Name: Nosocomiicoccus ampullae TRF-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14681

Type strain:

Species: Nosocomiicoccus ampullae

Strain Designation: TRF-1

Culture col. no.: DSM 19163, CIP 109506, LMG 24060, UCCCB22

Strain history: CIP <- 2007, M. Alves, Coimbra Univ., Coimbra, Portugal: strain TRF-1, "Jeotgalicoccus genus"

NCBI tax ID(s): 489910 (species)

SI-ID 302705

LMG 24060, CIP 109506, DSM 19163

Other strains from Nosocomiicoccus ampullae

N. ampullae CCUG 55627

Section

Nosocomiicoccus ampullae TRF-1 is an aerobe, mesophilic, Gram-positive human pathogen that was isolated from transfer spike, physiological saline flask in a health care center.

coccus-shaped
Gram-positive
aerobe
human pathogen
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	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Staphylococcaceae*
	Genus	*Nosocomiicoccus*
	Species	**Nosocomiicoccus ampullae**
	Full Scientific Name (LPSN)	Nosocomiicoccus ampullae Morais et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32599]	Gram stain	positive
[Ref.: #116345]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #32599]	Cell shape	coccus-shaped
[Ref.: #116345]	Cell shape	coccus-shaped

[Ref.: #32599]	Motility	no
[Ref.: #116345]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %94.228

[Ref.: #32599]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7944]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #7944]

Culture medium growth

[Ref.: #7944]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7944]

Culture medium composition

expand / minimize

[Ref.: #39787]

Culture medium

MEDIUM 45 - for Columbia agar with sheep blood

[Ref.: #39787]

Culture medium growth

[Ref.: #39787]

Culture medium composition

expand / minimize

[Ref.: #116345]

Culture medium

CIP Medium 45

[Ref.: #116345]

Culture medium growth

[Ref.: #116345]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7944]	growth	30 °C
[Ref.: #32599]	growth	30-45 °C
[Ref.: #32599]	optimum	37 °C
[Ref.: #39787]	growth	37 °C
[Ref.: #67772]	optimum	30-37 °C
[Ref.: #67772]	minimum	30 °C
[Ref.: #67772]	maximum	37 °C

[Ref.: #7944]	Temperature range	mesophilic
[Ref.: #32599]	Temperature range	mesophilic
[Ref.: #39787]	Temperature range	mesophilic
[Ref.: #67772]	Temperature range	mesophilic

		pH
[Ref.: #67772]	maximum	8.0
[Ref.: #67772]	minimum	7.5
[Ref.: #32599]	optimum	7.5-8
[Ref.: #32599]	growth	7.5-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32599]	Oxygen tolerance	aerobe
[Ref.: #116345]	Oxygen tolerance	obligate aerobe

[Ref.: #32599]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.973

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32599]		NaCl		growth	0-10	%

[Ref.: #7944]	Murein short key	A11.03
[Ref.: #7944]	Murein types	A3alpha L-Lys-Gly₂_-₄-L-Ser₁_-₂-Gly

[Ref.: #32599]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32599]	arabinose ChEBI	+	carbon source
[Ref.: #116345]	nitrate ChEBI	-	reduction
[Ref.: #116345]	nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #116345]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #32599]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #32599]	catalase	+	1.11.1.6
[Ref.: #116345]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #32599]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #32599]	gelatinase	+
[Ref.: #68382]	leucine arylamidase	-	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #116345]	oxidase	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #116345]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #116345]	11917	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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

[Ref.: #7944]	Sample type/isolated from	transfer spike, physiological saline flask in a health care center
[Ref.: #7944]	Country	Portugal
[Ref.: #7944]	Country ISO 3 Code	PRT
[Ref.: #7944]	Continent	Europe

[Ref.: #67772]	Sample type/isolated from	Surface of bottles of saline solution used in wound cleansing
[Ref.: #67772]	Sampling date	2005
[Ref.: #67772]	Country	Portugal
[Ref.: #67772]	Country ISO 3 Code	PRT
[Ref.: #67772]	Continent	Europe

[Ref.: #116345]	Sample type/isolated from	Saline flask
[Ref.: #116345]	Country	Portugal
[Ref.: #116345]	Country ISO 3 Code	PRT
[Ref.: #116345]	Continent	Europe
[Ref.: #116345]	Isolation date	2005
* marker position based on {}

Isolation sources categories

#Infection	#Medical device	-
#Infection	#Medical environment	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EU240886 (>99% sequence identity) for Nosocomiicoccus ampullae subclade from Microbeatlas

Aquatic Samples	1152
Soil Samples	1543
Animal Samples	15338
Plant Samples	342
Total Samples	18375

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

[Ref.: #7944]	Pathogenicity (human)	yes, in single cases
[Ref.: #7944]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #67772]	Biosafety level	1
[Ref.: #116345]	Biosafety level	1	Risk group (French classification)

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.: #7944]	Nosocomiicoccus ampullae strain TRF-1 16S ribosomal RNA gene, partial sequence	EU240886	1502	ENA	489910 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67772]	Nosocomiicoccus ampullae LUREC	GCA_001696685	scaffold	GenBank	489910 tax ID
[Ref.: #66792]	Nosocomiicoccus ampullae DSM 19163	GCA_019357495	complete	GenBank	489910 tax ID	*
[Ref.: #66792]	Nosocomiicoccus ampullae DSM 19163	GCA_014202595	scaffold	GenBank	489910 tax ID	*
[Ref.: #66792]	Nosocomiicoccus ampullae strain DSM 19163	489910.8	complete	PATRIC	489910 tax ID	*
[Ref.: #66792]	Nosocomiicoccus ampullae strain DSM 19163	489910.5	wgs	PATRIC	489910 tax ID	*
[Ref.: #66792]	Nosocomiicoccus ampullae DSM 19163	2861585789	draft	JGI IMG/M	489910 tax ID	*

[Ref.: #7944]

GC-content

33.5 mol%

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: Nosocomiicoccus ampullae DSM 19163 NCBI: GCA_019357495.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Nosocomiicoccus ampullae DSM 19163 NCBI: GCA_019357495.1
[Ref.: #69480]	flagellated	no	98.253	yes
[Ref.: #69480]	gram-positive	yes	91.226	yes
[Ref.: #69480]	anaerobic	no	98.185	yes
[Ref.: #69480]	aerobic	yes	93.161	yes
[Ref.: #69480]	halophile	yes	96.442	no
[Ref.: #69480]	spore-forming	no	90.357	yes
[Ref.: #69480]	motile	no	91.74	yes
[Ref.: #69480]	thermophile	no	99.586	no
[Ref.: #69480]	glucose-util	yes	84.121	no
[Ref.: #69480]	glucose-ferment	no	64.801	no

Availability in culture collections External links

[Ref.: #7944]

Culture collection no.

DSM 19163, CIP 109506, LMG 24060, UCCCB22

[Ref.: #83807]

SI-ID 302705

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Complete Genome Sequences of Two Nosocomiicoccus ampullae Strains and a Growth-Adapted Mutant.	Schuster CF, Sommer F, Strommenger B, Werner G, Layer F	Microbiol Resour Announc	10.1128/MRA.00747-21	2021	*
Phylogeny	Nosocomiicoccus ampullae gen. nov., sp. nov., isolated from the surface of bottles of saline solution used in wound cleansing.	Alves M, Nogueira C, de Magalhaes-Sant'ana A, Chung AP, Morais PV, da Costa MS	Int J Syst Evol Microbiol	10.1099/ijs.0.65753-0	2008	*

References

#7944

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19163

#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 )

#32599

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28812 (see below)

#39787 ; Curators of the CIP;

#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) .

#67772 The University of Coimbra Bacteria Culture Collection (UCCCB) ; Curators of the UCCCB;

#68382

Automatically annotated from API zym .

#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 )

#83807

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-ID302705.1 )

#116345 Collection of Institut Pasteur ; Curators of the CIP; CIP 109506

#28812

IJSEM 2939 2008 ( DOI 10.1099/ijs.0.65753-0 , PubMed 19060087 )

* These data were automatically processed and therefore are not curated

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Nosocomiicoccus ampullae DSM 19163

Nosocomiicoccus ampullae DSM 19163

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