Name: Gracilimonas mengyeensis DSM 21985
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 24739

Type strain:

Species: Gracilimonas mengyeensis

Culture col. no.: DSM 21985, ACCC 10717, YIM J14

Strain history: <- X.-L. Cui, YIM; YIM J14 <- J.-H. Liu and Y.-X. Wang

NCBI tax ID(s): 1302730 (species)

SI-ID 406532

DSM 21985

Special Collections

Section

Gracilimonas mengyeensis DSM 21985 is a facultative anaerobe, Gram-negative, rod-shaped bacterium that was isolated from sediment from a salt mine.

Gram-negative
rod-shaped
facultative anaerobe
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	*Balneolota*
	Class	*Balneolia*
	Order	*Balneolales*
	Family	*Balneolaceae*
	Genus	*Gracilimonas*
	Species	**Gracilimonas mengyeensis**
	Full Scientific Name (LPSN)	Gracilimonas mengyeensis Wang et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #31097]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %92.376

[Ref.: #31097]	Cell length	7.25 µm

[Ref.: #31097]	Cell width	0.4 µm

[Ref.: #31097]	Cell shape	rod-shaped

[Ref.: #31097]	Motility	no

[Ref.: #31097]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21195]

Culture medium

MEDIUM 514 PLUS ADDITIONAL SALT (DSMZ Medium 514b)

[Ref.: #21195]

Culture medium growth

[Ref.: #21195]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21195]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21195]	growth	28 °C
[Ref.: #31097]	growth	20-37 °C
[Ref.: #31097]	optimum	28 °C

	pH	Kind of pH		pH
[Ref.: #31097]			optimum	7.5
[Ref.: #31097]			growth	6.5-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31097]

Oxygen tolerance

facultative anaerobe

[Ref.: #31097]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31097]		NaCl		growth	02-15	%
[Ref.: #31097]		NaCl		optimum	6.5	%

[Ref.: #31097]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31097]	dextrin ChEBI	+	carbon source
[Ref.: #31097]	esculin ChEBI	+	hydrolysis
[Ref.: #31097]	galactose ChEBI	+	carbon source
[Ref.: #31097]	glucose ChEBI	+	carbon source
[Ref.: #31097]	glycerol ChEBI	+	carbon source
[Ref.: #31097]	lactose ChEBI	+	carbon source
[Ref.: #31097]	maltose ChEBI	+	carbon source
[Ref.: #31097]	nitrate ChEBI	+	reduction
[Ref.: #31097]	sorbitol ChEBI	+	carbon source
[Ref.: #31097]	sucrose ChEBI	+	carbon source
[Ref.: #31097]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #31097]	acid phosphatase	+	3.1.3.2
[Ref.: #31097]	alkaline phosphatase	+	3.1.3.1
[Ref.: #31097]	alpha-galactosidase	+	3.2.1.22
[Ref.: #31097]	catalase	+	1.11.1.6
[Ref.: #31097]	cytochrome oxidase	+	1.9.3.1
[Ref.: #31097]	urease	+	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	100	5 of 5
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	degradation of hexoses	66.67	12 of 18
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	polyamine pathway	65.22	15 of 23
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	vitamin B1 metabolism	61.54	8 of 13
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	degradation of sugar acids	60	15 of 25
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	histidine metabolism	58.62	17 of 29
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	non-pathway related	55.26	21 of 38
[Ref.: #66794]	vitamin B6 metabolism	54.55	6 of 11
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	46.15	6 of 13
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	carotenoid biosynthesis	45.45	10 of 22
[Ref.: #66794]	oxidative phosphorylation	45.05	41 of 91
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	degradation of sugar alcohols	43.75	7 of 16
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #21195]	Sample type/isolated from	sediment from a salt mine
[Ref.: #21195]	Geographic location (country and/or sea, region)	Yunnan Province, Mengye salt mine (22° 71' N 101° 63' E)
[Ref.: #21195]	Country	China
[Ref.: #21195]	Country ISO 3 Code	CHN
[Ref.: #21195]	Continent	Asia
[Ref.: #21195]	Geographic location	23.1833°/102.0500°
* marker position based on {}

Isolation sources categories

#Engineered	#Other	#Mine
#Condition	#Saline	-
#Environmental	#Terrestrial	#Sediment
#Environmental	#Terrestrial	#Geologic

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KC561141 (>99% sequence identity) for Gracilimonas mengyeensis subclade from Microbeatlas

Aquatic Samples	80
Soil Samples	11
Animal Samples
Plant Samples
Total Samples	91

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

[Ref.: #21195]

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.: #21195]	Gracilimonas mengyeensis strain YIM J14 16S ribosomal RNA gene, partial sequence	KC561141	1396	GenBank ENA	1302730 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Gracilimonas mengyeensis DSM 21985	GCA_900182705	contig	GenBank ENA	1302730 tax ID	*
[Ref.: #66792]	Gracilimonas mengyeensis strain DSM 21985	1302730.3	wgs	PATRIC	1302730 tax ID	*
[Ref.: #66792]	Gracilimonas mengyeensis DSM 21985	2724679790	draft	JGI IMG/M	1302730 tax ID	*

[Ref.: #21195]	GC-content	47.2 mol%	high performance liquid chromatography (HPLC)
[Ref.: #31097]	GC-content	47.2 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Gracilimonas mengyeensis strain DSM 21985 PATRIC: 1302730.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Gracilimonas mengyeensis strain DSM 21985 PATRIC: 1302730.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	92.376	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	88.536	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	84.146	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	58.022	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	89.125	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	56.506	no

Availability in culture collections External links

[Ref.: #21195]

Culture collection no.

DSM 21985, ACCC 10717, YIM J14

[Ref.: #88567]

SI-ID 406532

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Gracilimonas amylolytica sp. nov., isolated from deep-sea sediment.	Wu YH, Yan J, Fang C, Huo YY, Ma WL, Zhang DM, Wang CS, Xu XW	Int J Syst Evol Microbiol	10.1099/ijsem.0.002734	2018	*
Phylogeny	Rhodohalobacter halophilus gen. nov., sp. nov., a moderately halophilic member of the family Balneolaceae.	Xia J, Xie ZH, Dunlap CA, Rooney AP, Du ZJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.001806	2017	*
Phylogeny	Gracilimonas mengyeensis sp. nov., a moderately halophilic bacterium isolated from a salt mine in Yunnan, south-western China.	Wang YX, Li YP, Liu JH, Xiao W, Lai YH, Li ZY, Ding ZG, Wen ML, Cui XL	Int J Syst Evol Microbiol	10.1099/ijs.0.052043-0	2013	*

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 )

#21195

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21985

#31097

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #27426 (see below)

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 )

#88567

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-ID406532.1 )

#27426

IJSEM 3989 2013 ( DOI 10.1099/ijs.0.052043-0 , PubMed 23710054 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Gracilimonas mengyeensis in external resources:
SILVA
BRENDA
PANGAEA
GBIF

Gracilimonas mengyeensis strain DSM 21985

Gracilimonas mengyeensis strain DSM 21985

Change proposal

Change proposal