Strain identifier

BacDive ID: 140383

Type strain: Yes

Species: Flavobacterium gossypii

Strain Designation: JM-222

Strain history: CIP <- 2017, P. Kämpfer, Giessen Univ., Giessen, Germany: strain JM-222

NCBI tax ID(s): 1646119 (species)

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General

@ref: 42990

BacDive-ID: 140383

DSM-Number: 100397

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

description: Flavobacterium gossypii JM-222 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from root tissue of field grown cotton .

NCBI tax id

  • NCBI tax id: 1646119
  • Matching level: species

strain history

@refhistory
42990<- P. Kämpfer, Univ. Giessen, Germany; JM-222 <- J. McInroy
119713CIP <- 2017, P. Kämpfer, Giessen Univ., Giessen, Germany: strain JM-222

doi: 10.13145/bacdive140383.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Flavobacterium
  • species: Flavobacterium gossypii
  • full scientific name: Flavobacterium gossypii Kämpfer et al. 2017

@ref: 42990

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Flavobacterium

species: Flavobacterium gossypii

full scientific name: Flavobacterium gossypii Kämpfer et al. 2017

strain designation: JM-222

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43483negative2 µm1 µmrod-shapedno
69480negative99.993
119713negativerod-shapedno

colony morphology

  • @ref: 43483
  • colony color: Yellowish
  • colony shape: circular
  • medium used: Nutrient agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43483Nutrient agar (NA)yes
42990CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
119713CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
43483positivegrowth15-30
43483nogrowth50thermophilic
42990positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
43483positivegrowth6.5-10alkaliphile
43483nogrowth5.5
43483nogrowth11

Physiology and metabolism

oxygen tolerance

  • @ref: 43483
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
43483no
69481no100
69480no99.987

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4348317057cellobiose-builds acid from
4348318333D-arabitol-builds acid from
4348316899D-mannitol-builds acid from
4348316024D-mannose-builds acid from
4348317924D-sorbitol-builds acid from
4348365327D-xylose-builds acid from
4348316813galactitol-builds acid from
4348317113erythritol-builds acid from
4348330849L-arabinose-builds acid from
4348327374L-inositol-builds acid from
4348362345L-rhamnose-builds acid from
4348317716lactose-builds acid from
4348328053melibiose-builds acid from
4348337657methyl D-glucoside-builds acid from
4348316634raffinose-builds acid from
4348317814salicin-builds acid from
4348317992sucrose-builds acid from
4348327082trehalose-builds acid from
43483309162-oxoglutarate-carbon source
43483161933-hydroxybenzoate-carbon source
4348316865gamma-aminobutyric acid-carbon source
43483178794-hydroxybenzoate-carbon source
4348330089acetate-carbon source
4348317128adipate-carbon source
4348315963ribitol-carbon source
4348318305arbutin-carbon source
4348378208azelaate-carbon source
4348316958beta-alanine-carbon source
4348317057cellobiose-carbon source
4348316383cis-aconitate-carbon source
4348316947citrate-carbon source
4348315824D-fructose-carbon source
4348312936D-galactose-carbon source
4348316899D-mannitol-carbon source
4348316024D-mannose-carbon source
4348316988D-ribose-carbon source
4348317924D-sorbitol-carbon source
4348365327D-xylose-carbon source
43483370543-hydroxybutyrate-carbon source
4348324996lactate-carbon source
4348329806fumarate-carbon source
4348324265gluconate-carbon source
4348317859glutaric acid-carbon source
4348317754glycerol-carbon source
4348317268myo-inositol-carbon source
4348317240itaconate-carbon source
4348316977L-alanine-carbon source
4348330849L-arabinose-carbon source
4348329991L-aspartate-carbon source
4348315971L-histidine-carbon source
4348315603L-leucine-carbon source
4348315589L-malate-carbon source
4348315729L-ornithine-carbon source
4348317295L-phenylalanine-carbon source
4348317203L-proline-carbon source
4348362345L-rhamnose-carbon source
4348317115L-serine-carbon source
4348316828L-tryptophan-carbon source
4348368428maltitol-carbon source
4348317306maltose-carbon source
4348328053melibiose-carbon source
4348336986mesaconate-carbon source
4348328037N-acetylgalactosamine-carbon source
43483506227N-acetylglucosamine-carbon source
4348318401phenylacetate-carbon source
4348317272propionate-carbon source
4348317148putrescine-carbon source
4348315361pyruvate-carbon source
4348317814salicin-carbon source
434839300suberic acid-carbon source
4348317992sucrose-carbon source
4348315708trans-aconitate-carbon source
4348327082trehalose-carbon source
43483901464-nitrophenyl beta-D-glucuronide-hydrolysis
43483O-nitrophenyl-beta-D-galactopyranosid-hydrolysis
4348317634D-glucose+builds acid from
4348317306maltose+builds acid from
434832-deoxythymidine-5'-4-nitrophenyl phosphate+hydrolysis
43483911224-nitrophenyl alpha-D-glucopyranoside+hydrolysis
43483902594-nitrophenyl beta-D-glucopyranoside+hydrolysis
43483901484-nitrophenyl beta-D-xylopyranoside+hydrolysis
434833122bis-4-nitrophenyl phosphate+hydrolysis
4348391050bis-4-nitrophenyl-phenyl phosphonate+hydrolysis
4348355394bis-4-nitrophenyl-phosphorylcholine+hydrolysis
43483casein+hydrolysis
4348316991dna+hydrolysis
43483gamma-L-glutamate-4-nitroanilide+hydrolysis
434835291gelatin+hydrolysis
43483L-alanine 4-nitroanilide+hydrolysis
43483L-proline-4-nitroanilide+hydrolysis
4348328017starch+hydrolysis
4348318186tyrosine+hydrolysis
4348317634D-glucose+/-carbon source
4348316024D-mannose+/-carbon source
4348317306maltose+/-carbon source

metabolite production

@refChebi-IDmetaboliteproduction
4348316136hydrogen sulfideno
4348335581indoleno

enzymes

@refvalueactivityec
43483cytochrome oxidase+1.9.3.1
43483catalase+1.11.1.6
43483arginine dihydrolase-3.5.3.6
43483lysine decarboxylase-4.1.1.18
43483ornithine decarboxylase-4.1.1.17
43483urease-3.5.1.5
43483beta-galactosidase-3.2.1.23

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43483C15:0 anteiso2.5
    43483C15:011.1
    43483C15:0 2OH1
    43483C15:0 3OH1.9
    43483C15:1ω6c1.1
    43483C16:01.4
    43483C16:1ω7c / C15:0 iso 2OH7.8
    43483C17:1ω6c1.5
    43483C17:1ω8c2.1
    43483C15:0 iso22.9
    43483C15:0 iso 3OH6.2
    43483C15:1 iso G5.3
    43483C16:0 iso2.1
    43483C16:0 iso 3OH1.5
    43483C17:0 iso1.7
    43483C17:0 iso 3OH13.1
    43483C17:1 iso ω9c4
  • type of FA analysis: whole cell analysis
  • incubation medium: TSA
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 2
  • incubation_oxygen: aerobic
  • software version: Sherlock 2.11
  • library/peak naming table: TSBA4.1
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
42990root tissue of field grown cotton (Gossypium hirsutum)Gossypium hirsutumAlabama, AuburnUSAUSANorth America
43483root tissue of field-grown cottonAuburn, AlabamaUSAUSANorth America
119713EnvironmentUnited States of AmericaUSANorth America2000

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#Engineered#Agriculture#Field
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_159187.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_66;96_33925;97_43030;98_56248;99_159187&stattab=map
  • Last taxonomy: Flavobacterium gossypii
  • 16S sequence: KR047732
  • Sequence Identity:
  • Total samples: 128
  • soil counts: 70
  • aquatic counts: 15
  • animal counts: 33
  • plant counts: 10

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
429901Risk group (German classification)
1197131Risk group (French classification)

Sequence information

16S sequences

  • @ref: 42990
  • description: Flavobacterium gossypii 16S ribosomal RNA gene, partial sequence
  • accession: KR047732
  • length: 1423
  • database: ena
  • NCBI tax ID: 1646119

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Flavobacterium gossypii DSM 100397GCA_014138495scaffoldncbi1646119
66792Flavobacterium gossypii strain DSM 1003971646119.3wgspatric1646119
66792Flavobacterium gossypii DSM 1003972830104207draftimg1646119

GC content

@refGC-contentmethod
4348338.2high performance liquid chromatography (HPLC)
4299038.2fluorimetric

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno87.468yes
flagellatedno96.302yes
gram-positiveno98.467no
anaerobicno99.625yes
aerobicyes92.665no
halophileno93.857no
spore-formingno94.513yes
glucose-utilyes79.418no
thermophileno99.509no
glucose-fermentno91.741no

External links

@ref: 42990

culture collection no.: DSM 100397, CCM 8610, LMG 28821, CIP 111493, CIP 110906

straininfo link

  • @ref: 96674
  • straininfo: 408008

literature

  • topic: Phylogeny
  • Pubmed-ID: 28840797
  • title: Flavobacterium gossypii sp. nov. isolated from the root tissue of field-grown cotton.
  • authors: Kampfer P, Busse HJ, McInroy JA, Glaeser SP
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002115
  • year: 2017
  • mesh: Alabama, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/genetics, Flavobacterium/*classification/genetics/isolation & purification, Gossypium/*microbiology, Phosphatidylethanolamines/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, 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
42990Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100397Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100397)
43483Peter Kämpfer, Hans-Jürgen Busse, John A. McInroy, Stefanie P. GlaeserFlavobacterium gossypii sp. nov. isolated from the root tissue of field-grown cotton10.1099/ijsem.0.002115IJSEM 67: 3345-3350 201728840797
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
96674Reimer, 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-ID408008.1
119713Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20111493Collection of Institut Pasteur (CIP 111493)