Strain identifier

BacDive ID: 141059

Type strain: Yes

Species: Sphingomonas faucium

Strain Designation: E62-3

NCBI tax ID(s): 1762886 (species)

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General

@ref: 43938

BacDive-ID: 141059

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

description: Sphingomonas faucium E62-3 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from soil of Enshi Grand Canyon, Hubei province, PR China.

NCBI tax id

  • NCBI tax id: 1762886
  • Matching level: species

doi: 10.13145/bacdive141059.20230509.8.1

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 faucium
  • full scientific name: Sphingomonas faucium Liu et al. 2016

@ref: 43938

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Sphingomonadales

family: Sphingomonadaceae

genus: Sphingomonas

species: Sphingomonas faucium

strain designation: E62-3

type strain: yes

Morphology

cell morphology

  • @ref: 43938
  • gram stain: negative
  • cell length: 0.7-1.1 µm
  • cell width: 0.4-0.5 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 43938
  • colony color: yellow
  • colony shape: circular
  • incubation period: 3 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

@refnamegrowth
439381/10 tryptic soy agaryes
43938LB (Luria-Bertani) MEDIUMyes
43938MacConkey agarno
43938Nutrient agar (NA)yes
43938Reasoner's 2A agar (R2A)yes

culture temp

@refgrowthtypetemperaturerange
43938positivegrowth15-37
43938positiveoptimum28mesophilic

culture pH

@refabilitytypepHPH range
43938positivegrowth6.0-9.0alkaliphile
43938positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43938
  • oxygen tolerance: aerobe

halophily

  • @ref: 43938
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-0.5 %(w/v)

observation

  • @ref: 43938
  • observation: quinone Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4393830089acetate-assimilation
4393824265gluconate-assimilation
4393816977L-alanine-assimilation
4393815971L-histidine-assimilation
4393817203L-proline-assimilation
4393824996lactate-assimilation
4393817306maltose-assimilation
4393817272propionate-assimilation
4393817814salicin-assimilation
4393817992sucrose-assimilation
4393831011valerate-assimilation
4393816236ethanol-builds acid from
4393817716lactose-builds acid from
4393817234glucose-fermentation
43938casein-hydrolysis
439385291gelatin-hydrolysis
4393828017starch-hydrolysis
4393853426tween 80-hydrolysis
4393817632nitrate-reduction
4393817634D-glucose+assimilation
4393862345L-rhamnose+assimilation
4393828053melibiose+assimilation
4393816988D-ribose+builds acid from
4393865327D-xylose+builds acid from
4393830849L-arabinose+builds acid from
4393816991dna+hydrolysis
439384853esculin+hydrolysis
4393853424tween 20+hydrolysis

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitiveis resistant
439383393carbenicillinyesyes
4393848923erythromycinyesyes
43938100246norfloxacinyesyes
439387731ofloxacinyesyes
4393817334penicillinyesyes
439388232piperacillinyesyes
4393829007ceftriaxoneyesyes
4393850845doxycyclineyesyes
4393850694minocyclineyesyes
439383493cefoperazoneyesyes
439387507neomycinyesyes
439389332sulfamethoxazoleyesyes
4393823066cephalosporinyesyes
439383508ceftazidimeyesyes
439383515cefuroximeyesyes
439387809oxacillinyesyes
439385195furazolidoneyesyes
439383745clindamycinyesyes

metabolite production

@refChebi-IDmetaboliteproduction
4393815688acetoinno
4393816136hydrogen sulfideno
4393835581indoleyes

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
4393817234glucose-
4393815688acetoin-

enzymes

@refvalueactivityec
43938urease+3.5.1.5
43938arginine dihydrolase+3.5.3.6
43938catalase+1.11.1.6
43938cytochrome oxidase-1.9.3.1
43938beta-galactosidase+3.2.1.23
43938alpha-glucosidase+3.2.1.20
43938N-acetyl-beta-glucosaminidase+3.2.1.52
43938lipase (C 14)-
43938trypsin-3.4.21.4
43938beta-glucosidase-3.2.1.21
43938cystine arylamidase-3.4.11.3

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43938C14:02.3
    43938C14:0 2OH8.9
    43938C15:00.5
    43938C16:014.7
    43938C16:1ω5c1.8
    43938C16:1ω7c / C15:0 iso 2OH24.5
    43938C17:1ω6c1.7
    43938C18:1ω5c0.5
    43938C18:1ω7c36.4
    4393811-methyl C18:1ω7c6.4
    43938C19:0ω8c cyclo1.2
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A agar
  • agar/liquid: agar
  • incubation temperature: 28
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA40 4.10
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890 gas chromatograph
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 43938
  • sample type: soil of Enshi Grand Canyon, Hubei province, PR China
  • geographic location: Enshi Grand Canyon, Hubei province
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 30.4
  • longitude: 109.3
  • enrichment culture: 1/10 tryptic soy agar
  • enrichment culture duration: 1 week
  • enrichment culture temperature: 28

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_11538.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_4605;97_6989;98_8644;99_11538&stattab=map
  • Last taxonomy: Sphingomonas
  • 16S sequence: KU179043
  • Sequence Identity:
  • Total samples: 65
  • soil counts: 19
  • aquatic counts: 13
  • animal counts: 14
  • plant counts: 19

Sequence information

16S sequences

  • @ref: 43938
  • description: 16S rRNA gene sequence
  • accession: KU179043
  • database: nuccore

GC content

  • @ref: 43938
  • GC-content: 66.4
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 43938

culture collection no.: KCTC 42834, CCTCC AB 2015300

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27054358Sphingomonas faucium sp. nov., isolated from canyon soil.Liu D, Jin X, Sun X, Song Y, Feng L, Wang G, Li MInt J Syst Evol Microbiol10.1099/ijsem.0.0010642016Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Ubiquinone/analogs & derivatives/chemistryTranscriptome
Phylogeny29116039Sphingomonas colocasiae sp. nov., isolated from taro (Colocasia esculanta).Lin SY, Hameed A, Hsu YH, Liu YC, Hung MH, Lai WA, Young CCInt J Syst Evol Microbiol10.1099/ijsem.0.0024712017Bacterial Typing Techniques, Base Composition, Colocasia/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Sphingomonas/*classification/genetics/isolation & purification, Taiwan, Ubiquinone/chemistryTranscriptome
Phylogeny29872901Sphingomonas montis sp. nov., Isolated from Forest Soil of Low-Altitude Mountain.Chaudhary DK, Dahal RH, Kim JCurr Microbiol10.1007/s00284-018-1524-y2018*Altitude, DNA, Bacterial, Molecular Typing, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonas/chemistry/classification/genetics/*isolation & purificationTranscriptome

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
43938Dongmei Liu, Xin Jin, Xuelian Sun, Yali Song, Liling Feng, Gejiao Wang, Mingshun LiSphingomonas faucium sp. nov., isolated from canyon soil10.1099/ijsem.0.001064IJSEM 66: 2847-2852 201627054358
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/