Archive BacDiveID:10.13145/bacdive133644.20230509.8.1

Strain identifier

BacDive ID: 133644

Type strain:

Species: Fodinibius salinus

Strain history: <- X.-L. Cui, YIM <- J.-H. Liu and Y.-X. Wang, YIM

NCBI tax ID(s): 860790 (species)

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

General

@ref: 16044

BacDive-ID: 133644

DSM-Number: 21935

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

description: Fodinibius salinus DSM 21935 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from hypersaline environment.

NCBI tax id

NCBI tax id: 860790
Matching level: species

strain history

@ref: 16044
history: <- X.-L. Cui, YIM <- J.-H. Liu and Y.-X. Wang, YIM

doi: 10.13145/bacdive133644.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/balneolota
domain: Bacteria
phylum: Balneolota
class: Balneolia
order: Balneolales
family: Balneolaceae
genus: Fodinibius
species: Fodinibius salinus
full scientific name: Fodinibius salinus Wang et al. 2012

@ref: 16044

domain: Bacteria

phylum: Balneolaeota

class: Balneolia

order: Balneolales

family: Balneolaceae

genus: Fodinibius

species: Fodinibius salinus

full scientific name: Fodinibius salinus Wang et al. 2012

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
29903	negative	1.0-3.0 µm	0.3 µm	rod-shaped	no
69480	negative					99.986

pigmentation

@ref: 29903
production: yes

Culture and growth conditions

culture medium

@ref: 16044
name: MEDIUM 514 PLUS ADDITIONAL SALT (DSMZ Medium 514b)
growth: yes
link: https://mediadive.dsmz.de/medium/514b
composition: Name: MEDIUM 514 plus additional salt (DSMZ Medium 514b) Composition: NaCl 19.45 g/l Agar 17.5 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
16044	positive	growth	28	mesophilic
29903	positive	growth	25-45
29903	positive	optimum	37	mesophilic

culture pH

@ref	ability	type	pH	PH range
29903	positive	growth	6.0-9.0	alkaliphile
29903	positive	optimum	7.5-8.0

Physiology and metabolism

oxygen tolerance

@ref: 29903
oxygen tolerance: aerobe

spore formation

@ref	spore formation	confidence
29903	no
69481	no	100
69480	no	99.973

halophily

@ref	salt	growth	tested relation	concentration
29903	NaCl	positive	growth	4-23 %
29903	NaCl	positive	optimum	10-15 %

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
29903	16947	citrate	+	carbon source
29903	53423	tween 40	+	carbon source
29903	53426	tween 80	+	carbon source
29903	4853	esculin	+	hydrolysis
29903	17632	nitrate	+	reduction

enzymes

@ref	value	activity	ec
29903	catalase	+	1.11.1.6
29903	gelatinase	+
29903	cytochrome oxidase	+	1.9.3.1
29903	urease	+	3.5.1.5

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent	latitude	longitude
29903	hypersaline environment
16044	sediment from a salt mine	Yunnan,Fenggang salt mine (23°28' N 100° 43' E)	China	CHN	Asia	23.4667	100.717

isolation source categories

Cat1: #Condition
Cat2: #Saline

taxonmaps

@ref: 69479
File name: preview.99_129680.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_2060;96_50549;97_65079;98_86842;99_129680&stattab=map
Last taxonomy: Fodinibius salinus subclade
16S sequence: HM153810
Sequence Identity:
Total samples: 129
soil counts: 19
aquatic counts: 110

Safety information

risk assessment

@ref: 16044
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 16044
description: Fodinibius salinus strain YIM D17 16S ribosomal RNA gene, partial sequence
accession: HM153810
length: 1466
database: ena
NCBI tax ID: 860790

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Fodinibius salinus DSM 21935	GCA_008124865	contig	ncbi	860790
66792	Fodinibius salinus strain DSM 21935	860790.3	wgs	patric	860790
66792	Fodinibius salinus DSM 21935	2728369742	draft	img	860790

GC content

@ref	GC-content	method
16044	43.0	high performance liquid chromatography (HPLC)
29903	43

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	no	95.607	yes
flagellated	no	98.784	yes
gram-positive	no	98.098	yes
anaerobic	no	98.799	yes
halophile	yes	85.67	yes
spore-forming	no	93.423	yes
thermophile	no	88.067	yes
glucose-util	yes	85.467	no
aerobic	yes	85.903	yes
glucose-ferment	no	78.579	no

External links

@ref: 16044

culture collection no.: DSM 21935, ACCC 10716, YIM D17

straininfo link

@ref: 91541
straininfo: 403871

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	21441370	Fodinibius salinus gen. nov., sp. nov., a moderately halophilic bacterium isolated from a salt mine.	Wang YX, Liu JH, Xiao W, Zhang XX, Li YQ, Lai YH, Ji KY, Wen ML, Cui XL	Int J Syst Evol Microbiol	10.1099/ijs.0.025502-0	2011	Bacterial Typing Techniques, Bacteroidetes/chemistry/classification/genetics/isolation & purification, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/microbiology, Lipids/analysis, Mining, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Species Specificity	Genetics
Phylogeny	32123983	Aliifodinibius salipaludis sp. nov., Isolated from Saline-Alkaline Soil.	Zhao X, Miao S, Sun Y, Gong Q, Zhao J, Wang J, Zhang G	Curr Microbiol	10.1007/s00284-019-01863-w	2020	*Bacteria/chemistry/classification/genetics, China, Genome, Bacterial/genetics, Hydrogen-Ion Concentration, Soil Microbiology	Genetics

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
16044	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21935)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-21935
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
29903	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	26275	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
91541	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID403871.1	StrainInfo: A central database for resolving microbial strain identifiers