Bifidobacterium scaligerum (DSM 103140, TRE D, JCM 31792)

Name: Bifidobacterium scaligerum (DSM 103140, TRE D, JCM 31792)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159318

Type strain

Culture col. no. DSM 103140 TRE D JCM 31792

NCBI tax ID(s) 2052656

Special Collections DSMZ JCM

History DSMZ <- P. Mattarelli, Univ. Bologna, Italy; TRE D <- M. Modesto and S. Michelini JCM <-- P. Mattarelli; Dept. of Agric. Sci., Bologna Univ., Italy; TRE D.

Links

Bifidobacterium scaligerum DSM 103140 is a bacterium that was isolated from Feces of Saguinus oedipus.

genome sequence Bacteria

Name and taxonomic classification

SI-ID 404271

LMG 33149,JCM 31792,DSM 103140

@ref 20215

Last LPSN update 2026-05-29 08:44:10

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Bifidobacteriales

Family Bifidobacteriaceae

Genus Bifidobacterium

Species Bifidobacterium scaligerum

Full scientific name Bifidobacterium scaligerum Modesto et al. 2020

Morphology

Cell morphology

@ref	Motility	Confidence
125438		92

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
66141	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)
66141	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate anaerobe	93.672

Spore formation

@ref	Spore formation	Confidence
125439		98.93

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
66141	Feces of Saguinus oedipus	Saguinus oedipus	Bussolengo (Verona)	Italy	ITA	Europe
67770	Feces of an adult subject of the cotton top tamarin (Saguinus oedipus) housed under semi-naturalconditions in Parco Natura Viva - Garda Zoological Park	Saguinus oedipus	Bussolengo, Verona	Italy	ITA	Europe

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM280286v1 assembly for Bifidobacterium scaligerum TRE D	scaffold	GCA_002802865	2052656.3	2791355238	2052656	74.3

GC content

@ref	GC-content (mol%)	Method
67770	58.9	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM280286v1 assembly for Bifidobacterium scaligerum TRE D
NCBI: GCA_002802865

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	49.59	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	93.67	no
125439	motility	BacteriaNetⓘ	no	79.01	no
125439	spore_formation	BacteriaNetⓘ	no	98.93	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bifidobacterium scaligerum TRE D
NCBI: GCA_002802865.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	86.73	no
125438	anaerobic	anaerobicⓘ	yes	83.74	no
125438	aerobic	aerobicⓘ	no	91.23	no
125438	spore-forming	spore-formingⓘ	no	87.72	no
125438	thermophilic	thermophileⓘ	no	90.49	yes
125438	flagellated	motile2+ⓘ	no	92.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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
	Comparative prebiotic potential of galacto- and fructo-oligosaccharides, native inulin, and acacia gum in Kenyan infant gut microbiota during iron supplementation.	Momo Cabrera P, Rachmuhl C, Derrien M, Bourdet-Sicard R, Lacroix C, Geirnaert A.	ISME Commun	10.1093/ismeco/ycae033	2024
	Yeast mannan rich fraction positively influences microbiome uniformity, productivity associated taxa, and lay performance.	Leigh RJ, Corrigan A, Murphy RA, Taylor-Pickard J, Moran CA, Walsh F.	Anim Microbiome	10.1186/s42523-024-00295-7	2024
Phylogeny	Contrasting Diversity and Composition of Human Colostrum Microbiota in a Maternal Cohort With Different Ethnic Origins but Shared Physical Geography (Island Scale).	Xie W, Zhang H, Ni Y, Peng Y.	Front Microbiol	10.3389/fmicb.2022.934232	2022
Phylogeny	Bifidobacterium primatium sp. nov., Bifidobacterium scaligerum sp. nov., Bifidobacterium felsineum sp. nov. and Bifidobacterium simiarum sp. nov.: Four novel taxa isolated from the faeces of the cotton top tamarin (Saguinus oedipus) and the emperor tamarin (Saguinus imperator).	Modesto M, Puglisi E, Bonetti A, Michelini S, Spiezio C, Sandri C, Sgorbati B, Morelli L, Mattarelli P	Syst Appl Microbiol	10.1016/j.syapm.2018.07.005	2018

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 )
#66141	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103140
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 scaligerum (DSM 103140, TRE D, JCM 31792)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_002802865

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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