Gracilibacillus halophilus (DSM 17856, CGMCC 1.6303, YIM-C55.5)

Name: Gracilibacillus halophilus (DSM 17856, CGMCC 1.6303, YIM-C55.5)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1463

Type strain

Strain Designation YIM-C55.5

Culture col. no. DSM 17856 CGMCC 1.6303 YIM-C55.5

NCBI tax ID(s) 470864

Special Collections DSMZ Literature strains

History DSMZ <- Xiaolong Cui; YIM-C55.5

Links

Gracilibacillus halophilus YIM-C55.5 is an obligate aerobe, halophilic, spore-forming bacterium that forms circular colonies and was isolated from saline soil sample from a beach of the Xiaochaidamu salt lake.

colony-forming rod-shaped motile Gram-positive spore-forming halophilic obligate aerobe Bacteria 16S sequence genome sequence

Name and taxonomic classification

SI-ID 312280

CGMCC 1.6303,DSM 17856

@ref 20215

Last LPSN update 2026-05-29 08:25:16

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Gracilibacillus

Species Gracilibacillus halophilus

Full scientific name Gracilibacillus halophilus Chen et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Flagellum arrangement
23045	positive	4.0-8.0 µm	0.3-0.5 µm	rod-shaped		peritrichous

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
23045	1.0-1.5 mm	creamy white	circular	3 days	HSMA15 (pH 7.0)

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7142	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514; with strain-specific modifications) Composition: NaCl 150.0 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
23045	high-salt medium (HSMA15 (pH 7.0))

Culture temp

@ref	Growth	Type	Temperature (°C)
23045	positive	growth	28.0-60.0
23045	positive	optimum	45.0-50.0

Culture pH

@ref	Ability	Type	PH	PH range
23045	positive	optimum	7.0
23045	positive	growth	6.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
23045	obligate aerobe
125439	obligate aerobe	96.756

Spore formation

@ref	Spore description	Type of spore	Spore formation	Confidence
23045	ellipsoidal,terminal within swollen sporangia	endospore
125438				92.258

Halophily

@ref	Halophily level	Salt	Growth	Tested relation	Concentration
23045	halophilic	NaCl	positive	growth	7.0-30.0 %(w/v)
23045		NaCl		optimum	15.0 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23045	16651 ChEBI	(S)-lactate	-	respiration
23045	62064 ChEBI	2,3-butanediol	-	respiration
23045	16808 ChEBI	2-dehydro-D-gluconate	+	builds acid from
23045	17256 ChEBI	2-deoxyadenosine	-	respiration
23045	64552 ChEBI	2-hydroxybutyrate	-	respiration
23045	30916 ChEBI	2-oxoglutarate	-	respiration
23045	28644 ChEBI	2-oxopentanoate	-	respiration
23045	37054 ChEBI	3-hydroxybutyrate	-	respiration
23045	73918 ChEBI	3-O-methyl-D-glucose	-	respiration
23045	16724 ChEBI	4-hydroxybutyrate	-	respiration
23045	18101 ChEBI	4-hydroxyphenylacetic acid	-	respiration
23045	17426 ChEBI	5-dehydro-D-gluconate	+	builds acid from
23045	30089 ChEBI	acetate	+	respiration
23045	16335 ChEBI	adenosine	-	respiration
23045	40585 ChEBI	alpha-cyclodextrin	-	respiration
23045	17925 ChEBI	alpha-D-glucose	-	respiration
23045	36219 ChEBI	alpha-lactose	-	respiration
23045	16027 ChEBI	amp	-	respiration
23045	27613 ChEBI	amygdalin	+	builds acid from
23045	27613 ChEBI	amygdalin	+	oxidation
23045	27613 ChEBI	amygdalin	+	respiration
23045	22599 ChEBI	arabinose	+	oxidation
23045	18305 ChEBI	arbutin	-	builds acid from
23045	18305 ChEBI	arbutin	-	respiration
23045	495055 ChEBI	beta-cyclodextrin	-	respiration
23045		casein	-	hydrolysis
23045	17057 ChEBI	cellobiose	-	builds acid from
23045	17057 ChEBI	cellobiose	-	respiration
23045	17029 ChEBI	chitin	+	hydrolysis
23045	16947 ChEBI	citrate	-	carbon source
23045	15570 ChEBI	D-alanine	-	respiration
23045	17108 ChEBI	D-arabinose	+	builds acid from
23045	18333 ChEBI	D-arabitol	-	builds acid from
23045	18333 ChEBI	D-arabitol	-	respiration
23045	15824 ChEBI	D-fructose	+	builds acid from
23045	15824 ChEBI	D-fructose	+	respiration
23045	78697 ChEBI	D-fructose 6-phosphate	-	respiration
23045	28847 ChEBI	D-fucose	-	builds acid from
23045	12936 ChEBI	D-galactose	-	builds acid from
23045	12936 ChEBI	D-galactose	-	respiration
23045	18024 ChEBI	D-galacturonic acid	-	respiration
23045	8391 ChEBI	D-gluconate	-	respiration
23045	17634 ChEBI	D-glucose	+	builds acid from
23045	14314 ChEBI	D-glucose 6-phosphate	-	respiration
23045	62318 ChEBI	D-lyxose	-	builds acid from
23045	15588 ChEBI	D-malate	-	respiration
23045	16899 ChEBI	D-mannitol	+	builds acid from
23045	16899 ChEBI	D-mannitol	+	respiration
23045	16024 ChEBI	D-mannose	-	builds acid from
23045	16024 ChEBI	D-mannose	+	respiration
23045	27605 ChEBI	D-psicose	-	respiration
23045	16988 ChEBI	D-ribose	+	builds acid from
23045	16988 ChEBI	D-ribose	+	respiration
23045	17924 ChEBI	D-sorbitol	+	builds acid from
23045	17924 ChEBI	D-sorbitol	+	respiration
23045	16443 ChEBI	D-tagatose	-	respiration
23045	16443 ChEBI	D-tagatose	+	builds acid from
23045	16551 ChEBI	D-trehalose	-	builds acid from
23045	16551 ChEBI	D-trehalose	+	respiration
23045	65327 ChEBI	D-xylose	-	builds acid from
23045	65327 ChEBI	D-xylose	+	respiration
23045	23652 ChEBI	dextrin	-	respiration
23045	17113 ChEBI	erythritol	-	builds acid from
23045	4853 ChEBI	esculin	-	builds acid from
23045	4853 ChEBI	esculin	+	hydrolysis
23045	16813 ChEBI	galactitol	-	builds acid from
23045	5291 ChEBI	gelatin	+	hydrolysis
23045	28066 ChEBI	gentiobiose	-	builds acid from
23045	28066 ChEBI	gentiobiose	-	respiration
23045	24265 ChEBI	gluconate	-	builds acid from
23045	17234 ChEBI	glucose	-	fermentation
23045	17234 ChEBI	glucose	+	fermentation
23045	17234 ChEBI	glucose	+	oxidation
23045	29042 ChEBI	glucose 1-phosphate	-	respiration
23045	17754 ChEBI	glycerol	-	builds acid from
23045	17754 ChEBI	glycerol	-	respiration
23045	14336 ChEBI	glycerol 1-phosphate	-	respiration
23045	28087 ChEBI	glycogen	+	builds acid from
23045	28087 ChEBI	glycogen	+	respiration
23045	73784 ChEBI	glycyl-l-glutamate	-	respiration
23045	17596 ChEBI	inosine	-	respiration
23045	15443 ChEBI	inulin	-	builds acid from
23045	15443 ChEBI	inulin	-	respiration
23045	21217 ChEBI	L-alaninamide	-	respiration
23045	16977 ChEBI	L-alanine	+	respiration
23045	73786 ChEBI	L-alanylglycine	-	respiration
23045	30849 ChEBI	L-arabinose	-	builds acid from
23045	30849 ChEBI	L-arabinose	+	respiration
23045	18403 ChEBI	L-arabitol	-	builds acid from
23045	17196 ChEBI	L-asparagine	+	respiration
23045	18287 ChEBI	L-fucose	-	builds acid from
23045	18287 ChEBI	L-fucose	-	respiration
23045	29985 ChEBI	L-glutamate	-	respiration
23045	15589 ChEBI	L-malate	-	respiration
23045	18183 ChEBI	L-pyroglutamic acid	-	respiration
23045	62345 ChEBI	L-rhamnose	+	builds acid from
23045	62345 ChEBI	L-rhamnose	+	respiration
23045	17115 ChEBI	L-serine	-	respiration
23045	17266 ChEBI	L-sorbose	+	builds acid from
23045	65328 ChEBI	L-xylose	-	builds acid from
23045	75144 ChEBI	lactamide	-	respiration
23045	17716 ChEBI	lactose	-	builds acid from
23045	6359 ChEBI	lactulose	-	respiration
23045	17306 ChEBI	maltose	-	builds acid from
23045	17306 ChEBI	maltose	+	respiration
23045	61993 ChEBI	maltotriose	-	respiration
23045	28808 ChEBI	mannan	-	respiration
23045	6731 ChEBI	melezitose	-	builds acid from
23045	6731 ChEBI	melezitose	-	respiration
23045	28053 ChEBI	melibiose	+	builds acid from
23045	28053 ChEBI	melibiose	+	oxidation
23045	28053 ChEBI	melibiose	+	respiration
23045	74611 ChEBI	methyl (R)-lactate	-	respiration
23045	55507 ChEBI	methyl alpha-D-galactoside	-	respiration
23045	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from
23045	320061 ChEBI	methyl alpha-D-glucopyranoside	-	respiration
23045	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
23045	43943 ChEBI	methyl alpha-D-mannoside	-	respiration
23045	17540 ChEBI	methyl beta-D-galactoside	-	respiration
23045	320055 ChEBI	methyl beta-D-glucopyranoside	-	respiration
23045	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
23045	51850 ChEBI	methyl pyruvate	-	respiration
23045	75146 ChEBI	monomethyl succinate	-	respiration
23045	17268 ChEBI	myo-inositol	+	builds acid from
23045	17268 ChEBI	myo-inositol	+	oxidation
23045	17268 ChEBI	myo-inositol	+	respiration
23045	63154 ChEBI	N-acetyl-beta-D-mannosamine	-	respiration
23045	44337 ChEBI	N-acetyl-L-glutamate	-	respiration
23045	506227 ChEBI	N-acetylglucosamine	-	builds acid from
23045	506227 ChEBI	N-acetylglucosamine	-	respiration
23045	17632 ChEBI	nitrate	+	reduction
23045	18394 ChEBI	palatinose	-	respiration
23045	17272 ChEBI	propionate	-	respiration
23045	17148 ChEBI	putrescine	-	respiration
23045	15361 ChEBI	pyruvate	-	respiration
23045	16634 ChEBI	raffinose	-	builds acid from
23045	16634 ChEBI	raffinose	+	respiration
23045	26546 ChEBI	rhamnose	+	oxidation
23045	15963 ChEBI	ribitol	-	builds acid from
23045	17814 ChEBI	salicin	-	builds acid from
23045	17814 ChEBI	salicin	-	respiration
23045	32488 ChEBI	sedoheptulosan	-	respiration
23045	30911 ChEBI	sorbitol	+	oxidation
23045	17164 ChEBI	stachyose	-	respiration
23045	28017 ChEBI	starch	-	builds acid from
23045	28017 ChEBI	starch	+	hydrolysis
23045	143136 ChEBI	succinamate	-	respiration
23045	30031 ChEBI	succinate	-	respiration
23045	17992 ChEBI	sucrose	+	builds acid from
23045	17992 ChEBI	sucrose	+	oxidation
23045	17992 ChEBI	sucrose	+	respiration
23045	17748 ChEBI	thymidine	-	respiration
23045	63528 ChEBI	thymidine 5'-monophosphate	-	respiration
23045	32528 ChEBI	turanose	-	builds acid from
23045	32528 ChEBI	turanose	-	respiration
23045	53423 ChEBI	tween 40	-	respiration
23045	53426 ChEBI	tween 80	-	respiration
23045	53426 ChEBI	tween 80	+	hydrolysis
23045	16199 ChEBI	urea	-	hydrolysis
23045	16704 ChEBI	uridine	-	respiration
23045	16695 ChEBI	uridine 5'-monophosphate	-	respiration
23045	17151 ChEBI	xylitol	-	builds acid from
23045	17151 ChEBI	xylitol	-	respiration

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.	Resistance conc.
23045	28971	ampicillin	30 µg
23045	17698	chloramphenicol	30 µg
23045	17833	gentamicin		10 µg
23045	6104	kanamycin		30 µg
23045	6472	lincomycin	2 µg
23045	100147	nalidixic acid		20 µg
23045	28368	novobiocin	30 µg
23045	8309	polymyxin b		30 µg
23045	28077	rifampicin	5 µg
23045	17076	streptomycin		10 µg
23045	27902	tetracycline	30 µg

Metabolite production

@ref	Chebi-ID	Metabolite
23045	15688 ChEBI	acetoin
23045	16136 ChEBI	hydrogen sulfide
23045	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Citrate test	Methylred-test
23045	15688 ChEBI	acetoin	-
23045	16947 ChEBI	citrate		-
23045	17234 ChEBI	glucose			-

Enzymes

@ref	Value	Activity	Ec
23045	acid phosphatase	+	3.1.3.2
23045	alkaline phosphatase	+	3.1.3.1
23045	alpha-chymotrypsin	+	3.4.21.1
23045	alpha-fucosidase	-	3.2.1.51
23045	alpha-galactosidase	-	3.2.1.22
23045	alpha-glucosidase	+	3.2.1.20
23045	alpha-mannosidase	+	3.2.1.24
23045	beta-galactosidase	+	3.2.1.23
23045	beta-glucoronidase	-	3.2.1.31
23045	beta-glucosidase	+	3.2.1.21
23045	catalase	+	1.11.1.6
23045	cystine arylamidase	+	3.4.11.3
23045	cytochrome oxidase	+	1.9.3.1
23045	esterase (C 4)	+
23045	esterase lipase (C 8)	+
23045	leucine arylamidase	+	3.4.11.1
23045	lipase (C 14)	-
23045	N-acetyl-beta-glucosaminidase	-	3.2.1.52
23045	naphthol-AS-BI-phosphohydrolase	+
23045	trypsin	-	3.4.21.4
23045	valine arylamidase	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Terrestrial	#Coast
#Environmental	#Terrestrial	#Soil
#Condition	#Saline	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature
7142	saline soil sample from a beach of the Xiaochaidamu salt lake	Xiaochaidamu salt lake, Qaidam Basin, Qinghai Province, north-west China.	China	CHN	Asia
23045						high-salt medium (HSM, pH 7.5) agar supplemented with 20 % NaCl (w/v) (HSMA20, pH 7.5)	based on marine agar 2216, consisted of (per litre distilled water): 5.0 g casein peptone, 2.0 g yeast extract (Oxoid), 1.0 g lactalbumin hydrolysate (Oxoid), 8.0 g Na2SO4 , 6.4 g MgCl2.6H2O, 4.0 g KCl, 2.0 g MgSO4.7H2O, 2.0 g CaCl2 , 0.1 g iron(III) citrate, 0.16 g Na2CO3 , 0.08 g KBr, 34.0 mg SrCl2 , 22.0 mg H3BO3 , 4.0 mg sodium silicate, 2.4 mg NaF, 1.6 mg (NH4)NO3 and 8.0 mg Na2HPO4	7 days	55.0

Taxonmaps

69479

Global distribution of 16S sequence EU135704 (>99% sequence identity) for Gracilibacillus halophilus subclade from Microbeatlas

Aquatic Samples	17
Soil Samples	18
Animal Samples	63
Plant Samples	1
Total Samples	99

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7142	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM35960v1 assembly for Gracilibacillus halophilus YIM-C55.5	contig	GCA_000359605	1308866.3	2545824697	1308866	44.37

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7142	Gracilibacillus halophilus YIM-C55.5 strain YIM C55.5 16S ribosomal RNA gene, partial sequence	EU135704	1514		1308866

GC content

7142

GC-content (mol%)42.3

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM35960v1 assembly for Gracilibacillus halophilus YIM-C55.5
NCBI: GCA_000359605

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.76	no
125439	gram_stain	BacteriaNetⓘ	variable	53.80	no
125439	motility	BacteriaNetⓘ	yes	59.53	no
125439	spore_formation	BacteriaNetⓘ	yes	63.39	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Gracilibacillus halophilus YIM-C55.5
PATRIC: 1308866.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	86.55	no
125438	anaerobic	anaerobicⓘ	no	94.51	yes
125438	spore-forming	spore-formingⓘ	yes	92.26	yes
125438	aerobic	aerobicⓘ	yes	73.72	no
125438	thermophilic	thermophileⓘ	no	84.98	no
125438	flagellated	motile2+ⓘ	yes	84.30	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Gracilibacillus eburneus sp.nov., a moderately halophilic bacterium isolated from Xinjiang province, China.	Guan HL, Zhang YJ, Lu XJ, Jia M, Zhang ZY, Gao XH, Ma YC, Tian F, Tang SK	Arch Microbiol	10.1007/s00203-017-1450-6	2017
Phylogeny	Gracilibacillus bigeumensis sp. nov., a moderately halophilic bacterium from solar saltern soil.	Kim P, Lee JC, Park DJ, Shin KS, Kim JY, Kim CJ	Int J Syst Evol Microbiol	10.1099/ijs.0.034264-0	2011
Phylogeny	Gracilibacillus halophilus sp. nov., a moderately halophilic bacterium isolated from saline soil.	Chen YG, Cui XL, Zhang YQ, Li WJ, Wang YX, Xu LH, Peng Q, Wen ML, Jiang CL	Int J Syst Evol Microbiol	10.1099/ijs.0.65698-0	2008

References

#7142	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17856
#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 )
#23045	Yi-Guang Chen,Xiao-Long Cui,Yu-Qin Zhang,Wen-Jun Li,Yong-Xia Wang,Li-Hua Xu,Qian Peng,Meng-Liang Wen,Cheng-Lin Jiang: Gracilibacillus halophilus sp. nov., a moderately halophilic bacterium isolated from saline soil. IJSEM 58: 2403 - 2408 2008 ( DOI 10.1099/ijs.0.65698-0 , PubMed 18842864 )
#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) .
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Content

About us

Gracilibacillus halophilus (DSM 17856, CGMCC 1.6303, YIM-C55.5)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000359605

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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