Strain identifier

BacDive ID: 14227

Type strain: Yes

Species: Sphingomonas sanguinis

Strain history: CIP <- 1994, IFO, Sphingomonas sanguis <- E. Yabuuchi, Kansai Med. Univ., Japan <- NCTC <- CDC: strain B4562, Pseudomonas paucimobilis

NCBI tax ID(s): 1219054 (strain), 33051 (species)

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General

@ref: 5189

BacDive-ID: 14227

DSM-Number: 13885

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, motile, rod-shaped, human pathogen

description: Sphingomonas sanguinis DSM 13885 is an obligate aerobe, mesophilic, Gram-negative human pathogen that was isolated from blood.

NCBI tax id

NCBI tax idMatching level
33051species
1219054strain

strain history

@refhistory
5189<- JCM <- GIFU <- NCTC <- R. E. Weaver, CDC
67770GIFU 2397 <-- NCTC 11032 <-- R. E. Weaver DCD B4562.
122429CIP <- 1994, IFO, Sphingomonas sanguis <- E. Yabuuchi, Kansai Med. Univ., Japan <- NCTC <- CDC: strain B4562, Pseudomonas paucimobilis

doi: 10.13145/bacdive14227.20230509.8.1

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 sanguinis
  • full scientific name: Sphingomonas sanguinis corrig. Takeuchi et al. 1993

  • synonyms

    • @ref: 20215
    • synonym: Sphingomonas sanguis

@ref: 5189

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas sanguinis

full scientific name: Sphingomonas sanguinis Takeuchi et al. 1993

type strain: yes

Morphology

cell morphology

  • @ref: 122429
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5189BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
37284MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
122429CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
5189positivegrowth30mesophilic
37284positivegrowth30mesophilic
67770positivegrowth30mesophilic
122429positivegrowth22-37
122429nogrowth5psychrophilic
122429nogrowth10psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122429
  • oxygen tolerance: obligate aerobe

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
1224294853esculin+hydrolysis
12242917632nitrate-builds gas from
12242916301nitrite-builds gas from

antibiotic resistance

  • @ref: 122429
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12242935581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68369cytochrome oxidase-1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
122429oxidase+
122429alcohol dehydrogenase-1.1.1.1
122429gelatinase+/-
122429DNase+/-
122429catalase+1.11.1.6
122429lysine decarboxylase-4.1.1.18
122429ornithine decarboxylase-4.1.1.17
122429phenylalanine ammonia-lyase+4.3.1.24
122429urease-3.5.1.5

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
5189-----+-++++-++---+---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122429+++++-+++++++++++++-+++-++-----+--++-----+---++--+----+----+---------------+---++-----+-++++-++--++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
5189bloodUSAUSANorth America
67770Blood
122429Human, BloodUnited States of AmericaUSANorth America

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Fluids#Blood
#Infection#Patient

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
5189yes, in single cases1Risk group (German classification)
1224291Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Sphingomonas sanguinis 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceGQ907189761ena33051
20218Sphingomonas paucimobilis strain BCRC 13955 16S-23S ribosomal RNA intergenic spacer, complete sequenceEU014534758ena13689
20218Sphingomonas genospecies-1 16S ribosomal RNA, partial sequenceD38428156ena35807
20218Sphingomonas sanguinis gene for 16S rRNA, partial sequenceD137261414ena33051
20218Sphingomonas sanguinis gene for 16S ribosomal RNAD845291359ena33051
20218Sphingomonas sanguinis gene for 16S rRNA, partial sequence, strain: NBRC 13937AB6805281412ena33051

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingomonas paucimobilis strain NCTC1103213689.17wgspatric13689
66792Sphingomonas sanguinis NBRC 139371219054.3wgspatric1219054
66792Sphingomonas sanguinis NBRC 139372731957633draftimg1219054
67770Sphingomonas sanguinis NBRC 13937GCA_001591005contigncbi1219054

GC content

@refGC-contentmethod
6777061.8high performance liquid chromatography (HPLC)
6777062.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes67.212no
gram-positiveno97.078no
anaerobicno99.313no
aerobicyes95no
halophileno94.013no
spore-formingno93.745no
thermophileno98.749no
glucose-utilyes92.662no
flagellatedno91.069no
glucose-fermentno90.763yes

External links

@ref: 5189

culture collection no.: DSM 13885, GIFU 2397, IFO 13937, JCM 7514, NBRC 13937, NCTC 11032, ATCC 51382, BCRC 17636, CCUG 27654, CCUG 31194, CDC B4562, CIP 104197, IAM 12578, IAM 14273, LMG 10925, LMG 17325, LMG 2240

straininfo link

  • @ref: 83386
  • straininfo: 4987

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny25985831Sphingomonas morindae sp. nov., isolated from Noni (Morinda citrifolia L.) branch.Liu Y, Yao S, Lee YJ, Cao Y, Zhai L, Zhang X, Su J, Ge Y, Kim SG, Cheng CInt J Syst Evol Microbiol10.1099/ijs.0.0003402015Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Endophytes/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Molecular Sequence Data, Morinda/*microbiology, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/chemistryEnzymology
Phylogeny29087271Sphingomonas jatrophae sp. nov. and Sphingomonas carotinifaciens sp. nov., two yellow-pigmented endophytes isolated from stem tissues of Jatropha curcas L.Madhaiyan M, Alex THH, Cho H, Kim SJ, Weon HY, Kwon SW, Whitman WB, Ji LInt J Syst Evol Microbiol10.1099/ijsem.0.0024342017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Endophytes/classification/genetics/isolation & purification, Fatty Acids/chemistry, Jatropha/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Plant Stems/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Singapore, Spermidine/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/chemistryEnzymology
Phylogeny30010528Sphingomonas aeria sp. nov., isolated from air.Xue H, Piao CG, Wang XZ, Lin CL, Guo MW, Li YInt J Syst Evol Microbiol10.1099/ijsem.0.0029102018*Air Microbiology, Bacterial Typing Techniques, Base Composition, Beijing, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5189Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13885)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13885
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
37284Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16079
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
83386Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4987.1StrainInfo: A central database for resolving microbial strain identifiers
122429Curators of the CIPCollection of Institut Pasteur (CIP 104197)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104197