Strain identifier

BacDive ID: 140110

Type strain: Yes

Species: Chryseobacterium sediminis

Strain Designation: IMT-174

Strain history: CIP <- 2015, P. Kämpfer, Giessen Univ., Giessen, Germany: strain IMT-174

NCBI tax ID(s): 1679494 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 42717

BacDive-ID: 140110

DSM-Number: 29981

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Chryseobacterium sediminis IMT-174 is a mesophilic bacterium that was isolated from river sediment.

NCBI tax id

  • NCBI tax id: 1679494
  • Matching level: species

strain history

@refhistory
42717<- P. Kämpfer, Univ. Giessen, Germany; IMT-174 <- G. Harmon
122535CIP <- 2015, P. Kämpfer, Giessen Univ., Giessen, Germany: strain IMT-174

doi: 10.13145/bacdive140110.20230509.8.1

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 sediminis
  • full scientific name: Chryseobacterium sediminis Kämpfer et al. 2015

@ref: 42717

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Weeksellaceae

genus: Chryseobacterium

species: Chryseobacterium sediminis

full scientific name: Chryseobacterium sediminis Kämpfer et al. 2015

strain designation: IMT-174

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no93.268
6948099.995negative
122535nonegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
41951MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
42717TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yesName: 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 waterhttps://mediadive.dsmz.de/medium/545
122535CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
41951positivegrowth30mesophilic
42717positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.999

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
42717river sedimentAmacuro riverGuyanaGUYMiddle and South America
122535Environment, Sediment, Amacwo riverGuyanaFranceFRAEurope2011-02-02

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#River (Creek)
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_1681.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_76;96_753;97_878;98_1329;99_1681&stattab=map
  • Last taxonomy: Chryseobacterium
  • 16S sequence: KR349467
  • Sequence Identity:
  • Total samples: 347
  • soil counts: 79
  • aquatic counts: 106
  • animal counts: 148
  • plant counts: 14

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
427171Risk group (German classification)
1225351Risk group (French classification)

Sequence information

16S sequences

  • @ref: 42717
  • description: Chryseobacterium sediminis strain IMT-174 16S ribosomal RNA gene, partial sequence
  • accession: KR349467
  • length: 1396
  • database: ena
  • NCBI tax ID: 1679494

Genome sequences

  • @ref: 66792
  • description: Chryseobacterium sediminis IMT-174
  • accession: GCA_008386505
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 1679494

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.807no
flagellatedno96.507no
gram-positiveno97.971no
anaerobicno99.57no
aerobicyes93.776no
halophileno94.896no
spore-formingno93.971no
glucose-utilyes85.721no
thermophileno99.535yes
glucose-fermentno93.913no

External links

@ref: 42717

culture collection no.: DSM 29981, CIP 110895, LMG 28695

straininfo link

  • @ref: 96517
  • straininfo: 406377

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26283329Chryseobacterium sediminis sp. nov., isolated from a river sediment.Kampfer P, Busse HJ, McInroy JA, Glaeser SPInt J Syst Evol Microbiol10.1099/ijsem.0.0005272015Bacterial Typing Techniques, Base Composition, Chryseobacterium/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Guyana, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rivers/*microbiology, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny34748473Chryseobacterium panacisoli sp. nov., isolated from ginseng-cultivation soil with ginsenoside-converting activity.Keum DH, Yeon JM, Yun CS, Lee SY, Im WTInt J Syst Evol Microbiol10.1099/ijsem.0.0050862021Bacterial Typing Techniques, Base Composition, *Chryseobacterium/classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Ginsenosides/metabolism, Glycolipids/chemistry, Nucleic Acid Hybridization, *Panax/microbiology, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
41951Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/34489
42717Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29981Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29981)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
96517Reimer, 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 identifiers10.60712/SI-ID406377.1
122535Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110895Collection of Institut Pasteur (CIP 110895)