Strain identifier

BacDive ID: 14248

Type strain: Yes

Species: Sphingomonas molluscorum

Strain history: CIP <- 2006, KMM

NCBI tax ID(s): 418184 (species)

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General

@ref: 8194

BacDive-ID: 14248

DSM-Number: 19588

keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped

description: Sphingomonas molluscorum DSM 19588 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from marine mollusc.

NCBI tax id

  • NCBI tax id: 418184
  • Matching level: species

strain history

@refhistory
8194<- CIP <- KMM <- L. Romanenko, Russian Acad. of Science, Vladivostok
332842006, KMM
67770M. Uchino <-- L. A. Romanenko KMM 3882.
121006CIP <- 2006, KMM

doi: 10.13145/bacdive14248.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Sphingomonadaceae
  • genus: Sphingomonas
  • species: Sphingomonas molluscorum
  • full scientific name: Sphingomonas molluscorum Romanenko et al. 2007

@ref: 8194

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas molluscorum

full scientific name: Sphingomonas molluscorum Romanenko et al. 2007

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31827negative1.0-1.5 µm0.4-0.6 µmrod-shapedno
121006negativerod-shapedno

colony morphology

  • @ref: 121006

pigmentation

  • @ref: 31827
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8194TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
33284Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121006CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
8194positivegrowth30mesophilic
31827positivegrowth7-37
31827positiveoptimum26.5mesophilic
33284positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31827aerobe
121006obligate aerobe

spore formation

  • @ref: 31827
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31827NaClpositivegrowth0-4 %
31827NaClpositiveoptimum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3182722599arabinose+carbon source
3182724265gluconate+carbon source
3182717234glucose+carbon source
3182717716lactose+carbon source
3182715792malonate+carbon source
3182717306maltose+carbon source
3182737684mannose+carbon source
31827506227N-acetylglucosamine+carbon source
318274853esculin+hydrolysis
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837115443inulin-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837116988D-ribose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
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
12100617632nitrate-reduction
12100616301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12100635581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
31827catalase+1.11.1.6
31827cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
121006oxidase+
121006alcohol dehydrogenase-1.1.1.1
121006catalase+1.11.1.6
121006lysine decarboxylase-4.1.1.18
121006ornithine decarboxylase-4.1.1.17
121006urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase+3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121006-+++++++++++++++++--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
8194-----+-++++-+++-----+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121006---+/--+/----+/-+/-+/-+/--------+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/-+/--+/-+/----+/-+/-+/--+/------+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost speciesisolation date
8194marine molluscSea of Japan, Peter the Great BayRussiaRUSAsia
67770Marine bivalve (Anadara broughtoni)Peter the Great Bay, the Sea of JapanRussiaRUSAnadara broughtoni
121006Marine MollusePeter the Great bay, Sea of JapanRussian FederationRUSEurope2003

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Host#Invertebrates (Other)#Mollusca

taxonmaps

  • @ref: 69479
  • File name: preview.99_15592.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_348;97_8938;98_10958;99_15592&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: AB248285
  • Sequence Identity:
  • Total samples: 1810
  • soil counts: 320
  • aquatic counts: 504
  • animal counts: 909
  • plant counts: 77

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
81941Risk group (German classification)
1210061Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8194
  • description: Sphingomonas molluscorum gene for 16S rRNA, partial sequence, strain: An 18 (= KMM 3882)
  • accession: AB248285
  • length: 1381
  • database: ena
  • NCBI tax ID: 418184

GC content

@refGC-contentmethod
3182768.3
6777068.3high performance liquid chromatography (HPLC)

External links

@ref: 8194

culture collection no.: DSM 19588, CIP 109223, JCM 14122, KMM 3882, NRIC 0685, CCTCC AB 2016286

straininfo link

  • @ref: 83407
  • straininfo: 297317

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17267979Sphingomonas molluscorum sp. nov., a novel marine isolate with antimicrobial activity.Romanenko LA, Uchino M, Frolova GM, Tanaka N, Kalinovskaya NI, Latyshev N, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.64441-02007Aerobiosis, Animals, *Antibiosis, Arcidae/*microbiology, Bacterial Typing Techniques, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA, Glycosphingolipids/analysis/chemistry, Gram-Positive Bacteria/drug effects, Japan, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sphingomonas/*classification/cytology/*isolation & purification/physiologyGenetics
Phylogeny24425812Sphingomonas aerophila sp. nov. and Sphingomonas naasensis sp. nov., isolated from air and soil, respectively.Kim SJ, Moon JY, Lim JM, Ahn JH, Weon HY, Ahn TY, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.055269-02013*Air Microbiology, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistryGenetics
Phylogeny28933318Sphingomonas antarctica sp. nov., isolated from Antarctic tundra soil.Huang Y, Wei Z, Danzeng W, Kim MC, Zhu G, Zhang Y, Liu Z, Peng FInt J Syst Evol Microbiol10.1099/ijsem.0.0022532017Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, *Tundra, Ubiquinone/chemistryTranscriptome
Phylogeny31671048Sphingomonas paeninsulae sp. nov., isolated from soil sampled at Fildes Peninsula, Antarctica.Geng Y, Zhang Y, Qin K, Liu J, Tian J, Huang Y, Wei Z, Zhang F, Peng FInt J Syst Evol Microbiol10.1099/ijsem.0.0035042019Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/isolation & purification, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8194Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19588)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19588
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31827Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2809328776041
33284Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6941
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
69479João 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
83407Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297317.1StrainInfo: A central database for resolving microbial strain identifiers
121006Curators of the CIPCollection of Institut Pasteur (CIP 109223)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109223