Strain identifier

BacDive ID: 141103

Type strain: Yes

Species: Nocardioides immobilis

Strain Designation: FLL521

Strain history: <- Lingfei Lu, Huzhong Agricultural Univ.

NCBI tax ID(s): 2049295 (species)

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General

@ref: 44011

BacDive-ID: 141103

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

description: Nocardioides immobilis FLL521 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from the soil of an iron mine.

NCBI tax id

  • NCBI tax id: 2049295
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Lingfei Lu, Huzhong Agricultural Univ.

doi: 10.13145/bacdive141103.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Nocardioides
  • species: Nocardioides immobilis
  • full scientific name: Nocardioides immobilis Lu et al. 2017

@ref: 44011

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Propionibacteriales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides immobilis

strain designation: FLL521

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
44011negative1.0-1.8 µm0.5-0.7 µmrod-shapedno
69480positive100

colony morphology

  • @ref: 44011
  • colony size: 1-2 mm
  • colony color: white
  • incubation period: 3 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

  • @ref: 44011
  • name: Reasoners 2A agar
  • growth: yes
  • composition: per litre: 0.25 g tryptone, 0.25 g peptone, 0.5 g yeast extract, 0.5 g soluble starch, 0.5 g casaminoacids, 0.5 g glucose, 0.3 g sodium pyruvate, 0.3 g K2HPO4 ,0.1 g MgSO4 , 15 g agar, pH 7.2

culture temp

@refgrowthtypetemperaturerange
44011positivegrowth16-32
44011positiveoptimum28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
44011positivegrowth6.5-9.0alkaliphile
44011positivegrowth8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
44011aerobe
67771aerobe

spore formation

@refspore formationconfidence
44011no
69481no97
69480no99.212

halophily

  • @ref: 44011
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 0.5 %

observation

@refobservation
44011growth on R2A, but not on nutrientagar, lysogeny broth or tryptic soy broth media
44011MK-8(H 4 ) is the predominant respiratory quinone

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4401116150benzoate-assimilation
4401115356cysteine-assimilation
4401116024D-mannose-assimilation
44011606565hippurate-assimilation
4401116467L-arginine-assimilation
4401117716lactose-assimilation
4401125115malate-assimilation
4401163019potassium sodium L-tartrate-assimilation
4401153258sodium citrate-assimilation
4401130911sorbitol-assimilation
4401116988D-ribose-builds acid from
4401117268myo-inositol-builds acid from
4401130849L-arabinose-builds acid from
4401117716lactose-builds acid from
4401129864mannitol-builds acid from
4401116634raffinose-builds acid from
4401130911sorbitol-builds acid from
4401117992sucrose-builds acid from
4401127082trehalose-builds acid from
4401127922sorbose-carbon source
44011casein-hydrolysis
4401162968cellulose-hydrolysis
4401116467L-arginine-hydrolysis
4401128017starch-hydrolysis
4401153424tween 20-hydrolysis
4401117632nitrate-reduction
4401112936D-galactose+assimilation
4401116988D-ribose+assimilation
4401117203L-proline+assimilation
4401116828L-tryptophan+assimilation
4401115611sarcosine+assimilation
4401112936D-galactose+builds acid from
4401116024D-mannose+builds acid from
4401117234glucose+builds acid from
4401117306maltose+builds acid from
4401117057cellobiose+carbon source
4401115824D-fructose+carbon source
4401117754glycerol+carbon source
4401117268myo-inositol+carbon source
4401130849L-arabinose+carbon source
4401162345L-rhamnose+carbon source
4401117306maltose+carbon source
4401129864mannitol+carbon source
4401128044phenylalanine+carbon source
4401116634raffinose+carbon source
4401117992sucrose+carbon source
4401127082trehalose+carbon source
440115291gelatin+hydrolysis
4401153423tween 40+hydrolysis
4401153425tween 60+hydrolysis
4401153426tween 80+hydrolysis
4401116199urea+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
4401130854indole-3-acetateno
4401115138sulfideyes

enzymes

@refvalueactivityec
44011cytochrome oxidase-1.9.3.1
44011catalase+1.11.1.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    44011C17:0 anteiso1
    44011C16:03.3
    44011C16:1ω7c and/or C15:0 Iso 2OH1.4
    44011C17:04
    4401110-methyl C17:03.3
    44011C17:1ω6c2
    44011C17:1ω8c9.2
    44011C18:02
    4401110-methyl C18:01.9
    44011C18:1ω9c13.5
    44011C14:0 iso1.6
    44011C15:0 iso2.4
    44011C16:0 iso41.3
    44011C16:1 iso H1.8
    44011C17:0 iso4
    44011C18:0 iso2.6
  • type of FA analysis: whole cell analysis
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6.1
  • system: MIS MIDI
  • method/protocol: Sasser, 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
44011the soil of an iron mineShanxi ProvinceChinaCHNAsia
67771From Jianshan mountain's iron mineTaiyuan City Shanxi provinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_179311.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_18723;97_47549;98_72227;99_179311&stattab=map
  • Last taxonomy: Nocardioides immobilis subclade
  • 16S sequence: KY684256
  • Sequence Identity:
  • Total samples: 286
  • soil counts: 249
  • aquatic counts: 17
  • animal counts: 9
  • plant counts: 11

Sequence information

16S sequences

  • @ref: 44011
  • description: 16S rRNA gene sequence
  • accession: KY684256
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides immobilis CCTCC AB 2017083GCA_003515065contigncbi2049295
66792Nocardioides immobilis strain CCTCC AB 20170832049295.3wgspatric2049295
66792Nocardioides immobilis CCTCC AB 20170832834611595draftimg2049295

GC content

  • @ref: 44011
  • GC-content: 70.3
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno97no
motileno97.287yes
gram-positiveyes82.113yes
anaerobicno98.577yes
aerobicyes92.847yes
halophileno94.379no
spore-formingno73.626no
glucose-utilyes90.038no
flagellatedno98.389yes
thermophileno95.916no
glucose-fermentno90.665no

External links

@ref: 44011

culture collection no.: KCTC 39931, CCTCC AB 2017083

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29068272Nocardioides immobilis sp. nov., isolated from iron mine soil.Lu L, Cao M, Wang D, Yuan K, Zhuang W, Guo W, Wang GInt J Syst Evol Microbiol10.1099/ijsem.0.0024502017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Iron, *Mining, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Phylogeny30403584Nocardioides silvaticus sp. nov., isolated from forest soil.Li C, Shi K, Zhang Y, Wang GInt J Syst Evol Microbiol10.1099/ijsem.0.0030792018Actinomycetales/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny33470924Nocardioides stalactiti sp. nov., isolated from a cave stalactite surface.Zhou XK, Huang Y, Zhang TK, Liu JJ, Liu ZY, Zhu ML, Ma L, Liu T, Wang XJ, Mo MHInt J Syst Evol Microbiol10.1099/ijsem.0.0046362021Bacterial Typing Techniques, Base Composition, Caves/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nocardioides/*classification/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, 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
44011Lingfei Lu, Min Cao, Dan Wang, Kai Yuan, Weiping Zhuang, Wei Guo, Gejiao WangNocardioides immobilis sp. nov., isolated from iron mine soil10.1099/ijsem.0.002450IJSEM 67: 5230-5234 201729068272
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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