Strain identifier

BacDive ID: 24269

Type strain: Yes

Species: Noviherbaspirillum massiliense

Strain Designation: JC206

Strain history: <- J.-C. Lagier, Timone Hospital, Marseille, France; JC206

NCBI tax ID(s): 1465823 (species)

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General

@ref: 20983

BacDive-ID: 24269

DSM-Number: 25712

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile, rod-shaped

description: Noviherbaspirillum massiliense JC206 is an aerobe, mesophilic, motile bacterium that was isolated from human faeces of a healthy patient.

NCBI tax id

  • NCBI tax id: 1465823
  • Matching level: species

strain history

  • @ref: 20983
  • history: <- J.-C. Lagier, Timone Hospital, Marseille, France; JC206

doi: 10.13145/bacdive24269.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Oxalobacteraceae
  • genus: Noviherbaspirillum
  • species: Noviherbaspirillum massiliense
  • full scientific name: Noviherbaspirillum massiliense (Lagier et al. 2014) Chaudhary and Kim 2017

  • synonyms

    @refsynonym
    20215Herbaspirillum massiliense
    20215Noviherbaspirillum massiliense

@ref: 20983

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Noviherbaspirillum

species: Noviherbaspirillum massiliense

full scientific name: Noviherbaspirillum massiliense (Lagier et al. 2014) Chaudhary and Kim 2017

strain designation: JC206

type strain: yes

Morphology

cell morphology

  • @ref: 43245
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: polar

multimedia

  • @ref: 20983
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_25712.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43245Reasoner's 2A agar (R2A)yes
43245nutritient agar (NA)yes
43245trypticase soy agar (TSA)no
20983COLUMBIA BLOOD AGAR (DSMZ Medium 429)yeshttps://mediadive.dsmz.de/medium/429Name: COLUMBIA BLOOD AGAR (DSMZ Medium 429) Composition: Horse blood 40.0 g/l Columbia agar base

culture temp

@refgrowthtypetemperaturerange
20983positivegrowth37mesophilic
43245positiveoptimum37mesophilic
43245positivegrowth30-37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 43245
  • oxygen tolerance: aerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
432454853esculin+hydrolysis
4324517632nitrate-reduction
4324530089acetate+carbon source
4324517968butyrate+carbon source
4324530031succinate+carbon source
4324515361pyruvate-carbon source
4324528757fructose-growth
4324528260galactose-growth
4324517234glucose-growth
4324517716lactose-growth
4324517306maltose-growth
4324537684mannose-growth
4324530911sorbitol-growth
4324526546rhamnose-growth
4324518222xylose-growth
4324524265gluconate-growth
4324528885butanol-growth
4324516236ethanol-growth
4324517754glycerol-growth

metabolite production

  • @ref: 43245
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43245catalase+1.11.1.6
43245cytochrome oxidase+1.9.3.1
43245arginine dihydrolase+3.5.3.6

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
20983human faeces of a healthy patientSenegalSENAfrica
43245faecal flora of a healthy patientSenegalSENAfrica

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_8163.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_3405;97_4628;98_5941;99_8163&stattab=map
  • Last taxonomy: Noviherbaspirillum massiliense subclade
  • 16S sequence: JN657219
  • Sequence Identity:
  • Total samples: 1153
  • soil counts: 253
  • aquatic counts: 140
  • animal counts: 716
  • plant counts: 44

Safety information

risk assessment

  • @ref: 20983
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20983
  • description: Herbaspirillum massiliense JC206 16S ribosomal RNA gene, partial sequence
  • accession: JN657219
  • length: 1489
  • database: ena
  • NCBI tax ID: 1095769

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Noviherbaspirillum massiliense JC206GCA_000312045scaffoldncbi1095769
66792Noviherbaspirillum massiliense JC2062547132156draftimg1095769

GC content

@refGC-contentmethod
2098359.73sequence analysis
4324559.73genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes88.043yes
flagellatedyes80.194yes
gram-positiveno98.905no
anaerobicno97.384no
aerobicyes72.43no
halophileno92.227no
spore-formingno93.13no
glucose-utilno75.601yes
thermophileno93.316no
glucose-fermentno89.296no

External links

@ref: 20983

culture collection no.: DSM 25712, CSUR P159

straininfo link

  • @ref: 88210
  • straininfo: 402288

literature

topicPubmed-IDtitleauthorsjournalDOIyeartopic2mesh
Genetics23407294Non-contiguous finished genome sequence and description of Herbaspirillum massiliense sp. nov.Lagier JC, Gimenez G, Robert C, Raoult D, Fournier PEStand Genomic Sci10.4056/sigs.30864742012Phylogeny
Phylogeny27995870Noviherbaspirillum agri sp. nov., isolated from reclaimed grassland soil, and reclassification of Herbaspirillum massiliense (Lagier et al., 2014) as Noviherbaspirillum massiliense comb. nov.Chaudhary DK, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0017472017TranscriptomeBacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Grassland, Herbaspirillum/genetics, Nepal, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry
Phylogeny28629495Noviherbaspirillum denitrificans sp. nov., a denitrifying bacterium isolated from rice paddy soil and Noviherbaspirillum autotrophicum sp. nov., a denitrifying, facultatively autotrophic bacterium isolated from rice paddy soil and proposal to reclassify Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov.Ishii S, Ashida N, Ohno H, Segawa T, Yabe S, Otsuka S, Yokota A, Senoo KInt J Syst Evol Microbiol10.1099/ijsem.0.0018752017TranscriptomeBacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Denitrification, Fatty Acids/chemistry, Herbaspirillum/*classification/genetics/isolation & purification, *Oryza, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology
Phylogeny33063170Noviherbaspirillum galbum sp. nov., a bacterium isolated from soil.Park Y, Maeng S, Lee SE, Han JH, Lee YK, Oh J, Jigden B, Kang JH, Kim MKArch Microbiol10.1007/s00203-020-02076-72020Fatty Acids, Oxalobacteraceae/*classification/genetics, Phospholipids, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Soil Microbiology, Species Specificity
Phylogeny33164727Noviherbaspirillum aerium sp. nov., isolated from air.Xue H, Piao CG, Lin YH, Bian DR, Li YInt J Syst Evol Microbiol10.1099/ijsem.0.0045372020Transcriptome*Air Microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Oxalobacteraceae/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, Pigmentation, Putrescine/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry
Phylogeny33787987Noviherbaspirillum pedocola sp. nov., isolated from oil-contaminated experimental soil.Chaudhary DK, Dahal RH, Hong YArch Microbiol10.1007/s00203-021-02295-62021TranscriptomeBacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, *Oxalobacteraceae/classification/genetics, *Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/chemistry, *Soil Microbiology, Species Specificity

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
20983Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-25712Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25712)
43245Satoshi Ishii, Naoaki Ashida, Hiroki Ohno, Takahiro Segawa, Shuhei Yabe, Shigeto Otsuka, Akira Yokota, Keishi SenooNoviherbaspirillum denitrificans sp. nov., a denitrifying bacterium isolated from rice paddy soil and Noviherbaspirillum autotrophicum sp. nov., a denitrifying, facultatively autotrophic bacterium isolated from rice paddy soil and proposal to reclassify Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov.10.1099/ijsem.0.001875IJSEM 67: 1841-1848 201728629495
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
88210Reimer, 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 identifiers10.60712/SI-ID402288.1