Archive BacDiveID:10.13145/bacdive5713.20230509.8.1

Strain identifier

BacDive ID: 5713

Type strain:

Species: Bizionia paragorgiae

Strain history: <- KCTC <- S. B. Kim, KCTC <- O. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok, Russia

NCBI tax ID(s): 283786 (species)

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

General

@ref: 17397

BacDive-ID: 5713

DSM-Number: 23842

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

description: Bizionia paragorgiae DSM 23842 is a mesophilic, Gram-negative bacterium that was isolated from soft coral Paragoria arborea.

NCBI tax id

NCBI tax id: 283786
Matching level: species

strain history

@ref: 17397
history: <- KCTC <- S. B. Kim, KCTC <- O. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok, Russia

doi: 10.13145/bacdive5713.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacteroidota
domain: Bacteria
phylum: Bacteroidota
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Bizionia
species: Bizionia paragorgiae
full scientific name: Bizionia paragorgiae Nedashkovskaya et al. 2005

@ref: 17397

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Bizionia

species: Bizionia paragorgiae

full scientific name: Bizionia paragorgiae Nedashkovskaya et al. 2005

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: negative
confidence: 99.954

Culture and growth conditions

culture medium

@ref: 17397
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: 17397
growth: positive
type: growth
temperature: 25
range: mesophilic

Physiology and metabolism

spore formation

@ref	spore formation	confidence
69481	no	100
69480	no	99.993

Isolation, sampling and environmental information

isolation

@ref: 17397
sample type: soft coral Paragoria arborea
host species: Paragoria arborea
geographic location: Makarov Bay, Iturup Island, Sea of Okhotsk
country: Russia
origin.country: RUS
continent: Asia

isolation source categories

Cat1: #Host
Cat2: #Invertebrates (Other)
Cat3: #Cnidaria (Corals)

Safety information

risk assessment

@ref: 17397
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 17397
description: Bizionia paragorgiae strain KMM 6029 16S ribosomal RNA gene, partial sequence
accession: AY651070
length: 1425
database: ena
NCBI tax ID: 283786

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Bizionia paragorgiae DSM 23842	GCA_900107625	scaffold	ncbi	283786
66792	Bizionia paragorgiae strain DSM 23842	283786.6	wgs	patric	283786
66792	Bizionia paragorgiae DSM 23842	2622736593	draft	img	283786

GC content

@ref: 17397
GC-content: 37.6

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	no	88.383	no
glucose-ferment	no	92.778	no
flagellated	no	93.968	no
gram-positive	no	97.941	no
anaerobic	no	99.42	no
aerobic	yes	89.181	no
halophile	no	57.376	no
spore-forming	no	94.689	no
thermophile	no	99.741	yes
glucose-util	yes	78.021	no

External links

@ref: 17397

culture collection no.: DSM 23842, KCTC 12304, KMM 6029, LMG 22571

straininfo link

@ref: 75195
straininfo: 132530

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	15653903	Bizionia paragorgiae gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from the soft coral Paragorgia arborea.	Nedashkovskaya OI, Kim SB, Lysenko AM, Frolova GM, Mikhailov VV, Bae KS	Int J Syst Evol Microbiol	10.1099/ijs.0.63381-0	2005	Animals, Anthozoa/microbiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Flavobacteriaceae/chemistry/classification/genetics/isolation & purification, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA	Genetics
Phylogeny	26297143	Bizionia fulviae sp. nov., isolated from the gut of an egg cockle, Fulvia mutica.	Kim HS, Hyun DW, Kim PS, Lee JY, Shin NR, Yun JH, Whon TW, Kim MS, Jung MJ, Bae JW	Int J Syst Evol Microbiol	10.1099/ijs.0.000380	2015	Animals, Bacterial Typing Techniques, Base Composition, Cardiidae, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/classification, Molecular Sequence Data, Phosphatidylethanolamines, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry	Genetics
Phylogeny	26956595	Xanthomarina gelatinilytica gen. nov., sp. nov., isolated from seawater.	Vaidya B, Kumar R, Sharma G, Srinivas TNR, Anil Kumar P	Int J Syst Evol Microbiol	10.1099/ijsem.0.000515	2015	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/classification/genetics/isolation & purification, India, Molecular Sequence Data, Phospholipids/chemistry, Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry	Genetics
Phylogeny	32886593	Wocania indica gen. nov., sp. nov., isolated from deep sea hydrothermal sulfide in the northwest Indian Ocean, and proposal to reclassify Flaviramulus ichthyoenteri as Wocania ichthyoenteri comb. nov.	He Y, Zeng X, Xiong J, Lai Q, Li J, Shao Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.004439	2020	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/classification/isolation & purification, Hydrothermal Vents/microbiology, Indian Ocean, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry	Transcriptome

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
17397	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23842)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-23842
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
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	Nucleic Acids Res. 49: D498-D508 2020	33211880
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
75195	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID132530.1	StrainInfo: A central database for resolving microbial strain identifiers