Strain identifier

BacDive ID: 135526

Type strain: Yes

Species: Croceibacter atlanticus

Strain history: CIP <- 2003, KCTC

NCBI tax ID(s): 313588 (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 8.1 (current version)

General

@ref: 34673

BacDive-ID: 135526

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

description: Croceibacter atlanticus CIP 108009 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from Bermuda Atlantic Time Series station in the western Sargasso Sea.

NCBI tax id

  • NCBI tax id: 313588
  • Matching level: species

strain history

@refhistory
346732003, KCTC
67770IAM 15332 <-- CIP 108009 <-- KCTC 12090 <-- J.-C. Cho and S. J. Giovannoni HTCC2559.
34673CIP <- 2003, KCTC

doi: 10.13145/bacdive135526.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Croceibacter
  • species: Croceibacter atlanticus
  • full scientific name: Croceibacter atlanticus Cho and Giovannoni 2003

@ref: 34673

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Croceibacter

species: Croceibacter atlanticus

type strain: yes

Morphology

cell morphology

  • @ref: 34673
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

pigmentation

  • @ref: 34673
  • production: no
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
34673Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
34673CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
34673positivegrowth25mesophilic
67770positivegrowth23psychrophilic
34673positivegrowth15-30
34673nogrowth5psychrophilic
34673nogrowth37mesophilic
34673nogrowth41thermophilic
34673nogrowth45thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
34673NaClnogrowth0 %
34673NaClnogrowth2 %
34673NaClnogrowth4 %
34673NaClnogrowth6 %
34673NaClnogrowth8 %
34673NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
346734853esculin-hydrolysis
34673606565hippurate+hydrolysis
3467317632nitrate-reduction
3467316301nitrite-reduction
3467315792malonate-assimilation

metabolite production

  • @ref: 34673
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
3467315688acetoin-
3467317234glucose-

enzymes

@refvalueactivityec
34673oxidase-
34673beta-galactosidase+3.2.1.23
34673alcohol dehydrogenase-1.1.1.1
34673gelatinase+/-
34673amylase+
34673caseinase+3.4.21.50
34673catalase+1.11.1.6
34673tween esterase+
34673gamma-glutamyltransferase+2.3.2.2
34673lecithinase+
34673lipase-
34673lysine decarboxylase-4.1.1.18
34673ornithine decarboxylase-4.1.1.17
34673phenylalanine ammonia-lyase-4.3.1.24
34673protease+
34673tryptophan deaminase-
34673urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
34673-+++-++----+--------

Isolation, sampling and environmental information

isolation

  • @ref: 67770
  • sample type: Bermuda Atlantic Time Series station in the western Sargasso Sea
  • country: Atlantic Ocean

taxonmaps

  • @ref: 69479
  • File name: preview.99_4816.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16657;96_2378;97_2894;98_3606;99_4816&stattab=map
  • Last taxonomy: Croceibacter atlanticus subclade
  • 16S sequence: AY163576
  • Sequence Identity:
  • Total samples: 15592
  • soil counts: 293
  • aquatic counts: 13201
  • animal counts: 2030
  • plant counts: 68

Safety information

risk assessment

  • @ref: 34673
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 67770
  • description: Croceibacter atlanticus strain HTCC2559T 16S ribosomal RNA gene, partial sequence
  • accession: AY163576
  • length: 1489
  • database: ena
  • NCBI tax ID: 216432

Genome sequences

  • @ref: 67770
  • description: Croceibacter atlanticus HTCC2559
  • accession: GCA_000196315
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 216432

GC content

  • @ref: 67770
  • GC-content: 34.8

External links

@ref: 34673

culture collection no.: CIP 108009, KCTC 12090, ATCC BAA 628, JCM 21780, IAM 15332

straininfo link

  • @ref: 92872
  • straininfo: 97612

literature

  • topic: Phylogeny
  • Pubmed-ID: 12747413
  • title: Croceibacter atlanticus gen. nov., sp. nov., a novel marine bacterium in the family Flavobacteriaceae.
  • authors: Cho JC, Giovannoni SJ
  • journal: Syst Appl Microbiol
  • DOI: 10.1078/072320203322337344
  • year: 2003
  • mesh: Biodegradation, Environmental, Carbon/metabolism, Fatty Acids/analysis, Gram-Negative Aerobic Rods and Cocci/*classification/genetics/ultrastructure, Molecular Sequence Data, Phenotype, Phylogeny, Seawater/*microbiology, Sequence Analysis, DNA, *Water Microbiology
  • topic2: Genetics

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
34673Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108009Collection of Institut Pasteur (CIP 108009)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
92872Reimer, 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-ID97612.1