Strain identifier

BacDive ID: 141002

Type strain: Yes

Species: Novosphingobium humi

Strain Designation: R1-4

Strain history: C. O. Jeon; Chung-Ang Univ., South Korea; R1-4.

NCBI tax ID(s): 2282397 (species)

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General

@ref: 43889

BacDive-ID: 141002

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

description: Novosphingobium humi R1-4 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from soil in military shooting range, Jangseong, Republic of Korea.

NCBI tax id

  • NCBI tax id: 2282397
  • Matching level: species

strain history

  • @ref: 67770
  • history: C. O. Jeon; Chung-Ang Univ., South Korea; R1-4.

doi: 10.13145/bacdive141002.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Erythrobacteraceae
  • genus: Novosphingobium
  • species: Novosphingobium humi
  • full scientific name: Novosphingobium humi Hyeon et al. 2017

@ref: 43889

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Novosphingobium

species: Novosphingobium humi

strain designation: R1-4

type strain: yes

Morphology

cell morphology

  • @ref: 43889
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43889
  • colony color: whitish-yellow
  • medium used: R2A agar

Culture and growth conditions

culture medium

@refnamegrowth
43889LB (Luria-Bertani) MEDIUMyes
43889Nutrient agar (NA)yes
43889Reasoner's 2A agar (R2A)yes
43889Tryptic soy agaryes

culture temp

@refgrowthtypetemperaturerange
43889positivegrowth15-45
43889positiveoptimum30mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
43889positivegrowth6.0-9.0alkaliphile
43889positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43889
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
43889NaClnogrowth1 %(w/v)
43889NaClpositiveminimum0 %(w/v)

observation

@refobservation
43889quinone Q-10
67770quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4388917128adipate-assimilation
4388927689decanoate-assimilation
4388916899D-mannitol-assimilation
4388916024D-mannose-assimilation
4388930849L-arabinose-assimilation
43889506227N-acetylglucosamine-assimilation
4388918401phenylacetate-assimilation
4388932032potassium gluconate-assimilation
4388953258sodium citrate-assimilation
4388917234glucose-fermentation
43889casein-hydrolysis
438895291gelatin-hydrolysis
4388928017starch-hydrolysis
4388953426tween 80-hydrolysis
4388916199urea-hydrolysis
4388917634D-glucose+assimilation
4388925115malate+assimilation
4388917306maltose+assimilation
438894853esculin+hydrolysis
4388953424tween 20+hydrolysis
4388918186tyrosine+hydrolysis
4388917632nitrate+reduction

metabolite production

  • @ref: 43889
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43889cytochrome oxidase+1.9.3.1
43889catalase-1.11.1.6
43889alkaline phosphatase+3.1.3.1
43889esterase (C 4)+
43889esterase Lipase (C 8)+
43889leucine arylamidase+3.4.11.1
43889acid phosphatase+3.1.3.2
43889naphthol-AS-BI-phosphohydrolase+
43889beta-galactosidase+3.2.1.23
43889beta-glucuronidase+3.2.1.31
43889beta-glucosidase+3.2.1.21
43889lipase (C 14)-
43889valine arylamidase-
43889cystine arylamidase-3.4.11.3
43889trypsin-3.4.21.4
43889alpha-chymotrypsin-3.4.21.1
43889alpha-galactosidase-3.2.1.22
43889alpha-glucosidase-3.2.1.20
43889N-acetyl-beta-glucosaminidase-3.2.1.52
43889alpha-mannosidase-3.2.1.24
43889alpha-fucosidase-3.2.1.51
43889arginine dihydrolase-3.5.3.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43889C14:0 2OH4.2
    43889C16:09.4
    43889C16:1ω7c / C16:1ω6c35.4
    43889C18:1ω7c / C18:1ω6c37.8
    43889C19:0ω8c cyclo13.2
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A broth
  • agar/liquid: liquid
  • incubation temperature: 30
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890 gas chromatograph

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
43889soil in military shooting range, Jangseong, Republic of KoreaJangseongRepublic of KoreaKORAsia37.2833127.4R2A agar3 days30
67770Soil from a military shooting rangeRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_8439.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_3914;97_4812;98_6168;99_8439&stattab=map
  • Last taxonomy: Novosphingobium
  • 16S sequence: KY658458
  • Sequence Identity:
  • Total samples: 1265
  • soil counts: 85
  • aquatic counts: 554
  • animal counts: 552
  • plant counts: 74

Sequence information

16S sequences

  • @ref: 43889
  • description: 16S rRNA gene sequence
  • accession: KY658458
  • database: nuccore

Genome sequences

  • @ref: 66792
  • description: Novosphingobium humi KACC 19094
  • accession: GCA_028607105
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 2282397

GC content

@refGC-contentmethod
4388964.4real time PCR (RTD-PCR)
6777064.4thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno82.611yes
gram-positiveno97.613no
anaerobicno96.816yes
aerobicyes80.113no
halophileno95.219no
spore-formingno92.801no
glucose-fermentno89.345yes
thermophileno97.831yes
glucose-utilyes92.163no
motileyes56.315yes

External links

@ref: 43889

culture collection no.: KACC 19094, JCM 31879

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28829033Novosphingobium humi sp. nov., isolated from soil of a military shooting range.Hyeon JW, Kim K, Son AR, Choi E, Lee SK, Jeon COInt J Syst Evol Microbiol10.1099/ijsem.0.0020892017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Firearms, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistryTranscriptome
Phylogeny31804916Novosphingobium umbonatum sp. nov., isolated from a freshwater mesocosm.Sheu SY, Cai CY, Kwon SW, Chen WMInt J Syst Evol Microbiol10.1099/ijsem.0.0038892020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/chemistry, Sphingomonadaceae/*classification/isolation & purification, Taiwan, Ubiquinone/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
43889Jong Woo Hyeon, Kyungchul Kim, Ah Ryeong Son, Eunmi Choi, Sung Kuk Lee, Che Ok JeonNovosphingobium humi sp. nov., isolated from soil of a military shooting range10.1099/ijsem.0.002089IJSEM 67: 3083-3088 201728829033
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/
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/