Strain identifier
BacDive ID: 131418
Type strain: 
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)
version 9.3 (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
| @ref | history |
|---|---|
| 22645 | <- P. Kämpfer, Univ. Giessen, Germany; NXU-44 <- J. McInroy |
| 121312 | CIP <- 2015, P. Kämpfer, Giessen Univ., Giessen, Germany: strain NXU-44 |
doi: 10.13145/bacdive131418.20250331.9.3
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 | gram stain | confidence | motility | cell shape |
|---|---|---|---|---|
| 125439 | negative | 99.6 | ||
| 125438 | 90.5 | no | ||
| 125438 | negative | 96.727 | ||
| 121312 | negative | no | rod-shaped |
Culture and growth conditions
culture medium
| @ref | name | growth | composition | link |
|---|---|---|---|---|
| 42014 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
| 22645 | TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) | yes | Name: 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 water | https://mediadive.dsmz.de/medium/545 |
| 121312 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 42014 | positive | growth | 30 |
| 22645 | positive | growth | 28 |
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: aerobe
- confidence: 93.8
spore formation
- @ref: 125439
- spore formation: no
- confidence: 99.2
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent | isolation date |
|---|---|---|---|---|---|---|---|
| 22645 | rhizosphere of switchgrass Panicum virgatum | Panicum virgatum | Alabama, Auburn | USA | USA | North America | |
| 121312 | Environment, Soil, rhizosphere of switch grass | Alabama | United States of America | USA | North America | 1998-01-02 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Rhizosphere |
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 22645 | 1 | Risk group (German classification) |
| 121312 | 1 | Risk 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: nuccore
- NCBI tax ID: 1617283
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Flavobacterium nitrogenifigens DSM 29982 | GCA_900182675 | scaffold | ncbi | 1617283 |
| 66792 | Flavobacterium nitrogenifigens NXU-44 | GCA_003254565 | contig | ncbi | 1617283 |
| 66792 | Flavobacterium nitrogenifigens strain DSM 29982 | 1617283.5 | wgs | patric | 1617283 |
| 66792 | Flavobacterium nitrogenifigens DSM 29982 | 2724679792 | draft | img | 1617283 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 96.727 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 97.064 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 86.408 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 84.904 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 98.924 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 90.5 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 99.2 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 67.2 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 99.6 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | aerobe | 93.8 |
External links
@ref: 22645
culture collection no.: DSM 29982, CIP 110894, LMG 28694
straininfo link
- @ref: 89846
- straininfo: 396416
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 25994915 | Flavobacterium nitrogenifigens sp. nov., isolated from switchgrass (Panicum virgatum). | Kampfer P, Busse HJ, McInroy JA, Xu J, Glaeser SP | Int J Syst Evol Microbiol | 10.1099/ijs.0.000330 | 2015 | Alabama, 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/chemistry | Genetics |
| Phylogeny | 27357576 | Flavobacterium panacis sp. nov., isolated from rhizosphere of Panax ginseng. | Kim DH, Singh P, Farh Mel-A, Kim YJ, Nguyen NL, Lee HA, Yang DC | Antonie Van Leeuwenhoek | 10.1007/s10482-016-0720-7 | 2016 | Base 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/metabolism | Metabolism |
| Phylogeny | 30111073 | Flavobacterium amnigenum sp. nov. Isolated from a River. | Patil KS, Padakandla SR, Chae JC | J Microbiol Biotechnol | 10.4014/jmb.1806.06044 | 2018 | Base 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/analysis | Transcriptome |
| Phylogeny | 31562606 | Flavobacterium 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 L | J Microbiol | 10.1007/s12275-019-9194-4 | 2019 | Bacterial 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/analysis | Genetics |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |
| 22645 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29982 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29982) | |
| 42014 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/34488 | ||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 89846 | Reimer, 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 identifiers | 10.60712/SI-ID396416.1 | |
| 121312 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110894 | Collection of Institut Pasteur (CIP 110894) | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |