Strain identifier
BacDive ID: 158547
Type strain:
Species: Ruegeria marisrubri
Strain Designation: ZGT118
Strain history: U. Stingl ZGT118.
NCBI tax ID(s): 1685379 (species)
General
@ref: 65241
BacDive-ID: 158547
keywords: genome sequence, 16S sequence, Bacteria, aerobe, moderately halophilic, Gram-negative, rod-shaped, colony-forming
description: Ruegeria marisrubri ZGT118 is an aerobe, moderately halophilic, Gram-negative bacterium that forms circular colonies and was isolated from water sample.
NCBI tax id
- NCBI tax id: 1685379
- Matching level: species
strain history
- @ref: 67770
- history: U. Stingl ZGT118.
doi: 10.13145/bacdive158547.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Ruegeria
- species: Ruegeria marisrubri
- full scientific name: Ruegeria marisrubri Zhang et al. 2017
@ref: 65241
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Ruegeria
species: Ruegeria marisrubri
strain designation: ZGT118
type strain: yes
Morphology
cell morphology
- @ref: 65241
- gram stain: negative
- cell length: 2.0-5.0 µm
- cell width: 0.6-1.2 µm
- cell shape: rod-shaped
- motility: no
colony morphology
- @ref: 65241
- colony size: 3 mm
- colony color: beige
- colony shape: circular
- incubation period: 3 days
- medium used: marine agar
Culture and growth conditions
culture medium
@ref | name | growth |
---|---|---|
65241 | Marine agar (MA) | yes |
65241 | tryptic soy agar | no |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
65241 | positive | growth | 20-50 | |
65241 | positive | optimum | 37-40 | |
67770 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
65241 | positive | growth | 6-8.5 | alkaliphile |
65241 | positive | optimum | 7-7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 65241
- oxygen tolerance: aerobe
spore formation
- @ref: 65241
- spore formation: no
halophily
@ref | halophily level | salt | growth | tested relation | concentration |
---|---|---|---|---|---|
65241 | moderately halophilic | NaCl | positive | growth | 0.5-2.6 M |
65241 | moderately halophilic | NaCl | positive | optimum | 1.5-2.0 M |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
65241 | 16651 | (S)-lactate | - | carbon source |
65241 | 1 % sodium lactate | + | carbon source | |
65241 | 16763 | 2-oxobutanoate | + | carbon source |
65241 | 30916 | 2-oxoglutarate | - | carbon source |
65241 | 37054 | 3-hydroxybutyrate | - | carbon source |
65241 | 73918 | 3-O-methyl-D-glucose | - | carbon source |
65241 | 18101 | 4-hydroxyphenylacetic acid | - | carbon source |
65241 | 30089 | acetate | - | assimilation |
65241 | 30089 | acetate | - | carbon source |
65241 | 13705 | acetoacetate | - | carbon source |
65241 | 17925 | alpha-D-glucose | + | carbon source |
65241 | 36219 | alpha-lactose | + | carbon source |
65241 | 64552 | 2-hydroxybutyrate | + | carbon source |
65241 | 161680 | aztreonam | - | carbon source |
65241 | 73706 | bromosuccinate | - | carbon source |
65241 | casein | + | assimilation | |
65241 | 16947 | citrate | - | carbon source |
65241 | 18333 | D-arabitol | + | carbon source |
65241 | 29990 | D-aspartate | - | carbon source |
65241 | 17057 | cellobiose | + | carbon source |
65241 | 15824 | D-fructose | + | carbon source |
65241 | 78697 | D-fructose 6-phosphate | + | carbon source |
65241 | 28847 | D-fucose | - | carbon source |
65241 | 12936 | D-galactose | - | carbon source |
65241 | 18024 | D-galacturonic acid | - | carbon source |
65241 | 14314 | D-glucose 6-phosphate | - | carbon source |
65241 | 15748 | D-glucuronate | - | carbon source |
65241 | 15748 | D-glucuronate | + | carbon source |
65241 | 15588 | D-malate | - | carbon source |
65241 | 17306 | maltose | + | carbon source |
65241 | 16899 | D-mannitol | - | carbon source |
65241 | 16024 | D-mannose | + | carbon source |
65241 | 28053 | melibiose | + | carbon source |
65241 | 16634 | raffinose | + | carbon source |
65241 | 33801 | D-saccharate | - | carbon source |
65241 | 16523 | D-serine | - | carbon source |
65241 | 16523 | D-serine | + | carbon source |
65241 | 17924 | D-sorbitol | - | carbon source |
65241 | 16551 | D-trehalose | - | carbon source |
65241 | 32528 | turanose | - | carbon source |
65241 | 23652 | dextrin | + | carbon source |
65241 | 15740 | formate | - | carbon source |
65241 | 71321 | fusidate | + | carbon source |
65241 | 16537 | galactarate | - | carbon source |
65241 | 16865 | gamma-aminobutyric acid | + | carbon source |
65241 | 5291 | gelatin | - | carbon source |
65241 | 5291 | gelatin | + | assimilation |
65241 | 28066 | gentiobiose | + | carbon source |
65241 | 32323 | glucuronamide | - | carbon source |
65241 | 17754 | glycerol | + | carbon source |
65241 | 70744 | glycine-proline | + | carbon source |
65241 | 17596 | inosine | - | carbon source |
65241 | 16977 | L-alanine | - | carbon source |
65241 | 16467 | L-arginine | + | carbon source |
65241 | 29991 | L-aspartate | + | carbon source |
65241 | 18287 | L-fucose | - | carbon source |
65241 | 17464 | L-galactonic acid gamma-lactone | + | carbon source |
65241 | 29985 | L-glutamate | + | carbon source |
65241 | 15971 | L-histidine | - | carbon source |
65241 | 15589 | L-malate | - | carbon source |
65241 | 18183 | L-pyroglutamic acid | - | carbon source |
65241 | 62345 | L-rhamnose | - | carbon source |
65241 | 17115 | L-serine | + | carbon source |
65241 | 48607 | lithium chloride | - | carbon source |
65241 | 74611 | methyl (R)-lactate | + | carbon source |
65241 | 320055 | methyl beta-D-glucopyranoside | + | carbon source |
65241 | 51850 | methyl pyruvate | + | carbon source |
65241 | 17268 | myo-inositol | - | carbon source |
65241 | 63153 | N-acetyl-D-mannosamine | + | carbon source |
65241 | 28037 | N-acetylgalactosamine | - | carbon source |
65241 | 506227 | N-acetylglucosamine | + | carbon source |
65241 | 35418 | n-acetylneuraminate | + | carbon source |
65241 | 100147 | nalidixic acid | + | carbon source |
65241 | 17632 | nitrate | + | reduction |
65241 | 17309 | pectin | + | carbon source |
65241 | 75248 | potassium tellurite | + | carbon source |
65241 | 17272 | propionate | - | carbon source |
65241 | 26490 | quinate | - | carbon source |
65241 | 17814 | salicin | + | carbon source |
65241 | 75229 | sodium bromate | - | carbon source |
65241 | 64103 | sodium butyrate | - | carbon source |
65241 | 17164 | stachyose | - | carbon source |
65241 | 17992 | sucrose | + | carbon source |
65241 | 27897 | tryptophan | - | energy source |
65241 | 53423 | tween 40 | - | carbon source |
65241 | 53426 | tween 80 | - | assimilation |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is sensitive | sensitivity conc. | is resistant | resistance conc. |
---|---|---|---|---|---|---|---|
65241 | 28971 | ampicillin | yes | yes | 10 µg (disc) | ||
65241 | 18208 | penicillin g | yes | yes | 10 µg (disc) | ||
65241 | 17076 | streptomycin | yes | yes | 10 µg (disc) | ||
65241 | 48923 | erythromycin | yes | yes | 15 µg (disc) | ||
65241 | 17698 | chloramphenicol | yes | yes | 30 µg (disc) | ||
65241 | 6104 | kanamycin | yes | yes | 30 µg (disc) | ||
65241 | 27902 | tetracycline | yes | yes | 30 µg (disc) | ||
65241 | 8309 | polymyxin b | yes | yes | 30 µg (disc) | ||
65241 | 17833 | gentamicin | yes | yes | 10 µg (disc) | ||
65241 | 28001 | vancomycin | yes | yes | 30 µg (disc) |
metabolite production
- @ref: 65241
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 65241
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
65241 | catalase | + | 1.11.1.6 |
65241 | cytochrome oxidase | + | 1.9.3.1 |
65241 | alpha-glucosidase | + | 3.2.1.20 |
65241 | valine arylamidase | + | |
65241 | alkaline phosphatase | + | 3.1.3.1 |
65241 | esterase Lipase (C 8) | + | |
65241 | alpha-mannosidase | + | 3.2.1.24 |
65241 | alpha-fucosidase | + | 3.2.1.51 |
65241 | esterase (C 4) | + | |
65241 | beta-galactosidase | + | 3.2.1.23 |
65241 | trypsin | + | 3.4.21.4 |
65241 | leucine arylamidase | + | 3.4.11.1 |
65241 | acid phosphatase | - | 3.1.3.2 |
65241 | naphthol-AS-BI-phosphohydrolase | - | |
65241 | lipase (C 14) | - | |
65241 | cystine arylamidase | - | 3.4.11.3 |
65241 | alpha-chymotrypsin | - | 3.4.21.1 |
65241 | alpha-galactosidase | - | 3.2.1.22 |
65241 | beta-glucuronidase | - | 3.2.1.31 |
65241 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
65241 | tryptophan deaminase | - | 4.1.99.1 |
65241 | urease | - | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
@ref | sample type | sampling date | geographic location | country | origin.country | continent | latitude | longitude | enrichment culture | enrichment culture duration | enrichment culture temperature | isolation procedure |
---|---|---|---|---|---|---|---|---|---|---|---|---|
65241 | water sample | 2011 | brine-seawater interface at Erba Deep in the Red Sea | Saudi Arabia | SAU | Asia | 20.73 | 38.1833 | 50 % marine 2216 broth (MB; Difco) and 50 % sterilized in situ brine water | 1 week | 28 | 5 ml brine was used to inoculate 30 ml enrichment medium [50 % marine 2216 broth (MB; Difco) and 50 % sterilized in situ brine water]. The flasks were incubated at 28°C for 1 week, then plated onto marine 2216 agar (MA; Difco) plates amended to a final concentration of 10 % NaCl, and subsequently purified into single colonies using plates containing the same solidified media |
67770 | Brine-seawater interface at Erba Deep in the Red Sea | Saudi Arabia | SAU | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
taxonmaps
- @ref: 69479
- File name: preview.99_5943.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_588;97_3492;98_4418;99_5943&stattab=map
- Last taxonomy: Ruegeria marisrubri
- 16S sequence: KP726356
- Sequence Identity:
- Total samples: 472
- soil counts: 9
- aquatic counts: 327
- animal counts: 135
- plant counts: 1
Sequence information
16S sequences
- @ref: 65241
- description: 16S rRNA gene sequence
- accession: KP726356
- database: nuccore
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Ruegeria sp. ZGT118 | 1685379.3 | wgs | patric | 1685379 |
66792 | Ruegeria marisrubri ZGT118 | 2724679120 | draft | img | 1685379 |
67770 | Ruegeria marisrubri ZGT118 | GCA_001507595 | contig | ncbi | 1685379 |
GC content
- @ref: 65241
- GC-content: 62.94
- method: genome sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 68.247 | yes |
gram-positive | no | 98.422 | yes |
anaerobic | no | 97.544 | no |
aerobic | yes | 81.595 | no |
halophile | yes | 87.052 | yes |
spore-forming | no | 95.97 | no |
glucose-util | yes | 63.574 | yes |
flagellated | no | 87.169 | yes |
thermophile | no | 86.318 | no |
glucose-ferment | no | 91.436 | no |
External links
@ref: 65241
culture collection no.: JCM 19519, ACCC 19862
literature
- topic: Phylogeny
- Pubmed-ID: 29022541
- title: Ruegeria profundi sp. nov. and Ruegeria marisrubri sp. nov., isolated from the brine-seawater interface at Erba Deep in the Red Sea.
- authors: Zhang G, Haroon MF, Zhang R, Dong X, Wang D, Liu Y, Xun W, Dong X, Stingl U
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.002344
- year: 2017
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Indian Ocean, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, *Salts, Saudi Arabia, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry
- topic2: Transcriptome
Reference
@id | authors | title | doi/url | journal | pubmed |
---|---|---|---|---|---|
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 | ||
65241 | Guishan Zhang, Mohamed Fauzi Haroon, Ruifu Zhang, Xiaoyan Dong, Dandan Wang, Yunpeng Liu, Weibing Xun, Xiuzhu Dong, Ulrich Stingl | Ruegeria profundi sp. nov. and Ruegeria marisrubri sp. nov., isolated from the brine–seawater interface at Erba Deep in the Red Sea | 10.1099/ijsem.0.002344 | IJSEM 67: 4624-4631 2017 | 29022541 |
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 | ||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 |
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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ |