Strain identifier
BacDive ID: 132403
Type strain:
Species: Shimia abyssi
Strain history: Y. Nogi; Res. & Dev. Center for Mar. Biosci., JAMSTEC, Japan; JAMH 043.
NCBI tax ID(s): 1662395 (species)
General
@ref: 24192
BacDive-ID: 132403
DSM-Number: 100673
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, chemoorganotroph, Gram-negative, pleomorphic-shaped, colony-forming
description: Shimia abyssi DSM 100673 is an obligate aerobe, chemoorganotroph, Gram-negative bacterium that forms circular colonies and was isolated from sediment of a deep-sea cold-seep.
NCBI tax id
- NCBI tax id: 1662395
- Matching level: species
strain history
@ref | history |
---|---|
24192 | <- Y. Nogi, Japan Agency for Marine-Earth Sci. and Technol. (JAMSTEC), Extremobiosphere Res. Center, Yokosuka; JAMH 043 |
67770 | Y. Nogi; Res. & Dev. Center for Mar. Biosci., JAMSTEC, Japan; JAMH 043. |
doi: 10.13145/bacdive132403.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Shimia
- species: Shimia abyssi
- full scientific name: Shimia abyssi (Nogi et al. 2016) Wirth and Whitman 2018
synonyms
@ref synonym 20215 Thalassovita abyssi 20215 Thalassobius abyssi
@ref: 24192
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Shimia
species: Shimia abyssi
full scientific name: Shimia abyssi (Nogi et al. 2016) Wirth and Whitman 2018
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
43825 | negative | 1.5-2 µm | 0.7-1 µm | pleomorphic-shaped | no | |
69480 | negative | 99.997 |
colony morphology
- @ref: 43825
- colony size: 1-2 mm
- colony color: Ivory
- colony shape: circular
- incubation period: 2 days
- medium used: MA agar
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
43825 | Marine agar (MA) | yes | ||
24192 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
43825 | positive | growth | 10-30 | |
43825 | positive | optimum | 25 | mesophilic |
24192 | positive | growth | 25 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
43825 | positive | growth | 6.5-9.5 | alkaliphile |
43825 | positive | optimum | 7-7.5 |
Physiology and metabolism
oxygen tolerance
- @ref: 43825
- oxygen tolerance: obligate aerobe
nutrition type
- @ref: 43825
- type: chemoorganotroph
spore formation
@ref | spore formation | confidence |
---|---|---|
43825 | no | |
69481 | no | 100 |
69480 | no | 99.999 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
43825 | NaCl | positive | growth | 2-7 %(w/v) |
43825 | NaCl | positive | optimum | 2-3 %(w/v) |
43825 | NaCl | no | growth | 0-1 %(w/v) |
observation
- @ref: 67770
- observation: quinones: Q-10
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43825 | 30089 | acetate | - | builds acid from |
43825 | 16150 | benzoate | - | builds acid from |
43825 | 16947 | citrate | - | builds acid from |
43825 | 30849 | L-arabinose | - | builds acid from |
43825 | 17716 | lactose | - | builds acid from |
43825 | 16634 | raffinose | - | builds acid from |
43825 | 17992 | sucrose | - | builds acid from |
43825 | 27082 | trehalose | - | builds acid from |
43825 | 2509 | agar | - | hydrolysis |
43825 | 85146 | carboxymethylcellulose | - | hydrolysis |
43825 | casein | - | hydrolysis | |
43825 | 17029 | chitin | - | hydrolysis |
43825 | 4853 | esculin | - | hydrolysis |
43825 | 5291 | gelatin | - | hydrolysis |
43825 | 28017 | starch | - | hydrolysis |
43825 | 53424 | tween 20 | - | hydrolysis |
43825 | 53423 | tween 40 | - | hydrolysis |
43825 | 53426 | tween 80 | - | hydrolysis |
43825 | 16199 | urea | - | hydrolysis |
43825 | 16301 | nitrite | - | reduction |
43825 | 17057 | cellobiose | + | builds acid from |
43825 | 15824 | D-fructose | + | builds acid from |
43825 | 12936 | D-galactose | + | builds acid from |
43825 | 17634 | D-glucose | + | builds acid from |
43825 | 16899 | D-mannitol | + | builds acid from |
43825 | 16024 | D-mannose | + | builds acid from |
43825 | 65327 | D-xylose | + | builds acid from |
43825 | 17754 | glycerol | + | builds acid from |
43825 | 18287 | L-fucose | + | builds acid from |
43825 | 62345 | L-rhamnose | + | builds acid from |
43825 | 17306 | maltose | + | builds acid from |
43825 | 17268 | myo-inositol | + | builds acid from |
43825 | 44337 | N-acetyl-L-glutamate | + | builds acid from |
43825 | 15361 | pyruvate | + | builds acid from |
43825 | 53425 | tween 60 | + | hydrolysis |
43825 | 17632 | nitrate | + | reduction |
68369 | 25115 | malate | - | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | - | assimilation |
68369 | 24265 | gluconate | - | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | - | assimilation |
68369 | 16024 | D-mannose | - | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | - | assimilation |
68369 | 5291 | gelatin | - | hydrolysis |
68369 | 4853 | esculin | - | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is sensitive | sensitivity conc. | is resistant |
---|---|---|---|---|---|---|
43825 | 28971 | ampicillin | yes | yes | 10 µg (disc) | |
43825 | 204928 | cefotaxime | yes | yes | 30 µg (disc) | |
43825 | 17698 | chloramphenicol | yes | yes | 30 µg (disc) | |
43825 | 17833 | gentamicin | yes | yes | 10 µg (disc) | |
43825 | 6104 | kanamycin | yes | yes | 30 µg (disc) | |
43825 | 28368 | novobiocin | yes | yes | 30 µg (disc) | |
43825 | 17076 | streptomycin | yes | yes | 10 µg (disc) | |
43825 | 27902 | tetracycline | yes | yes | 30 µg (disc) | |
43825 | 8309 | polymyxin b | yes | yes | 300 µg (disc) | |
43825 | 18208 | penicillin g | yes | yes | 10 Unit (disc) | |
43825 | 3745 | clindamycin | yes | yes |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68369 | gelatinase | - | |
68369 | beta-glucosidase | - | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
24192 | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|
24192 | sediment of a deep-sea cold-seep | Sagami-Bay, off Hatsushima at a depth of 1097 m | Japan | JPN | Asia | 35.009 | 139.136 |
43825 | From sediment of the deep-sea cold-seep area off Hatsushima; depth: 1097 m | Sagami Bay | Japan | JPN | Asia | 35.15 | 141.267 |
67770 | Cold-seep sediment in Sagami Bay | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Sediment |
Safety information
risk assessment
- @ref: 24192
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24192
- description: Thalassobius abyssi gene for 16S ribosomal RNA, partial sequence
- accession: LC057677
- length: 1404
- database: ena
- NCBI tax ID: 1662395
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Shimia abyssi DSM 100673 | GCA_003014475 | contig | ncbi | 1662395 |
66792 | Thalassobius abyssi strain DSM 100673 | 1662395.5 | wgs | patric | 1662395 |
66792 | Shimia abyssi DSM 100673 | 2728369514 | draft | img | 1662395 |
GC content
- @ref: 24192
- GC-content: 58
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 89.669 | yes |
gram-positive | no | 98.248 | no |
anaerobic | no | 98.854 | no |
aerobic | yes | 91.335 | yes |
halophile | yes | 70.498 | no |
spore-forming | no | 96.615 | yes |
thermophile | no | 97.141 | yes |
glucose-util | yes | 59.3 | yes |
flagellated | no | 94.017 | yes |
glucose-ferment | no | 89.749 | no |
External links
@ref: 24192
culture collection no.: DSM 100673, JCM 30900, JAMH 043
straininfo link
- @ref: 90744
- straininfo: 397596
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 26554730 | Thalassobius abyssi sp. nov., a marine bacterium isolated from cold-seep sediment. | Nogi Y, Mori K, Makita H, Hatada Y | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000758 | 2015 | ||
Phylogeny | 33886449 | Shimia sediminis sp. nov., a bacterium isolated from marine sediment in the East China Sea. | Zhu S, Chen C, Cheng Y, Guo C, Peng N, Zhang W, He S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004782 | 2021 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
Reference
@id | authors | title | doi/url | catalogue | 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 | |||
24192 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100673 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100673) | |||
43825 | Yuichi Nogi, Kozue Mori, Hiroko Makita, Yuji Hatada | Thalassobius abyssi sp. nov., a marine bacterium isolated from cold-seep sediment | 10.1099/ijsem.0.000758 | IJSEM 66: 574-579 2016 | 26554730 | |
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/ | ||||
68369 | Automatically annotated from API 20NE | |||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
90744 | 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-ID397596.1 |