Name: Flavobacterium halmophilum HMSMF 1.1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6027

Type strain:

Species: Flavobacterium halmophilum

Strain Designation: HMSMF 1.1

Culture col. no.: DSM 5349, ATCC 19717, IAM 14439, NCMB 1971, JCM 21222, ACAM 71, CIP 105455, IFO 15537, LMG 4023, NBRC 15537, NCIB 8718, NCIMB 1971, NCIMB 8718

Strain history: CIP <- 1998, NCIMB <- Hopkins Marine station, Stanford Univ., Pacific Grove, California, USA: strain HMSMF 1.1 <- B. Elazari-Volcani

NCBI tax ID(s): 252 (species)

SI-ID 13675

LMG 4023, ATCC 19717, NCIB 8718, NCMB 1971, DSM 5349, IFO 15537, CIP 105455, NCIMB 1971, IAM 14439, CCM 2833, NCIMB 8718, NBRC 15537, JCM 21222, CGMCC 1.2317, VTT E-103155

Section

Flavobacterium halmophilum HMSMF 1.1 is a mesophilic, motile bacterium that was isolated from dead sea.

motile
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	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Flavobacterium*
	Species	Flavobacterium halmophilum
	Full Scientific Name (LPSN)	Flavobacterium halmophilum corrig. Elazari-Volcani 1940 (Approved Lists 1980)

	Synonym	Flavobacterium halmephilium
	Synonym	**Halomonas halmophila**

Information on morphological and physiological properties Morphology

[Ref.: #119796]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.951

[Ref.: #119796]	Cell shape	rod-shaped

[Ref.: #119796]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %97.249

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1996]

Culture medium

MEDIUM 514 PLUS ADDITIONAL SALT (DSMZ Medium 514b)

[Ref.: #1996]

Culture medium growth

[Ref.: #1996]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1996]

Culture medium composition

expand / minimize

[Ref.: #39297]

Culture medium

MEDIUM 117 - for Pseudoalteromonas haloplanktis, Cytophaga lytica and Halomonas halodenitrificans

[Ref.: #39297]

Culture medium growth

[Ref.: #39297]

Culture medium composition

expand / minimize

[Ref.: #119796]

Culture medium

CIP Medium 117

[Ref.: #119796]

Culture medium growth

[Ref.: #119796]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #119796]

Culture medium

CIP Medium 192

[Ref.: #119796]

Culture medium growth

[Ref.: #119796]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #1996]		growth	25 °C
[Ref.: #39297]		growth	25 °C
[Ref.: #67770]		growth	25 °C
[Ref.: #119796]		growth	15-30 °C
[Ref.: #119796]	no	growth	5 °C
[Ref.: #119796]	no	growth	37 °C
[Ref.: #119796]	no	growth	41 °C
[Ref.: #119796]	no	growth	45 °C

[Ref.: #1996]	Temperature range	mesophilic
[Ref.: #39297]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #119796]	Temperature range	psychrophilic
[Ref.: #119796]	Temperature range	mesophilic
[Ref.: #119796]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %98.808

	Salt	Tested relation		Salt conc.
[Ref.: #119796]	NaCl		growth	8-10	%
[Ref.: #119796]	NaCl	no	growth	0	%
[Ref.: #119796]	NaCl	no	growth	2	%
[Ref.: #119796]	NaCl	no	growth	4	%
[Ref.: #119796]	NaCl	no	growth	6	%

[Ref.: #67770]

Observation

quinones: Q-9

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	D-fructose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #119796]	esculin ChEBI	-	hydrolysis
[Ref.: #119796]	hippurate ChEBI	-	hydrolysis
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	maltose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #119796]	nitrate ChEBI	-	reduction
[Ref.: #119796]	nitrite ChEBI	-	reduction
[Ref.: #68371]	sucrose ChEBI	+	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #119796]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #119796]		acetoin ChEBI	-
[Ref.: #119796]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #119796]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #119796]	amylase	-
[Ref.: #119796]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #119796]	caseinase	-	3.4.21.50
[Ref.: #119796]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #119796]	gamma-glutamyltransferase	+	2.3.2.2
[Ref.: #119796]	gelatinase	-
[Ref.: #119796]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #119796]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #119796]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #119796]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #119796]	oxidase	-
[Ref.: #119796]	phenylalanine ammonia-lyase	+	4.3.1.24
[Ref.: #119796]	protease	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #119796]	tryptophan deaminase	-
[Ref.: #119796]	tween esterase	-
[Ref.: #119796]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #119796]	10084	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.: #119796]	1160	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #119796]	8713	-	+	+	+	-	+	-	-	-	-	-	-	-	-	-	+	-	-	-	-

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

[Ref.: #1996]	Sample type/isolated from	dead sea

[Ref.: #67770]	Sample type/isolated from	Dead Sea

[Ref.: #119796]	Sample type/isolated from	Environment, Dead sea
[Ref.: #119796]	Country	Israel
[Ref.: #119796]	Country ISO 3 Code	ISR
[Ref.: #119796]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	-
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Marine
#Condition	#Saline	-

What are isolation sources categories?

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

[Ref.: #1996]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #119796]	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 halmophila partial 16S rRNA gene, strain ATCC 19717	AJ306889	1530	ENA	252 tax ID	*
[Ref.: #20218]	Flavobacterium halmophilum 16S ribosomal RNA	M59153	1540	ENA	252 tax ID	*
[Ref.: #20218]	Halomonas halmophila gene for 16S rRNA, partial sequence, strain: NBRC 15537	AB680891	1463	ENA	252 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Halomonas halmophila NBRC 15537	GCA_006540005	contig	GenBank	252 tax ID
[Ref.: #66792]	Halomonas halmophila strain NBRC 15537	252.3	wgs	PATRIC	252 tax ID	*

[Ref.: #67770]

GC-content

63 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 halmophila strain NBRC 15537 PATRIC: 252.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Halomonas halmophila strain NBRC 15537 PATRIC: 252.3
[Ref.: #69480]	motile	yes	88.879	no
[Ref.: #69480]	gram-positive	no	98.787	no
[Ref.: #69480]	anaerobic	no	98.691	no
[Ref.: #69480]	aerobic	yes	93.645	no
[Ref.: #69480]	halophile	yes	93.104	no
[Ref.: #69480]	spore-forming	no	95.696	no
[Ref.: #69480]	glucose-util	yes	93.255	no
[Ref.: #69480]	flagellated	no	54.925	no
[Ref.: #69480]	thermophile	no	96.707	yes
[Ref.: #69480]	glucose-ferment	no	68.208	no

Availability in culture collections External links

[Ref.: #1996]

Culture collection no.

DSM 5349, ATCC 19717, IAM 14439, NCMB 1971, JCM 21222, ACAM 71, CIP 105455, IFO 15537, LMG 4023, NBRC 15537, NCIB 8718, NCIMB 1971, NCIMB 8718

[Ref.: #75513]

SI-ID 13675

References

#1996

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5349

#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 )

#39297 ; 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 .

#68382

Automatically annotated from API zym .

#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 )

#75513

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-ID13675.1 )

#119796 Collection of Institut Pasteur ; Curators of the CIP; CIP 105455
* These data were automatically processed and therefore are not curated

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Halomonas halmophila strain NBRC 15537

Halomonas halmophila strain NBRC 15537

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Change proposal