Strain identifier
BacDive ID: 13655
Type strain:
Species: Gemmobacter nectariphilus
Strain history: Y. Tanaka AST4.
NCBI tax ID(s): 1121271 (strain), 220343 (species)
General
@ref: 5913
BacDive-ID: 13655
DSM-Number: 15620
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Gemmobacter nectariphilus DSM 15620 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1121271 | strain |
220343 | species |
strain history
@ref | history |
---|---|
5913 | <- Y. Tanaka; AST4 |
67770 | Y. Tanaka AST4. |
doi: 10.13145/bacdive13655.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Paracoccaceae
- genus: Gemmobacter
- species: Gemmobacter nectariphilus
- full scientific name: Gemmobacter nectariphilus (Tanaka et al. 2004) Chen et al. 2013
synonyms
@ref synonym 20215 Wagnerdoeblera nectariphila 20215 Catellibacterium nectariphilum
@ref: 5913
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Gemmobacter
species: Gemmobacter nectariphilus
full scientific name: Gemmobacter nectariphilus (Tanaka et al. 2004) Chen et al. 2013
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell shape | motility | cell length | cell width | confidence |
---|---|---|---|---|---|---|
30689 | negative | rod-shaped | no | |||
29963 | negative | rod-shaped | no | 1.65 µm | 0.7 µm | |
69480 | negative | 99.999 |
pigmentation
@ref | production |
---|---|
29963 | no |
30689 | yes |
Culture and growth conditions
culture medium
- @ref: 5913
- name: NPB MEDIUM (DSMZ Medium 995)
- growth: yes
- link: https://mediadive.dsmz.de/medium/995
- composition: Name: NPB MEDIUM (DSMZ Medium 995) Composition: Agar 15.0 g/l Tryptone peptone 10.0 g/l D-Glucose 5.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 1.0 g/l KH2PO4 0.5 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
5913 | positive | growth | 30 | mesophilic |
30689 | positive | growth | 15-40 | |
29963 | positive | growth | 20-37 | |
30689 | positive | optimum | 30 | mesophilic |
29963 | positive | optimum | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
29963 | positive | growth | 06-08 |
30689 | positive | growth | 06-08 |
29963 | positive | optimum | 7 |
30689 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
29963 | aerobe |
30689 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
30689 | no | |
69481 | no | 90 |
69480 | no | 99.995 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30689 | NaCl | positive | growth | 0-2 % |
30689 | NaCl | positive | optimum | 1 % |
29963 | NaCl | positive | optimum | <3 % |
observation
@ref | observation |
---|---|
29963 | aggregates in chains |
67770 | quinones: Q-10 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29963 | 21217 | L-alaninamide | + | carbon source |
29963 | 29987 | glutamate | + | carbon source |
29963 | 28087 | glycogen | + | carbon source |
29963 | 24996 | lactate | + | carbon source |
29963 | 51850 | methyl pyruvate | + | carbon source |
29963 | 17822 | serine | + | carbon source |
29963 | 30031 | succinate | + | carbon source |
29963 | 53426 | tween 80 | + | carbon source |
enzymes
@ref | value | activity | ec |
---|---|---|---|
29963 | catalase | + | 1.11.1.6 |
29963 | cytochrome oxidase | + | 1.9.3.1 |
30689 | alkaline phosphatase | + | 3.1.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
5913 | activated sludge | Kawasaki plant of Ajinomoto Co. | Japan | JPN | Asia |
67770 | Activated sludge | Japan | JPN | Asia |
isolation source categories
- Cat1: #Engineered
- Cat2: #Waste
- Cat3: #Activated sludge
taxonmaps
- @ref: 69479
- File name: preview.99_1629.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_926;97_1078;98_1287;99_1629&stattab=map
- Last taxonomy: Gemmobacter nectariphilus subclade
- 16S sequence: AB101543
- Sequence Identity:
- Total samples: 7825
- soil counts: 639
- aquatic counts: 5101
- animal counts: 1734
- plant counts: 351
Safety information
risk assessment
- @ref: 5913
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 5913
- description: Catellibacterium nectariphilum gene for 16S ribosomal RNA, partial sequence
- accession: AB101543
- length: 1386
- database: ena
- NCBI tax ID: 1121271
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Catellibacterium nectariphilum DSM 15620 | 1121271.3 | wgs | patric | 1121271 |
66792 | Gemmobacter nectariphilus DSM 15620 | 2524614723 | draft | img | 1121271 |
67770 | Gemmobacter nectariphilus DSM 15620 | GCA_000429765 | scaffold | ncbi | 1121271 |
GC content
@ref | GC-content | method |
---|---|---|
5913 | 64.5 | |
67770 | 64.5 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 90 | no |
motile | no | 68.043 | no |
flagellated | no | 92.52 | no |
gram-positive | no | 98.217 | yes |
anaerobic | no | 98.401 | no |
aerobic | yes | 84.759 | no |
halophile | no | 65.349 | yes |
spore-forming | no | 96.429 | no |
thermophile | no | 94.529 | yes |
glucose-util | yes | 58.236 | no |
glucose-ferment | no | 88.778 | no |
External links
@ref: 5913
culture collection no.: DSM 15620, JCM 11959, NBRC 100046, AST 4, CGMCC 1.8899, CGMCC 1.8904
straininfo link
- @ref: 82838
- straininfo: 132013
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 15143049 | Catellibacterium nectariphilum gen. nov., sp. nov., which requires a diffusible compound from a strain related to the genus Sphingomonas for vigorous growth. | Tanaka Y, Hanada S, Manome A, Tsuchida T, Kurane R, Nakamura K, Kamagata Y | Int J Syst Evol Microbiol | 10.1099/ijs.0.02750-0 | 2004 | Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Microscopy, Electron, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/growth & development/*metabolism, Sewage/microbiology, Sphingomonas/*metabolism | Genetics |
Phylogeny | 19820000 | Catellibacterium aquatile sp. nov., isolated from fresh water, and emended description of the genus Catellibacterium Tanaka et al. 2004. | Liu Y, Xu CJ, Jiang JT, Liu YH, Song XF, Li H, Liu ZP | Int J Syst Evol Microbiol | 10.1099/ijs.0.017632-0 | 2009 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fresh Water/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/metabolism, Sodium Chloride/metabolism | Genetics |
Phylogeny | 22493172 | Description of Gemmobacter fontiphilus sp. nov., isolated from a freshwater spring, reclassification of Catellibacterium nectariphilum as Gemmobacter nectariphilus comb. nov., Catellibacterium changlense as Gemmobacter changlensis comb. nov., Catellibacterium aquatile as Gemmobacter aquaticus nom. nov., Catellibacterium caeni as Gemmobacter caeni comb. nov., Catellibacterium nanjingense as Gemmobacter nanjingensis comb. nov., and emended description of the genus Gemmobacter and of Gemmobacter aquatilis. | Chen WM, Cho NT, Huang WC, Young CC, Sheu SY | Int J Syst Evol Microbiol | 10.1099/ijs.0.042051-0 | 2012 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Natural Springs/*microbiology, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Taiwan | Genetics |
Phylogeny | 24014623 | Gemmobacter megaterium sp. nov., isolated from coastal planktonic seaweeds. | Liu JJ, Zhang XQ, Chi FT, Pan J, Sun C, Wu M | Int J Syst Evol Microbiol | 10.1099/ijs.0.050955-0 | 2013 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater, Seaweed/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Genetics |
Phylogeny | 29022543 | Gemmobacter straminiformis sp. nov., isolated from an artificial fountain. | Kang JY, Kim MJ, Chun J, Son KP, Jahng KY | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002403 | 2017 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/chemistry, *Water Microbiology | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
5913 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15620) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15620 | |||
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 | |||
29963 | 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 | 26332 | 28776041 | |
30689 | 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 | 27020 | 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) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
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 | |||
82838 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID132013.1 | StrainInfo: A central database for resolving microbial strain identifiers |