Strain identifier

BacDive ID: 14131

Type strain: Yes

Species: Sphingobacterium lactis

Strain history: <- S. Scherer, Research Center for Nutrition and Food Sci. (ZIEL), TU Munich, GERMANY; WCC4512 <- V. Schmidt

NCBI tax ID(s): 797291 (species)

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General

@ref: 16183

BacDive-ID: 14131

DSM-Number: 22361

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

description: Sphingobacterium lactis DSM 22361 is an aerobe, mesophilic, Gram-negative human pathogen that was isolated from raw milk.

NCBI tax id

  • NCBI tax id: 797291
  • Matching level: species

strain history

  • @ref: 16183
  • history: <- S. Scherer, Research Center for Nutrition and Food Sci. (ZIEL), TU Munich, GERMANY; WCC4512 <- V. Schmidt

doi: 10.13145/bacdive14131.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Sphingobacteriaceae
  • genus: Sphingobacterium
  • species: Sphingobacterium lactis
  • full scientific name: Sphingobacterium lactis Schmidt et al. 2012

@ref: 16183

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Sphingobacterium

species: Sphingobacterium lactis

full scientific name: Sphingobacterium lactis Schmidt et al. 2012

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30447negative1.7 µm0.65 µmrod-shapedno
69480negative99.993

pigmentation

  • @ref: 30447
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16183R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
16183NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16183positivegrowth28mesophilic
30447positivegrowth10-41

culture pH

  • @ref: 30447
  • ability: positive
  • type: growth
  • pH: 06-09
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 30447
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30447no
69481no100
69480no99.998

halophily

  • @ref: 30447
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3044715963ribitol+carbon source
3044722599arabinose+carbon source
3044717057cellobiose+carbon source
3044728757fructose+carbon source
3044717234glucose+carbon source
3044728087glycogen+carbon source
3044717716lactose+carbon source
3044717306maltose+carbon source
3044737684mannose+carbon source
3044728053melibiose+carbon source
30447506227N-acetylglucosamine+carbon source
3044716634raffinose+carbon source
3044717814salicin+carbon source
3044717992sucrose+carbon source
3044727082trehalose+carbon source
304474853esculin+hydrolysis

enzymes

@refvalueactivityec
30447catalase+1.11.1.6
30447cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 16183
  • sample type: raw milk
  • geographic location: Bavaria
  • country: Germany
  • origin.country: DEU
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Fluids#Milk
#Host#Mammals

Safety information

risk assessment

  • @ref: 16183
  • pathogenicity human: yes, in single cases
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16183
  • description: Sphingobacterium lactis partial 16S rRNA gene, strain DSM 22361
  • accession: FN908501
  • length: 1515
  • database: ena
  • NCBI tax ID: 797291

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingobacterium lactis DSM 22361GCA_011046555completencbi797291
66792Sphingobacterium lactis DSM 22361GCA_900107985contigncbi797291
66792Sphingobacterium lactis strain DSM 22361797291.3wgspatric797291
66792Sphingobacterium lactis strain DSM 22361797291.6completepatric797291
66792Sphingobacterium lactis DSM 223612675903147draftimg797291

GC content

@refGC-contentmethod
1618344.2high performance liquid chromatography (HPLC)
3044744.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno91.258yes
flagellatedno96.618yes
gram-positiveno97.657yes
anaerobicno98.572yes
aerobicyes85.816no
halophileno92.71no
spore-formingno95.757no
thermophileno99.519no
glucose-utilyes86.548yes
glucose-fermentno90.502no

External links

@ref: 16183

culture collection no.: DSM 22361, LMG 25272, WCC 4512

straininfo link

  • @ref: 83296
  • straininfo: 398885

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21856986Sphingobacterium lactis sp. nov. and Sphingobacterium alimentarium sp. nov., isolated from raw milk and a dairy environment.Schmidt VSJ, Wenning M, Scherer SInt J Syst Evol Microbiol10.1099/ijs.0.036327-02011Animals, Bacterial Typing Techniques, Base Composition, Chaperonin 60/genetics, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, *Environmental Microbiology, Fatty Acids/analysis, Milk/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingobacterium/*classification/genetics/*isolation & purificationGenetics
Phylogeny28629491Sphingobacterium alkalisoli sp. nov., isolated from a saline-alkaline soil.Xu L, Sun JQ, Wang LJ, Gao ZW, Sun LZ, Wu XLInt J Syst Evol Microbiol10.1099/ijsem.0.0018952017*Alkalies, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydrogen-Ion Concentration, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Salinity, Sequence Analysis, DNA, *Soil Microbiology, Sphingobacterium/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31967955Sphingobacterium olei sp. nov., isolated from oil-contaminated soil.Liu B, Yang X, Sheng M, Yang Z, Qiu J, Wang C, He JInt J Syst Evol Microbiol10.1099/ijsem.0.0040002020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, *Petroleum Pollution, Phosphatidylethanolamines/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingobacterium/*classification/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16183Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22361)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22361
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
30447Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2678228776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
83296Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398885.1StrainInfo: A central database for resolving microbial strain identifiers