Ligilactobacillus apodemi (DSM 16634, CIP 108913, ASB1)

Name: Ligilactobacillus apodemi (DSM 16634, CIP 108913, ASB1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6646

Type strain

Strain Designation ASB1, ASB-1

Culture col. no. DSM 16634 CIP 108913 ASB1 NCIMB 14359 JCM 16172 1 more

NCBI tax ID(s) 307126

Special Collections DSMZ JCM CIP Literature strains

History <- R. Osawa; ASB1 CIP 108913 <-- DSM 16634 <-- R. Osawa ASB1. CIP <- 2005, DSMZ <- R. Osawa, Kobe Univ., Kobe, Japan: strain ASB-1

Links

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

Gram-positive rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 292425

LMG 25505,DSM 16634,CIP 108913,JCM 16172

@ref 20215

Last LPSN update 2026-02-09 11:19:17

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Lactobacillaceae

Genus Ligilactobacillus

Species Ligilactobacillus apodemi

Full scientific name Ligilactobacillus apodemi (Osawa et al. 2006) Zheng et al. 2020

Synonyms (1)

Lactobacillus apodemi

BacDive ID	Other strains from **Ligilactobacillus apodemi** (4)	Type strain
6645	L. apodemi ASB7, DSM 16748
6647	L. apodemi ASB2, DSM 16635
6648	L. apodemi ASB6, DSM 16648
6649	L. apodemi ASB8, DSM 16649

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31735	positive	05-06 µm	0.5-1 µm	rod-shaped
116423	positive			rod-shaped
125438	positive				92.292

Pigmentation

31735

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6537	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
38184	MEDIUM 40- for Lactobacillus and Leuconostoc		Distilled water make up to (1000.000 ml);Man Rogosa Sharp agar (68.000 g)
116423	CIP Medium 40	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6537	positive	growth	37	mesophilic
31735	positive	growth	25-45
31735	positive	optimum	25-37	mesophilic
38184	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic
116423	positive	growth	30-37	mesophilic
116423	negative	growth	10
116423	negative	growth	15
116423	negative	growth	22

Culture pH

@ref	Ability	Type	PH
31735	positive	optimum	7
31735	positive	growth	7

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
6537	anaerobe
6537	microaerophile
31735	anaerobe
116423	facultative anaerobe
125439	microaerophile	99.2

Spore formation

31735

Spore formationno

Observation

31735

Observationaggregates in chains

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	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	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	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
31735	28757 ChEBI	fructose	+	carbon source
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
31735	28260 ChEBI	galactose	+	carbon source
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
31735	17234 ChEBI	glucose	+	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
31735	24996 ChEBI	lactate	+	carbon source
31735	17716 ChEBI	lactose	+	carbon source
31735	17306 ChEBI	maltose	+	carbon source
31735	37684 ChEBI	mannose	+	carbon source
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
31735	28053 ChEBI	melibiose	+	carbon source
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
31735	506227 ChEBI	N-acetylglucosamine	+	carbon source
116423	17632 ChEBI	nitrate	-	reduction
116423	17632 ChEBI	nitrate	+	respiration
116423	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
31735	16634 ChEBI	raffinose	+	carbon source
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
31735	17992 ChEBI	sucrose	+	carbon source
31735	27082 ChEBI	trehalose	+	carbon source
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
116423	15688 ChEBI	acetoin	-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
116423	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
68382	beta-galactosidase	+	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
116423	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
116423	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
116423	ornithine decarboxylase	-	4.1.1.17
116423	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
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
116423	-	-	-	-	-	+	+	-	-	-	+	+	-	+	-	+	-	-	+	-

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
6537	-	-	-	-	-	+	-	-	-	-	-	+	+	+	-	-	-	-	-	-	-	-	+	-	+	+	+	+	+	+	+	+	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-
6537	-	-	-	-	-	-	-	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	+	-	+	+	+	+	+	+	+	+	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-
116423	not determinedn.d.	-	-	-	-	-	-	-	-	-	+/-	+/-	+/-	+/-	-	-	-	-	-	-	-	-	+/-	-	+/-	+/-	+/-	+/-	+/-	+/-	+/-	+/-	+/-	-	-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Muridae (Mouse/Rat)
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
6537	feces, wild Japanese wood mouse	Kyotanabe	Japan	JPN	Asia
67770	Wild mouse feces	Kyotanabe	Japan	JPN	Asia
116423	Animal, Wild Japanese wood mouse	Kyotanabe	Japan	JPN	Asia	2002

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6537	1	Risk group (German classification) According to TRBA 466
116423	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	ASM143440v1 assembly for Ligilactobacillus apodemi DSM 16634 = JCM 16172	scaffold	GCA_001434405	1423724.4	2675903500	1423724	66.35
67770	ASM61588v1 assembly for Ligilactobacillus apodemi DSM 16634 = JCM 16172	contig	GCA_000615885	1236952.3	2585427873	1423724	58.62

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Lactobacillus apodemi gene for 16S ribosomal RNA, partial sequence, strain: DSM 16634	AB370874	1487	307126
6537	Lactobacillus apodemi 16S rRNA gene, type strain ASB1T	AJ871178	1532	307126
67770	Lactobacillus apodemi JCM 16172 gene for 16S rRNA, partial sequence	LC519852	1504	307126

GC content

@ref	GC-content (mol%)	Method
6537	38.5
67770	38.5	high performance liquid chromatography (HPLC)
67770	38.6	genome sequence analysis

Genome-based predictions

Predictions

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	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	microaerophile	99.20	no
125439	gram_stain	BacteriaNetⓘ	positive	77.10	no
125439	motility	BacteriaNetⓘ	no	70.50	no
125439	spore_formation	BacteriaNetⓘ	no	74.30	no

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	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.29	yes
125438	anaerobic	anaerobicⓘ	no	82.88	no
125438	spore-forming	spore-formingⓘ	no	87.45	no
125438	aerobic	aerobicⓘ	no	94.87	yes
125438	thermophilic	thermophileⓘ	no	96.00	yes
125438	flagellated	motile2+ⓘ	no	89.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples.	Gonzalez E, Pitre FE, Brereton NJB.	Environ Microbiol	10.1111/1462-2920.14632	2019
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 )
#28011	IJSEM 1693 2006 ( DOI 10.1099/ijs.0.64147-0 , PubMed 16825652 )
#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
#38184	; Curators of the CIP;
#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 .
#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 .
#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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Ligilactobacillus apodemi (DSM 16634, CIP 108913, ASB1)

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

Observation

Metabolite utilization

Metabolite tests

Enzymes

API zym

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001434405

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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