Name: Paucilactobacillus hokkaidonensis LOOC260
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24132

Type strain:

Species: Paucilactobacillus hokkaidonensis

Strain Designation: LOOC260

Culture col. no.: DSM 26202, CIP 110792, JCM 18461, KCTC 21044

Strain history: CIP <- 2014, DSMZ <- M. Tohno, NARO, Tochigi, Japan: strain LOOC260

NCBI tax ID(s): 1291742 (strain), 1193095 (species)

SI-ID 390269

JCM 18461, DSM 26202, LMG 28400, CIP 110792

Other strains from Paucilactobacillus hokkaidonensis

P. hokkaidonensis JCM 18460
P. hokkaidonensis JCM 18462
P. hokkaidonensis JCM 18463

Section

Paucilactobacillus hokkaidonensis LOOC260 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from timothy grass silage.

Gram-positive
rod-shaped
anaerobe
mesophilic
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	*Bacillota*
	Class	*Bacilli*
	Order	*Lactobacillales*
	Family	*Lactobacillaceae*
	Genus	*Paucilactobacillus*
	Species	**Paucilactobacillus hokkaidonensis**
	Full Scientific Name (LPSN)	Paucilactobacillus hokkaidonensis (Tohno et al. 2013) Zheng et al. 2020

Synonym

Lactobacillus hokkaidonensis

Information on morphological and physiological properties Morphology

[Ref.: #30898]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #119929]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #30898]	Cell length	2.25 µm

[Ref.: #30898]	Cell width	1 µm

[Ref.: #30898]	Cell shape	rod-shaped
[Ref.: #119929]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #30898]	Motility	no
[Ref.: #119929]	Motility	no
[Ref.: #67771]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %97.437

[Ref.: #30898]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #41596]

Culture medium

MEDIUM 40- for Lactobacillus and Leuconostoc

[Ref.: #41596]

Culture medium growth

[Ref.: #41596]

Culture medium composition

expand / minimize

[Ref.: #20992]

Culture medium

MRS MEDIUM (DSMZ Medium 11)

[Ref.: #20992]

Culture medium growth

[Ref.: #20992]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20992]

Culture medium composition

expand / minimize

[Ref.: #119929]

Culture medium

CIP Medium 40

[Ref.: #119929]

Culture medium growth

[Ref.: #119929]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #20992]	growth	25 °C
[Ref.: #30898]	growth	04-37 °C
[Ref.: #30898]	optimum	25 °C
[Ref.: #41596]	growth	25 °C
[Ref.: #67770]	growth	30 °C
[Ref.: #67771]	growth	25 °C

[Ref.: #20992]	Temperature range	mesophilic
[Ref.: #30898]	Temperature range	mesophilic
[Ref.: #41596]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30898]			growth	4.0-7.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #20992]	Oxygen tolerance	anaerobe
[Ref.: #20992]	Oxygen tolerance	microaerophile
[Ref.: #30898]	Oxygen tolerance	facultative anaerobe
[Ref.: #67771]	Oxygen tolerance	microaerophile

[Ref.: #30898]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.997

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30898]		NaCl		growth	0-4	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #30898]	arabinose ChEBI	+	carbon source
[Ref.: #68371]	arbutin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	cellobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gentiobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #30898]	glucose ChEBI	+	carbon source
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #30898]	maltose ChEBI	+	carbon source
[Ref.: #68371]	maltose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #30898]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #30898]	ribose ChEBI	+	carbon source
[Ref.: #68371]	salicin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	sucrose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #30898]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30898]		acid phosphatase	+	3.1.3.2
[Ref.: #30898]		alpha-galactosidase	+	3.2.1.22

API® 50CH acid:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #20992]	14794	-	-	-	-	+	+	+	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
[Ref.: #20992]	14793	-	-	-	-	+	+	+	-	-	+	-	+	-	-	-	-	-	-	-	-	-	-	+/-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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

[Ref.: #20992]	Sample type/isolated from	timothy grass (Phleum pratense L.) silage
[Ref.: #20992]	Host species	Phleum pratense
[Ref.: #20992]	Geographic location (country and/or sea, region)	Hokkaido
[Ref.: #20992]	Country	Japan
[Ref.: #20992]	Country ISO 3 Code	JPN
[Ref.: #20992]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Timothy grass (Phleum pratense L.) silage produced
[Ref.: #67770]	Host species	Phleum pratense
[Ref.: #67770]	Geographic location (country and/or sea, region)	Hokkaido
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From timothy grass, `Phleum pratense` L. silage
[Ref.: #67771]	Geographic location (country and/or sea, region)	Hokkaido
[Ref.: #67771]	Country	Japan
[Ref.: #67771]	Country ISO 3 Code	JPN
[Ref.: #67771]	Continent	Asia

[Ref.: #119929]	Sample type/isolated from	Timothy grass, Phleum pratense L. silage
[Ref.: #119929]	Geographic location (country and/or sea, region)	Hokkaido
[Ref.: #119929]	Country	Japan
[Ref.: #119929]	Country ISO 3 Code	JPN
[Ref.: #119929]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host

#Plants

#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC521988 (>99% sequence identity) for Paucilactobacillus hokkaidonensis from Microbeatlas

Aquatic Samples	211
Soil Samples	146
Animal Samples	1507
Plant Samples	170
Total Samples	2034

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #20992]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #119929]	Biosafety level	1	Risk group (French classification)

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.: #67770]	Lactobacillus hokkaidonensis JCM 18461 gene for 16S rRNA, partial sequence	LC521988	1515	ENA	1291742 tax ID
[Ref.: #20992]	Lactobacillus hokkaidonensis gene for 16S ribosomal RNA, partial sequence	AB721549	1502	ENA	1291742 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67771]	Paucilactobacillus hokkaidonensis DSM 26202	GCA_001437505	scaffold	GenBank	1193095 tax ID
[Ref.: #66792]	Paucilactobacillus hokkaidonensis JCM 18461	GCA_001311505	contig	GenBank	1291742 tax ID	*
[Ref.: #66792]	Lactobacillus hokkaidonensis JCM 18461	1291742.4	wgs	PATRIC	1291742 tax ID	*
[Ref.: #66792]	Lactobacillus hokkaidonensis JCM 18461 strain LOOC260	1291742.5	plasmid	PATRIC	1291742 tax ID	*
[Ref.: #66792]	Lactobacillus hokkaidonensis JCM 18461 strain LOOC260	1291742.6	plasmid	PATRIC	1291742 tax ID	*
[Ref.: #66792]	Lactobacillus hokkaidonensis strain DSM 26202	1193095.8	wgs	PATRIC	1193095 tax ID	*

[Ref.: #20992]	GC-content	39.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30898]	GC-content	39.4 mol%
[Ref.: #67770]	GC-content	38.1 mol%	genome sequence analysis
[Ref.: #67770]	GC-content	39-39.8 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	39.0-39.08 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: Paucilactobacillus hokkaidonensis JCM 18461 LOOC260 NCBI: GCA_000829395.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paucilactobacillus hokkaidonensis JCM 18461 LOOC260 NCBI: GCA_000829395.1
[Ref.: #69480]	motile	no	96.368	yes
[Ref.: #69480]	flagellated	no	98.332	yes
[Ref.: #69480]	gram-positive	yes	96.233	yes
[Ref.: #69480]	anaerobic	no	95.43	no
[Ref.: #69480]	aerobic	no	96.165	no
[Ref.: #69480]	halophile	yes	94.333	no
[Ref.: #69480]	spore-forming	no	93.878	yes
[Ref.: #69480]	glucose-util	yes	88.147	no
[Ref.: #69480]	thermophile	no	99.69	yes
[Ref.: #69480]	glucose-ferment	yes	89.25	no

Availability in culture collections External links

[Ref.: #20992]

Culture collection no.

DSM 26202, CIP 110792, JCM 18461, KCTC 21044

[Ref.: #88090]

SI-ID 390269

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lactobacillus wasatchensis sp. nov., a non-starter lactic acid bacteria isolated from aged Cheddar cheese.	Oberg CJ, Oberg TS, Culumber MD, Ortakci F, Broadbent JR, McMahon DJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.000689	2015	*
Phylogeny	Lactobacillus hokkaidonensis sp. nov., isolated from subarctic timothy grass (Phleum pratense L.) silage.	Tohno M, Kitahara M, Uegaki R, Irisawa T, Ohkuma M, Tajima K	Int J Syst Evol Microbiol	10.1099/ijs.0.047027-0	2012	*
Metabolism	Complete genome sequence and analysis of Lactobacillus hokkaidonensis LOOC260(T), a psychrotrophic lactic acid bacterium isolated from silage.	Tanizawa Y, Tohno M, Kaminuma E, Nakamura Y, Arita M	BMC Genomics	10.1186/s12864-015-1435-2	2015	*

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 )

#20992

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26202

#30898

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 #27228 (see below)

#41596 ; Curators of the CIP;

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

#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 .

#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 )

#88090

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID390269.1 )

#119929 Collection of Institut Pasteur ; Curators of the CIP; CIP 110792

#27228

IJSEM 2526 2013 ( DOI 10.1099/ijs.0.047027-0 , PubMed 23223820 )

* These data were automatically processed and therefore are not curated

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Paucilactobacillus hokkaidonensis JCM 18461 LOOC260

Paucilactobacillus hokkaidonensis JCM 18461 LOOC260

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