Strain identifier

BacDive ID: 159868

Type strain: Yes

Species: Nocardioides allogilvus

Strain history: <- Wenjun Li, Sun Sat-Sen Univ.

NCBI tax ID(s): 2072017 (species)

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General

@ref: 66607

BacDive-ID: 159868

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

description: Nocardioides allogilvus KCTC 49020 is an aerobe, Gram-positive, coccus-shaped bacterium that forms circular colonies and was isolated from soil collected at a karst cave.

NCBI tax id

  • NCBI tax id: 2072017
  • Matching level: species

strain history

  • @ref: 67771
  • history: <- Wenjun Li, Sun Sat-Sen Univ.

doi: 10.13145/bacdive159868.20240916.9.1

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 allogilvus
  • full scientific name: Nocardioides allogilvus Zhang et al. 2018

@ref: 66607

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Propionibacteriales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides allogilvus

type strain: yes

Morphology

cell morphology

  • @ref: 66607
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

colony morphology

  • @ref: 66607
  • colony color: pale yellow
  • colony shape: circular
  • incubation period: 4 days
  • medium used: R2A medium

Culture and growth conditions

culture medium

@refnamegrowth
66607Czapek's agaryes
66607Gause's synthetic agarno
66607ISP 2yes
66607ISP 3yes
66607ISP 4yes
66607ISP 5no
66607Nutrient agar (NA)yes
66607potato-dextrose agarno
66607Reasoner's 2A agar (R2A)yes

culture temp

@refgrowthtypetemperature
66607positiveoptimum28
66607positivegrowth4-35
67771positivegrowth28

culture pH

  • @ref: 66607
  • ability: positive
  • type: growth
  • pH: 8.0-10.0
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
66607aerobe
67771aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

halophily

  • @ref: 66607
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-6 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6660715748D-glucuronate+carbon source
6660716634raffinose+carbon source
6660716899D-mannitol+carbon source
6660717057cellobiose+carbon source
6660717115L-serine+carbon source
6660717164stachyose+carbon source
6660717306maltose+carbon source
6660717309pectin+carbon source
6660717596inosine+carbon source
6660717716lactose+carbon source
6660717814salicin+carbon source
6660717992sucrose+carbon source
6660718287L-fucose+carbon source
6660726490quinate+carbon source
6660727082trehalose+carbon source
6660728053melibiose+carbon source
6660728800N-acetylgalactosamine+carbon source
6660728847D-fucose+carbon source
6660729991L-aspartate+carbon source
6660730612D-glucarate+carbon source
6660732323glucuronamide+carbon source
6660732528turanose+carbon source
6660735418n-acetylneuraminate+carbon source
6660753423tween 40+carbon source
6660759640N-acetylglucosamine+carbon source
6660762345L-rhamnose+carbon source
6660763153N-acetyl-D-mannosamine+carbon source
66607739183-O-methyl-D-glucose+carbon source
66607100147nalidixic acid+carbon source
66607320055methyl beta-D-glucopyranoside+carbon source
666075291gelatin-hydrolysis
6660728017starch-hydrolysis
6660753426tween 80-hydrolysis
6660762968cellulose-hydrolysis
66607milk-hydrolysis
6660753423tween 40+hydrolysis
6660753424tween 20+hydrolysis
6660753425tween 60+hydrolysis
6660717632nitrate+reduction

metabolite production

  • @ref: 66607
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

@refvalueactivityec
66607alpha-fucosidase-3.2.1.51
66607alpha-mannosidase-3.2.1.24
66607beta-D-fucosidase-3.2.1.38
66607beta-galactosidase-3.2.1.23
66607beta-glucosidase-3.2.1.21
66607beta-glucuronidase-3.2.1.31
66607chymotrypsin-3.4.4.5
66607N-acetyl-beta-glucosaminidase-3.2.1.52
66607trypsin-3.4.21.4
66607urease-3.5.1.5
66607acid phosphatase+3.1.3.2
66607alkaline phosphatase+3.1.3.1
66607alpha-glucosidase+3.2.1.20
66607catalase+1.11.1.6
66607cystine arylamidase+3.4.11.3
66607cytochrome oxidase+1.9.3.1
66607esterase (C 4)+
66607esterase Lipase (C 8)+
66607leucine arylamidase+3.4.11.1
66607lipase (C 14)+
66607naphthol-AS-BI-phosphohydrolase+
66607valine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    66607C19:0 iso1
    66607C17:1 iso w9c / C16:0 10-methyl4
    66607C16:0 anteiso0.5
    66607C17:00.5
    66607C17:0 iso0.5
    66607C17:1 w6c0.6
    66607C14:0 iso0.7
    66607C17:0 anteiso1.1
    66607C20:1 w9c1.2
    66607C16:01.6
    66607C18:1 iso H1.7
    66607C18:0 iso2.2
    66607C18:1 2OH2.7
    66607C14:0 anteiso22.2
    66607C16:0 iso25.4
    66607C16:1 w7c / C16:1 w6c3.7
    66607C19:1 w11c / C19:1 w9c3.9
    66607C16:1 iso H7.7
    66607C18:1 w9c7.9
    66607C17:1 w8c8.4
  • type of FA analysis: whole cell analysis
  • incubation medium: TSA
  • incubation temperature: 28
  • incubation time: 3
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • method/protocol: Sasser, 1990

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
66607soil collected at a karst caveLuoyang County, Henan ProvinceChinaCHNAsia33.7667111.567ISP 2supplemented with nystatin (50 mg/l), nalidixic acid (20 mg/l)14 days28
67771From soil of karst caveHenan provinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Geologic
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_6858.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_851;97_993;98_5048;99_6858&stattab=map
  • Last taxonomy: Nocardioides
  • 16S sequence: MG800321
  • Sequence Identity:
  • Total samples: 21802
  • soil counts: 13298
  • aquatic counts: 2750
  • animal counts: 3378
  • plant counts: 2376

Sequence information

16S sequences

  • @ref: 66607
  • description: Nocardioides allogilvus 16S ribosomal RNA gene, partial sequence
  • accession: MG800321
  • length: 1471
  • database: nuccore
  • NCBI tax ID: 2072017

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides allogilvus KCTC 49020GCA_003047285contigncbi2072017
66792Nocardioides sp. KCTC 490202144186.3wgspatric2072017
66792Nocardioides allogilvus KCTC 490202855286858draftimg2072017

GC content

  • @ref: 66607
  • GC-content: 69.90
  • method: genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes89.73yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no96.482no
69480spore-formingspore-formingAbility to form endo- or exosporesno65.1no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.284no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno97yes
69480flagellatedmotile2+Ability to perform flagellated movementno89no

External links

@ref: 66607

culture collection no.: KCTC 49020, CGMCC 4.7457, CFH 30205

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29927366Nocardioides allogilvus sp. nov., a novel actinobacterium isolated from a karst cave.Zhang LY, Ming H, Zhao ZL, Ji WL, Salam N, Jiao JY, Fang BZ, Li WJ, Nie GXInt J Syst Evol Microbiol10.1099/ijsem.0.0028632018Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Phylogeny33877575Description of Nocardioides piscis sp. nov., Sphingomonas piscis sp. nov. and Sphingomonas sinipercae sp. nov., isolated from the intestine of fish species Odontobutis interrupta (Korean spotted sleeper) and Siniperca scherzeri (leopard mandarin fish).Hyun DW, Jeong YS, Lee JY, Sung H, Lee SY, Choi JW, Kim HS, Kim PS, Bae JWJ Microbiol10.1007/s12275-021-1036-52021Animals, Base Composition, DNA, Bacterial/genetics/metabolism, Fishes/microbiology, Intestines/microbiology, Nocardioides/*classification/genetics/*isolation & purification/metabolism, Phospholipids/metabolism, Phylogeny, Republic of Korea, Sphingomonas/*classification/genetics/*isolation & purification/metabolismMetabolism

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
66607Ling-Yu Zhang, Hong Ming, Zhuo-Li Zhao, Wei-Li Ji, Nimaichand Salam, Jian-Yu Jiao, Bao-Zhu Fang, Wen-Jun Li and Guo-Xing NieNocardioides allogilvus sp. nov., a novel actinobacterium isolated from a karst cave10.1099/ijsem.0.002863IJSEM 68: 2485-2490 201829927366
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
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