Name: Bifidobacterium jacchi DSM 103362
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 159320

Type strain:

Species: Bifidobacterium jacchi

Culture col. no.: DSM 103362, JCM 31788, MRM 9.3

Strain history: P. Mattarelli; Dept. of Agric. Sci., Bologna Univ., Italy; MRM 9.3.

NCBI tax ID(s): 2490545 (species)

SI-ID 404258

DSM 103362

Section

Bifidobacterium jacchi DSM 103362 is an aerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from Faeces of Saguinus oedipus.

colony-forming
Gram-positive
rod-shaped
aerobe
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Bifidobacteriales*
	Family	*Bifidobacteriaceae*
	Genus	*Bifidobacterium*
	Species	**Bifidobacterium jacchi**
	Full Scientific Name (LPSN)	Bifidobacterium jacchi Modesto et al. 2019

Information on morphological and physiological properties Morphology

[Ref.: #67988]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #67988]	Cell length	8.0-12.0 µm

[Ref.: #67988]	Cell width	2 µm

[Ref.: #67988]	Cell shape	rod-shaped

[Ref.: #67988]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %95.125

[Ref.: #67988]	Colony size	1.0-2.0 mm
[Ref.: #67988]	Colony color	white
[Ref.: #67988]	Colony shape	circular
[Ref.: #67988]	Incubation period	3 days
[Ref.: #67988]	Cultivation medium used	TPY agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #66143]

Culture medium

BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)

[Ref.: #66143]

Culture medium growth

[Ref.: #66143]

Culture medium link

Medium recipe at MediaDive

[Ref.: #66143]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #66143]	growth	37 °C
[Ref.: #67770]	growth	37 °C
[Ref.: #67988]	growth	22-48 °C
[Ref.: #67988]	optimum	37 °C

[Ref.: #66143]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67988]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #67988]			optimum	7
[Ref.: #67988]			growth	4.0-7.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67988]	Oxygen tolerance	aerobe
[Ref.: #67988]	Oxygen tolerance	microaerophile
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.281

[Ref.: #67988]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999
[Ref.: #69481]	Ability of spore formation	no Confidence in %91

[Ref.: #67988]	Observation	cells form a branched structure with 'Y' at the both side
[Ref.: #67988]	Observation	The peptidoglycan type is L-Orn - L-Ser - L-Ala
[Ref.: #67988]	Observation	Colonies on the surface of are white, smooth and circular with entire edges, while the embedded colonies are lens-shaped or elliptical

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #67988]	amygdalin ChEBI	-	builds acid from
[Ref.: #67988]	arbutin ChEBI	+	builds acid from
[Ref.: #67988]	cellobiose ChEBI	-	builds acid from
[Ref.: #67988]	D-arabinose ChEBI	-	builds acid from
[Ref.: #67988]	D-arabitol ChEBI	-	builds acid from
[Ref.: #67988]	D-fructose ChEBI	+	builds acid from
[Ref.: #67988]	D-fucose ChEBI	-	builds acid from
[Ref.: #67988]	D-galactose ChEBI	+	builds acid from
[Ref.: #67988]	D-glucose ChEBI	+	builds acid from
[Ref.: #67988]	D-lyxose ChEBI	-	builds acid from
[Ref.: #67988]	D-mannitol ChEBI	+	builds acid from
[Ref.: #67988]	D-mannose ChEBI	+	builds acid from
[Ref.: #67988]	D-ribose ChEBI	+	builds acid from
[Ref.: #67988]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #67988]	D-tagatose ChEBI	-	builds acid from
[Ref.: #67988]	D-xylose ChEBI	-	builds acid from
[Ref.: #67988]	erythritol ChEBI	-	builds acid from
[Ref.: #67988]	esculin ChEBI	-	hydrolysis
[Ref.: #67988]	esculin ferric citrate	-	builds acid from
[Ref.: #67988]	galactitol ChEBI	-	builds acid from
[Ref.: #67988]	gentiobiose ChEBI	-	builds acid from
[Ref.: #67988]	glycerol ChEBI	-	builds acid from
[Ref.: #67988]	glycogen ChEBI	-	builds acid from
[Ref.: #67988]	inulin ChEBI	-	builds acid from
[Ref.: #67988]	L-arabinose ChEBI	+	builds acid from
[Ref.: #67988]	L-arabitol ChEBI	-	builds acid from
[Ref.: #67988]	L-fucose ChEBI	-	builds acid from
[Ref.: #67988]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #67988]	L-sorbose ChEBI	-	builds acid from
[Ref.: #67988]	L-xylose ChEBI	-	builds acid from
[Ref.: #67988]	lactose ChEBI	+	builds acid from
[Ref.: #67988]	maltose ChEBI	+	builds acid from
[Ref.: #67988]	melezitose ChEBI	-	builds acid from
[Ref.: #67988]	melibiose ChEBI	+/-	builds acid from
[Ref.: #67988]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from
[Ref.: #67988]	methyl alpha-D-mannoside ChEBI	-	builds acid from
[Ref.: #67988]	methyl beta-D-xylopyranoside ChEBI	+	builds acid from
[Ref.: #67988]	myo-inositol ChEBI	-	builds acid from
[Ref.: #67988]	N-acetylglucosamine ChEBI	+/-	builds acid from
[Ref.: #67988]	nitrate ChEBI	-	reduction
[Ref.: #67988]	potassium 2-dehydro-D-gluconate	-	builds acid from
[Ref.: #67988]	potassium 5-dehydro-D-gluconate	-	builds acid from
[Ref.: #67988]	potassium gluconate ChEBI	-	builds acid from
[Ref.: #67988]	raffinose ChEBI	+	builds acid from
[Ref.: #67988]	ribitol ChEBI	-	builds acid from
[Ref.: #67988]	salicin ChEBI	-	builds acid from
[Ref.: #67988]	starch ChEBI	-	builds acid from
[Ref.: #67988]	sucrose ChEBI	+	builds acid from
[Ref.: #67988]	trehalose ChEBI	+	builds acid from
[Ref.: #67988]	turanose ChEBI	+/-	builds acid from
[Ref.: #67988]	xylitol ChEBI	-	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #67988]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #67988]	alkaline phosphatase	+/-	3.1.3.1
[Ref.: #67988]	alpha-galactosidase	+	3.2.1.22
[Ref.: #67988]	alpha-glucosidase	+	3.2.1.20
[Ref.: #67988]	beta-galactosidase	+	3.2.1.23
[Ref.: #67988]	catalase	-	1.11.1.6
[Ref.: #67988]	cytochrome oxidase	-	1.9.3.1
[Ref.: #67988]	fructose-6-phosphate phosphoketolase	+	4.1.2.22
[Ref.: #67988]	glycin arylamidase	+/-
[Ref.: #67988]	histidine arylamidase	+
[Ref.: #67988]	L-arginine arylamidase	+
[Ref.: #67988]	leucine arylamidase	+	3.4.11.1
[Ref.: #67988]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #67988]	phenylalanine arylamidase	+
[Ref.: #67988]	proline-arylamidase	+	3.4.11.5
[Ref.: #67988]	serine arylamidase	+
[Ref.: #67988]	tyrosine arylamidase	+
[Ref.: #67988]	urease	-	3.5.1.5
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #66143]	Sample type/isolated from	Faeces of Saguinus oedipus
[Ref.: #66143]	Geographic location (country and/or sea, region)	Verona
[Ref.: #66143]	Country	Italy
[Ref.: #66143]	Country ISO 3 Code	ITA
[Ref.: #66143]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Feces of a baby common marmoset (Callithrix jacchus)
[Ref.: #67770]	Host species	Callithrix jacchus
[Ref.: #67770]	Country	Italy
[Ref.: #67770]	Country ISO 3 Code	ITA
[Ref.: #67770]	Continent	Europe

[Ref.: #67988]	Sample type/isolated from	faeces of a baby common marmoset
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KP718960 (>99% sequence identity) for Bifidobacterium from Microbeatlas

Aquatic Samples	64
Soil Samples	68
Animal Samples	11142
Plant Samples	19
Total Samples	11293

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.: #66143]	Bifidobacterium sp. MRM 9.03 16S ribosomal RNA gene, partial sequence	KP718960	1466	ENA	1630179 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67988]	Bifidobacterium jacchi MRM 9.3	GCA_009078285	scaffold	GenBank	2490545 tax ID

[Ref.: #67988]

GC-content

61.5 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: Bifidobacterium jacchi MRM 9.3 NCBI: GCA_009078285.1
[Ref.: #69481]	spore-forming	no	91	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Bifidobacterium jacchi MRM 9.3 NCBI: GCA_009078285.1
[Ref.: #69480]	flagellated	no	96.154	no
[Ref.: #69480]	gram-positive	yes	93.459	yes
[Ref.: #69480]	anaerobic	yes	97.592	no
[Ref.: #69480]	aerobic	no	96.577	no
[Ref.: #69480]	halophile	no	82.098	no
[Ref.: #69480]	spore-forming	no	96.066	no
[Ref.: #69480]	thermophile	no	97.799	yes
[Ref.: #69480]	glucose-util	yes	89.009	no
[Ref.: #69480]	motile	no	94.933	no
[Ref.: #69480]	glucose-ferment	yes	82.927	no

Availability in culture collections External links

[Ref.: #66143]

Culture collection no.

DSM 103362, JCM 31788, MRM 9.3

[Ref.: #111819]

SI-ID 404258

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Bifidobacterium jacchi sp. nov., isolated from the faeces of a baby common marmoset (Callithrix jacchus).	Modesto M, Watanabe K, Arita M, Satti M, Oki K, Sciavilla P, Patavino C, Camma C, Michelini S, Sgorbati B, Mattarelli P	Int J Syst Evol Microbiol	10.1099/ijsem.0.003518	2019	*

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 )

#66143

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103362

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#67988

Monica Modesto, Koichi Watanabe, Masanori Arita, Maria Satti, Kaihei Oki, Piero Sciavilla, Claudio Patavino, Cesare Cammà, Samanta Michelini, Barbara Sgorbati, Paola Mattarelli: Bifidobacterium jacchi sp. nov., isolated from the faeces of a baby common marmoset (Callithrix jacchus). IJSEM 69: 2477 - 2485 2019 ( DOI 10.1099/ijsem.0.003518 )

#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 )

#111819

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-ID404258.1 )

* These data were automatically processed and therefore are not curated

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Bifidobacterium jacchi MRM 9.3

Bifidobacterium jacchi MRM 9.3

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