Strain identifier

BacDive ID: 10492

Type strain: Yes

Species: Neisseria bacilliformis

Strain history: <- CCUG; CCUG 50858 <- X. Y. Han, Univ. Texas; MDA2833

NCBI tax ID(s): 267212 (species)

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General

@ref: 16803

BacDive-ID: 10492

DSM-Number: 23338

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-negative

description: Neisseria bacilliformis DSM 23338 is a microaerophile, mesophilic, Gram-negative bacterium that was isolated from submandibular wound of a 53-year-old man.

NCBI tax id

  • NCBI tax id: 267212
  • Matching level: species

strain history

  • @ref: 16803
  • history: <- CCUG; CCUG 50858 <- X. Y. Han, Univ. Texas; MDA2833

doi: 10.13145/bacdive10492.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Neisseriales
  • family: Neisseriaceae
  • genus: Neisseria
  • species: Neisseria bacilliformis
  • full scientific name: Neisseria bacilliformis Han et al. 2006

@ref: 16803

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Neisseriales

family: Neisseriaceae

genus: Neisseria

species: Neisseria bacilliformis

full scientific name: Neisseria bacilliformis Han et al. 2006

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.985

colony morphology

  • @ref: 16803
  • type of hemolysis: gamma

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16803BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
16803COLUMBIA 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

culture temp

@refgrowthtypetemperaturerange
16803positivegrowth37mesophilic
59021positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
16803microaerophile
59021microaerophile

spore formation

@refspore formationconfidence
69481no96
69480no99.998

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6837715824D-fructose-builds acid from
6837717306maltose-builds acid from
6837717992sucrose-builds acid from
6837718257ornithine-degradation
6837716199urea-hydrolysis
6837727897tryptophan-energy source

metabolite production

  • @ref: 68377
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68377
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
16803catalase-1.11.1.6
16803cytochrome-c oxidase+1.9.3.1
68377tryptophan deaminase-4.1.99.1
68377proline-arylamidase+3.4.11.5
68377alkaline phosphatase-3.1.3.1
68377urease-3.5.1.5
68377ornithine decarboxylase-4.1.1.17

API NH

@refPENGLUFRUMALSACODCURELIPPALbeta GALProAGGTIND
16803-+-----+/---++-
16803+--------++--
16803-+--------++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudesampling date
16803submandibular wound of a 53-year-old manTexas, HoustonUSAUSANorth America29.7499-95.3584
59021Human wound,53-yr-old man,submandibular,carcinomaTX,HoustonUSAUSANorth America2003

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body-Site#Oral cavity and airways
#Host Body-Site#Other#Wound
#Host#Human#Male

taxonmaps

  • @ref: 69479
  • File name: preview.99_3733.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15355;96_1209;97_2312;98_2851;99_3733&stattab=map
  • Last taxonomy: Kingella
  • 16S sequence: AY560519
  • Sequence Identity:
  • Total samples: 22798
  • soil counts: 389
  • aquatic counts: 782
  • animal counts: 21492
  • plant counts: 135

Safety information

risk assessment

  • @ref: 16803
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16803
  • description: Neisseria bacilliformis 16S ribosomal RNA gene, partial sequence
  • accession: AY560519
  • length: 1489
  • database: ena
  • NCBI tax ID: 888742

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Neisseria bacilliformis DSM 23338GCA_014055025completencbi267212
66792Neisseria bacilliformis ATCC BAA-1200888742.3wgspatric888742
66792Neisseria bacilliformis strain DSM 23338267212.13completepatric267212

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno96no
motileno88.144no
flagellatedno95.157no
gram-positiveno98.419no
anaerobicno97.52yes
aerobicno95.334yes
halophileno76.819no
spore-formingno97.404no
thermophileno98.381yes
glucose-utilno50.683no
glucose-fermentno89.059no

External links

@ref: 16803

culture collection no.: DSM 23338, ATCC BAA 1200, CCUG 50858, MDA 2833

straininfo link

  • @ref: 79769
  • straininfo: 214792

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16455901Neisseria bacilliformis sp. nov. isolated from human infections.Han XY, Hong T, Falsen EJ Clin Microbiol10.1128/JCM.44.2.474-479.20062006Bacterial Typing Techniques, Culture Media, DNA, Bacterial/analysis, DNA, Ribosomal, Fatty Acids/analysis, Genes, rRNA, Humans, Molecular Sequence Data, Neisseria/*classification/genetics/*isolation & purification/physiology, Neisseriaceae Infections/*microbiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Sequence Analysis, DNA, Species SpecificityCultivation
Phylogeny36309905Kingella pumchi sp. nov., an organism isolated from human vertebral puncture tissue.Xiao M, Liu R, Du J, Liu R, Zhai L, Wang H, Yao S, Xu YCAntonie Van Leeuwenhoek10.1007/s10482-022-01786-w2022

Reference

@idauthorscataloguedoi/urltitle
16803Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23338)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23338
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
59021Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 50858)https://www.ccug.se/strain?id=50858
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)
68377Automatically annotated from API NH
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
79769Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID214792.1StrainInfo: A central database for resolving microbial strain identifiers