Name: Vagococcus bubulae SS1994
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 157225

Type strain:

Species: Vagococcus bubulae

Strain Designation: SS1994

Culture col. no.: CCUG 70831, LMG 30164

NCBI tax ID(s): 1977868 (species)

SI-ID 411579

CCUG 70831

Special Collections

Section

When using BacDive for research please cite our paper

Vagococcus bubulae SS1994 is a microaerophile, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from Ground beef.

colony-forming
Gram-positive
rod-shaped
mesophilic
microaerophile
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	*Bacillota*
	Class	*Bacilli*
	Order	*Lactobacillales*
	Family	*Enterococcaceae*
	Genus	*Vagococcus*
	Species	**Vagococcus bubulae**
	Full Scientific Name (LPSN)	Vagococcus bubulae Shewmaker et al. 2019

Information on morphological and physiological properties Morphology

[Ref.: #67899]	Gram stain	positive
[Ref.: #125438]	Gram stain	positive Confidence in %90.415

[Ref.: #67899]	Cell shape	rod-shaped
[Ref.: #67899]	Cell shape	coccus-shaped

[Ref.: #67899]	Motility	no

[Ref.: #67899]	Type of hemolysis	alpha
[Ref.: #67899]	Hemolysis ability	1
[Ref.: #67899]	Colony size	1 mm
[Ref.: #67899]	Colony color	grey-white
[Ref.: #67899]	Colony shape	circular
[Ref.: #67899]	Incubation period	1 days
[Ref.: #67899]	Cultivation medium used	trypticase soy agar supplemented with 5 % sheep blood

Information on culture and growth conditions Culture and growth conditions

	Kind of temperature		Temperature
[Ref.: #63753]		growth	37 °C
[Ref.: #67899]		growth	35 °C
[Ref.: #67899]		growth	30 °C
[Ref.: #67899]		growth	10 °C
[Ref.: #67899]	no	growth	45 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #63753]

Oxygen tolerance

microaerophile

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #67899]		NaCl		growth	6.5	%

[Ref.: #67899]

Observation

No gas is produced in Mann-Rogosa-Sharp broth.

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #67899]	alpha-cyclodextrin ChEBI	-	builds acid from
[Ref.: #67899]	arginine ChEBI	-	hydrolysis
[Ref.: #67899]	bile acid ChEBI	+	growth
[Ref.: #67899]	D-arabinose ChEBI	+	builds acid from
[Ref.: #67899]	D-arabitol ChEBI	-	builds acid from
[Ref.: #67899]	D-mannitol ChEBI	+	builds acid from
[Ref.: #67899]	D-ribose ChEBI	+	builds acid from
[Ref.: #67899]	D-sorbitol ChEBI	+	builds acid from
[Ref.: #67899]	D-tagatose ChEBI	+	builds acid from
[Ref.: #67899]	D-xylose ChEBI	+	builds acid from
[Ref.: #67899]	esculin ChEBI	+	hydrolysis
[Ref.: #67899]	glycerol ChEBI	+	builds acid from
[Ref.: #67899]	glycogen ChEBI	-	builds acid from
[Ref.: #67899]	hippurate ChEBI	+	hydrolysis
[Ref.: #67899]	inulin ChEBI	+	builds acid from
[Ref.: #67899]	L-arabinose ChEBI	+	builds acid from
[Ref.: #67899]	L-sorbose ChEBI	-	builds acid from
[Ref.: #67899]	L-xylose ChEBI	+	builds acid from
[Ref.: #67899]	lactose ChEBI	+	builds acid from
[Ref.: #67899]	maltose ChEBI	+	builds acid from
[Ref.: #67899]	melibiose ChEBI	+	builds acid from
[Ref.: #67899]	methyl alpha-D-glucopyranoside ChEBI	+	builds acid from
[Ref.: #67899]	methyl beta-D-glucopyranoside ChEBI	+	builds acid from
[Ref.: #67899]	pullulan ChEBI	+	builds acid from
[Ref.: #67899]	pyruvate ChEBI	+	growth
[Ref.: #67899]	raffinose ChEBI	+	builds acid from
[Ref.: #67899]	starch ChEBI	-	hydrolysis
[Ref.: #67899]	sucrose ChEBI	+	builds acid from
[Ref.: #67899]	tellurite ChEBI	-	growth
[Ref.: #67899]	trehalose ChEBI	+	builds acid from
[Ref.: #67899]	urea ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #67899]		acetoin ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #67899]	alkaline phosphatase	-	3.1.3.1
[Ref.: #67899]	alpha-galactosidase	+	3.2.1.22
[Ref.: #67899]	beta-galactosidase	+	3.2.1.23
[Ref.: #67899]	beta-glucosidase	+	3.2.1.21
[Ref.: #67899]	beta-glucuronidase	-	3.2.1.31
[Ref.: #67899]	beta-mannosidase	-	3.2.1.25
[Ref.: #67899]	catalase	-	1.11.1.6
[Ref.: #67899]	leucine aminopeptidase	+	3.4.1.1
[Ref.: #67899]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #67899]	pyrrolidonyl arylamidase	+	3.4.19.3

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

[Ref.: #63753]	Sample type/isolated from	Ground beef
[Ref.: #63753]	Sampling date	2002
[Ref.: #63753]	Geographic location (country and/or sea, region)	Oregon
[Ref.: #63753]	Country	USA
[Ref.: #63753]	Country ISO 3 Code	USA
[Ref.: #63753]	Continent	North America

[Ref.: #67899]	Sample type/isolated from	ground beef
* marker position based on {}

Isolation sources categories

#Engineered

#Food production

#Meat

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KY937952 (>99% sequence identity) for Vagococcus from Microbeatlas

Aquatic Samples	4
Soil Samples	43
Animal Samples	221
Plant Samples
Total Samples	268

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.: #67899]	Vagococcus bubulae strain SS1994 16S ribosomal RNA gene, partial sequence	KY937952	1480	GenBank ENA	1977868 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67899]	Vagococcus bubulae SS1994	GCA_003950315	contig	GenBank ENA	1977868 tax ID

[Ref.: #67899]

GC-content

33.6 mol%

genome sequence analysis

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: Vagococcus bubulae SS1994 NCBI: GCA_003950315.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	90.415	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	85.964	yes
[Ref.: #125438]	aerobic	aerobicⓘ	no	95.503	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	71.105	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	95.496	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	89	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Vagococcus bubulae SS1994 NCBI: GCA_003950315
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	60.8
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	60.5
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	variable	68.2
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	microaerophile	89.6

Availability in culture collections External links

[Ref.: #63753]

Culture collection no.

CCUG 70831, LMG 30164

[Ref.: #110324]

SI-ID 411579

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Vagococcus bubulae sp. nov., isolated from ground beef, and Vagococcus vulneris sp. nov., isolated from a human foot wound.	Shewmaker PL, Whitney AM, Gulvik CA, Humrighouse BW, Gartin J, Moura H, Barr JR, Moore ERB, Karlsson R, Pinto TCA, Teixeira LM	Int J Syst Evol Microbiol	10.1099/ijsem.0.003459	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 )

#63753 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 70831

#67899

Patricia L. Shewmaker, Anne M. Whitney, Christopher A. Gulvik, Ben W. Humrighouse, Jarrett Gartin, Hercules Moura, John R. Barr, Edward R. B. Moore, Roger Karlsson, Tatiana C. A. Pinto, Lucia M. Teixeira: Vagococcus bubulae sp. nov., isolated from ground beef, and Vagococcus vulneris sp. nov., isolated from a human foot wound. IJSEM 69: 2268 - 2276 2019 ( DOI 10.1099/ijsem.0.003459 )

#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 .

#110324

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-ID411579.1 )

#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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