Strain identifier

BacDive ID: 14681

Type strain: Yes

Species: Nosocomiicoccus ampullae

Strain Designation: TRF-1

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

NCBI tax ID(s): 489910 (species)

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General

@ref: 7944

BacDive-ID: 14681

DSM-Number: 19163

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, coccus-shaped

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

NCBI tax id

  • NCBI tax id: 489910
  • Matching level: species

strain history

@refhistory
7944<- M. Alves and C. Nogueira, Institute of Microbiolgy, University of Coimbra, Portugal; TRF-1
67772Alves, M. University of Coimbra
116345CIP <- 2007, M. Alves, Coimbra Univ., Coimbra, Portugal: strain TRF-1, "Jeotgalicoccus genus"

doi: 10.13145/bacdive14681.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Staphylococcaceae
  • genus: Nosocomiicoccus
  • species: Nosocomiicoccus ampullae
  • full scientific name: Nosocomiicoccus ampullae Morais et al. 2008

@ref: 7944

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Staphylococcaceae

genus: Nosocomiicoccus

species: Nosocomiicoccus ampullae

full scientific name: Nosocomiicoccus ampullae Morais et al. 2008

strain designation: TRF-1

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
32599positivecoccus-shapedno
116345positivecoccus-shapedno
125438positive91.945

pigmentation

  • @ref: 32599
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7944COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
39787MEDIUM 45 - for Columbia agar with sheep bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Sheepblood (100.000 ml)
116345CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45

culture temp

@refgrowthtypetemperature
7944positivegrowth30
32599positivegrowth30-45
32599positiveoptimum37
39787positivegrowth37
67772positiveoptimum30-37
67772positiveminimum30
67772positivemaximum37

culture pH

@refabilitytypepH
32599positivegrowth7.5-8
32599positiveoptimum7.5-8
67772positivemaximum8.0
67772positiveminimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32599aerobe
116345obligate aerobe

spore formation

  • @ref: 32599
  • spore formation: no

halophily

  • @ref: 32599
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

murein

  • @ref: 7944
  • murein short key: A11.03
  • type: A3alpha L-Lys-Gly2-4-L-Ser1-2-Gly

observation

  • @ref: 32599
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3259922599arabinose+carbon source
11634517632nitrate-reduction
11634516301nitrite-reduction

metabolite production

  • @ref: 116345
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
32599alkaline phosphatase+3.1.3.1
32599catalase+1.11.1.6
32599gelatinase+
32599cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase-3.2.1.20
68382beta-galactosidase-3.2.1.23
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
116345oxidase-
116345catalase+1.11.1.6
116345urease-3.5.1.5
68382beta-glucosidase-3.2.1.21
68382beta-glucuronidase-3.2.1.31
68382trypsin-3.4.21.4

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116345--++----------------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dateisolation date
7944transfer spike, physiological saline flask in a health care centerPortugalPRTEurope
67772Surface of bottles of saline solution used in wound cleansingPortugalPRTEurope2005
116345Saline flaskPortugalPRTEurope2005

isolation source categories

Cat1Cat2
#Infection#Medical device
#Infection#Medical environment

taxonmaps

  • @ref: 69479
  • File name: preview.99_9129.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_735;97_858;98_6709;99_9129&stattab=map
  • Last taxonomy: Nosocomiicoccus ampullae subclade
  • 16S sequence: EU240886
  • Sequence Identity:
  • Total samples: 18375
  • soil counts: 1543
  • aquatic counts: 1152
  • animal counts: 15338
  • plant counts: 342

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
7944yes, in single cases1Risk group (German classification)
677721
1163451Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7944
  • description: Nosocomiicoccus ampullae strain TRF-1 16S ribosomal RNA gene, partial sequence
  • accession: EU240886
  • length: 1502
  • database: nuccore
  • NCBI tax ID: 489910

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nosocomiicoccus ampullae DSM 19163GCA_019357495completencbi489910
66792Nosocomiicoccus ampullae DSM 19163GCA_014202595scaffoldncbi489910
66792Nosocomiicoccus ampullae strain DSM 19163489910.8completepatric489910
66792Nosocomiicoccus ampullae strain DSM 19163489910.5wgspatric489910
66792Nosocomiicoccus ampullae DSM 191632861585789draftimg489910
67772Nosocomiicoccus ampullae LURECGCA_001696685scaffoldncbi489910

GC content

  • @ref: 7944
  • GC-content: 33.5

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes91.945yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no94.969yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes69.038yes
125438spore-formingspore-formingAbility to form endo- or exosporesno78.069no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.158yes
125438motile2+flagellatedAbility to perform flagellated movementno89.304no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes61.8
125439BacteriaNetmotilityAbility to perform movementyes57.7
125439BacteriaNetgram_stainReaction to gram-stainingpositive73
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthaerobe73.2

External links

@ref: 7944

culture collection no.: DSM 19163, CIP 109506, LMG 24060, UCCCB22

straininfo link

  • @ref: 83807
  • straininfo: 302705

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19060087Nosocomiicoccus 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 MSInt J Syst Evol Microbiol10.1099/ijs.0.65753-02008*Environmental Microbiology, Fatty Acids/analysis, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, *Sodium Chloride, Species Specificity, Staphylococcaceae/chemistry/*classification/genetics/*physiology, Wounds and Injuries/therapyGenetics
Genetics34913718Complete Genome Sequences of Two Nosocomiicoccus ampullae Strains and a Growth-Adapted Mutant.Schuster CF, Sommer F, Strommenger B, Werner G, Layer FMicrobiol Resour Announc10.1128/MRA.00747-212021

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7944Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19163)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19163
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
32599Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2881228776041
39787Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7257
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67772Curators of the UCCCBhttps://ucccb.uc.pt/
68382Automatically annotated from API zym
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
83807Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID302705.1StrainInfo: A central database for resolving microbial strain identifiers
116345Curators of the CIPCollection of Institut Pasteur (CIP 109506)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109506
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1