Strain identifier

BacDive ID: 5705

Type strain: Yes

Species: Chryseobacterium humi

Strain Designation: ECP37

Strain history: CIP <- 2010, DSMZ <- C. Pires, UCP, Porto, Portugal: strain ECP37

NCBI tax ID(s): 493375 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 15822

BacDive-ID: 5705

DSM-Number: 21580

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Chryseobacterium humi ECP37 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from contaminated industrial soil.

NCBI tax id

  • NCBI tax id: 493375
  • Matching level: species

strain history

@refhistory
15822<- C. Pires, Escola Superior Biotecnol. (UCP), Porto, Portugal; ECP37
119982CIP <- 2010, DSMZ <- C. Pires, UCP, Porto, Portugal: strain ECP37

doi: 10.13145/bacdive5705.20230509.8.1

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 humi
  • full scientific name: Chryseobacterium humi Pires et al. 2010

  • synonyms

    • @ref: 20215
    • synonym: Halpernia humi

@ref: 15822

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium humi

full scientific name: Chryseobacterium humi Pires et al. 2010

strain designation: ECP37

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29291negative2.05 µm0.55 µmrod-shapedno
69480no90.742
69480negative99.967
119982negativerod-shapedno

pigmentation

  • @ref: 29291
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15822TRYPTONE 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
34511MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119982CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
15822positivegrowth28mesophilic
29291positivegrowth04-37
29291positiveoptimum27.5mesophilic
34511positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
29291positivegrowth06-09alkaliphile
29291positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29291aerobe
119982obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
29291NaClpositivegrowth0-7 %
29291NaClpositiveoptimum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2929122599arabinose+carbon source
2929117057cellobiose+carbon source
2929117234glucose+carbon source
2929128087glycogen+carbon source
2929117306maltose+carbon source
2929137684mannose+carbon source
292914853esculin+hydrolysis
11998217632nitrate-reduction
11998216301nitrite-reduction

metabolite production

  • @ref: 119982
  • 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
119982oxidase+
119982catalase+1.11.1.6
119982urease-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
119982-+-+-++--+++---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15822contaminated industrial soilnorthern Portugal, EstarrejaPortugalPRTEurope
119982Environment, Contaminated industrial soilEstarrejaPortugalPRTEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Engineered#Industrial
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_116675.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_19049;97_23613;98_58371;99_116675&stattab=map
  • Last taxonomy: Chryseobacterium humi
  • 16S sequence: EU360966
  • Sequence Identity:
  • Total samples: 77
  • soil counts: 30
  • aquatic counts: 29
  • animal counts: 17
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
158221Risk group (German classification)
1199821Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15822
  • description: Chryseobacterium humi strain ECP37 16S ribosomal RNA gene, partial sequence
  • accession: EU360966
  • length: 1480
  • database: ena
  • NCBI tax ID: 493375

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Halpernia humi DSM 21580GCA_900108025contigncbi493375
66792Chryseobacterium humi strain DSM 21580493375.5wgspatric493375
66792Chryseobacterium humi DSM 215802684622890draftimg493375

GC content

@refGC-contentmethod
1582234high performance liquid chromatography (HPLC)
2929134

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.44yes
anaerobicno99.383no
halophileno90.861no
spore-formingno96.811no
glucose-utilyes84.412yes
aerobicyes87.011no
thermophileno99.027yes
motileno94.169yes
flagellatedno97.645yes
glucose-fermentno92.002no

External links

@ref: 15822

culture collection no.: DSM 21580, LMG 24684, NBRC 104927, CIP 110175

straininfo link

  • @ref: 75187
  • straininfo: 358562

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
Biotechnology26676544Mine land valorization through energy maize production enhanced by the application of plant growth-promoting rhizobacteria and arbuscular mycorrhizal fungi.Moreira H, Pereira SI, Marques AP, Rangel AO, Castro PMEnviron Sci Pollut Res Int10.1007/s11356-015-5914-42015Biodegradation, Environmental, Biomass, Cadmium, Glomeromycota, Metals, Heavy/analysis, *Mining, Mycorrhizae/*physiology, Plant Development, Plant Roots, Rhizobium, *Rhizosphere, Soil, *Soil Microbiology, Soil Pollutants/*analysis, Zea mays/chemistry/*growth & development

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15822Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21580)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21580
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
29291Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2570728776041
34511Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8005
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)
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
75187Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID358562.1StrainInfo: A central database for resolving microbial strain identifiers
119982Curators of the CIPCollection of Institut Pasteur (CIP 110175)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110175