Strain identifier

BacDive ID: 132574

Type strain: Yes

Species: Filimonas zeae

Strain Designation: 772

Strain history: <- J. L. Gao, Beijing Academy of Agriculture and Forestry Science; 772

NCBI tax ID(s): 1737353 (species)

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General

@ref: 24363

BacDive-ID: 132574

DSM-Number: 100760

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, motile, filament-shaped, colony-forming

description: Filimonas zeae 772 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from surface-sterilized root tissue of maize plant.

NCBI tax id

  • NCBI tax id: 1737353
  • Matching level: species

strain history

  • @ref: 24363
  • history: <- J. L. Gao, Beijing Academy of Agriculture and Forestry Science; 772

doi: 10.13145/bacdive132574.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Chitinophagia
  • order: Chitinophagales
  • family: Chitinophagaceae
  • genus: Filimonas
  • species: Filimonas zeae
  • full scientific name: Filimonas zeae Gao et al. 2016

@ref: 24363

domain: Bacteria

phylum: Bacteroidetes

class: Chitinophagia

order: Sphingobacteriales

family: Chitinophagaceae

genus: Filimonas

species: Filimonas zeae

full scientific name: Filimonas zeae Gao et al. 2016

strain designation: 772

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43949negative2.9-14.6 µm0.2-0.4 µmfilament-shapedyesgliding
69480negative99.998

colony morphology

  • @ref: 43949
  • colony size: 0.5 mm
  • colony color: yellowish
  • colony shape: circular
  • incubation period: 4 days
  • medium used: Luria-Bertani agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43949CCM nitrogen free mediumyes
43949LB (Luria-Bertani) MEDIUMyes
43949Nutrient agar (NA)yes
43949Reasoner's 2A agar (R2A)yes
43949Tryptic soy agaryes
24363R2A 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
43949positivegrowth15-37
43949positiveoptimum28-30mesophilic
24363positivegrowth28mesophilic

culture pH

@refabilitytypepH
43949positivegrowth5.0-7.0
43949positiveoptimum6

Physiology and metabolism

oxygen tolerance

  • @ref: 43949
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.965

halophily

  • @ref: 43949
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 5 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4394917128adipate-assimilation
4394927689decanoate-assimilation
4394916899D-mannitol-assimilation
4394925115malate-assimilation
43949506227N-acetylglucosamine-assimilation
4394918401phenylacetate-assimilation
4394932032potassium gluconate-assimilation
4394953258sodium citrate-assimilation
4394916947citrate-carbon source
4394916899D-mannitol-carbon source
4394915978glycerol 3-phosphate-carbon source
4394917464L-galactonic acid gamma-lactone-carbon source
4394951850methyl pyruvate-carbon source
4394917992sucrose-carbon source
4394927613amygdalin-fermentation
4394922599arabinose-fermentation
4394917634D-glucose-fermentation
4394916899D-mannitol-fermentation
4394917924D-sorbitol-fermentation
4394917234glucose-fermentation
4394917268myo-inositol-fermentation
4394930849L-arabinose-fermentation
4394962345L-rhamnose-fermentation
4394928053melibiose-fermentation
4394917992sucrose-fermentation
43949casein-hydrolysis
4394916991dna-hydrolysis
4394928017starch-hydrolysis
4394917632nitrate-reduction
4394917634D-glucose+assimilation
4394917925alpha-D-glucose+carbon source
4394936219alpha-lactose+carbon source
4394917057cellobiose+carbon source
4394912936D-galactose+carbon source
4394918024D-galacturonic acid+carbon source
4394915748D-glucuronate+carbon source
4394916024D-mannose+carbon source
43949495056gamma-cyclodextrin+carbon source
439495291gelatin+carbon source
4394928066gentiobiose+carbon source
4394970744glycine-proline+carbon source
4394962345L-rhamnose+carbon source
4394917306maltose+carbon source
4394928053melibiose+carbon source
43949320055methyl beta-D-glucopyranoside+carbon source
4394917309pectin+carbon source
4394917814salicin+carbon source
4394975198tetrazolium blue+carbon source
4394975193tetrazolium violet+carbon source
4394927082trehalose+carbon source
439494853esculin+hydrolysis
439495291gelatin+hydrolysis
4394918186tyrosine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
4394915688acetoinno
4394916136hydrogen sulfideno
4394935581indoleno

enzymes

@refvalueactivityec
43949catalase+1.11.1.6
43949cytochrome oxidase+1.9.3.1
43949beta-galactosidase+3.2.1.23
43949arginine dihydrolase-3.5.3.6
43949lysine decarboxylase-4.1.1.18
43949urease-3.5.1.5
43949tryptophan deaminase-4.1.99.1
43949gelatinase-
43949ornithine decarboxylase-4.1.1.17
43949alkaline phosphatase+3.1.3.1
43949esterase (C 4)+
43949esterase Lipase (C 8)+
43949leucine arylamidase+3.4.11.1
43949valine arylamidase+
43949cystine arylamidase+3.4.11.3
43949trypsin+3.4.21.4
43949acid phosphatase+3.1.3.2
43949naphthol-AS-BI-phosphohydrolase+
43949alpha-chymotrypsin+3.4.21.1
43949alpha-galactosidase+3.2.1.22
439496-phospho-beta-galactosidase+3.2.1.85
43949alpha-glucosidase+3.2.1.20
43949beta-glucosidase+3.2.1.21
43949N-acetyl-beta-glucosaminidase+3.2.1.52
43949lipase (C 14)-
43949beta-glucuronidase-3.2.1.31
43949alpha-mannosidase-3.2.1.24
43949alpha-fucosidase-3.2.1.51

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43949C13:1 AT 12-131
    43949C14:02
    43949C15:0 2OH1
    43949C16:09.2
    43949C16:0 2OH1
    43949C16:0 3OH3.1
    43949C16:1ω5c9.6
    43949C15:0 iso23.8
    43949C15:0 iso 2OH / C16:1ω7c6.2
    43949C15:0 iso 3OH1.5
    43949C15:1 iso G23.6
    43949C17:0 iso 3OH6.7
  • type of FA analysis: whole cell analysis
  • incubation medium: Tryptic soy agar
  • agar/liquid: agar
  • incubation temperature: 28
  • software version: Sherlock 4.5
  • library/peak naming table: TSBA4.1
  • system: MIS MIDI
  • instrument: Hewlett Packard 6890 gas chromatograph
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperature
24363surface-sterilized root tissue of maize plantBeijing, Fangshan DistrictChinaCHNAsia
43949surface-sterilized root tissue of maize planted in the Fangshan District of Beijing, ChinaFangshan District of BeijingChinaCHNAsiaCCM nitrogen free medium3 days28

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part

taxonmaps

  • @ref: 69479
  • File name: preview.99_124941.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_185;96_2206;97_59799;98_83929;99_124941&stattab=map
  • Last taxonomy: Filimonas
  • 16S sequence: KR610522
  • Sequence Identity:
  • Total samples: 1878
  • soil counts: 823
  • aquatic counts: 457
  • animal counts: 336
  • plant counts: 262

Safety information

risk assessment

  • @ref: 24363
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24363
  • description: Filimonas zeae strain 772 16S ribosomal RNA gene, partial sequence
  • accession: KR610522
  • length: 1408
  • database: ena
  • NCBI tax ID: 1737353

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Filimonas zeae CGMCC 1.15290GCA_014641615scaffoldncbi1737353
66792Filimonas zeae strain CGMCC 1.152901737353.3wgspatric1737353
66792Filimonas zeae DSM 1007602861385466draftimg1737353

GC content

  • @ref: 24363
  • GC-content: 44.9
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno97.341yes
gram-positiveno97.582no
anaerobicno99.029no
aerobicyes87.721no
halophileno96.634no
spore-formingno92.443no
thermophileno99.402yes
glucose-utilyes88.939no
motileno91.293no
glucose-fermentno88.799no

External links

@ref: 24363

culture collection no.: DSM 100760, CGMCC 1.15290

straininfo link

  • @ref: 90891
  • straininfo: 401437

literature

  • topic: Phylogeny
  • Pubmed-ID: 27118116
  • title: Filimonas zeae sp. nov., an endophytic bacterium isolated from maize root.
  • authors: Gao JL, Sun P, Wang XM, Qiu TL, Lv FY, Yang MM, Lu M, Sun JG
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001116
  • year: 2016
  • mesh: Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, Beijing, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry, Zea mays/*microbiology
  • 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
24363Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100760Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100760)
43949Jun-Lian Gao, Pengbo Sun, Xu-Ming Wang, Tian-Lei Qiu, Fan-Yang Lv, Ming-Ming Yang, Mengzhu Lu, Jian-Guang SunFilimonas zeae sp. nov., an endophytic bacterium isolated from maize root10.1099/ijsem.0.001116IJSEM 66: 2730-2734 201627118116
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/
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
90891Reimer, 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-ID401437.1