Lacticaseibacillus saniviri (DSM 24301, JCM 17471, YIT 12363)

Name: Lacticaseibacillus saniviri (DSM 24301, JCM 17471, YIT 12363)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6701

Type strain

Culture col. no. DSM 24301 JCM 17471 YIT 12363

NCBI tax ID(s) 931533

Special Collections DSMZ JCM Literature strains

History DSMZ <- K. Oki, Yakult Central Inst. Microbiol. Res., Kunitachi, Japan; YIT 12363 <- K. Watanabe JCM <-- K. Oki YIT 12363.

Links

Lacticaseibacillus saniviri DSM 24301 is a microaerophile, Gram-positive, rod-shaped bacterium that was isolated from feces of a Japanese healthy adult male.

Gram-positive rod-shaped microaerophile genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 398599

JCM 17471,DSM 24301

@ref 20215

Last LPSN update 2026-05-29 08:26:28

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Lactobacillaceae

Genus Lacticaseibacillus

Species Lacticaseibacillus saniviri

Full scientific name Lacticaseibacillus saniviri (Oki et al. 2012) Zheng et al. 2020

Synonyms (1)

Lactobacillus saniviri

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30248	positive	1.5-3.0 µm	1 µm	rod-shaped
125438					91.5
125438	positive				92.566

Pigmentation

30248

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17626	MRS MEDIUM (DSMZ Medium 11)		Medium recipe at MediaDive	Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
17626	positive	growth	37
67770	positive	growth	37

Culture pH

@ref	Ability	Type	PH	PH range
30248	positive	growth	4.0-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
17626	microaerophile
30248	facultative anaerobe
125439	obligate aerobe	94.173

Spore formation

30248

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30248	NaCl	positive	growth	5 %

Murein

@ref	Murein short key	Type
17626	A11.31	A4alpha L-Lys-D-Asp

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	17057 ChEBI	cellobiose	+	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	15824 ChEBI	D-fructose	+	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	16899 ChEBI	D-mannitol	+	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
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	+	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
30248	17754 ChEBI	glycerol	+	carbon source
68371	17754 ChEBI	glycerol	+	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
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	18287 ChEBI	L-fucose	-	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	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
30248	28053 ChEBI	melibiose	+	carbon source
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	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
30248	16634 ChEBI	raffinose	+	carbon source
68371	16634 ChEBI	raffinose	+	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
30248	33942 ChEBI	ribose	+	carbon source
30248	17814 ChEBI	salicin	+	carbon source
68371	17814 ChEBI	salicin	+	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
30248	17992 ChEBI	sucrose	+	carbon source
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

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	acetate fermentation	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	teichoic acid biosynthesis	100	1 of 1
66794	ribulose monophosphate pathway	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	acetoin degradation	100	3 of 3
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	palmitate biosynthesis	90.91	20 of 22
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	pentose phosphate pathway	81.82	9 of 11
66794	glycogen metabolism	80	4 of 5
66794	methylglyoxal degradation	80	4 of 5
66794	pyrimidine metabolism	75.56	34 of 45
66794	glycogen biosynthesis	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	purine metabolism	73.4	69 of 94
66794	flavin biosynthesis	73.33	11 of 15
66794	photosynthesis	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	Entner Doudoroff pathway	70	7 of 10
66794	starch degradation	70	7 of 10
66794	valine metabolism	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	NAD metabolism	66.67	12 of 18
66794	cyanate degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	oxidative phosphorylation	62.64	57 of 91
66794	gluconeogenesis	62.5	5 of 8
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	isoleucine metabolism	62.5	5 of 8
66794	phenylalanine metabolism	61.54	8 of 13
66794	vitamin B1 metabolism	61.54	8 of 13
66794	threonine metabolism	60	6 of 10
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	non-pathway related	57.89	22 of 38
66794	propanol degradation	57.14	4 of 7
66794	serine metabolism	55.56	5 of 9
66794	metabolism of disaccharids	54.55	6 of 11
66794	adipate degradation	50	1 of 2
66794	sulfopterin metabolism	50	2 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
66794	butanoate fermentation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	lactate fermentation	50	2 of 4
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	methionine metabolism	46.15	12 of 26
66794	alanine metabolism	44.83	13 of 29
66794	d-mannose degradation	44.44	4 of 9
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	glutathione metabolism	42.86	6 of 14
66794	tetrahydrofolate metabolism	42.86	6 of 14
66794	mevalonate metabolism	42.86	3 of 7
66794	isoprenoid biosynthesis	42.31	11 of 26
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	degradation of pentoses	39.29	11 of 28
66794	glutamate and glutamine metabolism	39.29	11 of 28
66794	lipid metabolism	38.71	12 of 31
66794	lysine metabolism	38.1	16 of 42
66794	d-xylose degradation	36.36	4 of 11
66794	tryptophan metabolism	34.21	13 of 38
66794	enterobactin biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	lipid A biosynthesis	33.33	3 of 9
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	cysteine metabolism	33.33	6 of 18
66794	sphingosine metabolism	33.33	2 of 6
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	octane oxidation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	chorismate metabolism	33.33	3 of 9
66794	urea cycle	30.77	4 of 13
66794	leucine metabolism	30.77	4 of 13
66794	phenol degradation	30	6 of 20
66794	myo-inositol biosynthesis	30	3 of 10
66794	arginine metabolism	29.17	7 of 24
66794	reductive acetyl coenzyme A pathway	28.57	2 of 7
66794	citric acid cycle	28.57	4 of 14
66794	degradation of sugar acids	28	7 of 25
66794	histidine metabolism	27.59	8 of 29
66794	proline metabolism	27.27	3 of 11
66794	carnitine metabolism	25	2 of 8
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	CMP-KDO biosynthesis	25	1 of 4
66794	sulfate reduction	23.08	3 of 13
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	ascorbate metabolism	22.73	5 of 22
66794	arachidonic acid metabolism	22.22	4 of 18
66794	nitrate assimilation	22.22	2 of 9
66794	tyrosine metabolism	21.43	3 of 14
66794	heme metabolism	21.43	3 of 14

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
17626	-	+	-	-	-	+	-	-	-	-	+	+	+	+	-	-	-	-	+	-	-	-	+	+	+	+	+	+	+	-	-	+	+	-	-	+	-	-	-	+	-	-	+	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Patient	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)
#Host	#Human	#Male

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
17626	feces of a Japanese healthy adult male	Japan	JPN	Asia
67770	Feces of a healthy Japanese male

Taxonmaps

69479

Global distribution of 16S sequence LC519994 (>99% sequence identity) for Lacticaseibacillus saniviri subclade from Microbeatlas

Aquatic Samples	132
Soil Samples	107
Animal Samples	1244
Plant Samples	44
Total Samples	1527

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17626	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
67770	ASM143746v1 assembly for Lacticaseibacillus saniviri JCM 17471 = DSM 24301	scaffold	GCA_001437465	1293598.4	2663763364	1293598	61.09
67770	ASM131178v1 assembly for Lacticaseibacillus saniviri JCM 17471 = DSM 24301	contig	GCA_001311785	1293598.3	2728369696	1293598	37.6

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Lactobacillus saniviri strain DSM 24301 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence	JN644756	2250	1293598
17626	Lactobacillus saniviri gene for 16S rRNA, partial sequence	AB602569	1558	1293598
67770	Lactobacillus saniviri JCM 17471 gene for 16S rRNA, partial sequence	LC519994	1502	1293598

GC content

@ref	GC-content (mol%)	Method
17626	48.1	high performance liquid chromatography (HPLC)
30248	48.7
67770	47.7	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM143746v1 assembly for Lacticaseibacillus saniviri JCM 17471 = DSM 24301
NCBI: GCA_001437465

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.17	no
125439	gram_stain	BacteriaNetⓘ	positive	49.29	no
125439	motility	BacteriaNetⓘ	yes	49.76	no
125439	spore_formation	BacteriaNetⓘ	no	69.08	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lactobacillus saniviri JCM 17471 = DSM 24301
PATRIC: 1293598.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.57	yes
125438	anaerobic	anaerobicⓘ	no	88.24	yes
125438	spore-forming	spore-formingⓘ	no	81.19	yes
125438	aerobic	aerobicⓘ	no	93.42	yes
125438	thermophilic	thermophileⓘ	no	96.00	yes
125438	flagellated	motile2+ⓘ	no	91.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Evolutionary paths toward multi-level convergence of lactic acid bacteria in fructose-rich environments.	Konno N, Maeno S, Tanizawa Y, Arita M, Endo A, Iwasaki W.	Commun Biol	10.1038/s42003-024-06580-0	2024
	A sugar utilization phenotype contributes to the formation of genetic exchange communities in lactic acid bacteria.	Takenaka S, Kawashima T, Arita M.	FEMS Microbiol Lett	10.1093/femsle/fnab117	2021
Phylogeny	Lacticaseibacillus parahuelsenbergensis sp. nov., Lacticaseibacillus styriensis sp. nov. and Lacticaseibacillus zeae subsp. silagei subsp. nov., isolated from different grass and corn silage.	Grabner F M, Grabner H M, Schein H, Schrank A, Toglhofer M, Weidenholzer E, Ruckert-Reed C, Busche T, Buchebner-Jance M.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006441	2024
Phylogeny	Lactobacillus brantae sp. nov., isolated from faeces of Canada geese (Branta canadensis).	Volokhov DV, Amselle M, Beck BJ, Popham DL, Whittaker P, Wang H, Kerrigan E, Chizhikov VE	Int J Syst Evol Microbiol	10.1099/ijs.0.033852-0	2011
Phylogeny	Lactobacillus saniviri sp. nov. and Lactobacillus senioris sp. nov., isolated from human faeces.	Oki K, Kudo Y, Watanabe K	Int J Syst Evol Microbiol	10.1099/ijs.0.031658-0	2011

References

#17626	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24301
#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 )
#26590	IJSEM 601 2012 ( DOI 10.1099/ijs.0.031658-0 , PubMed 21515698 )
#30248	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 #26590
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68371	Automatically annotated from API 50CH acid .
#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

Lacticaseibacillus saniviri (DSM 24301, JCM 17471, YIT 12363)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Murein

Metabolite utilization

Pathway annotation

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001437465

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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