Name: Ligilactobacillus apodemi ASB1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 6646

Type strain:

Species: Ligilactobacillus apodemi

Strain Designation: ASB1, ASB-1

Culture col. no.: DSM 16634, CIP 108913, JCM 16172, NCIMB 14359

Strain history: CIP <- 2005, DSMZ <- R. Osawa, Kobe Univ., Kobe, Japan: strain ASB-1

NCBI tax ID(s): 307126 (species)

SI-ID 292425

DSM 16634, CIP 108913, JCM 16172

Special Collections

Other strains from Ligilactobacillus apodemi

Section

When using BacDive for research please cite our paper

Ligilactobacillus apodemi ASB1 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from feces, wild Japanese wood mouse.

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	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacillota*
	Class	*Bacilli*
	Order	*Lactobacillales*
	Family	*Lactobacillaceae*
	Genus	*Ligilactobacillus*
	Species	**Ligilactobacillus apodemi**
	Full Scientific Name (LPSN)	Ligilactobacillus apodemi (Osawa et al. 2006) Zheng et al. 2020

Synonym

Lactobacillus apodemi

Information on morphological and physiological properties Morphology

[Ref.: #31735]	Gram stain	positive
[Ref.: #116423]	Gram stain	positive
[Ref.: #125438]	Gram stain	positive Confidence in %92.292

[Ref.: #31735]	Cell length	05-06 µm

[Ref.: #31735]	Cell width	0.5-1 µm

[Ref.: #31735]	Cell shape	rod-shaped
[Ref.: #116423]	Cell shape	rod-shaped

[Ref.: #31735]	Motility	no
[Ref.: #116423]	Motility	no

[Ref.: #31735]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6537]

Culture medium

MRS MEDIUM (DSMZ Medium 11)

[Ref.: #6537]

Culture medium growth

[Ref.: #6537]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6537]

Culture medium composition

expand / minimize

[Ref.: #38184]

Culture medium

MEDIUM 40- for Lactobacillus and Leuconostoc

[Ref.: #38184]

Culture medium growth

[Ref.: #38184]

Culture medium composition

expand / minimize

[Ref.: #116423]

Culture medium

CIP Medium 40

[Ref.: #116423]

Culture medium growth

[Ref.: #116423]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #6537]		growth	37 °C
[Ref.: #31735]		growth	25-45 °C
[Ref.: #31735]		optimum	25-37 °C
[Ref.: #38184]		growth	37 °C
[Ref.: #67770]		growth	37 °C
[Ref.: #116423]		growth	30-37 °C
[Ref.: #116423]	negative	growth	10 °C
[Ref.: #116423]	negative	growth	15 °C
[Ref.: #116423]	negative	growth	22 °C

	pH	Kind of pH		pH
[Ref.: #31735]			optimum	7
[Ref.: #31735]			growth	7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #6537]	Oxygen tolerance	anaerobe
[Ref.: #6537]	Oxygen tolerance	microaerophile
[Ref.: #31735]	Oxygen tolerance	anaerobe
[Ref.: #116423]	Oxygen tolerance	facultative anaerobe
[Ref.: #125439]	Oxygen tolerance	microaerophile Confidence in %99.2

[Ref.: #31735]

Ability of spore formation

[Ref.: #31735]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin 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-fucose 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-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.: #31735]	fructose ChEBI	+	carbon source
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31735]	galactose ChEBI	+	carbon source
[Ref.: #68371]	gentiobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31735]	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.: #31735]	lactate ChEBI	+	carbon source
[Ref.: #31735]	lactose ChEBI	+	carbon source
[Ref.: #31735]	maltose ChEBI	+	carbon source
[Ref.: #31735]	mannose ChEBI	+	carbon source
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31735]	melibiose ChEBI	+	carbon source
[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.: #31735]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #116423]	nitrate ChEBI	-	reduction
[Ref.: #116423]	nitrate ChEBI	+	respiration
[Ref.: #116423]	nitrite ChEBI	-	reduction
[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.: #31735]	raffinose ChEBI	+	carbon source
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #31735]	sucrose ChEBI	+	carbon source
[Ref.: #31735]	trehalose ChEBI	+	carbon source
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #116423]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #116423]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	+	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #116423]	catalase	-	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #116423]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #116423]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #116423]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #6537]	15148	-	-	-	-	-	+	-	-	-	-	-	+	+	+	-	-	-	-	-	-	-	-	+	-	+	+	+	+	+	+	+	+	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-
[Ref.: #6537]	15147	-	-	-	-	-	-	-	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	+	-	+	+	+	+	+	+	+	+	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-
[Ref.: #116423]	11422	not determinedn.d.	-	-	-	-	-	-	-	-	-	+/-	+/-	+/-	+/-	-	-	-	-	-	-	-	-	+/-	-	+/-	+/-	+/-	+/-	+/-	+/-	+/-	+/-	+/-	-	-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #116423]	11544	-	-	-	-	-	+	+	-	-	-	+	+	-	+	-	+	-	-	+	-

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

[Ref.: #6537]	Sample type/isolated from	feces, wild Japanese wood mouse
[Ref.: #6537]	Geographic location (country and/or sea, region)	Kyotanabe
[Ref.: #6537]	Country	Japan
[Ref.: #6537]	Country ISO 3 Code	JPN
[Ref.: #6537]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Wild mouse feces
[Ref.: #67770]	Geographic location (country and/or sea, region)	Kyotanabe
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia

[Ref.: #116423]	Sample type/isolated from	Animal, Wild Japanese wood mouse
[Ref.: #116423]	Geographic location (country and/or sea, region)	Kyotanabe
[Ref.: #116423]	Country	Japan
[Ref.: #116423]	Country ISO 3 Code	JPN
[Ref.: #116423]	Continent	Asia
[Ref.: #116423]	Isolation date	2002
* marker position based on {}

Isolation sources categories

#Host	#Mammals	#Muridae (Mouse/Rat)
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence LC519852 (>99% sequence identity) for Ligilactobacillus apodemi from Microbeatlas

Aquatic Samples	731
Soil Samples	1119
Animal Samples	66125
Plant Samples	277
Total Samples	68252

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

[Ref.: #6537]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #116423]	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.: #6537]	Lactobacillus apodemi 16S rRNA gene, type strain ASB1T	AJ871178	1532	GenBank ENA	307126 tax ID
[Ref.: #67770]	Lactobacillus apodemi JCM 16172 gene for 16S rRNA, partial sequence	LC519852	1504	GenBank ENA	307126 tax ID
[Ref.: #20218]	Lactobacillus apodemi gene for 16S ribosomal RNA, partial sequence, strain: DSM 16634	AB370874	1487	GenBank ENA	307126 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.: #67770]	Ligilactobacillus apodemi DSM 16634 = JCM 16172	GCA_001434405	scaffold	GenBank ENA	1423724 tax ID
[Ref.: #67770]	Ligilactobacillus apodemi DSM 16634 = JCM 16172	GCA_000615885	contig	GenBank ENA	1423724 tax ID
[Ref.: #66792]	Lactobacillus apodemi DSM 16634 = JCM 16172	1423724.4	wgs	PATRIC	1423724 tax ID	*
[Ref.: #66792]	Lactobacillus apodemi JCM 16172	1236952.3	wgs	PATRIC	1423724 tax ID	*
[Ref.: #66792]	Ligilactobacillus apodemi JCM 16172	2585427873	draft	JGI IMG/M	1423724 tax ID	*
[Ref.: #66792]	Ligilactobacillus apodemi DSM 16634	2675903500	draft	JGI IMG/M	1423724 tax ID	*

[Ref.: #6537]	GC-content	38.5 mol%
[Ref.: #67770]	GC-content	38.5 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	38.6 mol%	genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Lactobacillus apodemi DSM 16634 = JCM 16172 PATRIC: 1423724.4
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	92.292	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	82.882	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	87.446	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	94.865	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	96	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	89	yes

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Ligilactobacillus apodemi DSM 16634 = JCM 16172 NCBI: GCA_001434405
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	microaerophile	99.2
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	77.1
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	70.5
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	74.3

Availability in culture collections External links

[Ref.: #6537]

Culture collection no.

DSM 16634, CIP 108913, JCM 16172, NCIMB 14359

[Ref.: #76120]

SI-ID 292425

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lactobacillus apodemi sp. nov., a tannase-producing species isolated from wild mouse faeces.	Osawa R, Fujisawa T, Pukall R	Int J Syst Evol Microbiol	10.1099/ijs.0.64147-0	2006	*

References

#6537

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16634

#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 )

#31735

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 #28011 (see below)

#38184 ; 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;

#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 .

#76120

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-ID292425.1 )

#116423 Collection of Institut Pasteur ; Curators of the CIP; CIP 108913

#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 .

#28011

IJSEM 1693 2006 ( DOI 10.1099/ijs.0.64147-0 , PubMed 16825652 )

* These data were automatically processed and therefore are not curated

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Lactobacillus apodemi DSM 16634 = JCM 16172

Ligilactobacillus apodemi DSM 16634 = JCM 16172

Change proposal

Change proposal