Strain identifier
BacDive ID: 14130
Type strain: 
Species: Sphingobacterium alimentarium
Strain history: <- S. Scherer, Research Center for Nutrition and Food Sci. (ZIEL), TU Munich, GERMANY; WCC4521 <- V. Schmidt
NCBI tax ID(s): 797292 (species)
version 8.1 (current version)
General
@ref: 16184
BacDive-ID: 14130
DSM-Number: 22362
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Sphingobacterium alimentarium DSM 22362 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from dairy environment.
NCBI tax id
- NCBI tax id: 797292
- Matching level: species
strain history
- @ref: 16184
- history: <- S. Scherer, Research Center for Nutrition and Food Sci. (ZIEL), TU Munich, GERMANY; WCC4521 <- V. Schmidt
doi: 10.13145/bacdive14130.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Sphingobacteriia
- order: Sphingobacteriales
- family: Sphingobacteriaceae
- genus: Sphingobacterium
- species: Sphingobacterium alimentarium
- full scientific name: Sphingobacterium alimentarium Schmidt et al. 2012
@ref: 16184
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Sphingobacterium
species: Sphingobacterium alimentarium
full scientific name: Sphingobacterium alimentarium Schmidt et al. 2012
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 30447 | negative | 1.75 µm | 0.8 µm | rod-shaped | no | |
| 69480 | no | 92.513 | ||||
| 69480 | negative | 99.995 |
pigmentation
- @ref: 30447
- production: yes
Culture and growth conditions
culture medium
- @ref: 16184
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 16184 | positive | growth | 28 | mesophilic |
| 30447 | positive | growth | 10-41 |
culture pH
- @ref: 30447
- ability: positive
- type: growth
- pH: 06-09
- PH range: alkaliphile
Physiology and metabolism
oxygen tolerance
- @ref: 30447
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 30447 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.999 |
halophily
- @ref: 30447
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-3 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 30447 | 17057 | cellobiose | + | carbon source |
| 30447 | 28757 | fructose | + | carbon source |
| 30447 | 17234 | glucose | + | carbon source |
| 30447 | 28087 | glycogen | + | carbon source |
| 30447 | 17716 | lactose | + | carbon source |
| 30447 | 17306 | maltose | + | carbon source |
| 30447 | 37684 | mannose | + | carbon source |
| 30447 | 28053 | melibiose | + | carbon source |
| 30447 | 506227 | N-acetylglucosamine | + | carbon source |
| 30447 | 16634 | raffinose | + | carbon source |
| 30447 | 17814 | salicin | + | carbon source |
| 30447 | 17992 | sucrose | + | carbon source |
| 30447 | 27082 | trehalose | + | carbon source |
| 30447 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 30447 | catalase | + | 1.11.1.6 |
| 30447 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
- @ref: 16184
- sample type: dairy environment
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
- Cat1: #Engineered
- Cat2: #Food production
- Cat3: #Dairy product
taxonmaps
- @ref: 69479
- File name: preview.99_8328.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15366;96_3821;97_4714;98_6061;99_8328&stattab=map
- Last taxonomy: Sphingobacterium alimentarium subclade
- 16S sequence: FN908502
- Sequence Identity:
- Total samples: 14527
- soil counts: 2932
- aquatic counts: 3015
- animal counts: 7572
- plant counts: 1008
Safety information
risk assessment
- @ref: 16184
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16184
- description: Sphingobacterium alimentarium partial 16S rRNA gene, strain DSM 22362
- accession: FN908502
- length: 1492
- database: ena
- NCBI tax ID: 797292
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sphingobacterium alimentarium DSM 22362 | GCA_004342685 | contig | ncbi | 797292 |
| 66792 | Sphingobacterium alimentarium strain DSM 22362 | 797292.3 | wgs | patric | 797292 |
| 66792 | Sphingobacterium alimentarium DSM 22362 | 2791354870 | draft | img | 797292 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 16184 | 39.3 | high performance liquid chromatography (HPLC) |
| 30447 | 39.3 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 91.742 | yes |
| flagellated | no | 96.845 | yes |
| gram-positive | no | 97.8 | yes |
| anaerobic | no | 98.866 | yes |
| halophile | no | 92.833 | no |
| spore-forming | no | 95.569 | yes |
| thermophile | no | 99.432 | yes |
| glucose-util | yes | 87.556 | yes |
| aerobic | yes | 88.13 | yes |
| glucose-ferment | no | 90.966 | no |
External links
@ref: 16184
culture collection no.: DSM 22362, LMG 25273, WCC 4521
straininfo link
- @ref: 83295
- straininfo: 361451
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21856986 | Sphingobacterium lactis sp. nov. and Sphingobacterium alimentarium sp. nov., isolated from raw milk and a dairy environment. | Schmidt VSJ, Wenning M, Scherer S | Int J Syst Evol Microbiol | 10.1099/ijs.0.036327-0 | 2011 | Animals, Bacterial Typing Techniques, Base Composition, Chaperonin 60/genetics, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Environmental Microbiology, Fatty Acids/analysis, Milk/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingobacterium/*classification/genetics/*isolation & purification | Genetics |
| Phylogeny | 22904214 | Sphingobacterium thermophilum sp. nov., of the phylum Bacteroidetes, isolated from compost. | Yabe S, Aiba Y, Sakai Y, Hazaka M, Kawahara K, Yokota A | Int J Syst Evol Microbiol | 10.1099/ijs.0.042481-0 | 2012 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Japan, Manure/microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purification | Genetics |
| Phylogeny | 26303282 | Sphingobacterium rhinocerotis sp. nov., isolated from the faeces of Rhinoceros unicornis. | Li GD, Chen X, Li QY, Xu FJ, Qiu SM, Jiang Y, Jiang CL | Antonie Van Leeuwenhoek | 10.1007/s10482-015-0563-7 | 2015 | Animals, Feces/*microbiology, Lipid Metabolism, Perissodactyla/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sphingobacterium/*classification/genetics/isolation & purification/metabolism | Metabolism |
| Phylogeny | 29388539 | Sphingobacterium bovisgrunnientis sp. nov., isolated from yak milk. | Kaur M, Singh H, Sharma S, Mishra S, Tanuku NRS, Pinnaka AK | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002562 | 2018 | Animals, Bacterial Typing Techniques, Base Composition, Cattle/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Milk/*microbiology, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingobacterium/*classification/genetics/isolation & purification | Transcriptome |
| Phylogeny | 32048984 | Sphingobacterium cavernae sp. nov., a novel bacterium isolated from soil sampled at Tiandong Cave. | Zhou XK, Huang Y, Li M, Zhang XF, Wei YQ, Cha QY, Zhang TK, Wang XJ, Liu JJ, Liu ZY, Qin SC, Mo MH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004044 | 2020 | Bacterial Typing Techniques, Base Composition, Caves/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingobacterium/*classification/isolation & purification, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 16184 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22362) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22362 | ||||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
| 30447 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 26782 | 28776041 | ||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 69479 | João 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 | ||||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
| 83295 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID361451.1 | StrainInfo: A central database for resolving microbial strain identifiers |