Name: Stenotrophomonas tumulicola T5916-2-1b
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 140908

Type strain:

Species: Stenotrophomonas tumulicola

Strain Designation: T5916-2-1b

Culture col. no.: JCM 30961, NCIMB 15009

Strain history: J. Sugiyama; TechnoSuruga Lab. Co., Ltd., Japan; T5916-2-1b.

NCBI tax ID(s): 1685415 (species)

Other strains from Stenotrophomonas tumulicola

S. tumulicola JCM 28316
S. tumulicola JCM 30962
S. tumulicola JCM 30963
S. tumulicola JCM 30965
S. tumulicola JCM 30966
S. tumulicola JCM 30967
S. tumulicola JCM 30968
S. tumulicola JCM 30969

Section

Stenotrophomonas tumulicola T5916-2-1b is an obligate aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from A viscous gel appearing on the mural painting on the west wall inside the stone chamber of Takamatsuzuka Tumulus.

colony-forming
Gram-negative
motile
rod-shaped
obligate 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	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Lysobacteraceae*
	Genus	*Stenotrophomonas*
	Species	**Stenotrophomonas tumulicola**
	Full Scientific Name (LPSN)	Stenotrophomonas tumulicola Handa et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43754]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.993

[Ref.: #43754]	Cell length	1.5-2.5 µm

[Ref.: #43754]	Cell width	0.8 µm

[Ref.: #43754]	Cell shape	rod-shaped

[Ref.: #43754]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %92.819

[Ref.: #43754]	Flagellum arrangement	monotrichous, polar

[Ref.: #43754]	Colony color	Yellowish
[Ref.: #43754]	Colony shape	circular
[Ref.: #43754]	Incubation period	1 day
[Ref.: #43754]	Cultivation medium used	Nutrient agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43754]

Culture medium

Nutrient agar (NA)

[Ref.: #43754]

Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #43754]			growth	10-37 °C
[Ref.: #67770]			growth	30 °C

[Ref.: #67770]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #43754]			growth	5-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43754]

Oxygen tolerance

obligate aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.991

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43754]		NaCl		growth	5	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43754]	cellobiose ChEBI	-	assimilation
[Ref.: #43754]	esculin ChEBI	+	hydrolysis
[Ref.: #43754]	ethanol ChEBI	+	assimilation
[Ref.: #43754]	gelatin ChEBI	+	hydrolysis
[Ref.: #43754]	glucose ChEBI	+	assimilation
[Ref.: #43754]	glucose ChEBI	+/-	builds acid from
[Ref.: #43754]	L-arabinose ChEBI	-	assimilation
[Ref.: #43754]	L-histidine ChEBI	+	assimilation
[Ref.: #43754]	lactose ChEBI	+	assimilation
[Ref.: #43754]	malate ChEBI	+	assimilation
[Ref.: #43754]	maltose ChEBI	+	assimilation
[Ref.: #43754]	maltose ChEBI	+	builds acid from
[Ref.: #43754]	mannose ChEBI	+	assimilation
[Ref.: #43754]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #43754]	nitrate ChEBI	-	reduction
[Ref.: #43754]	sodium chloride ChEBI	+	assimilation
[Ref.: #43754]	starch ChEBI	-	hydrolysis
[Ref.: #43754]	tween 80 ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #43754]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #43754]	beta-galactosidase	-	3.2.1.23
[Ref.: #43754]	catalase	+	1.11.1.6
[Ref.: #43754]	chymotrypsin	-	3.4.4.5
[Ref.: #43754]	cytochrome oxidase	-	1.9.3.1
[Ref.: #43754]	esterase (C 4)	-
[Ref.: #43754]	lipase (C 14)	-
[Ref.: #43754]	urease	-	3.5.1.5

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

[Ref.: #43754]	Sample type/isolated from	A viscous gel (biofilm) appearing on the mural painting (Byakko) on the west wall inside the stone chamber of Takamatsuzuka Tumulus
[Ref.: #43754]	Geographic location (country and/or sea, region)	Asuka-mura, Takaichi County, Nara Prefecture
[Ref.: #43754]	Country	Japan
[Ref.: #43754]	Country ISO 3 Code	JPN
[Ref.: #43754]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Yellow-cream visous gel (biofilm) from Takamatsuzuka Tumulus in Asuka-mura
[Ref.: #67770]	Geographic location (country and/or sea, region)	Nara Pref.
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Other	#Painting
#Environmental	#Biofilm	-
#Environmental	#Terrestrial	#Geologic

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC066089 (>99% sequence identity) for Stenotrophomonas from Microbeatlas

Aquatic Samples	340
Soil Samples	455
Animal Samples	566
Plant Samples	1192
Total Samples	2553

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.: #43754]	16S rRNA gene sequence	LC066089		GenBank

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Stenotrophomonas tumulicola JCM 30961	GCA_014117215	scaffold	GenBank	1685415 tax ID	*
[Ref.: #66792]	Stenotrophomonas tumulicola strain JCM 30961	1685415.3	wgs	PATRIC	1685415 tax ID	*

[Ref.: #43754]

GC-content

66 mol%

high performance liquid chromatography (HPLC)

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: Stenotrophomonas tumulicola JCM 30961 NCBI: GCA_014117215.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Stenotrophomonas tumulicola JCM 30961 NCBI: GCA_014117215.1
[Ref.: #69480]	motile	yes	90.307	yes
[Ref.: #69480]	flagellated	no	78.361	yes
[Ref.: #69480]	gram-positive	no	98.049	yes
[Ref.: #69480]	anaerobic	no	98.754	yes
[Ref.: #69480]	aerobic	yes	94.14	yes
[Ref.: #69480]	halophile	no	90.409	no
[Ref.: #69480]	spore-forming	no	95.395	no
[Ref.: #69480]	thermophile	no	98.927	no
[Ref.: #69480]	glucose-util	yes	88.627	yes
[Ref.: #69480]	glucose-ferment	no	90.835	no

Availability in culture collections External links

[Ref.: #43754]

Culture collection no.

JCM 30961, NCIMB 15009

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Stenotrophomonas bentonitica sp. nov., isolated from bentonite formations.	Sanchez-Castro I, Ruiz-Fresneda MA, Bakkali M, Kampfer P, Glaeser SP, Busse HJ, Lopez-Fernandez M, Martinez-Rodriguez P, Merroun ML	Int J Syst Evol Microbiol	10.1099/ijsem.0.002016	2017	*
Phylogeny	Stenotrophomonas tumulicola sp. nov., a major contaminant of the stone chamber interior in the Takamatsuzuka Tumulus.	Handa Y, Tazato N, Nagatsuka Y, Koide T, Kigawa R, Sano C, Sugiyama J	Int J Syst Evol Microbiol	10.1099/ijsem.0.000843	2015	*
	Identification and environment-friendly biocontrol potential of five different bacteria against Aphis punicae and Aphis illinoisensis (Hemiptera: Aphididae).	Baazeem A, Alotaibi SS, Khalaf LK, Kumar U, Zaynab M, Alharthi S, Darwish H, Alghamdi A, Jat SK, Al-Barty A, Albogami B, Noureldeen A, Ravindran B	Front Microbiol	10.3389/fmicb.2022.961349	2022	*

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 )

#43754

Yutaka Handa, Nozomi Tazato, Yuka Nagatsuka, Tomomi Koide, Rika Kigawa, Chie Sano, Junta Sugiyama: Stenotrophomonas tumulicola sp. nov., a major contaminant of the stone chamber interior in the Takamatsuzuka Tumulus. IJSEM 66: 1119 - 1124 2016 ( DOI 10.1099/ijsem.0.000843 , PubMed 26653171 )

#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;

#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 )

* These data were automatically processed and therefore are not curated

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Stenotrophomonas tumulicola JCM 30961

Stenotrophomonas tumulicola JCM 30961

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