Bifidobacterium indicum (CCUG 34986, LMG 18911, DSM 20216)

Name: Bifidobacterium indicum (CCUG 34986, LMG 18911, DSM 20216)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1700

Type strain

Strain Designation C-215

Culture col. no. CCUG 34986 LMG 18911 DSM 20216 ATCC 25911 C-215 5 more

NCBI tax ID(s) 1687

Special Collections DSMZ CCUG JCM KCTC

History <- V. Scardovi, C-215 ATCC 25911 <-- V. Scardovi C-215 (Bifidobacterium indicum).

Links

Bifidobacterium indicum C-215 is an anaerobe, mesophilic prokaryote that was isolated from hindgut of honeybee.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 9632

LMG 11584,ATCC 25911,CCUG 34986,DSM 20216,LMG 18911,JCM 5819,CCRC 14675,KCTC 3233,AS 1.2279,BCRC 14675,CGMCC 1.2279

@ref 20215

Last LPSN update 2025-12-16 09:47:10

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Bifidobacteriales

Family Bifidobacteriaceae

Genus Bifidobacterium

Species Bifidobacterium indicum

Full scientific name Bifidobacterium indicum Scardovi and Trovatelli 1969 (Approved Lists 1980)

Synonyms (1)

Bifidobacterium coryneforme

BacDive ID	Other strains from **Bifidobacterium indicum** (1)	Type strain
1707	B. indicum C 410, DSM 20214, ATCC 25912, CCUG 34985, ... (type strain)

Morphology

Cell morphology

@ref	Motility	Confidence
125438		96

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8610	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)	Range
8610	positive	growth	37	mesophilic
52435	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
8610	anaerobe
52435	anaerobe

Spore formation

@ref	Spore formation	Confidence
125438		90.546
125439		97.4

Murein

@ref	Murein short key	Type
8610	A11.31	A4alpha L-Lys-D-Asp

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
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	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	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	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	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	+	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		Potassium 2-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	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

Fatty acid profile

Metadata FA analysis

@ref

52435

Fatty acid	Percentage	ECL
C16:0	28.4	16
C18:2 ω6,9c/C18:0 ANTE	22.4	17.724
C18:1 ω9c	18.3	17.769
C18:0	11.3	18
Unidentified	4.8	18.184
C19:0 CYCLO ω9c	4.2	18.87
Unidentified	2.7	19.33
C14:0	2.4	14
C16:1 ω7c	2.2	15.819
C17:0 anteiso	1.7	16.722
C18:1 ω6c	1.6	17.858

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
8610	-	-	-	-	+	-	-	-	-	-	+/-	+	+	-	-	-	-	-	-	-	-	-	-	-	+/-	+	+/-	-	-	-	+	+/-	-	-	-	+	-	-	-	+/-	-	-	-	-	-	-	-	-	-	-
8610	-	-	-	-	+	+	+	-	-	-	+	+	+	-	-	-	-	-	-	-	-	+	-	+	+	+	+	+	+	+	+	+	-	-	-	+	-	-	-	+	+	-	-	-	-	-	-	+	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Arthropoda	#Insecta
#Host Body-Site	#Gastrointestinal tract	-

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent	Host species
8610	hindgut of honeybee
52435	Honeybee hindgut,Apis mellifica caucasica	Norway	NOR	Europe
67770	Hindgut of honeybee Apis mellifica caucasica				Apis mellifica caucasica

Taxonmaps

69479

Global distribution of 16S sequence LC071833 (>99% sequence identity) for Bifidobacterium from Microbeatlas

Aquatic Samples	210
Soil Samples	246
Animal Samples	15035
Plant Samples	108
Total Samples	15599

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8610	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
66792	ASM73786v1 assembly for Bifidobacterium coryneforme LMG18911	complete	GCA_000737865	1687.3	2597490194	1687	97.06
124043	ASM3698689v1 assembly for Bifidobacterium coryneforme JCM 5819	contig	GCA_036986895	1687.31		1687	74.86
124043	ASM3698687v1 assembly for Bifidobacterium coryneforme CGMCC 1.2279	contig	GCA_036986875	1687.30		1687	74.86
67770	DSM-20216 assembly for Bifidobacterium coryneforme DSM 20216	contig	GCA_000771345	1437599.3	2693429521	1437599	64.04

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Bifidobacterium coryneforme strain ATCC 25911 16S ribosomal RNA gene, partial sequence	M58733	1473	1687
20218	Bifidobacterium coryneforme ATCC25911 16S-23S intergenic spacer	U09523	459	1687
20218	Bifidobacterium coryneforme strain CCUG 34986 16S ribosomal RNA gene, partial sequence	EF187238	1370	1687
20218	Bifidobacterium coryneforme gene for 16S rRNA, partial sequence, strain: JCM 5819	AB116297	475	1687
20218	Bifidobacterium coryneforme gene for 16S rRNA, partial sequence, strain: JCM 5819	AB507093	668	1687
67770	Bifidobacterium coryneforme gene for 16S ribosomal RNA, partial sequence	AB437358	1507	1687
67770	Bifidobacterium coryneforme gene for 16S ribosomal RNA, partial sequence, strain: JCM 5819	LC071833	1452	1687

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Bifidobacterium coryneforme strain LMG 18911
PATRIC: 1687.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.40	no
125439	motility	BacteriaNetⓘ	no	55.10	no
125439	gram_stain	BacteriaNetⓘ	positive	67.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	79.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bifidobacterium coryneforme LMG18911
NCBI: GCA_000737865.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	85.67	no
125438	anaerobic	anaerobicⓘ	yes	79.25	yes
125438	aerobic	aerobicⓘ	no	94.58	yes
125438	spore-forming	spore-formingⓘ	no	90.55	no
125438	thermophilic	thermophileⓘ	no	95.50	no
125438	flagellated	motile2+ⓘ	no	96.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	The Type Strain of Bifidobacterium indicum Scardovi and Trovatelli 1969 (Approved Lists 1980) is ATCC 25912, not DSM 20214, and Rejection to Reclassify Bifidobacterium coryneforme as Bifidobacterium indicum.	Jiang CS, Li CY, Gu CT.	Curr Microbiol	10.1007/s00284-024-03712-x	2024
	Exploring the biodiversity of Bifidobacterium asteroides among honey bee microbiomes.	Lugli GA, Fontana F, Tarracchini C, Mancabelli L, Milani C, Turroni F, Ventura M.	Environ Microbiol	10.1111/1462-2920.16223	2022
	Effects of a supplemented diet containing 7 probiotic strains (Honeybeeotic) on honeybee physiology and immune response: analysis of hemolymph cytology, phenoloxidase activity, and gut microbiome.	Robino P, Galosi L, Bellato A, Vincenzetti S, Gonella E, Ferrocino I, Serri E, Biagini L, Roncarati A, Nebbia P, Menzio C, Rossi G.	Biol Res	10.1186/s40659-024-00533-x	2024
Genetics	Natural diversity of the honey bee (Apis mellifera) gut bacteriome in various climatic and seasonal states.	Papp M, Bekesi L, Farkas R, Makrai L, Judge MF, Maroti G, Tozser D, Solymosi N.	PLoS One	10.1371/journal.pone.0273844	2022
	Beneficial Bacteria and Plant Extracts Promote Honey Bee Health and Reduce Nosema ceranae Infection.	Garrido PM, Porrini MP, Alberoni D, Baffoni L, Scott D, Mifsud D, Eguaras MJ, Di Gioia D.	Probiotics Antimicrob Proteins	10.1007/s12602-022-10025-7	2024
	Prevalence of Antibiotic Resistance Genes among Human Gut-Derived Bifidobacteria.	Duranti S, Lugli GA, Mancabelli L, Turroni F, Milani C, Mangifesta M, Ferrario C, Anzalone R, Viappiani A, van Sinderen D, Ventura M.	Appl Environ Microbiol	10.1128/aem.02894-16	2017
Phylogeny	Investigation of the evolutionary development of the genus Bifidobacterium by comparative genomics.	Lugli GA, Milani C, Turroni F, Duranti S, Ferrario C, Viappiani A, Mancabelli L, Mangifesta M, Taminiau B, Delcenserie V, van Sinderen D, Ventura M.	Appl Environ Microbiol	10.1128/aem.02004-14	2014
Genetics	Characterization of Bifidobacterium asteroides Isolates.	Pino A, Benkaddour B, Inturri R, Amico P, Vaccaro SC, Russo N, Vaccalluzzo A, Agolino G, Caggia C, Miloud H, Randazzo CL.	Microorganisms	10.3390/microorganisms10030655	2022
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
Pathogenicity	Exploring the Ecology of Bifidobacteria and Their Genetic Adaptation to the Mammalian Gut.	Duranti S, Longhi G, Ventura M, van Sinderen D, Turroni F.	Microorganisms	10.3390/microorganisms9010008	2020
Phylogeny	Phylogenetic Analysis of the Bifidobacterium Genus Using Glycolysis Enzyme Sequences.	Brandt K, Barrangou R.	Front Microbiol	10.3389/fmicb.2016.00657	2016
Genetics	Genome-Wide Assessment of Stress-Associated Genes in Bifidobacteria.	Schopping M, Vesth T, Jensen K, Franzen CJ, Zeidan AA.	Appl Environ Microbiol	10.1128/aem.02251-21	2022
	The genus bifidobacterium: From genomics to functionality of an important component of the mammalian gut microbiota running title: Bifidobacterial adaptation to and interaction with the host.	Alessandri G, van Sinderen D, Ventura M.	Comput Struct Biotechnol J	10.1016/j.csbj.2021.03.006	2021
Phylogeny	Genomic encyclopedia of type strains of the genus Bifidobacterium.	Milani C, Lugli GA, Duranti S, Turroni F, Bottacini F, Mangifesta M, Sanchez B, Viappiani A, Mancabelli L, Taminiau B, Delcenserie V, Barrangou R, Margolles A, van Sinderen D, Ventura M.	Appl Environ Microbiol	10.1128/aem.02308-14	2014
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
Cultivation	A new selective medium for Bifidobacterium spp.	Nebra Y, Blanch AR.	Appl Environ Microbiol	10.1128/aem.65.11.5173-5176.1999	1999
Phylogeny	Identification of species belonging to the Bifidobacterium genus by PCR-RFLP analysis of a hsp60 gene fragment.	Baffoni L, Stenico V, Strahsburger E, Gaggia F, Di Gioia D, Modesto M, Mattarelli P, Biavati B.	BMC Microbiol	10.1186/1471-2180-13-149	2013
Enzymology	Detection of Bifidobacterium animalis subsp. lactis (Bb12) in the intestine after feeding of sows and their piglets.	Solano-Aguilar G, Dawson H, Restrepo M, Andrews K, Vinyard B, Urban JF.	Appl Environ Microbiol	10.1128/aem.00309-08	2008
Metabolism	Diversity, ecology and intestinal function of bifidobacteria.	Bottacini F, Ventura M, van Sinderen D, O'Connell Motherway M.	Microb Cell Fact	10.1186/1475-2859-13-s1-s4	2014
	Designing primers and evaluation of the efficiency of propidium monoazide - Quantitative polymerase chain reaction for counting the viable cells of Lactobacillus gasseri and Lactobacillus salivarius.	Lai CH, Wu SR, Pang JC, Ramireddy L, Chiang YC, Lin CK, Tsen HY.	J Food Drug Anal	10.1016/j.jfda.2016.10.004	2017
Cultivation	Bile salt toxicity to some bifidobacteria strains: role of conjugated bile salt hydrolase and pH.	Grill JP, Perrin S, Schneider F	Can J Microbiol	10.1139/w00-066	2000
	Bifidobacterium mizhiense sp. nov., isolated from the gut of honeybee (Apis mellifera).	Li TT, Zhang HX, Gu CT.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005390	2022

References

#8610	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20216
#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 )
#52435	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 34986
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 indicum (CCUG 34986, LMG 18911, DSM 20216)

Name and taxonomic classification