Strain identifier

BacDive ID: 5706

Type strain: Yes

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)

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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 idMatching level
1121288strain
493376species

strain history

@refhistory
15821<- C. Pires, Escola Superior Biotecnol. (UCP), Porto, Portugal; 3A10
121516CIP <- 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

@refgram staincell lengthcell widthcell shapemotilityconfidence
29291negative1.8 µm0.6 µmrod-shapedno
69480no92.171
69480negative99.994
121516negativerod-shapedyes

pigmentation

  • @ref: 29291
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15821TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://mediadive.dsmz.de/medium/545Name: 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
40741MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121516CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
15821positivegrowth28mesophilic
29291positivegrowth10-37
29291positiveoptimum30mesophilic
40741positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
29291positivegrowth06-09alkaliphile
29291positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29291aerobe
121516obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.99

halophily

@refsaltgrowthtested relationconcentration
29291NaClpositivegrowth0-6 %
29291NaClpositiveoptimum2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2929117128adipate+carbon source
2929122599arabinose+carbon source
2929128757fructose+carbon source
2929117234glucose+carbon source
2929128087glycogen+carbon source
2929117716lactose+carbon source
2929125115malate+carbon source
2929117306maltose+carbon source
2929129864mannitol+carbon source
2929137684mannose+carbon source
29291506227N-acetylglucosamine+carbon source
2929126546rhamnose+carbon source
2929130911sorbitol+carbon source
2929117992sucrose+carbon source
2929118222xylose+carbon source
292914853esculin+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837115824D-fructose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12151617632nitrate-reduction
12151616301nitrite-reduction

metabolite production

  • @ref: 121516
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

enzymes

@refvalueactivityec
29291catalase+1.11.1.6
29291gelatinase+
29291cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)+
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
121516oxidase+
121516catalase+1.11.1.6
121516urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121516-+++++++++++---+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121516----------+/--+/---------------+/--------+/--------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15821rhizosphere sediment sample from a polluted siteNorthwest Portugal, EstarrejaPortugalPRTEurope
121516Environment, Rhizosphere sediment, sample from a polluted siteEstarrejaPortugalPRTEurope

isolation source categories

Cat1Cat2Cat3
#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

@refbiosafety levelbiosafety level comment
158211Risk group (German classification)
1215161Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Chryseobacterium palustre gene for 16S rRNA, partial sequence, strain: NBRC 104928AB6822251442ena493376
15821Chryseobacterium palustre strain 3A10 16S ribosomal RNA gene, partial sequenceEU3609671444ena1121288

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Kaistella palustris DSM 21579GCA_000422265scaffoldncbi1121288
66792Chryseobacterium palustre DSM 215791121288.4wgspatric1121288
66792Chryseobacterium palustre DSM 215792523533629draftimg1121288

GC content

@refGC-contentmethod
1582143
1582142.4
1582141.5sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.564no
flagellatedno97.491yes
gram-positiveno98.243yes
anaerobicno99.067yes
aerobicyes87.936yes
halophileno85.057no
spore-formingno96.218no
thermophileno99.248yes
glucose-utilyes87.315no
glucose-fermentno92.443no

External links

@ref: 15821

culture collection no.: DSM 21579, LMG 24685, NBRC 104928, CIP 110180

straininfo link

  • @ref: 75188
  • straininfo: 358561

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19651727Chryseobacterium palustre sp. nov. and Chryseobacterium humi sp. nov., isolated from industrially contaminated sediments.Pires C, Carvalho MF, De Marco P, Magan N, Castro PMLInt J Syst Evol Microbiol10.1099/ijs.0.010348-02009Base 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 PollutantsGenetics
Phylogeny33724915Kaistella 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 FInt J Syst Evol Microbiol10.1099/ijsem.0.0047402021

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
15821Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21579)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21579
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
29291Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604125707
40741Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8010
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
75188Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID358561.1StrainInfo: A central database for resolving microbial strain identifiers
121516Curators of the CIPCollection of Institut Pasteur (CIP 110180)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110180