Strain identifier

BacDive ID: 158323

Type strain: Yes

Species: Nocardia rhizosphaerihabitans

Strain history: <- S. Qin, Jangsu Normal University, The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province; KLBMP S0039

NCBI tax ID(s): 1691570 (species)

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General

@ref: 64999

BacDive-ID: 158323

DSM-Number: 101726

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive

description: Nocardia rhizosphaerihabitans DSM 101726 is an aerobe, spore-forming, mesophilic bacterium that was isolated from coastal soil.

NCBI tax id

  • NCBI tax id: 1691570
  • Matching level: species

strain history

  • @ref: 64999
  • history: <- S. Qin, Jangsu Normal University, The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province; KLBMP S0039

doi: 10.13145/bacdive158323.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Nocardiaceae
  • genus: Nocardia
  • species: Nocardia rhizosphaerihabitans
  • full scientific name: Nocardia rhizosphaerihabitans Ding et al. 2018

@ref: 64999

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Nocardia

species: Nocardia rhizosphaerihabitans

full scientific name: Nocardia rhizosphaerihabitans Ding et al. 2018

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
65296positiveno
125439positive99.7
125439no92.4

multicellular morphology

  • @ref: 65296
  • forms multicellular complex: yes
  • complex color: yellowish white to white
  • further description: forms extensively branched, yellowish white to white substrate mycelium and white to gray–white aerial mycelium that fragments into short to elongated rod-like elements on tested media

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
64999TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
65296ISP2yes
65296ISP5yes
65296ISP6yes
65296tryptic soy agaryes
65296potato-dextrose agaryes
65296ISP3yes
65296ISP4yes
65296ISP7yes
65296Czapek's agaryes

culture temp

@refgrowthtypetemperature
64999positivegrowth28
65296positivegrowth10-37
65296positiveoptimum28

culture pH

@refabilitytypepHPH range
65296positivegrowth5-10alkaliphile
65296positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
65296aerobe
125438aerobe90.359
125439obligate aerobe98.8

halophily

@refsaltgrowthtested relationconcentration
65296NaClpositivegrowth0-5 %(w/v)
65296NaClpositiveoptimum1-3 %(w/v)

observation

  • @ref: 65296
  • observation: weakly acid-alcohol-fast

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6529616708adenine-hydrolysis
6529627613amygdalin+builds acid from
65296casein-hydrolysis
6529617057cellobiose-carbon source
6529662968cellulose-hydrolysis
6529615824D-fructose+carbon source
6529612936D-galactose-carbon source
6529617634D-glucose+carbon source
6529616024D-mannose+carbon source
6529616988D-ribose-carbon source
6529623652dextrin+carbon source
6529633946erythrose-carbon source
652965291gelatin-hydrolysis
6529615428glycine+nitrogen source
6529628087glycogen+builds acid from
6529617368hypoxanthine-hydrolysis
6529617268myo-inositol-carbon source
6529616977L-alanine+nitrogen source
6529630849L-arabinose+builds acid from
6529630849L-arabinose+carbon source
6529616467L-arginine+nitrogen source
6529615971L-histidine+nitrogen source
6529618019L-lysine+nitrogen source
6529617203L-proline+nitrogen source
6529617115L-serine+nitrogen source
6529617716lactose-carbon source
6529617306maltose+carbon source
6529637684mannose+builds acid from
6529674863methyl beta-D-xylopyranoside+builds acid from
65296milk+assimilation
6529616634raffinose-carbon source
6529626546rhamnose+carbon source
6529628017starch-hydrolysis
6529617992sucrose+builds acid from
6529627082trehalose+builds acid from
6529627082trehalose+carbon source
6529653424tween 20-hydrolysis
6529653423tween 40-hydrolysis
6529653426tween 80-hydrolysis
6529618222xylose-carbon source

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.group ID
652967809oxacillinyesyes1 µg (disc)
652963745clindamycinyesyes2 µg (disc)
65296100241ciprofloxacinyesyes5 µg (disc)
65296100246norfloxacinyesyes10 µg (disc)
6529648923erythromycinyesyes15 µg (disc)
6529663598levofloxacinyesyes5 µg (disc)
6529617334penicillinyesyes10 µg (disc)
652963732clarithromycinyesyes15 µg (disc)
6529650694minocyclineyesyes30 µg (disc)
652968309polymyxin byesyes30 µg (disc)
6529628001vancomycinyesyes30 µg (disc)
652969215spectinomycinyesyes100 µg (disc)
6529645924trimethoprimyesyes1.25 µg (disc)26
652969332sulfamethoxazoleyesyes23.75 µg (disc)26

metabolite production

  • @ref: 65296
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
65296urease+3.5.1.5
65296catalase+1.11.1.6

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65296C14:00.4
    65296C16:028.2
    65296C17:00.5
    65296C18:031.1
    65296C18:0 10-methyl, TBSA17.7
    65296C18:1ω9c12.2
    65296C20:00.3
    65296C16:1ω7c and/or C16:1ω6c7.9
    65296C19:1ω11c and/or C19:1ω9c0.5
  • type of FA analysis: whole cell analysis
  • incubation medium: tryptic soy broth
  • agar/liquid: liquid
  • incubation temperature: 28
  • incubation time: 5
  • software version: Sherlock 6.0
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
64999coastal soilJiangsu Province, Lianyungang region (34° 20' 29.4'' N, 119° 8' 25.4 E)ChinaCHNAsia34.3415119.14
65296rhizosphere soil of Lycium Linncoastal region in Lianyungang, Jiangsu ProvinceChinaCHNAsiastarch-arginine agar5.0 g glucose, 5.0 g soluble starch, 1.0 g yeast extract, 2.0 g hydrolyzed casein, 2.0 g CaCO3, 15.0 g agar, 1000 ml H2O, pH 7.2] supplemented with 3 % (w/v) NaCl and nystatin and nalidixic acid21 days28

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Plant#Rhizosphere
#Environmental#Terrestrial#Soil
#Host#Plants#Tree

taxonmaps

  • @ref: 69479
  • File name: preview.99_825.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_280;98_507;99_825&stattab=map
  • Last taxonomy: Nocardia
  • 16S sequence: KP972636
  • Sequence Identity:
  • Total samples: 542
  • soil counts: 198
  • aquatic counts: 84
  • animal counts: 206
  • plant counts: 54

Safety information

risk assessment

  • @ref: 64999
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessiondatabaselengthNCBI tax ID
65296Nocardia rhizosphaerihabitans strain KLBMP S0039 16S ribosomal RNA gene, partial sequenceKP972636nuccore
64999Nocardia rhizosphaerihabitans strain KLBMP S0039 16S ribosomal RNA gene, partial sequenceKP972636.3nuccore14071691570

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardia rhizosphaerihabitans CGMCC 4.7329GCA_014646295scaffoldncbi1691570
66792Nocardia rhizosphaerihabitans strain CGMCC 4.73291691570.3wgspatric1691570

GC content

  • @ref: 65296
  • GC-content: 68.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes89.75yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.667yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.359no
125438spore-formingspore-formingAbility to form endo- or exosporesyes58.643no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.9yes
125438motile2+flagellatedAbility to perform flagellated movementno89.4no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes86.3
125439BacteriaNetmotilityAbility to perform movementno92.4
125439BacteriaNetgram_stainReaction to gram-stainingpositive99.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe98.8

External links

@ref: 64999

culture collection no.: DSM 101726, CGMCC 4.7329, KCTC 39693, KLBMP S0039

straininfo link

  • @ref: 111133
  • straininfo: 408094

literature

  • topic: Phylogeny
  • Pubmed-ID: 29125460
  • title: Nocardia rhizosphaerihabitans sp. nov., a novel actinomycete isolated from a coastal soil.
  • authors: Ding P, Bai JL, Wang TT, Sun Y, Cao CL, Jiang JH, Qin S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002481
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Lycium/*microbiology, Nocardia/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
64999Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-101726Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101726)
65296Peng Ding, Juan-Luan Bai, Tian-Tian Wang, Yong Sun, Cheng-Liang Cao, Ji-Hong Jiang, Sheng QinNocardia rhizosphaerihabitans sp. nov., a novel actinomycete isolated from a coastal soil10.1099/ijsem.0.002481IJSEM 68: 192-197 201829125460
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
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/
111133Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID408094.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG