Name: Lysobacter firmicutimachus PB-6250
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 132648

Type strain:

Species: Lysobacter firmicutimachus

Strain Designation: PB-6250, PB6250

Culture col. no.: DSM 102073, FERM BP-2938, LMG 28994

Strain history: <- H. Groß, Pharmaceutical Biology, University of Tuebingen, Germany <- NITE-IPOD <- T. Yoshida <- Shionogi Research Laboratories, Shionogi Co, Ltd., Osaka, Japan; PB-6250

NCBI tax ID(s): 1792846 (species)

SI-ID 398165

DSM 102073

Special Collections

Section

Lysobacter firmicutimachus PB-6250 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from soil.

colony-forming
Gram-negative
rod-shaped
aerobe
16S sequence
Bacteria

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	*Lysobacterales*
	Family	*Lysobacteraceae*
	Genus	*Lysobacter*
	Species	**Lysobacter firmicutimachus**
	Full Scientific Name (LPSN)	Lysobacter firmicutimachus Miess et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #24955]	Gram stain	negative

[Ref.: #24955]	Cell length	2.0-4.0 µm

[Ref.: #24955]	Cell width	0.9 µm

[Ref.: #24955]	Cell shape	rod-shaped

[Ref.: #24955]	Colony color	cream-yellow
[Ref.: #24955]	Colony shape	circular

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24437]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #24437]

Culture medium growth

[Ref.: #24437]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #24955]

Culture medium

NA (Nutrient Agar)

[Ref.: #24955]

Culture medium growth

[Ref.: #24955]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #24955]

Culture medium growth

[Ref.: #24955]

Culture medium

LB medium (lysogeny broth)

[Ref.: #24955]

Culture medium growth

[Ref.: #24955]

Culture medium

TSA (Trypticase soy agar)

[Ref.: #24955]

Culture medium growth

[Ref.: #24955]

Culture medium

Marine agar (MA)

[Ref.: #24955]

Culture medium growth

[Ref.: #24955]

Culture medium

MacConkey agar

[Ref.: #24955]

Culture medium growth

[Ref.: #24437]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #24437]

Culture medium growth

[Ref.: #24437]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24437]

Culture medium composition

expand / minimize

	Kind of temperature		Temperature
[Ref.: #24437]		growth	28 °C
[Ref.: #24955]		growth	15.0-37.0 °C
[Ref.: #24955]		optimum	25.0-28.0 °C
[Ref.: #24955]	no	growth	42 °C

	pH	Kind of pH		pH
[Ref.: #24955]			optimum	5.5
[Ref.: #24955]			growth	5.5-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #24955]

Oxygen tolerance

aerobe

[Ref.: #24955]

Ability of spore formation

[Ref.: #24437]

Name of produced compound

plusbacins

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #24955]		NaCl		growth	<0.5	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #24955]	esculin ChEBI	+	hydrolysis
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #24955]	gelatin ChEBI	+	hydrolysis
[Ref.: #68369]	gelatin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #24955]	glucose ChEBI	-	fermentation
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #24955]	nitrate ChEBI	-	reduction
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #24955]		acetoin ChEBI	no
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Metabolite	Voges-Proskauer-test	Methylred-test	Indole test
[Ref.: #24955]	acetoin ChEBI	-
[Ref.: #24955]	glucose ChEBI		-
[Ref.: #68369]	indole ChEBI			-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #24955]	acid phosphatase	+	3.1.3.2
[Ref.: #24955]	alkaline phosphatase	+	3.1.3.1
[Ref.: #24955]	alpha-fucosidase	-	3.2.1.51
[Ref.: #24955]	alpha-galactosidase	-	3.2.1.22
[Ref.: #24955]	alpha-glucosidase	-	3.2.1.20
[Ref.: #24955]	alpha-mannosidase	-	3.2.1.24
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #24955]	beta-galactosidase	-	3.2.1.23
[Ref.: #24955]	beta-glucosidase	-	3.2.1.21
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #24955]	beta-glucuronidase	-	3.2.1.31
[Ref.: #24955]	catalase	+	1.11.1.6
[Ref.: #24955]	cystine arylamidase	-	3.4.11.3
[Ref.: #24955]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #24955]	esterase (C 4)	+
[Ref.: #24955]	esterase lipase (C 8)	+
[Ref.: #68369]	gelatinase	+		* from API 20NE
[Ref.: #24955]	leucine arylamidase	+	3.4.11.1
[Ref.: #24955]	lipase (C 14)	-
[Ref.: #24955]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #24955]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #24955]	trypsin	+	3.4.21.4
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #24955]	valine arylamidase	-
	Only first 10 entries are displayed. Click here to see all.

API® 20NE:

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

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #24437]	25307	-	-	-	-	-	+	+	-	-	-	+	-	+	+	-	-	-	+	-	-	+
[Ref.: #24437]	24302	-	-	-	-	-	+	+	-	+	-	+	-	+	+	-	-	-	+	-	-	+

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

[Ref.: #24437]	Sample type/isolated from	soil
[Ref.: #24437]	Geographic location (country and/or sea, region)	Okinawa Prefecture, Okinawa-honto
[Ref.: #24437]	Country	Japan
[Ref.: #24437]	Country ISO 3 Code	JPN
[Ref.: #24437]	Continent	Asia

[Ref.: #24955]	Enrichment culture	tryptic soy agar (TSA, BBL 11768)
[Ref.: #24955]	Enrichment culture temperature	28 ̊C
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KU593484 (>99% sequence identity) for Lysobacter firmicutimachus from Microbeatlas

Aquatic Samples	112
Soil Samples	251
Animal Samples	45
Plant Samples	39
Total Samples	447

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

[Ref.: #24437]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #24437]	Lysobacter firmicutimachus strain PB-6250 16S ribosomal RNA gene, partial sequence	KU593484	1551	GenBank ENA	1792846 tax ID

[Ref.: #24437]

GC-content

68.7 mol%

high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #24437]

Culture collection no.

DSM 102073, FERM BP-2938, LMG 28994

[Ref.: #90961]

SI-ID 398165

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Reclassification of Pseudomonas sp. PB-6250T as Lysobacter firmicutimachus sp. nov.	Miess H, van Trappen S, Cleenwerck I, De Vos P, Gross H	Int J Syst Evol Microbiol	10.1099/ijsem.0.001329	2016	*
Phylogeny	Lysobacter tabacisoli sp. nov., isolated from rhizosphere soil of Nicotiana tabacum L.	Xiao M, Zhou XK, Chen X, Duan YQ, Alkhalifah DHM, Im WT, Hozzein WN, Chen W, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003164	2018	*

References

#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 )

#24437

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 102073

#24955

H. v. T. Miess, Stefanie,Cleenwerck, Ilse,De Vos, Paul,Gross, Harald: Reclassification of Pseudomonas sp. PB-6250T as Lysobacter firmicutimachus sp. nov. IJSEM 66: 4162 - 4166 2016 ( DOI 10.1099/ijsem.0.001329 , PubMed 27468934 )

#68369

Automatically annotated from API 20NE .

#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 .

#90961

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-ID398165.1 )

* These data were automatically processed and therefore are not curated

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