Leifsonia shinshuensis (CCUG 51930, CIP 106805, DSM 15165)

Name: Leifsonia shinshuensis (CCUG 51930, CIP 106805, DSM 15165)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7340

Type strain

Strain Designation DB102, DBI02

Culture col. no. CCUG 51930 CIP 106805 DSM 15165 JCM 10591 DB102 5 more

NCBI tax ID(s) 150026

Special Collections DSMZ CCUG JCM KCTC CIP

History <- JCM <- T. Yorifuji; DB102 T. Yorifuji DB102. CIP <- 2000, JCM <- T. Yorifuji: strain DBI02

Links

Leifsonia shinshuensis DB102 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from forest soil.

Gram-positive motile rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 69140

CIP 106805,JCM 10591,DSM 15165,IAM 15088,CCUG 51930,BCRC 17580,CCRC 17580,NBRC 103132

@ref 20215

Last LPSN update 2026-02-09 11:19:27

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Leifsonia

Species Leifsonia shinshuensis

Full scientific name Leifsonia shinshuensis Suzuki et al. 2000

BacDive ID	Other strains from **Leifsonia shinshuensis** (1)	Type strain
156439	L. shinshuensis CCUG 61758

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
122590	positive	rod-shaped
125439	positive			98.9

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
5734	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)	Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
39586	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122590	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
5734	positive	growth	28	mesophilic
39586	positive	growth	30	mesophilic
59368	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic
122590	positive	growth	25-37	mesophilic
122590	negative	growth	10
122590	negative	growth	15
122590	negative	growth	41
122590	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
59368	aerobe
122590	obligate aerobe
125439	obligate aerobe	98.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
122590	NaCl	positive	growth	0-4 %
122590	NaCl		growth	6 %
122590	NaCl		growth	8 %
122590	NaCl		growth	10 %

Murein

@ref	Murein short key	Type
5734	B07	B2gamma {Gly} [L-Dab] D-Glu-D-Dab

Observation

67770

Observationquinones: MK-11, MK-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	-	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
122590	4853 ChEBI	esculin	+	hydrolysis
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
122590	606565 ChEBI	hippurate	-	hydrolysis
68371	30849 ChEBI	L-arabinose	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	-	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
122590	17632 ChEBI	nitrate	-	reduction
122590	17632 ChEBI	nitrate	-	respiration
122590	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
122590	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
122590	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
122590	15688 ChEBI	acetoin	-
122590	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
122590	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	+	3.2.1.24	from API zym
122590	amylase	-
68382	beta-galactosidase	+	3.2.1.23	from API zym
122590	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
122590	caseinase	-	3.4.21.50
122590	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
122590	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
122590	gamma-glutamyltransferase	-	2.3.2.2
122590	gelatinase	-
122590	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
122590	lipase	-
68382	lipase (C 14)	-		from API zym
122590	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
122590	ornithine decarboxylase	-	4.1.1.17
122590	oxidase	-
122590	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
122590	tryptophan deaminase	-
122590	tween esterase	+
122590	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
122590	-	-	+	+	-	+	-	-	-	-	+	+	-	+	-	+	+	-	+	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
122590	not determinedn.d.	+/-	-	-	-	-	-	-	-	+/-	-	-	+/-	-	-	-	-	+/-	+/-	-	-	-	-	-	-	+/-	+/-	+/-	+/-	-	-	-	-	+/-	-	-	-	-	-	-	-	-	-	-	+/-	-	-	+/-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
122590	not determinedn.d.	-	+	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
5734	forest soil	Nagano pref.	Japan	JPN	Asia
59368	Soil	Nagano Pref.	Japan	JPN	Asia
67770	Soil	Nagano Pref.	Japan	JPN	Asia
122590	Environment, Soil	Nagano	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB028940 (>99% sequence identity) for Leifsonia from Microbeatlas

Aquatic Samples	554
Soil Samples	2218
Animal Samples	672
Plant Samples	396
Total Samples	3840

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5734	1	Risk group (German classification) According to TRBA 466
122590	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM1341037v1 assembly for Leifsonia shinshuensis DSM 15165	contig	GCA_013410375	150026.7	2856442703	150026	72.52
124043	ASM3954004v1 assembly for Leifsonia shinshuensis JCM 10591	contig	GCA_039540045			150026	60.41
124043	ASM4242932v1 assembly for Leifsonia shinshuensis JCM 10591	scaffold	GCA_042429325			150026	30.73

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Leifsonia shinshuensis strain DB102 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence	DQ232614	2145		150026
5734	Microbacteriaceae str. DB102 gene for 16S rRNA, partial sequence	AB028940	1395		97974

GC content

@ref	GC-content (mol%)	Method
5734	70.7	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Leifsonia shinshuensis DSM 15165
NCBI: GCA_013410375

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	69.50	no
125439	motility	BacteriaNetⓘ	no	65.40	no
125439	gram_stain	BacteriaNetⓘ	positive	98.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Leifsonia shinshuensis strain DSM 15165
PATRIC: 150026.7

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	89.47	no
125438	anaerobic	anaerobicⓘ	no	98.18	yes
125438	spore-forming	spore-formingⓘ	no	73.20	no
125438	aerobic	aerobicⓘ	yes	89.41	no
125438	thermophilic	thermophileⓘ	no	95.88	yes
125438	flagellated	motile2+ⓘ	no	77.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Leifsonia gen. nov., a genus for 2,4-diaminobutyric acid-containing actinomycetes to accommodate "Corynebacterium aquaticum" Leifson 1962 and Clavibacter xyli subsp. cynodontis Davis et al. 1984.	Suzuki KI, Suzuki M, Sasaki J, Park YH, Komagata KK	J Gen Appl Microbiol	10.2323/jgam.45.253	1999
Phylogeny	Leifsonia kribbensis sp. nov., isolated from soil.	Dastager SG, Lee JC, Ju YJ, Park DJ, Kim CJ	Int J Syst Evol Microbiol	10.1099/ijs.0.001925-0	2009

References

#5734	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15165
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#39586	; Curators of the CIP;
#59368	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 51930
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#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 .
#122590	Collection of Institut Pasteur ; Curators of the CIP; CIP 106805
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 )

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Leifsonia shinshuensis (CCUG 51930, CIP 106805, DSM 15165)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

Murein

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API zym

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_013410375

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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