Name: Gracilimonas amylolytica LA399
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 158807

Type strain:

Species: Gracilimonas amylolytica

Strain Designation: LA399

Culture col. no.: CGMCC 1.16248, KCTC 52885

Strain history: <- Yue-Hong Wu, Second Institute of Oceanography SOA

NCBI tax ID(s): 1749045 (species)

Section

Gracilimonas amylolytica LA399 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from deep-sea sediment.

colony-forming
Gram-negative
rod-shaped
aerobe
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 amylolytica**
	Full Scientific Name (LPSN)	Gracilimonas amylolytica Wu et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #65570]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #65570]	Cell length	1.1-1.8 µm

[Ref.: #65570]	Cell width	0.4-0.5 µm

[Ref.: #65570]	Cell shape	rod-shaped

[Ref.: #65570]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %92.116

[Ref.: #65570]	Colony color	pink
[Ref.: #65570]	Colony shape	circular
[Ref.: #65570]	Incubation period	3 days
[Ref.: #65570]	Cultivation medium used	MA

[Ref.: #65570]	Pigment production	yes
[Ref.: #65570]	Pigment name	carotenoid-like

Information on culture and growth conditions Culture and growth conditions

[Ref.: #65570]

Culture medium

Marine agar (MA)

[Ref.: #65570]

Culture medium growth

		Temperature
[Ref.: #65570]	growth	20-40 °C
[Ref.: #65570]	optimum	37 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #65570]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #65570]			optimum	7.0
[Ref.: #65570]			growth	6.5-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #65570]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #69480]	Ability of spore formation	no Confidence in %99.981
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Salt	Tested relation		Salt conc.
[Ref.: #65570]	NaCl		growth	0-10.0	%(w/v)
[Ref.: #65570]	NaCl		optimum	3.0-5.0	%(w/v)
[Ref.: #65570]	Marine salts	no	growth	0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65570]	cellobiose ChEBI	-	builds acid from
[Ref.: #65570]	cellobiose ChEBI	+	growth
[Ref.: #65570]	citrate ChEBI	-	growth
[Ref.: #65570]	D-fructose ChEBI	-	builds acid from
[Ref.: #65570]	D-fructose ChEBI	+	growth
[Ref.: #65570]	D-galactose ChEBI	+	builds acid from
[Ref.: #65570]	D-galactose ChEBI	+	growth
[Ref.: #65570]	D-mannose ChEBI	+	builds acid from
[Ref.: #65570]	D-mannose ChEBI	+	growth
[Ref.: #65570]	D-ribose ChEBI	-	builds acid from
[Ref.: #65570]	D-ribose ChEBI	+	growth
[Ref.: #65570]	esculin ChEBI	+	hydrolysis
[Ref.: #65570]	ethanol ChEBI	-	builds acid from
[Ref.: #65570]	gelatin ChEBI	+	hydrolysis
[Ref.: #65570]	glucose ChEBI	+	builds acid from
[Ref.: #65570]	glucose ChEBI	+	fermentation
[Ref.: #65570]	glucose ChEBI	+	growth
[Ref.: #65570]	L-arabinose ChEBI	+	growth
[Ref.: #65570]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #65570]	L-rhamnose ChEBI	+	growth
[Ref.: #65570]	lactose ChEBI	+	builds acid from
[Ref.: #65570]	lactose ChEBI	+	growth
[Ref.: #65570]	maltose ChEBI	+	builds acid from
[Ref.: #65570]	mannitol ChEBI	-	builds acid from
[Ref.: #65570]	melezitose ChEBI	-	builds acid from
[Ref.: #65570]	myo-inositol ChEBI	-	builds acid from
[Ref.: #65570]	nitrate ChEBI	-	reduction
[Ref.: #65570]	raffinose ChEBI	-	builds acid from
[Ref.: #65570]	raffinose ChEBI	+	growth
[Ref.: #65570]	ribitol ChEBI	-	builds acid from
[Ref.: #65570]	ribitol ChEBI	+	growth
[Ref.: #65570]	sodium acetate ChEBI	+	growth
[Ref.: #65570]	sodium gluconate ChEBI	+	growth
[Ref.: #65570]	sodium pyruvate ChEBI	+	growth
[Ref.: #65570]	sorbitol ChEBI	-	builds acid from
[Ref.: #65570]	sorbose ChEBI	+	builds acid from
[Ref.: #65570]	sorbose ChEBI	+	growth
[Ref.: #65570]	starch ChEBI	+	hydrolysis
[Ref.: #65570]	sucrose ChEBI	-	builds acid from
[Ref.: #65570]	sucrose ChEBI	+	growth
[Ref.: #65570]	trehalose ChEBI	-	builds acid from
[Ref.: #65570]	tween 20 ChEBI	-	hydrolysis
[Ref.: #65570]	tween 40 ChEBI	-	hydrolysis
[Ref.: #65570]	tween 80 ChEBI	+	hydrolysis
[Ref.: #65570]	xylose ChEBI	+	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #65570]	acetoin ChEBI	yes
[Ref.: #65570]	hydrogen sulfide ChEBI	no
[Ref.: #65570]	indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #65570]		acetoin ChEBI	+

	Enzyme	Enzyme activity	EC number
[Ref.: #65570]	arginine dihydrolase	+	3.5.3.6
[Ref.: #65570]	beta-galactosidase	-	3.2.1.23
[Ref.: #65570]	catalase	+	1.11.1.6
[Ref.: #65570]	cytochrome oxidase	+	1.9.3.1
[Ref.: #65570]	lysine decarboxylase	-	4.1.1.18
[Ref.: #65570]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #65570]	tryptophan deaminase	+	4.1.99.1
[Ref.: #65570]	urease	-	3.5.1.5

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

[Ref.: #65570]	Sample type/isolated from	deep-sea sediment
[Ref.: #65570]	Sampling date	2013-09
[Ref.: #65570]	Country	Pacific Ocean
[Ref.: #65570]	Geographic location	10.1669°/-154.2330°
[Ref.: #65570]	Enrichment culture	natural seawater agar
[Ref.: #65570]	Enrichment culture composition	supplemented with 0.05 % peptone, 0.01 % yeast extract and 1.5 % agar (w/v), pH 7.2-7.4
[Ref.: #65570]	Enrichment culture duration	30 days
[Ref.: #65570]	Enrichment culture temperature	25-28 ̊C

[Ref.: #67771]	Sample type/isolated from	From Deep Sea Sediment
[Ref.: #67771]	Geographic location (country and/or sea, region)	East Pacific Ocean
[Ref.: #67771]	Country	China
[Ref.: #67771]	Country ISO 3 Code	CHN
[Ref.: #67771]	Continent	Asia
[Ref.: #67771]	Geographic location	10.1667°/-154.2330°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

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.: #65570]	16S rRNA gene sequence	KT985637		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Gracilimonas amylolytica LA399	GCA_002911695	scaffold	GenBank	1749045 tax ID	*
[Ref.: #66792]	Gracilimonas amylolytica LA399	2833079920	draft	JGI IMG/M	1749045 tax ID	*

[Ref.: #65570]

GC-content

45.3 mol%

genome sequence analysis

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: Gracilimonas amylolytica LA399 NCBI: GCA_002911695.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Gracilimonas amylolytica LA399 NCBI: GCA_002911695.1
[Ref.: #69480]	flagellated	no	96.799	yes
[Ref.: #69480]	gram-positive	no	97.954	no
[Ref.: #69480]	anaerobic	no	98.827	yes
[Ref.: #69480]	aerobic	yes	82.997	no
[Ref.: #69480]	halophile	yes	88.422	no
[Ref.: #69480]	spore-forming	no	92.842	no
[Ref.: #69480]	glucose-util	yes	88.197	yes
[Ref.: #69480]	thermophile	no	92.478	no
[Ref.: #69480]	motile	no	93.244	no
[Ref.: #69480]	glucose-ferment	no	63.601	yes

Availability in culture collections External links

[Ref.: #65570]

Culture collection no.

CGMCC 1.16248, KCTC 52885

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	*

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 )

#65570

Yue-Hong Wu, Jing Yan, Chen Fang, Ying-Yi Huo, Wei-Lin Ma, De-Min Zhang, Chun-Sheng Wang and Xue-Wei Xu: Gracilimonas amylolytica sp. nov., isolated from deep-sea sediment. IJSEM 68: 1713 - 1718 2018 ( DOI 10.1099/ijsem.0.002734 , PubMed 29611802 )

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

* These data were automatically processed and therefore are not curated

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