Strain identifier

BacDive ID: 17206

Type strain: Yes

Species: Negativicoccus succinicivorans

Strain history: CIP <- 2008, J.P. Carlier, Inst. Pasteur, Paris, France <- H. Jean-Pierre, Montpellier Hosp., Montpellier, France: strain AIP 149.07

NCBI tax ID(s): 620903 (species)

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General

@ref: 15594

BacDive-ID: 17206

DSM-Number: 21255

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, coccus-shaped, human pathogen

description: Negativicoccus succinicivorans DSM 21255 is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from human toe wound.

NCBI tax id

  • NCBI tax id: 620903
  • Matching level: species

strain history

@refhistory
15594<- J.-P. Carlier; AIP 149.07 {2008} <- H. Jean-Pierre; ADV 07/08/06-B-1388
123366CIP <- 2008, J.P. Carlier, Inst. Pasteur, Paris, France <- H. Jean-Pierre, Montpellier Hosp., Montpellier, France: strain AIP 149.07

doi: 10.13145/bacdive17206.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Negativicutes
  • order: Veillonellales
  • family: Veillonellaceae
  • genus: Negativicoccus
  • species: Negativicoccus succinicivorans
  • full scientific name: Negativicoccus succinicivorans Marchandin et al. 2010

@ref: 15594

domain: Bacteria

phylum: Firmicutes

class: Negativicutes

order: Selenomonadales

family: Veillonellaceae

genus: Negativicoccus

species: Negativicoccus succinicivorans

full scientific name: Negativicoccus succinicivorans Marchandin et al. 2010

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotility
29435negative0.4 µmcoccus-shapedno
123366negativecoccus-shapedno

colony morphology

  • @ref: 60825
  • incubation period: 2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15594COLUMBIA 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
15594CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
33327MEDIUM 704 - for AcidaminococcaceaeyesDistilled water make up to (1000.000 ml);Glucose (5.000 g);Yeast extract(20.000 g);Succinic acid (13.500 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);Hemin solution - M00149 (25.000 ml)
123366CIP Medium 704yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=704

culture temp

@refgrowthtypetemperaturerange
15594positivegrowth37mesophilic
33327positivegrowth37mesophilic
60825positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
15594anaerobe
29435anaerobe
60825anaerobe
123366microaerophile

spore formation

  • @ref: 29435
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12336617632nitrate-reduction
12336616301nitrite-reduction

metabolite production

  • @ref: 123366
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29435alkaline phosphatase+3.1.3.1
123366catalase-1.11.1.6
123366urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic location
15594human toe woundFranceFRAEurope
60825Human wound,toeFranceFRAEurope2006-08-09Montpellier
123366Human, ToeFranceFRAEuropeMontpellier

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body-Site#Other#Wound
#Host Body-Site#Limb#Foot

taxonmaps

  • @ref: 69479
  • File name: preview.99_2337.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_314;96_1263;97_1498;98_1824;99_2337&stattab=map
  • Last taxonomy: Negativicoccus
  • 16S sequence: FJ715930
  • Sequence Identity:
  • Total samples: 48341
  • soil counts: 894
  • aquatic counts: 1038
  • animal counts: 46229
  • plant counts: 180

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
15594yes, in single cases1Risk group (German classification)
1233661Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15594
  • description: Negativicoccus succinicivorans strain ADV 07/08/06-B-1388 16S ribosomal RNA gene, partial sequence
  • accession: FJ715930
  • length: 1401
  • database: ena
  • NCBI tax ID: 620903

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Negativicoccus succinicivorans DSM 21255GCA_014207605scaffoldncbi620903
66792Negativicoccus succinicivorans strain DSM 21255620903.10wgspatric620903
66792Negativicoccus succinicivorans DSM 212552861593547draftimg620903

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno98.214yes
gram-positiveno94.68yes
anaerobicyes98.264yes
aerobicno96.231no
halophileno70.107no
spore-formingno93.745yes
glucose-utilyes57.568no
thermophileno97.115yes
motileno93.571no
glucose-fermentno65.72no

External links

@ref: 15594

culture collection no.: DSM 21255, CCUG 56017, CIP 109806, ADV 07/08/06-B-1388, AIP 149.07

straininfo link

  • @ref: 86205
  • straininfo: 370213

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19667386Negativicoccus succinicivorans gen. nov., sp. nov., isolated from human clinical samples, emended description of the family Veillonellaceae and description of Negativicutes classis nov., Selenomonadales ord. nov. and Acidaminococcaceae fam. nov. in the bacterial phylum Firmicutes.Marchandin H, Teyssier C, Campos J, Jean-Pierre H, Roger F, Gay B, Carlier JP, Jumas-Bilak EInt J Syst Evol Microbiol10.1099/ijs.0.013102-02009Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Gram-Negative Bacteria/classification/genetics, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Veillonellaceae/classification/*genetics/isolation & purificationPathogenicity
Phylogeny32303967Draft genome and description of Negativicoccus massiliensis strain Marseille-P2082, a new species isolated from the gut microbiota of an obese patient.Togo AH, Diop A, Tall ML, Million M, Khelaifia S, Maraninchi M, Raoult D, Fournier PE, Dubourg GAntonie Van Leeuwenhoek10.1007/s10482-020-01414-52020Adult, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Feces/microbiology, Female, *Gastrointestinal Microbiome, Genes, Bacterial/genetics, Genome, Bacterial, Genomics, Humans, *Obesity, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Veillonellaceae/*classification/genetics/*isolation & purification/physiologyGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15594Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21255)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21255
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
29435Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2584128776041
33327Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7590
60825Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56017)https://www.ccug.se/strain?id=56017
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)
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
86205Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID370213.1StrainInfo: A central database for resolving microbial strain identifiers
123366Curators of the CIPCollection of Institut Pasteur (CIP 109806)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109806