Archive BacDiveID:10.13145/bacdive2879.20230509.8.1

Strain identifier

BacDive ID: 2879

Type strain:

Species: Colwellia chukchiensis

Strain Designation: BCw111

Strain history: <- Y. Yu, Polar Res. Institute of China, Shanghai, PR China; BCw111

NCBI tax ID(s): 641665 (species)

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

General

@ref: 16411

BacDive-ID: 2879

DSM-Number: 22576

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

description: Colwellia chukchiensis BCw111 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from sea water .

NCBI tax id

NCBI tax id: 641665
Matching level: species

strain history

@ref: 16411
history: <- Y. Yu, Polar Res. Institute of China, Shanghai, PR China; BCw111

doi: 10.13145/bacdive2879.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Gammaproteobacteria
order: Alteromonadales
family: Colwelliaceae
genus: Colwellia
species: Colwellia chukchiensis
full scientific name: Colwellia chukchiensis Yu et al. 2011
synonyms
- @ref: 20215
- synonym: Cognaticolwellia chukchiensis

@ref: 16411

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Colwelliaceae

genus: Colwellia

species: Colwellia chukchiensis

full scientific name: Colwellia chukchiensis Yu et al. 2011

strain designation: BCw111

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
29834	negative	2.8 µm	0.75 µm	rod-shaped	yes
69480					yes	98.746
69480	negative					99.98

pigmentation

@ref: 29834
production: no

Culture and growth conditions

culture medium

@ref: 16411
name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
growth: yes
link: https://mediadive.dsmz.de/medium/514
composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
16411	positive	growth	25	mesophilic
29834	positive	growth	0-30
29834	positive	optimum	24	psychrophilic

culture pH

@ref	ability	type	pH	PH range
29834	positive	growth	5.0-10.5	alkaliphile
29834	positive	optimum	7.5

Physiology and metabolism

oxygen tolerance

@ref: 29834
oxygen tolerance: facultative anaerobe

spore formation

@ref	spore formation	confidence
69481	no	100
69480	no	99.994

halophily

@ref	salt	growth	tested relation	concentration
29834	NaCl	positive	growth	0.5-8 %
29834	NaCl	positive	optimum	4.3 %

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
29834	16947	citrate	+	carbon source
29834	28260	galactose	+	carbon source
29834	17234	glucose	+	carbon source
29834	53426	tween 80	+	carbon source
29834	4853	esculin	+	hydrolysis
29834	17632	nitrate	+	reduction

enzymes

@ref	value	activity	ec
29834	alkaline phosphatase	+	3.1.3.1
29834	catalase	+	1.11.1.6
29834	gelatinase	+
29834	cytochrome oxidase	+	1.9.3.1
29834	urease	+	3.5.1.5

Isolation, sampling and environmental information

isolation

@ref: 16411
sample type: sea water (60 m water depth)
geographic location: Chukchi Sea (73°00'00'' N 169°32'44'' W)
latitude: 73
longitude: -169.546

isolation source categories

Cat1: #Environmental
Cat2: #Aquatic
Cat3: #Marine

taxonmaps

@ref: 69479
File name: preview.99_5623.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_82;96_438;97_1201;98_4190;99_5623&stattab=map
Last taxonomy: Colwellia
16S sequence: FJ889599
Sequence Identity:
Total samples: 377
aquatic counts: 372
animal counts: 5

Safety information

risk assessment

@ref: 16411
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 16411
description: Colwellia chukchiensis strain BCw111 16S ribosomal RNA gene, partial sequence
accession: FJ889599
length: 1463
database: ena
NCBI tax ID: 641665

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Colwellia chukchiensis CGMCC 1.9127	GCA_002104455	contig	ncbi	641665
66792	Colwellia chukchiensis CGMCC 1.9127	GCA_900109795	scaffold	ncbi	641665
66792	Colwellia chukchiensis strain CGMCC 1.9127	641665.3	wgs	patric	641665
66792	Colwellia chukchiensis strain CGMCC1.9127	641665.4	wgs	patric	641665
66792	Colwellia chukchiensis CGMCC 1.9127	2843543880	draft	img	641665
66792	Colwellia chukchiensis CGMCC 1.9127	2667527443	draft	img	641665

GC content

@ref	GC-content	method
16411	41.3	high performance liquid chromatography (HPLC)
29834	41.3

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
glucose-ferment	no	77.844	no
motile	yes	90.789	yes
flagellated	yes	83.976	no
gram-positive	no	99.19	yes
anaerobic	no	98.33	yes
aerobic	yes	57.923	yes
halophile	yes	60.071	no
spore-forming	no	96.856	no
thermophile	no	99.159	yes
glucose-util	yes	89.022	yes

External links

@ref: 16411

culture collection no.: DSM 22576, CGMCC 1.9127, LMG 25329

straininfo link

@ref: 72402
straininfo: 362758

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	20495042	Colwellia chukchiensis sp. nov., a psychrotolerant bacterium isolated from the Arctic Ocean.	Yu Y, Li HR, Zeng YX	Int J Syst Evol Microbiol	10.1099/ijs.0.022111-0	2010	Alteromonadaceae/classification/genetics/isolation & purification/physiology, Anaerobiosis, Arctic Regions, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cold Temperature, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA	Genetics
Phylogeny	25201915	Colwellia aquaemaris sp. nov., isolated from the Cynoglossus semilaevis culture tank in a recirculating mariculture system.	Liu Y, Liu LZ, Zhong ZP, Zhou YG, Liu Y, Liu ZP	Int J Syst Evol Microbiol	10.1099/ijs.0.063305-0	2014	Alteromonadaceae/classification/genetics/isolation & purification, Aquaculture, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry	Genetics
Genetics	29371370	Draft Genome Sequences of Two Psychrotolerant Strains, Colwellia polaris MCCC 1C00015(T) and Colwellia chukchiensis CGMCC 1.9127(T).	Zhang C, Guo W, Wang Y, Chen X	Genome Announc	10.1128/genomeA.01575-17	2018

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed	journal
16411	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22576)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-22576
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
29834	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	26210	28776041
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)
66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates		33211880	Nucleic Acids Res. 49: D498-D508 2020
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
72402	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID362758.1	StrainInfo: A central database for resolving microbial strain identifiers

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

synonyms

Morphology

cell morphology

pigmentation

Culture and growth conditions

culture medium

culture temp

culture pH

Physiology and metabolism

oxygen tolerance

spore formation

halophily

metabolite utilization

enzymes

Isolation, sampling and environmental information

isolation

isolation source categories

taxonmaps

Safety information

risk assessment

Sequence information

16S sequences

Genome sequences

GC content

Genome-based predictions

predictions

External links

straininfo link

literature

Reference