Archive BacDiveID:10.13145/bacdive17840.20230509.8.1

Strain identifier

BacDive ID: 17840

Type strain:

Species: Demequina flava

Strain Designation: HR08-7

Strain history: <- M. Hamada, NBRC, NITE (Natl. Inst. of Technol. and Evaluation), Kisarazu, Japan; HR08-7

NCBI tax ID(s): 1095025 (species)

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

General

@ref: 17791

BacDive-ID: 17840

DSM-Number: 24865

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

description: Demequina flava HR08-7 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from marine sediment.

NCBI tax id

NCBI tax id: 1095025
Matching level: species

strain history

@ref: 17791
history: <- M. Hamada, NBRC, NITE (Natl. Inst. of Technol. and Evaluation), Kisarazu, Japan; HR08-7

doi: 10.13145/bacdive17840.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/actinomycetota
domain: Bacteria
phylum: Actinomycetota
class: Actinomycetes
order: Micrococcales
family: Demequinaceae
genus: Demequina
species: Demequina flava
full scientific name: Demequina flava Hamada et al. 2013

@ref: 17791

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Demequinaceae

genus: Demequina

species: Demequina flava

full scientific name: Demequina flava Hamada et al. 2013

strain designation: HR08-7

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
30586	positive	4 µm	0.7 µm	rod-shaped	no
69480					no	94.664
69480	positive					100

colony morphology

@ref: 17791
incubation period: 3-7 days

pigmentation

@ref: 30586
production: yes

Culture and growth conditions

culture medium

@ref: 17791
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
17791	positive	growth	28	mesophilic
30586	positive	growth	10-28
30586	positive	optimum	28	mesophilic

culture pH

@ref	ability	type	pH	PH range
30586	positive	growth	07-09	alkaliphile
30586	positive	optimum	7.5

Physiology and metabolism

oxygen tolerance

@ref: 30586
oxygen tolerance: anaerobe

spore formation

@ref	spore formation	confidence
30586	no
69481	no	100
69480	no	99.995

halophily

@ref: 30586
salt: NaCl
growth: positive
tested relation: growth
concentration: 0-10 %

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
30586	22599	arabinose	+	carbon source
30586	17057	cellobiose	+	carbon source
30586	28757	fructose	+	carbon source
30586	28260	galactose	+	carbon source
30586	17234	glucose	+	carbon source
30586	25017	leucine	+	carbon source
30586	17306	maltose	+	carbon source
30586	37684	mannose	+	carbon source
30586	17814	salicin	+	carbon source
30586	18222	xylose	+	carbon source
30586	4853	esculin	+	hydrolysis

enzymes

@ref: 30586
value: acid phosphatase
activity: +
ec: 3.1.3.2

Isolation, sampling and environmental information

isolation

@ref: 17791
sample type: marine sediment
geographic location: Hokkaido, Rishiri Island
country: Japan
origin.country: JPN
continent: Asia

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

taxonmaps

@ref: 69479
File name: preview.99_5713.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_657;97_760;98_2540;99_5713&stattab=map
Last taxonomy: Demequina
16S sequence: AB674956
Sequence Identity:
Total samples: 170
soil counts: 26
aquatic counts: 22
animal counts: 118
plant counts: 4

Safety information

risk assessment

@ref: 17791
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 17791
description: Demequina flava gene for 16S rRNA, partial sequence
accession: AB674956
length: 1476
database: ena
NCBI tax ID: 1095025

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Demequina flava NBRC 105854	GCA_000975035	scaffold	ncbi	1095025
66792	Demequina flava strain NBRC 105854	1095025.3	wgs	patric	1095025
66792	Demequina flava NBRC 105854	2667527640	draft	img	1095025

GC content

@ref	GC-content	method
17791	64.5	high performance liquid chromatography (HPLC)
30586	64.5

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	no	92.543	yes
flagellated	no	97.678	no
gram-positive	yes	94.766	yes
anaerobic	no	98.07	yes
aerobic	no	66.67	yes
halophile	no	68.313	no
spore-forming	no	86.89	no
glucose-util	yes	88.195	yes
thermophile	no	99.422	no
glucose-ferment	no	66.965	no

External links

@ref: 17791

culture collection no.: DSM 24865, NBRC 105854

straininfo link

@ref: 86831
straininfo: 403882

literature

topic: Phylogeny
Pubmed-ID: 22389288
title: Demequina flava sp. nov. and Demequina sediminicola sp. nov., isolated from sea sediment.
authors: Hamada M, Tamura T, Yamamura H, Suzuki KI, Hayakawa M
journal: Int J Syst Evol Microbiol
DOI: 10.1099/ijs.0.039297-0
year: 2012
mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis, Water Microbiology
topic2: Genetics

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
17791	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24865)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-24865
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
30586	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	26917	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)
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
86831	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID403882.1	StrainInfo: A central database for resolving microbial strain identifiers