Name: Bifidobacterium ramosum DSM 100688
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 132546

Type strain:

Species: Bifidobacterium ramosum

Culture col. no.: DSM 100688, JCM 30944, TRE M

Strain history: P. Mattarelli; Dept. of Agric. Sci., Bologna Univ., Italy; TRE M.

NCBI tax ID(s): 1798158 (species)

SI-ID 407015

DSM 100688

Special Collections

DSMZ
JCM

Section

When using BacDive for research please cite our paper

Bifidobacterium ramosum DSM 100688 is a mesophilic bacterium that was isolated from faeces of an adult cotton-top tamarin L..

mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Bifidobacteriales*
	Family	*Bifidobacteriaceae*
	Genus	*Bifidobacterium*
	Species	**Bifidobacterium ramosum**
	Full Scientific Name (LPSN)	Bifidobacterium ramosum Michelini et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #125439]	Gram stain	positive Confidence in %96.3

[Ref.: #125438]	Motility	no Confidence in %91.5

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24335]

Culture medium

BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)

[Ref.: #24335]

Culture medium growth

[Ref.: #24335]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24335]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #24335]			growth	37 °C
[Ref.: #67770]			growth	37 °C

Information on physiology and metabolism Physiology and metabolism

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	amygdalin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	arbutin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	cellobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	esculin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gentiobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycerol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	lactose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	maltose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	N-acetylglucosamine ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	sucrose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #24335]	15690	-	-	-	-	-	-	-	-	-	+	+	+	+	+	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	+	-	-	-	-	-	+	+	-	+	-	-	-	-	-	-	-	-	-	-

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

[Ref.: #24335]	Sample type/isolated from	faeces of an adult cotton-top tamarin (Saguinus oedipus) L.
[Ref.: #24335]	Host species	Saguinus oedipus
[Ref.: #24335]	Geographic location (country and/or sea, region)	Verona, Bussolengo, Parco Natura Viva
[Ref.: #24335]	Country	Italy
[Ref.: #24335]	Country ISO 3 Code	ITA
[Ref.: #24335]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Faeces of an adult subject of the cotton-top tamarin
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KU051447 (>99% sequence identity) for Bifidobacterium ramosum subclade from Microbeatlas

Aquatic Samples	165
Soil Samples	246
Animal Samples	19947
Plant Samples	28
Total Samples	20386

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #24335]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #24335]	Bifidobacterium ramosum strain TRE M 16S ribosomal RNA gene, partial sequence	KU051447	1382	GenBank ENA	1798158 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Bifidobacterium ramosum DSM 100688	GCA_009299505	contig	GenBank ENA	1798158 tax ID	*
[Ref.: #66792]	Bifidobacterium ramosum strain DSM 100688	1798158.5	wgs	PATRIC	1798158 tax ID	*

[Ref.: #24335]

GC-content

63 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bifidobacterium ramosum strain DSM 100688 PATRIC: 1798158.5
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	88.864	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	67.494	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	87.292	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	92	yes
[Ref.: #125438]	aerobic	aerobicⓘ	no	82.834	no
[Ref.: #125438]	motile2+	flagellatedⓘ	no	91.5	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Bifidobacterium ramosum DSM 100688 NCBI: GCA_009299505
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	82.6
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	71.7
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	96.3
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	72.6

Availability in culture collections External links

[Ref.: #24335]

Culture collection no.

DSM 100688, JCM 30944, TRE M

[Ref.: #90871]

SI-ID 407015

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Bifidobacterium aerophilum sp. nov., Bifidobacterium avesanii sp. nov. and Bifidobacterium ramosum sp. nov.: Three novel taxa from the faeces of cotton-top tamarin (Saguinus oedipus L.).	Michelini S, Modesto M, Filippini G, Spiezio C, Sandri C, Biavati B, Pisi A, Mattarelli P	Syst Appl Microbiol	10.1016/j.syapm.2016.04.005	2016	*

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 )

#24335

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100688

#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 .

#90871

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-ID407015.1 )

#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 .

* These data were automatically processed and therefore are not curated

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Bifidobacterium ramosum strain DSM 100688

Bifidobacterium ramosum DSM 100688

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