Strain identifier

BacDive ID: 131418

Type strain: Yes

Species: Flavobacterium nitrogenifigens

Strain Designation: NXU-44

Strain history: CIP <- 2015, P. Kämpfer, Giessen Univ., Giessen, Germany: strain NXU-44

NCBI tax ID(s): 1617283 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 22645

BacDive-ID: 131418

DSM-Number: 29982

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

description: Flavobacterium nitrogenifigens NXU-44 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from rhizosphere of switchgrass Panicum virgatum.

NCBI tax id

  • NCBI tax id: 1617283
  • Matching level: species

strain history

@refhistory
22645<- P. Kämpfer, Univ. Giessen, Germany; NXU-44 <- J. McInroy
121312CIP <- 2015, P. Kämpfer, Giessen Univ., Giessen, Germany: strain NXU-44

doi: 10.13145/bacdive131418.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Flavobacterium
  • species: Flavobacterium nitrogenifigens
  • full scientific name: Flavobacterium nitrogenifigens Kämpfer et al. 2015

@ref: 22645

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium nitrogenifigens

full scientific name: Flavobacterium nitrogenifigens Kämpfer et al. 2015

strain designation: NXU-44

type strain: yes

Morphology

cell morphology

  • @ref: 121312
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
42014MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
22645TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yesName: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled waterhttps://mediadive.dsmz.de/medium/545
121312CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
42014positivegrowth30mesophilic
22645positivegrowth28mesophilic

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
22645rhizosphere of switchgrass Panicum virgatumPanicum virgatumAlabama, AuburnUSAUSANorth America
121312Environment, Soil, rhizosphere of switch grassAlabamaUnited States of AmericaUSANorth America1998-01-02

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
226451Risk group (German classification)
1213121Risk group (French classification)

Sequence information

16S sequences

  • @ref: 22645
  • description: Flavobacterium nitrogenifigens strain NXU-44 16S ribosomal RNA gene, partial sequence
  • accession: KP711654
  • length: 1413
  • database: ena
  • NCBI tax ID: 1617283

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium nitrogenifigens DSM 29982GCA_900182675scaffoldncbi1617283
66792Flavobacterium nitrogenifigens NXU-44GCA_003254565contigncbi1617283
66792Flavobacterium nitrogenifigens strain DSM 299821617283.5wgspatric1617283
66792Flavobacterium nitrogenifigens DSM 299822724679792draftimg1617283

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno81.852no
flagellatedno93.635no
gram-positiveno98.441no
anaerobicno99.659no
aerobicyes89.729no
halophileno96.732no
spore-formingno92.431no
thermophileno99.316no
glucose-utilyes92.95no
glucose-fermentno87.045no

External links

@ref: 22645

culture collection no.: DSM 29982, CIP 110894, LMG 28694

straininfo link

  • @ref: 89846
  • straininfo: 396416

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny25994915Flavobacterium nitrogenifigens sp. nov., isolated from switchgrass (Panicum virgatum).Kampfer P, Busse HJ, McInroy JA, Xu J, Glaeser SPInt J Syst Evol Microbiol10.1099/ijs.0.0003302015Alabama, Bacterial Typing Techniques, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Flavobacterium/*classification/genetics/isolation & purification, Molecular Sequence Data, *Nitrogen Fixation, Panicum/*microbiology, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny27357576Flavobacterium panacis sp. nov., isolated from rhizosphere of Panax ginseng.Kim DH, Singh P, Farh Mel-A, Kim YJ, Nguyen NL, Lee HA, Yang DCAntonie Van Leeuwenhoek10.1007/s10482-016-0720-72016Base Composition, Cell Wall/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Flavobacterium/*classification/genetics/*isolation & purification/physiology, Panax/*microbiology, Phosphatidylethanolamines/metabolism, Phosphatidylserines/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhizosphere, Soil Microbiology, Species Specificity, Vitamin K 2/metabolismMetabolism
Phylogeny30111073Flavobacterium amnigenum sp. nov. Isolated from a River.Patil KS, Padakandla SR, Chae JCJ Microbiol Biotechnol10.4014/jmb.1806.060442018Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacterium/chemistry/*classification/genetics, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rivers/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisTranscriptome
Phylogeny31562606Flavobacterium zhairuonensis sp. nov., a gliding bacterium isolated from marine sediment of the East China Sea.Debnath SC, Miyah AMA, Chen C, Sheng H, Xu XW, Wu YH, Zheng DQ, Xu JZ, Di YN, Wang PM, Shen LJ Microbiol10.1007/s12275-019-9194-42019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacterium/*classification/genetics/*isolation & purification/physiology, Genome, Bacterial/genetics, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Nucleic Acid Hybridization, Phosphatidylethanolamines/analysis, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride, Temperature, Vitamin K 2/analogs & derivatives/analysisGenetics

Reference

@idauthorstitledoi/urlcatalogue
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
22645Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29982Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29982)
42014Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/34488
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
89846Reimer, 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-ID396416.1
121312Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110894Collection of Institut Pasteur (CIP 110894)