Strain identifier

BacDive ID: 140492

Type strain: Yes

Species: Flexivirga endophytica

Strain history: <- Wenjun Li

NCBI tax ID(s): 1849103 (species)

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General

@ref: 43104

BacDive-ID: 140492

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

description: Flexivirga endophytica KCTC 39536 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from leaf sample of Sweet Basil.

NCBI tax id

  • NCBI tax id: 1849103
  • Matching level: species

strain history

@refhistory
67770W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; YIM 7505.
67771<- Wenjun Li

doi: 10.13145/bacdive140492.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Dermacoccaceae
  • genus: Flexivirga
  • species: Flexivirga endophytica
  • full scientific name: Flexivirga endophytica Gao et al. 2016

@ref: 43104

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Micrococcales

family: Dermacoccaceae

genus: Flexivirga

species: Flexivirga endophytica

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43104positive0.6-0.8 µm0.6-0.8 µmcoccus-shapedno
69480no93.653
69480positive100

colony morphology

  • @ref: 43104
  • colony color: orange-yellow
  • medium used: plant agar 8

Culture and growth conditions

culture medium

  • @ref: 43104
  • name: plant agar 8
  • growth: yes
  • composition: yeast extract 0.5 g/l, aspartic acid 2 g/l, KNO3 0.5 g/l, K2HPO4x3H2O 0.5 g/l, MgSO4x7H2O 0.5 g/l, CaCO3 0.5 g/l, NaCl 2 g/l, trace salts solution 1 ml/l, nalidixic acid 25 mg/l, nystatin 50 mg/l

culture temp

@refgrowthtypetemperaturerange
43104positiveoptimum28-35mesophilic
43104positivegrowth20-45
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepH
43104positivegrowth5.0-8.0
43104positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43104aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no92
69480no99.925

halophily

@refsaltgrowthtested relationconcentration
43104NaClpositivegrowth0-7 %
43104NaClpositiveoptimum0-3 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4310417632nitrate+reduction
431045291gelatin+hydrolysis
4310453424tween 20+hydrolysis
4310453423tween 40+hydrolysis
4310453425tween 60+hydrolysis
4310453426tween 80+hydrolysis
43104casein-hydrolysis
4310428017starch-hydrolysis
4310417108D-arabinose+carbon source
4310429016arginine+carbon source
4310417057cellobiose+carbon source
4310415824D-fructose+carbon source
4310417634D-glucose+carbon source
4310429985L-glutamate+carbon source
4310417754glycerol+carbon source
4310417306maltose+carbon source
4310416899D-mannitol+carbon source
4310416024D-mannose+carbon source
4310462345L-rhamnose+carbon source
4310417115L-serine+carbon source
4310417992sucrose+carbon source
4310427082trehalose+carbon source
4310418333D-arabitol-carbon source
4310428847D-fucose-carbon source
4310417716lactose-carbon source
4310416988D-ribose-carbon source
4310465327D-xylose-carbon source
431044853esculin+hydrolysis
4310417634D-glucose+assimilation
4310430849L-arabinose+assimilation
4310416024D-mannose+assimilation
4310416899D-mannitol+assimilation
43104506227N-acetylglucosamine+assimilation
4310417306maltose+assimilation
4310432032potassium gluconate+assimilation
4310417128adipate+assimilation
4310425115malate+assimilation
4310453258sodium citrate+assimilation
4310418401phenylacetate+assimilation
4310427689decanoate-assimilation
4310417234glucose-fermentation
43104506227N-acetylglucosamine+builds acid from
431044853esculin+builds acid from
4310422599arabinose+builds acid from
4310417057cellobiose+builds acid from
4310415824D-fructose+builds acid from
4310417634D-glucose+builds acid from
4310417754glycerol+builds acid from
43104581435-dehydro-D-gluconate+builds acid from
4310462318D-lyxose+builds acid from
4310416899D-mannitol+builds acid from
4310462345L-rhamnose+builds acid from
4310417992sucrose+builds acid from
4310427082trehalose+builds acid from
4310432528turanose+builds acid from
4310418333D-arabitol+builds acid from
4310415963ribitol-builds acid from
4310427613amygdalin-builds acid from
4310422605arabinitol-builds acid from
4310418305arbutin-builds acid from
4310416813galactitol-builds acid from
4310417113erythritol-builds acid from
4310433984fucose-builds acid from
4310412936D-galactose-builds acid from
4310428066gentiobiose-builds acid from
4310424265gluconate-builds acid from
4310428087glycogen-builds acid from
4310417268myo-inositol-builds acid from
4310415443inulin-builds acid from
43104168082-dehydro-D-gluconate-builds acid from
4310417716lactose-builds acid from
4310417306maltose-builds acid from
4310416024D-mannose-builds acid from
431046731melezitose-builds acid from
4310428053melibiose-builds acid from
43104320061methyl alpha-D-glucopyranoside-builds acid from
4310443943methyl alpha-D-mannoside-builds acid from
4310474863methyl beta-D-xylopyranoside-builds acid from
4310416634raffinose-builds acid from
4310416988D-ribose-builds acid from
4310417814salicin-builds acid from
4310430911sorbitol-builds acid from
4310417266L-sorbose-builds acid from
4310428017starch-builds acid from
4310416443D-tagatose-builds acid from
4310417151xylitol-builds acid from
4310418222xylose-builds acid from

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.group ID
431042637amikacinyesyes30 µg (disc)
431043517cefuroxime sodiumyesyes30 µg (disc)
4310417698chloramphenicolyesyes30 µg (disc)
43104100241ciprofloxacinyesyes5 µg (disc)
4310448923erythromycinyesyes15 µg (disc)
4310417833gentamicinyesyes10 µg (disc)
43104100246norfloxacinyesyes10 µg (disc)
4310428368novobiocinyesyes30 µg (disc)
4310486455optochinyesyes5 µg (disc)
431047809oxacillinyesyes1 µg (disc)
4310417334penicillinyesyes10 Unit (disc)
431048232piperacillinyesyes100 µg (disc)
4310459062polymyxinyesyes300 Unit (disc)
431049332sulfamethoxazoleyesyes23.75 µg (disc)26
4310427902tetracyclineyesyes30 µg (disc)
4310445924trimethoprimyesyes1.25 µg (disc)26
4310428001vancomycinyesyes30 µg (disc)

metabolite production

  • @ref: 43104
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43104catalase+1.11.1.6
43104cytochrome oxidase-1.9.3.1
43104alkaline phosphatase+3.1.3.1
43104esterase (C 4)+
43104esterase Lipase (C 8)+
43104leucine arylamidase+3.4.11.1
43104valine arylamidase+
43104cystine arylamidase+3.4.11.3
43104trypsin+3.4.21.4
43104acid phosphatase+3.1.3.2
43104naphthol-AS-BI-phosphohydrolase+
43104alpha-glucosidase+3.2.1.20
43104beta-glucosidase+3.2.1.21
43104N-acetyl-beta-glucosaminidase+3.2.1.52
43104alpha-mannosidase+3.2.1.24
43104alpha-chymotrypsin+3.4.21.1
43104beta-galactosidase+3.2.1.23
43104lipase (C 14)-
43104alpha-galactosidase-3.2.1.22
43104beta-glucuronidase-3.2.1.31
43104beta-D-fucosidase-3.2.1.38
43104arginine dihydrolase+3.5.3.6
43104urease+3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43104C16:0 iso34
    43104C15:0 iso8.9
    43104C17:0 anteiso7.9
    43104C16:0 10-methyl/iso-C17:1ω9c6.8
    43104C16:1 iso H6.1
    43104C17:1 anteiso ω9c5.1
  • type of FA analysis: whole cell analysis
  • incubation medium: TSA (Difco)
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 4
  • software version: Sherlock 6.1
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture durationenrichment culture temperature
43104leaf sample of Sweet BasilImpression Tobacco farm, Shilin County, Yunnan ProvinceChinaCHNAsia24103plant agar 84 weeks30
67771from the leaf of Sweet BasilChinaCHNAsia
67770Leaf of Sweet Basil from Impression Tobacco farm in Shilin CountyYunnan Province, south-west ChinaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Leaf (Phyllosphere)

taxonmaps

  • @ref: 69479
  • File name: preview.99_80437.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_20999;97_42858;98_55991;99_80437&stattab=map
  • Last taxonomy: Flexivirga endophytica subclade
  • 16S sequence: KX151661
  • Sequence Identity:
  • Total samples: 305
  • soil counts: 63
  • aquatic counts: 57
  • animal counts: 181
  • plant counts: 4

Sequence information

16S sequences

  • @ref: 43104
  • description: Flexivirga sp. YIM 7505 16S ribosomal RNA gene, partial sequence
  • accession: KX151661
  • length: 1516
  • database: nuccore
  • NCBI tax ID: 1849103

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flexivirga endophytica CGMCC 1.15085GCA_014640635contigncbi1849103
66792Flexivirga endophytica KCTC 39536GCA_014652735scaffoldncbi1849103
66792Flexivirga endophytica strain CGMCC 1.150851849103.3wgspatric1849103
66792Flexivirga endophytica strain KCTC 395361849103.4wgspatric1849103

GC content

  • @ref: 67770
  • GC-content: 66.7
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno92no
motileno95.21yes
flagellatedno98.446no
gram-positiveyes88.964yes
anaerobicno99.107yes
aerobicyes92.349yes
halophileno91.726no
spore-formingno63.487no
glucose-utilyes89.186no
thermophileno97.772no
glucose-fermentno87.557yes

External links

@ref: 43104

culture collection no.: KCTC 39536, CGMCC 1.15085, YIM 7505, JCM 30628

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27264701Flexivirga endophytica sp. nov., an endophytic actinobacterium isolated from a leaf of Sweet Basil.Gao R, Liu BB, Yang W, Song PF, Chen W, Salam N, Duan YQ, Li QQ, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0012112016Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Ocimum basilicum/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Leaves/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny27902309Flexivirga oryzae sp. nov., isolated from soil of a rice paddy, and emended description of the genus Flexivirga Anzai et al. 2012.Hyeon JW, Kim HR, Lee HJ, Jeong SE, Choi SH, Jeon COInt J Syst Evol Microbiol10.1099/ijsem.0.0016572017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Oryza/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31800390Flexivirga caeni sp. nov., isolated from activated sludge.Keum DH, Lee YJ, Lee SY, Im WTInt J Syst Evol Microbiol10.1099/ijsem.0.0039102020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny33249533Flexivirga aerilata sp. nov., Isolated from an Automobile Air Conditioning System.Chaudhary DK, Lee H, Dahal RH, Kim DH, Cha IT, Lee KE, Kim DUCurr Microbiol10.1007/s00284-020-02300-z2020Actinobacteria, *Air Conditioning, *Automobiles, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids, Nucleic Acid Hybridization, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNATranscriptome

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
43104Rui Gao, Bing-Bing Liu, Wei Yang, Peng-Fei Song, Wei Chen, Nimaichand Salam, Yan-Qing Duan, Qing-Qing Li, Wen-Jun LiFlexivirga endophytica sp. nov., an endophytic actinobacterium isolated from a leaf of Sweet Basil10.1099/ijsem.0.001211IJSEM 66: 3388-3392 201627264701
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/
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