-mannitol | - | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 15824 | D-fructose | - | builds acid from |
68371 | 12936 | D-galactose | - | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 65327 | D-xylose | - | builds acid from |
68371 | 16988 | D-ribose | - | builds acid from |
68371 | 30849 | L-arabinose | - | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | - | builds acid from |
121516 | 17632 | nitrate | - | reduction |
121516 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 121516
- Chebi-ID: 35581
- metabolite: indole
- production: yes
enzymes
@ref | value | activity | ec |
---|---|---|---|
29291 | catalase | + | 1.11.1.6 |
29291 | gelatinase | + | |
29291 | cytochrome oxidase | + | 1.9.3.1 |
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 |
121516 | oxidase | + | |
121516 | catalase | + | 1.11.1.6 |
121516 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121516 | - | + | + | + | + | + | + | + | + | + | + | + | - | - | - | + | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121516 | - | - | - | - | - | - | - | - | - | - | +/- | - | +/- | - | - | - | - | - | - | - | - | - | - | - | - | - | - | +/- | - | - | - | - | - | - | - | +/- | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
15821 | rhizosphere sediment sample from a polluted site | Northwest Portugal, Estarreja | Portugal | PRT | Europe |
121516 | Environment, Rhizosphere sediment, sample from a polluted site | Estarreja | Portugal | PRT | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Contamination | |
#Environmental | #Terrestrial | #Sediment |
#Host Body-Site | #Plant | #Rhizosphere |
taxonmaps
- @ref: 69479
- File name: preview.99_2053.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_1132;97_1328;98_1605;99_2053&stattab=map
- Last taxonomy: Chryseobacterium palustre subclade
- 16S sequence: AB682225
- Sequence Identity:
- Total samples: 494
- soil counts: 43
- aquatic counts: 130
- animal counts: 313
- plant counts: 8
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
15821 | 1 | Risk group (German classification) |
121516 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Chryseobacterium palustre gene for 16S rRNA, partial sequence, strain: NBRC 104928 | AB682225 | 1442 | ena | 493376 |
15821 | Chryseobacterium palustre strain 3A10 16S ribosomal RNA gene, partial sequence | EU360967 | 1444 | ena | 1121288 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Kaistella palustris DSM 21579 | GCA_000422265 | scaffold | ncbi | 1121288 |
66792 | Chryseobacterium palustre DSM 21579 | 1121288.4 | wgs | patric | 1121288 |
66792 | Chryseobacterium palustre DSM 21579 | 2523533629 | draft | img | 1121288 |
GC content
@ref | GC-content | method |
---|---|---|
15821 | 43 | |
15821 | 42.4 | |
15821 | 41.5 | sequence analysis |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 91.564 | no |
flagellated | no | 97.491 | yes |
gram-positive | no | 98.243 | yes |
anaerobic | no | 99.067 | yes |
aerobic | yes | 87.936 | yes |
halophile | no | 85.057 | no |
spore-forming | no | 96.218 | no |
thermophile | no | 99.248 | yes |
glucose-util | yes | 87.315 | no |
glucose-ferment | no | 92.443 | no |
External links
@ref: 15821
culture collection no.: DSM 21579, LMG 24685, NBRC 104928, CIP 110180
straininfo link
- @ref: 75188
- straininfo: 358561
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 19651727 | Chryseobacterium palustre sp. nov. and Chryseobacterium humi sp. nov., isolated from industrially contaminated sediments. | Pires C, Carvalho MF, De Marco P, Magan N, Castro PML | Int J Syst Evol Microbiol | 10.1099/ijs.0.010348-0 | 2009 | Base Composition, Base Sequence, Chemical Industry, Chryseobacterium/chemistry/*classification/physiology, DNA, Bacterial/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Phylogeny, Portugal, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, *Soil Microbiology, *Soil Pollutants | Genetics |
Phylogeny | 33724915 | Kaistella flava sp. nov., isolated from Antarctic tundra soil, and emended descriptions of Kaistella yonginensis, Kaistella jeonii, Kaistella antarctica and Kaistella chaponensis. | Peng X, Zhang Y, Lu Y, Zhou X, Wei Z, Sun Y, Kuang C, Lu L, Geng Y, Qin K, Liu J, Peng F | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004740 | 2021 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
15821 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21579) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21579 | ||||
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 | ||
29291 | 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 | 28776041 | 25707 | ||
40741 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/8010 | |||||
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) | ||||
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 | ||||
75188 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID358561.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
121516 | Curators of the CIP | Collection of Institut Pasteur (CIP 110180) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110180 |