Archive BacDiveID:10.13145/bacdive13800.20230509.8.1

Strain identifier

BacDive ID: 13800

Type strain:

Species: Sulfitobacter donghicola

Strain Designation: DSW-25

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 1300350 (strain), 421000 (species)

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

General

@ref: 17285

BacDive-ID: 13800

DSM-Number: 23563

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

description: Sulfitobacter donghicola DSW-25 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater.

NCBI tax id

NCBI tax id	Matching level
421000	species
1300350	strain

strain history

@ref	history
17285	<- JCM; JCM 14565 <- J. H. Yoon
67770	Y.-H. Yoon DSW-25.
67771	<- JH Yoon, KRIBB

doi: 10.13145/bacdive13800.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Alphaproteobacteria
order: Rhodobacterales
family: Roseobacteraceae
genus: Sulfitobacter
species: Sulfitobacter donghicola
full scientific name: Sulfitobacter donghicola Yoon et al. 2007

@ref: 17285

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Sulfitobacter

species: Sulfitobacter donghicola

full scientific name: Sulfitobacter donghicola Yoon et al. 2007

strain designation: DSW-25

type strain: yes

Morphology

cell morphology

@ref: 67771
gram stain: negative

Culture and growth conditions

culture medium

@ref: 17285
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
17285	positive	growth	25	mesophilic
67770	positive	growth	25	mesophilic
67771	positive	growth	25	mesophilic

Physiology and metabolism

oxygen tolerance

@ref: 67771
oxygen tolerance: aerobe

observation

@ref: 67770
observation: quinones: Q-10

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
17285	seawater	East Sea	Republic of Korea	KOR	Asia
67770	Seawater
67771	From seawater	East Sea	Republic of Korea	KOR	Asia

isolation source categories

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

taxonmaps

@ref: 69479
File name: preview.99_6147.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_252;97_275;98_3138;99_6147&stattab=map
Last taxonomy: Sulfitobacter donghicola
16S sequence: EF202614
Sequence Identity:
Total samples: 1015
soil counts: 44
aquatic counts: 931
animal counts: 28
plant counts: 12

Safety information

risk assessment

@ref: 17285
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 17285
description: Sulfitobacter donghicola strain DSW-25 16S ribosomal RNA gene, partial sequence
accession: EF202614
length: 1418
database: ena
NCBI tax ID: 1300350

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Sulfitobacter donghicola DSW-25 = KCTC 12864 = JCM 14565	1300350.3	wgs	patric	1300350
66792	Sulfitobacter donghicola DSW-25 = KCTC 12864 = JCM 14565	1300350.4	wgs	patric	1300350
66792	Sulfitobacter donghicola DSW-25, KCTC 12864	2574180243	draft	img	1300350
66792	Sulfitobacter donghicola JCM 14565	2588253841	draft	img	1300350
67770	Sulfitobacter donghicola DSW-25 = KCTC 12864 = JCM 14565	GCA_000712275	contig	ncbi	1300350
67770	Sulfitobacter donghicola DSW-25 = KCTC 12864 = JCM 14565	GCA_000622405	contig	ncbi	1300350

GC content

@ref: 17285
GC-content: 56.9
method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
motile	no	63.411	no
gram-positive	no	97.826	yes
anaerobic	no	98.849	no
halophile	yes	65.05	no
spore-forming	no	96.468	no
thermophile	no	97.391	yes
glucose-util	no	60.688	no
flagellated	no	92.685	no
aerobic	yes	92.664	yes
glucose-ferment	no	91.187	no

External links

@ref: 17285

culture collection no.: DSM 23563, JCM 14565, KCTC 12864

straininfo link

@ref: 82978
straininfo: 309510

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	17684258	Description of Sulfitobacter donghicola sp. nov., isolated from seawater of the East Sea in Korea, transfer of Staleya guttiformis Labrenz et al. 2000 to the genus Sulfitobacter as Sulfitobacter guttiformis comb. nov. and emended description of the genus Sulfitobacter.	Yoon JH, Kang SJ, Lee MH, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.65071-0	2007	DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/classification/genetics/physiology, Seawater/microbiology	Genetics
Phylogeny	25278561	Sulfitobacter pseudonitzschiae sp. nov., isolated from the toxic marine diatom Pseudo-nitzschia multiseries.	Hong Z, Lai Q, Luo Q, Jiang S, Zhu R, Liang J, Gao Y	Int J Syst Evol Microbiol	10.1099/ijs.0.064972-0	2014	Atlantic Ocean, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diatoms/microbiology, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry	Genetics
Phylogeny	36334148	Sulfitobacter albidus sp. nov., isolated from marine sediment of Jeju Island.	Kim M, Cha IT, Lee KE, Park SJ	Arch Microbiol	10.1007/s00203-022-03305-x	2022	RNA, Ribosomal, 16S/genetics, Phylogeny, Seawater/microbiology, DNA, Bacterial/genetics, Bacterial Typing Techniques, Nucleic Acid Hybridization, Geologic Sediments, Sequence Analysis, DNA, Fatty Acids/chemistry, Phospholipids/chemistry	Transcriptome

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
17285	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23563)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-23563
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
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
67771	Curators of the KCTC		https://kctc.kribb.re.kr/En/Kctc
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
82978	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID309510.1	StrainInfo: A central database for resolving microbial strain identifiers