Bifidobacterium lemurum (DSM 28807, JCM 30168, LMC 13)

Name: Bifidobacterium lemurum (DSM 28807, JCM 30168, LMC 13)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130215

Type strain

Culture col. no. DSM 28807 JCM 30168 LMC 13 KCTC 15888

NCBI tax ID(s) 1603886

Special Collections DSMZ JCM KCTC

History DSMZ <- P. Mattarelli, Univ. Bologna, Dep. of Agricul. Scs., Italy; LMC 13 <- M. Modesto JCM <-- P. Mattarelli; Bologna Univ., Italy; LMC 13.

Links

Bifidobacterium lemurum DSM 28807 is an anaerobe bacterium that was isolated from faeces of a 5-year-old ring-tailed lemur .

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 406419

JCM 30168,DSM 28807

@ref 20215

Last LPSN update 2026-05-29 08:37:19

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Bifidobacteriales

Family Bifidobacteriaceae

Genus Bifidobacterium

Species Bifidobacterium lemurum

Full scientific name Bifidobacterium lemurum Modesto et al. 2015

Morphology

Cell morphology

@ref	Motility	Confidence
125438		92.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21533	BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)		Medium recipe at MediaDive	Name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) Composition: Glucose 10.0 g/l Casein peptone 10.0 g/l Bacto Soytone 5.0 g/l Meat extract 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l MnSO4 x H2O 0.05 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Tween 80 Resazurin Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
21533	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

21533

Oxygen toleranceanaerobe

Spore formation

@ref	Spore formation	Confidence
125439		94.455

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	+	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
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

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
21533	-	-	-	-	-	+	+	-	-	-	+	+	+	+	-	-	+	-	-	-	-	-	-	+	+/-	+	+	-	-	+	+	+	-	-	-	+	-	-	-	+	+	-	-	-	-	-	-	+	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Primates
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
21533	faeces of a 5-year-old ring-tailed lemur (Lemur catta)	Lemur catta	Verona, Parco Natura Viva	Italy	ITA	Europe
67770	Feces of a ring-tailed lemur (Lemur catta)	Lemur catta

Taxonmaps

69479

Global distribution of 16S sequence KJ658281 (>99% sequence identity) for Bifidobacterium from Microbeatlas

Aquatic Samples	530
Soil Samples	177
Animal Samples	24203
Plant Samples	47
Total Samples	24957

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21533	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1489817v1 assembly for Bifidobacterium lemurum DSM 28807	complete	GCA_014898175	1603886.10	8006884007	1603886	95.28
67770	ASM225966v1 assembly for Bifidobacterium lemurum DSM 28807	contig	GCA_002259665	1603886.6	2791355242	1603886	70.57
67770	ASM189516v1 assembly for Bifidobacterium lemurum DSM 28807	contig	GCA_001895165	1603886.3	2791355249	1603886	68.63

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21533	Bifidobacterium lemurum strain LMC 13 16S ribosomal RNA gene, partial sequence	KJ658281	1400		1603886

GC content

@ref	GC-content (mol%)	Method
21533	57.2	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: ASM1489817v1 assembly for Bifidobacterium lemurum DSM 28807
NCBI: GCA_014898175

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	67.56	no
125439	motility	BacteriaNetⓘ	no	77.72	no
125439	gram_stain	BacteriaNetⓘ	positive	66.87	no
125439	spore_formation	BacteriaNetⓘ	no	94.46	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bifidobacterium lemurum DSM 28807
NCBI: GCA_014898175.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.67	no
125438	anaerobic	anaerobicⓘ	yes	78.15	yes
125438	aerobic	aerobicⓘ	no	90.55	yes
125438	spore-forming	spore-formingⓘ	no	89.78	no
125438	thermophilic	thermophileⓘ	no	92.60	yes
125438	flagellated	motile2+ⓘ	no	92.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Substrate recognition mode of a glycoside hydrolase family 42 beta-galactosidase from Bifidobacterium longum subspecies infantis (BiBga42A) revealed by crystallographic and mutational analyses.	Gotoh A, Hidaka M, Sakurama H, Nishimoto M, Kitaoka M, Sakanaka M, Fushinobu S, Katayama T.	Microbiome Res Rep	10.20517/mrr.2023.14	2023
	Genetic insights into the dark matter of the mammalian gut microbiota through targeted genome reconstruction.	Lugli GA, Alessandri G, Milani C, Viappiani A, Fontana F, Tarracchini C, Mancabelli L, Argentini C, Ruiz L, Margolles A, van Sinderen D, Turroni F, Ventura M.	Environ Microbiol	10.1111/1462-2920.15559	2021
Genetics	Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family.	Lugli GA, Milani C, Turroni F, Duranti S, Mancabelli L, Mangifesta M, Ferrario C, Modesto M, Mattarelli P, Jiri K, van Sinderen D, Ventura M.	BMC Genomics	10.1186/s12864-017-3955-4	2017
Genetics	Tracking the Taxonomy of the Genus Bifidobacterium Based on a Phylogenomic Approach.	Lugli GA, Milani C, Duranti S, Mancabelli L, Mangifesta M, Turroni F, Viappiani A, van Sinderen D, Ventura M.	Appl Environ Microbiol	10.1128/aem.02249-17	2018
Genetics	Short-chain fatty acids in breast milk and their relationship with the infant gut microbiota.	Xi M, Yan Y, Duan S, Li T, Szeto IM, Zhao A.	Front Microbiol	10.3389/fmicb.2024.1356462	2024
Genetics	Host-Diet Effect on the Metabolism of Bifidobacterium.	Satti M, Modesto M, Endo A, Kawashima T, Mattarelli P, Arita M.	Genes (Basel)	10.3390/genes12040609	2021
Genetics	Genome-Based Taxonomic Classification of the Phylum Actinobacteria.	Nouioui I, Carro L, Garcia-Lopez M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Goker M.	Front Microbiol	10.3389/fmicb.2018.02007	2018
Genetics	Draft Genome Sequence of Bifidobacterium lemurum DSM 28807(T) Isolated from the Gastrointestinal Tracts of Ring-Tailed Lemurs (Lemur catta).	Toh H, Matsubara T, Tomida S, Mimura I, Arakawa K, Kikusui T, Morita H	Genome Announc	10.1128/genomeA.01656-16	2017
Phylogeny	Bifidobacterium eulemuris sp. nov., isolated from faeces of black lemurs (Eulemur macaco).	Michelini S, Modesto M, Pisi AM, Filippini G, Sandri C, Spiezio C, Biavati B, Sgorbati B, Mattarelli P	Int J Syst Evol Microbiol	10.1099/ijsem.0.000924	2016
Phylogeny	Bifidobacterium lemurum sp. nov., from faeces of the ring-tailed lemur (Lemur catta).	Modesto M, Michelini S, Stefanini I, Sandri C, Spiezio C, Pisi A, Filippini G, Biavati B, Mattarelli P	Int J Syst Evol Microbiol	10.1099/ijs.0.000162	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 )
#21533	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28807
#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 .
#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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Bifidobacterium lemurum (DSM 28807, JCM 30168, LMC 13)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014898175

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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