Name: Halomonas halophila F 5-7
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6016

Type strain:

Species: Halomonas halophila

Strain Designation: F 5-7, F5-7

Culture col. no.: DSM 4770, CCM 3662, JCM 20791, ATCC 49969, CGMCC 1.2316, CIP 103512, IAM 13009, LMG 6456, NBRC 102604, NCIMB 12996

Strain history: CIP <- 1992, A.R. Cormenzana, Granada Univ., Spain: strain F5-7

NCBI tax ID(s): 29573 (species)

SI-ID 2164

LMG 6456, CCM 3662, DSM 4770, ATCC 49969, CIP 103512, NCIMB 12996, IAM 13009, JCM 20791, CGMCC 1.2316, NBRC 102604

Other strains from Halomonas halophila

H. halophila JCM 32864
H. halophila JCM 32866

Section

Halomonas halophila F 5-7 is a facultative anaerobe, mesophilic, motile bacterium that was isolated from hypersaline soil.

motile
facultative anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Oceanospirillales*
	Family	*Halomonadaceae*
	Genus	*Halomonas*
	Species	**Halomonas halophila**
	Full Scientific Name (LPSN)	Halomonas halophila (Quesada et al. 1984) Dobson and Franzmann 1996

Synonym

Deleya halophila

Information on morphological and physiological properties Morphology

[Ref.: #119808]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.988

[Ref.: #119808]	Cell shape	rod-shaped

[Ref.: #119808]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %98.15

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1816]

Culture medium

MEDIUM 514 PLUS ADDITIONAL SALT (DSMZ Medium 514b)

[Ref.: #1816]

Culture medium growth

[Ref.: #1816]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1816]

Culture medium composition

expand / minimize

[Ref.: #1816]

Culture medium

MARINOCOCCUS ALBUS - MEDIUM (DSMZ Medium 434)

[Ref.: #1816]

Culture medium growth

[Ref.: #1816]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1816]

Culture medium composition

expand / minimize

[Ref.: #38128]

Culture medium

Marine agar (MA)

[Ref.: #38128]

Culture medium growth

[Ref.: #38128]

Culture medium composition

expand / minimize

[Ref.: #119808]

Culture medium

CIP Medium 13

[Ref.: #119808]

Culture medium growth

[Ref.: #119808]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #1816]	growth	28 °C
[Ref.: #1816]	growth	30 °C
[Ref.: #38128]	growth	25 °C
[Ref.: #67770]	growth	30 °C
[Ref.: #119808]	growth	5-41 °C

[Ref.: #1816]	Temperature range	mesophilic
[Ref.: #38128]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #119808]

Oxygen tolerance

facultative anaerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.976

	Salt	Tested relation		Salt conc.
[Ref.: #119808]	NaCl		growth	4-10	%
[Ref.: #119808]	NaCl	no	growth	0	%
[Ref.: #119808]	NaCl	no	growth	2	%

[Ref.: #67770]

Observation

quinones: Q-9

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	arbutin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	cellobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gentiobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	maltose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #119808]	nitrate ChEBI	+	reduction
[Ref.: #119808]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	sucrose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #119808]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #119808]	catalase	+	1.11.1.6
[Ref.: #119808]	gelatinase	-
[Ref.: #119808]	oxidase	+
[Ref.: #119808]	tryptophan deaminase	-
[Ref.: #119808]	urease	-	3.5.1.5

API® 50CH acid:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #119808]	9293	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

API® Biotype100:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #119808]	434	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #1816]	Sample type/isolated from	hypersaline soil

[Ref.: #67770]	Sample type/isolated from	Hypersaline soil near Alicante in southeast Spain

[Ref.: #119808]	Sample type/isolated from	Environment, Hypersaline soils
[Ref.: #119808]	Geographic location (country and/or sea, region)	Santa Pola
[Ref.: #119808]	Country	Spain
[Ref.: #119808]	Country ISO 3 Code	ESP
[Ref.: #119808]	Continent	Europe
[Ref.: #119808]	Isolation date	1983
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Condition	#Saline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AM941744 (>99% sequence identity) for Halomonas from Microbeatlas

Aquatic Samples	667
Soil Samples	73
Animal Samples	115
Plant Samples	14
Total Samples	869

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #1816]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #119808]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	Halomonas halophila partial 16S rRNA gene, strain CCM 3662	AM941744	1461	ENA	29573 tax ID	*
[Ref.: #20218]	Halomonas halophila partial 16S rRNA gene, strain DSM 4770	FN257740	1475	ENA	29573 tax ID	*
[Ref.: #20218]	Deleya halophila (DSM 4770) 16S ribosomal RNA (16S rRNA) gene	M93353	1478	ENA	29573 tax ID	*
[Ref.: #20218]	Halomonas halophila genes for 16S ribosomal RNA, internal transcribed spacer 1 and 23S ribosomal RNA, partial and complete sequence, clone: 1182	AB367215	1182	ENA	29573 tax ID	*
[Ref.: #20218]	Halomonas halophila gene for 16S rRNA, partial sequence, strain: NBRC 102604	AB681879	1463	ENA	29573 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Halomonas halophila NBRC 102604	GCA_007989465	contig	GenBank	29573 tax ID	*
[Ref.: #66792]	Halomonas halophila strain NBRC 102604	29573.3	wgs	PATRIC	29573 tax ID	*

[Ref.: #67770]

GC-content

66.7 mol%

thermal denaturation, midpoint method (Tm)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Halomonas halophila strain NBRC 102604 PATRIC: 29573.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Halomonas halophila strain NBRC 102604 PATRIC: 29573.3
[Ref.: #69480]	gram-positive	no	98.821	no
[Ref.: #69480]	anaerobic	no	98.581	no
[Ref.: #69480]	halophile	yes	94.188	no
[Ref.: #69480]	spore-forming	no	95.624	no
[Ref.: #69480]	glucose-util	yes	96.579	no
[Ref.: #69480]	motile	yes	90.308	no
[Ref.: #69480]	flagellated	yes	64.538	no
[Ref.: #69480]	thermophile	no	98.575	yes
[Ref.: #69480]	aerobic	yes	89.311	no
[Ref.: #69480]	glucose-ferment	no	68.979	no

Availability in culture collections External links

[Ref.: #1816]

Culture collection no.

DSM 4770, CCM 3662, JCM 20791, ATCC 49969, CGMCC 1.2316, CIP 103512, IAM 13009, LMG 6456, NBRC 102604, NCIMB 12996

[Ref.: #75502]

SI-ID 2164

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Halomonas smyrnensis sp. nov., a moderately halophilic, exopolysaccharide-producing bacterium.	Poli A, Nicolaus B, Denizci AA, Yavuzturk B, Kazan D	Int J Syst Evol Microbiol	10.1099/ijs.0.037036-0	2012	*
Phylogeny	Structural elucidation of a novel phosphoglycolipid isolated from six species of Halomonas.	Giordano A, Vella FM, Romano I, Gambacorta A	J Lipid Res	10.1194/jlr.M700152-JLR200	2007	*
Cultivation	Growth rate and some physiological features of Deleya halophila CCM 3662 at different salt concentrations.	Ferrer MR, del Moral A, Quesada E, Ramos-Cormenzana A	Ann Inst Pasteur Microbiol	10.1016/0769-2609(87)90053-6	1987	*

References

#1816

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 4770

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#38128 ; Curators of the CIP;

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68371

Automatically annotated from API 50CH acid .

#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.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: 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: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#75502

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID2164.1 )

#119808 Collection of Institut Pasteur ; Curators of the CIP; CIP 103512
* These data were automatically processed and therefore are not curated

Change proposal

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Halomonas halophila strain NBRC 102604

Halomonas halophila strain NBRC 102604

Change proposal

Change proposal