Strain identifier

BacDive ID: 158691

Type strain: Yes

Species: Sphingobacterium bovisgrunnientis

Strain Designation: YK2

Strain history: <- P. Anil Kumar, Microbial Type Culture Collection and Gene Bank(MTCC), CSIR-IMTECH(Institute of Microbial Technology)

NCBI tax ID(s): 1874697 (species)

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General

@ref: 65428

BacDive-ID: 158691

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming

description: Sphingobacterium bovisgrunnientis YK2 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from yak milk.

NCBI tax id

  • NCBI tax id: 1874697
  • Matching level: species

strain history

@refhistory
67770P. Anil Kumar; MTCC, India; YK2.
67771<- P. Anil Kumar, Microbial Type Culture Collection and Gene Bank(MTCC), CSIR-IMTECH(Institute of Microbial Technology)

doi: 10.13145/bacdive158691.20230509.8.1

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 bovisgrunnientis
  • full scientific name: Sphingobacterium bovisgrunnientis Kaur et al. 2018

@ref: 65428

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Sphingobacteriaceae

genus: Sphingobacterium

species: Sphingobacterium bovisgrunnientis

strain designation: YK2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
65428negative1.6-3.2 µm0.7-1.2 µmrod-shapedno
69480no90.123
69480negative99.995

colony morphology

  • @ref: 65428
  • colony size: 2-3 mm
  • colony color: yellowish
  • colony shape: circular
  • incubation period: 3 days
  • medium used: trypto-soya agar

pigmentation

  • @ref: 65428
  • production: no
  • name: Flexirubin-type pigments

Culture and growth conditions

culture medium

  • @ref: 65428
  • name: trypto-soya agar
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
65428positivegrowth25-42
65428positiveoptimum37mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
65428positivegrowth5-11alkaliphile
65428positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69480no99.979
69481no100

halophily

  • @ref: 65428
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 0-0.5 %(w/v)

observation

  • @ref: 65428
  • observation: the polar lipids consisted of PE, APL1 and L1-L6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
65428581435-dehydro-D-gluconate-assimilation
6542815963ribitol-assimilation
654282509agar-hydrolysis
6542822599arabinose-assimilation
6542822605arabinitol-assimilation
65428casein-hydrolysis
6542823399coumarate-assimilation
6542817108D-arabinose-assimilation
6542817057cellobiose-assimilation
6542817634D-glucose-assimilation
6542816899D-mannitol-assimilation
6542816024D-mannose-assimilation
6542817924D-sorbitol-assimilation
6542816443D-tagatose-assimilation
6542816551D-trehalose-assimilation
6542824996lactate-assimilation
6542816813galactitol-assimilation
6542817113erythritol-assimilation
654284853esculin+hydrolysis
6542828757fructose-assimilation
6542828260galactose-assimilation
654285291gelatin-hydrolysis
6542817234glucose-assimilation
6542817754glycerol-assimilation
6542815443inulin-assimilation
6542816087isocitrate-assimilation
6542830849L-arabinose-assimilation
6542818403L-arabitol-assimilation
6542815971L-histidine-assimilation
6542815589L-malate-assimilation
6542817716lactose-assimilation
6542815792malonate+assimilation
6542817306maltose-assimilation
65428maltose hydrate-assimilation
6542829864mannitol-assimilation
6542837684mannose+assimilation
654286731melezitose-assimilation
6542828053melibiose-assimilation
6542843943methyl alpha-D-mannoside-assimilation
6542837657methyl D-glucoside+assimilation
6542817268myo-inositol-assimilation
6542817632nitrate-reduction
6542818394palatinose-assimilation
6542816634raffinose-assimilation
6542826546rhamnose-assimilation
6542817814salicin-assimilation
6542853258sodium citrate-assimilation
6542884997sodium gluconate-assimilation
6542862983sodium malonate-assimilation
6542830911sorbitol-assimilation
6542827922sorbose-assimilation
6542817992sucrose-assimilation
6542827082trehalose-assimilation
6542853424tween 20+hydrolysis
6542853423tween 40+hydrolysis
6542853425tween 60+hydrolysis
6542853426tween 80-hydrolysis
6542816199urea-hydrolysis
6542817151xylitol-assimilation
6542818222xylose-assimilation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
654286472lincomycinyesyes2 µg (disc)
6542827902tetracyclineyesyes30 µg (disc)
654283506cefprozilyesyes30 µg (disc)
6542827644chlortetracyclinyesyes30 µg (disc)
6542828001vancomycinyesyes30 µg (disc)
6542817698chloramphenicolyesyes30 µg (disc)
654289215spectinomycinyesyes100 µg (disc)
6542818208penicillin gyesyes2 Unit
6542828669bacitracinyesyes8 Unit
65428474053cefazolinyesyes30 µg (disc)
6542828368novobiocinyesyes30 µg (disc)
654286104kanamycinyesyes30 µg (disc)
654282676amoxicillinyesyes30 µg (disc)
654283508ceftazidimeyesyes30 µg (disc)
654288309polymyxin byesyes300 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
6542835581indoleno
6542815138sulfideno

enzymes

@refvalueactivityec
65428catalase+1.11.1.6
65428cytochrome oxidase+1.9.3.1
65428tryptophan deaminase-4.1.99.1
65428phenylalanine arylamidase+
65428proline-arylamidase+3.4.11.5
65428pyrrolidonyl arylamidase+3.4.19.3
65428beta-galactosidase+3.2.1.23
65428glutamyl arylamidase pNA+
65428beta-glucosidase+3.2.1.21
65428tyrosine arylamidase+
65428alpha-galactosidase+3.2.1.22
65428beta-N-acetylgalactosaminidase+
65428arginine arylamidase+
65428glutamyl-glutamate arylamidase+
65428glycin arylamidase+
65428beta-xylosidase-
65428alanine arylamidase-3.4.11.2
65428proline-arylamidase-3.4.11.5
65428ornithine decarboxylase-4.1.1.17
65428lysine decarboxylase-4.1.1.18
65428beta-glucuronidase-3.2.1.31
65428gamma-glutamyltransferase-2.3.2.2
65428lipase (C 14)-
65428urease-3.5.1.5
65428alpha-galactosidase-3.2.1.22
65428phosphatase-
65428glycin arylamidase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65428C12:00.2
    65428C13:0 iso0.3
    65428C14:00.1
    65428C14:1 ! 5c0.5
    65428C15:0 2OH0.2
    65428C15:0 iso33.4
    65428C15:0 iso 3OH2.2
    65428C15:0 anteiso0.3
    65428C15:1ω6c1.1
    65428C15:1 iso F4.1
    65428C16:00.8
    65428C16:0 3OH0.5
    65428C16:0 iso 3OH0.2
    65428C16:1ω5c0.6
    65428C17:00.1
    65428C17:0 2OH0.3
    65428C17:0 3OH0.4
    65428C17:0 iso0.3
    65428C17:0 anteiso0.3
    65428C17:0 iso 3OH18.6
    65428C17:1ω8c0.5
    65428C17:1 iso ω9c9.5
    65428C18:0 3-OHω9c0.2
    65428C18:1ω9c0.5
    65428C18:3ω6,9,12c0.1
    65428C18:1 iso H0.1
    65428C19:0 iso0.3
    65428C20:0 iso0.2
    65428C13:0 3-OH and/or iso-C15:1 I2
    65428C16:1ω7c and/or C16:1ω6c and/or iso-C120.8
    65428anteiso-C 17:1 B and/or iso-C 17:1 I1.3
  • type of FA analysis: whole cell analysis
  • incubation medium: tryptone soya agar medium
  • incubation temperature: 37
  • incubation time: 2
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: 6890
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperature
65428yak milkLeh, Jammu and KashmirIndiaINDAsiatryptone soya agar medium5 days30
67770Yak milk collected from LehJammu and KashmirIndiaINDAsia
67771From Yak MilkChangla, LehIndiaINDAsia

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body Product#Fluids#Milk

taxonmaps

  • @ref: 69479
  • File name: preview.99_124050.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15366;96_3821;97_4714;98_28503;99_124050&stattab=map
  • Last taxonomy: Sphingobacterium bovisgrunnientis
  • 16S sequence: LT599836
  • Sequence Identity:
  • Total samples: 1060
  • soil counts: 224
  • aquatic counts: 234
  • animal counts: 582
  • plant counts: 20

Sequence information

16S sequences

  • @ref: 65428
  • description: 16S rRNA gene sequence
  • accession: LT599836
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphingobacterium bovisgrunnientis KCTC 52685GCA_009829085contigncbi1874697
66792Sphingobacterium bovisgrunnientis strain KCTC 526851874697.3wgspatric1874697
66792Sphingobacterium bovisgrunnientis KCTC 526852896326849draftimg1874697

GC content

  • @ref: 67770
  • GC-content: 38.9
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.076yes
gram-positiveno97.148yes
anaerobicno99.201no
aerobicyes91.217yes
halophileno92.8yes
spore-formingno93.95no
glucose-utilyes90.673no
flagellatedno96.501no
thermophileno99.431yes
glucose-fermentno88.95no

External links

@ref: 65428

culture collection no.: MTCC 12631, KCTC 52685, JCM 31951

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29388539Sphingobacterium bovisgrunnientis sp. nov., isolated from yak milk.Kaur M, Singh H, Sharma S, Mishra S, Tanuku NRS, Pinnaka AKInt J Syst Evol Microbiol10.1099/ijsem.0.0025622018Animals, Bacterial Typing Techniques, Base Composition, Cattle/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Milk/*microbiology, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sphingobacterium/*classification/genetics/isolation & purificationTranscriptome
Phylogeny32048984Sphingobacterium cavernae sp. nov., a novel bacterium isolated from soil sampled at Tiandong Cave.Zhou XK, Huang Y, Li M, Zhang XF, Wei YQ, Cha QY, Zhang TK, Wang XJ, Liu JJ, Liu ZY, Qin SC, Mo MHInt J Syst Evol Microbiol10.1099/ijsem.0.0040442020Bacterial Typing Techniques, Base Composition, Caves/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingobacterium/*classification/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
65428Manpreet Kaur, Harjodh Singh, Shivani Sharma, Sunita Mishra, Naga Radha Srinivas Tanuku, Anil Kumar PinnakaSphingobacterium bovisgrunnientis sp. nov., isolated from yak milk10.1099/ijsem.0.002562IJSEM 68: 636-642 201829388539
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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