Strain identifier

BacDive ID: 132403

Type strain: Yes

Species: Shimia abyssi

Strain history: Y. Nogi; Res. & Dev. Center for Mar. Biosci., JAMSTEC, Japan; JAMH 043.

NCBI tax ID(s): 1662395 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refhistory
24192<- Y. Nogi, Japan Agency for Marine-Earth Sci. and Technol. (JAMSTEC), Extremobiosphere Res. Center, Yokosuka; JAMH 043
67770Y. 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

    @refsynonym
    20215Thalassovita abyssi
    20215Thalassobius 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

@refgram staincell lengthcell widthcell shapemotilityconfidence
43825negative1.5-2 µm0.7-1 µmpleomorphic-shapedno
69480negative99.997

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

@refnamegrowthlinkcomposition
43825Marine agar (MA)yes
24192BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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

@refgrowthtypetemperaturerange
43825positivegrowth10-30
43825positiveoptimum25mesophilic
24192positivegrowth25mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
43825positivegrowth6.5-9.5alkaliphile
43825positiveoptimum7-7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 43825
  • oxygen tolerance: obligate aerobe

nutrition type

  • @ref: 43825
  • type: chemoorganotroph

spore formation

@refspore formationconfidence
43825no
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
43825NaClpositivegrowth2-7 %(w/v)
43825NaClpositiveoptimum2-3 %(w/v)
43825NaClnogrowth0-1 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4382530089acetate-builds acid from
4382516150benzoate-builds acid from
4382516947citrate-builds acid from
4382530849L-arabinose-builds acid from
4382517716lactose-builds acid from
4382516634raffinose-builds acid from
4382517992sucrose-builds acid from
4382527082trehalose-builds acid from
438252509agar-hydrolysis
4382585146carboxymethylcellulose-hydrolysis
43825casein-hydrolysis
4382517029chitin-hydrolysis
438254853esculin-hydrolysis
438255291gelatin-hydrolysis
4382528017starch-hydrolysis
4382553424tween 20-hydrolysis
4382553423tween 40-hydrolysis
4382553426tween 80-hydrolysis
4382516199urea-hydrolysis
4382516301nitrite-reduction
4382517057cellobiose+builds acid from
4382515824D-fructose+builds acid from
4382512936D-galactose+builds acid from
4382517634D-glucose+builds acid from
4382516899D-mannitol+builds acid from
4382516024D-mannose+builds acid from
4382565327D-xylose+builds acid from
4382517754glycerol+builds acid from
4382518287L-fucose+builds acid from
4382562345L-rhamnose+builds acid from
4382517306maltose+builds acid from
4382517268myo-inositol+builds acid from
4382544337N-acetyl-L-glutamate+builds acid from
4382515361pyruvate+builds acid from
4382553425tween 60+hydrolysis
4382517632nitrate+reduction
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistant
4382528971ampicillinyesyes10 µg (disc)
43825204928cefotaximeyesyes30 µg (disc)
4382517698chloramphenicolyesyes30 µg (disc)
4382517833gentamicinyesyes10 µg (disc)
438256104kanamycinyesyes30 µg (disc)
4382528368novobiocinyesyes30 µg (disc)
4382517076streptomycinyesyes10 µg (disc)
4382527902tetracyclineyesyes30 µg (disc)
438258309polymyxin byesyes300 µg (disc)
4382518208penicillin gyesyes10 Unit (disc)
438253745clindamycinyesyes

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
24192-------+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
24192sediment of a deep-sea cold-seepSagami-Bay, off Hatsushima at a depth of 1097 mJapanJPNAsia35.009139.136
43825From sediment of the deep-sea cold-seep area off Hatsushima; depth: 1097 mSagami BayJapanJPNAsia35.15141.267
67770Cold-seep sediment in Sagami BayJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Shimia abyssi DSM 100673GCA_003014475contigncbi1662395
66792Thalassobius abyssi strain DSM 1006731662395.5wgspatric1662395
66792Shimia abyssi DSM 1006732728369514draftimg1662395

GC content

  • @ref: 24192
  • GC-content: 58
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno89.669yes
gram-positiveno98.248no
anaerobicno98.854no
aerobicyes91.335yes
halophileyes70.498no
spore-formingno96.615yes
thermophileno97.141yes
glucose-utilyes59.3yes
flagellatedno94.017yes
glucose-fermentno89.749no

External links

@ref: 24192

culture collection no.: DSM 100673, JCM 30900, JAMH 043

straininfo link

  • @ref: 90744
  • straininfo: 397596

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26554730Thalassobius abyssi sp. nov., a marine bacterium isolated from cold-seep sediment.Nogi Y, Mori K, Makita H, Hatada YInt J Syst Evol Microbiol10.1099/ijsem.0.0007582015
Phylogeny33886449Shimia 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 SInt J Syst Evol Microbiol10.1099/ijsem.0.0047822021Bacterial 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/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
24192Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100673Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100673)
43825Yuichi Nogi, Kozue Mori, Hiroko Makita, Yuji HatadaThalassobius abyssi sp. nov., a marine bacterium isolated from cold-seep sediment10.1099/ijsem.0.000758IJSEM 66: 574-579 201626554730
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
90744Reimer, 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 identifiers10.60712/SI-ID397596.1