Strain identifier

BacDive ID: 132455

Type strain: Yes

Species: Nakamurella endophytica

Strain Designation: 2Q3S-4-2

Strain history: CGMCC 4.7308 <-- L. Tuo; Inst. of Med. Biotechnol., Chin. Acad. Med. Sci. & Peking Union Med. Coll., China; 2Q3S-4-2.

NCBI tax ID(s): 1748367 (species)

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General

@ref: 24244

BacDive-ID: 132455

DSM-Number: 100722

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-positive, coccus-shaped, colony-forming

description: Nakamurella endophytica 2Q3S-4-2 is an aerobe, Gram-positive, coccus-shaped bacterium that forms circular colonies and was isolated from surface-sterilized bark of Kandelia candel.

NCBI tax id

  • NCBI tax id: 1748367
  • Matching level: species

strain history

@refhistory
24244<- L. Tuo, Chinese Acad. Sci. (CAS), Beijing; 2Q3S-4-2
67770CGMCC 4.7308 <-- L. Tuo; Inst. of Med. Biotechnol., Chin. Acad. Med. Sci. & Peking Union Med. Coll., China; 2Q3S-4-2.

doi: 10.13145/bacdive132455.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Nakamurellales
  • family: Nakamurellaceae
  • genus: Nakamurella
  • species: Nakamurella endophytica
  • full scientific name: Nakamurella endophytica Tuo et al. 2016

@ref: 24244

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nakamurellaceae

genus: Nakamurella

species: Nakamurella endophytica

full scientific name: Nakamurella endophytica Tuo et al. 2016

strain designation: 2Q3S-4-2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
43733positive0.8-1.2 µmcoccus-shaped
69480no96.278
69480positive100

colony morphology

  • @ref: 43733
  • colony color: Vivid orange-yellow
  • colony shape: circular
  • medium used: ISP2 agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43733ISP 2 agaryes
43733ISP 3 agaryes
43733ISP 4 agarno
43733ISP 5 agarno
43733ISP2 agaryes
43733Reasoner's 2A agar (R2A)yes
24244R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43733positivegrowth20-37
43733positiveoptimum28-30mesophilic
24244positivegrowth28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
43733positivegrowth5-9alkaliphile
43733positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43733
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
43733no
69481yes98
69480no93.962

halophily

@refsaltgrowthtested relationconcentrationhalophily level
43733NaClpositivegrowth0-2 %(w/v)
43733NaClpositiveoptimum0 %(w/v)non-halophilic

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4373317128adipate-assimilation
4373327689decanoate-assimilation
4373317634D-glucose-assimilation
4373316899D-mannitol-assimilation
4373316024D-mannose-assimilation
4373330849L-arabinose-assimilation
4373325115malate-assimilation
4373317306maltose-assimilation
43733506227N-acetylglucosamine-assimilation
4373318401phenylacetate-assimilation
4373332032potassium gluconate-assimilation
4373353258sodium citrate-assimilation
4373317234glucose-fermentation
4373328017starch-hydrolysis
4373353423tween 40-hydrolysis
4373353426tween 80-hydrolysis
4373315588D-malate-oxidation
4373315589L-malate-oxidation
43733167632-oxobutanoate-oxidation
43733309162-oxoglutarate-oxidation
43733739183-O-methyl-D-glucose-oxidation
43733181014-hydroxyphenylacetic acid-oxidation
4373330089acetate-oxidation
43733645522-hydroxybutyrate-oxidation
437338295beta-hydroxybutyrate-oxidation
4373373706bromosuccinate-oxidation
4373316947citrate-oxidation
4373315570D-alanine-oxidation
4373329990D-aspartate-oxidation
4373333801D-saccharate-oxidation
4373316523D-serine-oxidation
4373323652dextrin-oxidation
4373315740formate-oxidation
4373316537galactarate-oxidation
4373316865gamma-aminobutyric acid-oxidation
4373370744glycine-proline-oxidation
4373317596inosine-oxidation
4373316467L-arginine-oxidation
4373329991L-aspartate-oxidation
4373318287L-fucose-oxidation
4373329985L-glutamate-oxidation
4373315971L-histidine-oxidation
4373318183L-pyroglutamic acid-oxidation
4373317115L-serine-oxidation
4373328053melibiose-oxidation
4373374611methyl (R)-lactate-oxidation
4373337657methyl D-glucoside-oxidation
4373317268myo-inositol-oxidation
4373328037N-acetylgalactosamine-oxidation
4373317272propionate-oxidation
4373326490quinate-oxidation
4373316634raffinose-oxidation
4373317164stachyose-oxidation
4373317632nitrate-reduction
437334853esculin+builds acid from
43733casein+hydrolysis
4373316651(S)-lactate+oxidation
4373313705acetoacetate+oxidation
4373317925alpha-D-glucose+oxidation
4373336219alpha-lactose+oxidation
4373317057cellobiose+oxidation
4373318333D-arabitol+oxidation
4373315824D-fructose+oxidation
4373378697D-fructose 6-phosphate+oxidation
4373328847D-fucose+oxidation
4373315895D-galactonic acid lactone+oxidation
4373312936D-galactose+oxidation
4373318024D-galacturonic acid+oxidation
437338391D-gluconate+oxidation
4373314314D-glucose 6-phosphate+oxidation
4373315748D-glucuronate+oxidation
4373316899D-mannitol+oxidation
4373316024D-mannose+oxidation
4373317924D-sorbitol+oxidation
437335291gelatin+oxidation
4373328066gentiobiose+oxidation
4373332323glucuronamide+oxidation
4373317754glycerol+oxidation
4373362345L-rhamnose+oxidation
4373317306maltose+oxidation
4373351850methyl pyruvate+oxidation
4373363154N-acetyl-beta-D-mannosamine+oxidation
43733506227N-acetylglucosamine+oxidation
4373335418n-acetylneuraminate+oxidation
4373317309pectin+oxidation
4373317814salicin+oxidation
4373317992sucrose+oxidation
4373327082trehalose+oxidation
4373332528turanose+oxidation
4373353423tween 40+oxidation
43733581435-dehydro-D-gluconate+/-builds acid from
4373362318D-lyxose+/-builds acid from
4373316988D-ribose+/-builds acid from
4373316443D-tagatose+/-builds acid from
4373365327D-xylose+/-builds acid from
4373362345L-rhamnose+/-builds acid from
4373317814salicin+/-builds acid from

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitiveis resistant
4373371321fusidateyesyes
4373348607lithium chlorideyesyes
4373350694minocyclineyesyes
4373375273niaproofyesyes
4373329673rifamycin svyesyes
4373375229sodium bromateyesyes
4373375198tetrazolium blueyesyes
4373345735troleandomycinyesyes
43733161680aztreonamyesyes
4373332735guanidinium chlorideyesyes
437336472lincomycinyesyes
43733100147nalidixic acidyesyes
4373375248potassium telluriteyesyes
4373364103sodium butyrateyesyes
437331 % sodium lactateyesyes
4373375193tetrazolium violetyesyes
4373328001vancomycinyesyes

metabolite production

  • @ref: 43733
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

metabolite tests

  • @ref: 43733
  • Chebi-ID: 17234
  • metabolite: glucose
  • methylred-test: -

enzymes

@refvalueactivityec
43733catalase+1.11.1.6
43733cytochrome oxidase-1.9.3.1
43733acid phosphatase+3.1.3.2
43733alkaline phosphatase+3.1.3.1
43733esterase Lipase (C 8)+
43733alpha-glucosidase+3.2.1.20
43733beta-glucosidase+3.2.1.21
43733leucine arylamidase+3.4.11.1
43733naphthol-AS-BI-phosphohydrolase+
43733valine arylamidase+/-
43733N-acetyl-beta-glucosaminidase-3.2.1.52
43733alpha-chymotrypsin-3.4.21.1
43733cystine arylamidase-3.4.11.3
43733esterase (C 4)-
43733alpha-fucosidase-3.2.1.51
43733alpha-galactosidase-3.2.1.22
43733beta-galactosidase-3.2.1.23
43733beta-glucuronidase-3.2.1.31
43733lipase (C 14)-
43733alpha-mannosidase-3.2.1.24
43733trypsin-3.4.21.4
43733urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitude
24244surface-sterilized bark of Kandelia candelKandelia candelMacao, Cotai Ecological ZonesChinaCHNAsia22.1333113.55
43733Surface-sterilized bark of Kandelia candel collected from Cotai Ecological ZonesMacaoChinaCHNAsia22.141113.575
67770Surface-sterilized bark of Kandelia candel from Cotai Ecological ZonesKandelia candelMacaoChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#Host#Plants#Tree
#Host Body-Site#Plant#Bark
#Host Body-Site#Plant#Sterilized plant part

taxonmaps

  • @ref: 69479
  • File name: preview.99_8608.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_3989;97_4905;98_6280;99_8608&stattab=map
  • Last taxonomy: Nakamurella endophytica subclade
  • 16S sequence: KT971019
  • Sequence Identity:
  • Total samples: 809
  • soil counts: 599
  • aquatic counts: 52
  • animal counts: 43
  • plant counts: 115

Safety information

risk assessment

  • @ref: 24244
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24244
  • description: Nakamurella endophytica strain 2Q3S-4-2 16S ribosomal RNA gene, partial sequence
  • accession: KT971019
  • length: 1475
  • database: ena
  • NCBI tax ID: 1748367

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nakamurella endophytica CGMCC 4.7308GCA_014646215scaffoldncbi1748367
66792Nakamurella endophytica strain CGMCC 4.73081748367.3wgspatric1748367

GC content

  • @ref: 24244
  • GC-content: 67.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes98no
flagellatedno98.745no
gram-positiveyes90.44yes
anaerobicno99.482no
aerobicyes93.398yes
halophileno96.461yes
spore-formingno89.627yes
thermophileno97.04yes
glucose-utilyes84.979no
motileno90.813no
glucose-fermentno87.243no

External links

@ref: 24244

culture collection no.: DSM 100722, CGMCC 4.7308, JCM 31778

straininfo link

  • @ref: 90793
  • straininfo: 400713

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny26813967Nakamurella endophytica sp. nov., a novel endophytic actinobacterium isolated from the bark of Kandelia candel.Tuo L, Li FN, Pan Z, Lou I, Guo M, Ming-Yuen Lee S, Chen L, Hu L, Sun CHInt J Syst Evol Microbiol10.1099/ijsem.0.0009232016Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Peptidoglycan/chemistry, *Phylogeny, Plant Bark/*microbiology, RNA, Ribosomal, 16S/genetics, Rhizophoraceae/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny28820108Nakamurella intestinalis sp. nov., isolated from the faeces of Pseudorhynchus japonicus.Kim SJ, Cho H, Joa JH, Hamada M, Ahn JH, Weon HY, Kwon SWInt J Syst Evol Microbiol10.1099/ijsem.0.0020592017Actinomycetales/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Feces/*microbiology, Orthoptera/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

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
24244Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100722Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100722)
43733Li Tuo, Fei-Na Li, Zhen Pan, Inchio Lou, Min Guo, Simon Ming-Yuen Lee, Li Chen, Lin Hu, Cheng-Hang SunNakamurella endophytica sp. nov., a novel endophytic actinobacterium isolated from the bark of Kandelia candel10.1099/ijsem.0.000923IJSEM 66: 1577-1582 201626813967
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/
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
90793Reimer, 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-ID400713.1