Holzapfeliella floricola (DSM 23037, JCM 16512, NRIC 0774)

Name: Holzapfeliella floricola (DSM 23037, JCM 16512, NRIC 0774)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6698

Type strain

Strain Designation Ryu1-2

Culture col. no. DSM 23037 JCM 16512 NRIC 0774 Ryu1-2 KCTC 21006

NCBI tax ID(s) 679249

Special Collections DSMZ JCM KCTC

History DSMZ <- S. Kawasaki, Dept. Bio-Science, Tokyo Univ. Agriculture, Japan; NRIC 0774 JCM <-- S. Kawasaki Ryu1-2.

Links

Holzapfeliella floricola Ryu1-2 is a bacterium that was isolated from flower of Caltha palustris.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 406305

LMG 29183,JCM 16512,DSM 23037

@ref 20215

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

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Lactobacillaceae

Genus Holzapfeliella

Species Holzapfeliella floricola

Full scientific name Holzapfeliella floricola (Kawasaki et al. 2011) Deshmukh and Oren 2023

Synonyms (2)

Holzapfelia floricola
Lactobacillus floricola

Morphology

Cell morphology

@ref	Motility	Confidence	Gram stain
125438		94
125438		92.982	positive

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16663	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)
16663	positive	growth	30
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	97.675

Spore formation

@ref	Spore formation	Confidence
125439		93.621

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	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
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
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
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	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

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	ribulose monophosphate pathway	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ethanol fermentation	100	2 of 2
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	threonine metabolism	80	8 of 10
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	ppGpp biosynthesis	75	3 of 4
66794	pentose phosphate pathway	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	photosynthesis	71.43	10 of 14
66794	purine metabolism	68.09	64 of 94
66794	acetoin degradation	66.67	2 of 3
66794	gluconeogenesis	62.5	5 of 8
66794	phenylalanine metabolism	61.54	8 of 13
66794	glycolysis	58.82	10 of 17
66794	methionine metabolism	57.69	15 of 26
66794	cysteine metabolism	55.56	10 of 18
66794	serine metabolism	55.56	5 of 9
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	NAD metabolism	55.56	10 of 18
66794	butanoate fermentation	50	2 of 4
66794	ketogluconate metabolism	50	4 of 8
66794	coenzyme A metabolism	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	sulfopterin metabolism	50	2 of 4
66794	suberin monomers biosynthesis	50	1 of 2
66794	pyrimidine metabolism	46.67	21 of 45
66794	vitamin B1 metabolism	46.15	6 of 13
66794	oxidative phosphorylation	45.05	41 of 91
66794	chorismate metabolism	44.44	4 of 9
66794	d-mannose degradation	44.44	4 of 9
66794	tetrahydrofolate metabolism	42.86	6 of 14
66794	propanol degradation	42.86	3 of 7
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	mevalonate metabolism	42.86	3 of 7
66794	non-pathway related	42.11	16 of 38
66794	arachidonate biosynthesis	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	methylglyoxal degradation	40	2 of 5
66794	glutamate and glutamine metabolism	39.29	11 of 28
66794	leucine metabolism	38.46	5 of 13
66794	urea cycle	38.46	5 of 13
66794	isoleucine metabolism	37.5	3 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
66794	metabolism of disaccharids	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	cyanate degradation	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	lipid A biosynthesis	33.33	3 of 9
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	valine metabolism	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	lysine metabolism	33.33	14 of 42
66794	arginine metabolism	33.33	8 of 24
66794	degradation of sugar alcohols	31.25	5 of 16
66794	propionate fermentation	30	3 of 10
66794	Entner Doudoroff pathway	30	3 of 10
66794	lipid metabolism	29.03	9 of 31
66794	tryptophan metabolism	28.95	11 of 38
66794	reductive acetyl coenzyme A pathway	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	vitamin B6 metabolism	27.27	3 of 11
66794	flavin biosynthesis	26.67	4 of 15
66794	cyclohexanol degradation	25	1 of 4
66794	acetate fermentation	25	1 of 4
66794	glycogen biosynthesis	25	1 of 4
66794	degradation of aromatic, nitrogen containing compounds	25	3 of 12
66794	CMP-KDO biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	ascorbate metabolism	22.73	5 of 22
66794	nitrate assimilation	22.22	2 of 9
66794	glutathione metabolism	21.43	3 of 14
66794	alanine metabolism	20.69	6 of 29

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
16663	-	-	-	-	-	-	-	-	-	-	+/-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Flower

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
16663	flower of Caltha palustris	Caltha palustris	Oze National Park	Japan	JPN	Asia
67770	Flower, buttercup (Caltha palustris)	Caltha palustris	Oze National Park	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence LC519858 (>99% sequence identity) for Holzapfelia floricola subclade from Microbeatlas

Aquatic Samples	112
Soil Samples	88
Animal Samples	2097
Plant Samples	145
Total Samples	2442

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16663	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	ASM143660v1 assembly for Holzapfeliella floricola DSM 23037 = JCM 16512	scaffold	GCA_001436605	1423744.4	2667527860	1423744	67.81
67770	ASM131146v1 assembly for Holzapfeliella floricola DSM 23037 = JCM 16512	contig	GCA_001311465	1423744.3	2728369687	1423744	30.64

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16663	Lactobacillus floricola gene for 16S rRNA, partial sequence, strain: Ryu1-2	AB523780	1566		1423744
67770	Lactobacillus floricola JCM 16512 gene for 16S rRNA, partial sequence	LC519858	1514		679249

GC content

@ref	GC-content (mol%)	Method
16663	48.0	high performance liquid chromatography (HPLC)
67770	34.5	genome sequence analysis
67770	48	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: ASM143660v1 assembly for Holzapfeliella floricola DSM 23037 = JCM 16512
BV-BRC: 1423744.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.68	no
125439	gram_stain	BacteriaNetⓘ	positive	60.63	no
125439	motility	BacteriaNetⓘ	no	73.31	no
125439	spore_formation	BacteriaNetⓘ	no	93.62	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lactobacillus floricola DSM 23037 = JCM 16512
PATRIC: 1423744.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.98	no
125438	anaerobic	anaerobicⓘ	no	82.14	no
125438	spore-forming	spore-formingⓘ	no	89.29	no
125438	aerobic	aerobicⓘ	no	89.93	no
125438	thermophilic	thermophileⓘ	no	98.00	yes
125438	flagellated	motile2+ⓘ	no	94.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Holzapfeliella saturejae sp. nov. isolated from flowers of winter savoury Satureja montana L.	Alcantara C, Peiroten N, Ramon-Nunez LA, Landete JM, Monedero V, Zuniga M.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006654	2025
Phylogeny	Lactobacillus floricola sp. nov., lactic acid bacteria isolated from mountain flowers.	Kawasaki S, Kurosawa K, Miyazaki M, Yagi C, Kitajima Y, Tanaka S, Irisawa T, Okada S, Sakamoto M, Ohkuma M, Niimura Y	Int J Syst Evol Microbiol	10.1099/ijs.0.022988-0	2010

References

#16663	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23037
#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 )
#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 )

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Holzapfeliella floricola (DSM 23037, JCM 16512, NRIC 0774)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

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_001436605

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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