Strain identifier

BacDive ID: 140265

Type strain: Yes

Species: Defluviitalea raffinosedens

Strain Designation: A6

Strain history: <- S. Ma, Biogas Inst. of Ministry of Agriculture, Chengdu, P.R. China; A6

NCBI tax ID(s): 1450156 (species)

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General

@ref: 42872

BacDive-ID: 140265

DSM-Number: 28090

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-positive, rod-shaped, colony-forming

description: Defluviitalea raffinosedens A6 is an anaerobe, thermophilic, Gram-positive bacterium that forms circular colonies and was isolated from anaerobic batch digester treating animal manure and rice straw.

NCBI tax id

  • NCBI tax id: 1450156
  • Matching level: species

strain history

  • @ref: 42872
  • history: <- S. Ma, Biogas Inst. of Ministry of Agriculture, Chengdu, P.R. China; A6

doi: 10.13145/bacdive140265.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Defluviitaleaceae
  • genus: Defluviitalea
  • species: Defluviitalea raffinosedens
  • full scientific name: Defluviitalea raffinosedens Ma et al. 2017

@ref: 42872

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Defluviitaleaceae

genus: Defluviitalea

species: Defluviitalea raffinosedens

full scientific name: Defluviitalea raffinosedens Ma et al. 2017

strain designation: A6

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43176positive2.5-7.6 µm1-0.58 µmrod-shapedno
69480positive100

colony morphology

  • @ref: 43176
  • colony color: white
  • colony shape: circular
  • incubation period: 2 days
  • medium used: basal carbonate yeast extract and trypticase medium (BCTY)

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43176basal carbonate yeast extract and trypticase medium (BCTY)yes
42872PY + X MEDIUM (DSMZ Medium 104b)yeshttps://mediadive.dsmz.de/medium/104bName: PY + X MEDIUM (DSMZ Medium 104b) Composition: Yeast extract 10.0 g/l D-Glucose 5.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Sodium resazurin 0.0005 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
43176positiveoptimum50thermophilic
43176positivegrowth40-65thermophilic
42872positivegrowth50thermophilic

culture pH

@refabilitytypepH
43176positivegrowth6.5-8.0
43176positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
43176anaerobe
69480anaerobe99.201

spore formation

@refspore formationconfidence
43176no
69480yes100

halophily

@refsaltgrowthtested relationconcentration
43176NaClpositivegrowth0-20 %(w/v)
43176NaClpositiveoptimum0 %(w/v)

observation

  • @ref: 43176
  • observation: yeast extract is required for growth

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4317617634D-glucose+fermentation
4317617306maltose+fermentation
4317665327D-xylose+fermentation
4317612936D-galactose+fermentation
4317615824D-fructose+fermentation
4317616988D-ribose+fermentation
4317617716lactose+fermentation
4317616024D-mannose+fermentation
4317616634raffinose+fermentation
4317617992sucrose+fermentation
4317617108D-arabinose+fermentation
4317617057cellobiose+fermentation
43176yeast extract+fermentation
4317616899D-mannitol-fermentation
4317662345L-rhamnose-fermentation
43176peptone-fermentation
4317630089acetate-fermentation
4317617272propionate-fermentation
4317615361pyruvate-fermentation
4317624996lactate-fermentation
4317662968cellulose-hydrolysis

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43176C12:00.7
    43176C14:018.1
    43176C13:0 3-OH2.9
    43176C16:030.6
    43176C16:0 OH3.2
    43176C16:1ω7c5.6
    43176C17:1 iso30.3
    43176Unknown5.7
  • type of FA analysis: whole cell analysis
  • system: MIS MIDI
  • method/protocol: Miller 1982
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedure
42872anaerobic batch digester treating animal manure and rice strawChinaCHNAsia
43176anaerobic batch digester treating animal manure and rice strawenriched mediumbasal medium containing 1 g yeast extract and 5 g sodium acetate or 3 g sodium propionate1 week55serially dilution and hungate roll-tube technique

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Anaerobic digestor
#Host#Mammals
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_150148.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_2004;96_8630;97_10378;98_12728;99_150148&stattab=map
  • Last taxonomy: Defluviitalea raffinosedens
  • 16S sequence: KF766957
  • Sequence Identity:
  • Total samples: 94
  • soil counts: 21
  • aquatic counts: 25
  • animal counts: 27
  • plant counts: 21

Safety information

risk assessment

  • @ref: 42872
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 42872
  • description: Defluviitalea raffinosedens strain A6 16S ribosomal RNA gene, partial sequence
  • accession: KF766957
  • length: 1413
  • database: ena
  • NCBI tax ID: 1450156

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Defluviitalea raffinosedens DSM 28090GCA_016908775contigncbi1450156
66792Defluviitalea raffinosedens strain DSM 280901450156.4wgspatric1450156
66792Defluviitalea raffinosedens DSM 280902901198348draftimg1450156

GC content

  • @ref: 42872
  • GC-content: 36.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes86no
motileyes84.619no
gram-positiveyes83.722yes
anaerobicyes99.034yes
halophileno92.618yes
spore-formingyes78.153yes
glucose-utilyes88.622no
aerobicno98.228yes
flagellatedyes63.988no
glucose-fermentyes75.836no
thermophileyes70.012no

External links

@ref: 42872

culture collection no.: DSM 28090, ACCC 19951

straininfo link

  • @ref: 96571
  • straininfo: 397090

literature

  • topic: Phylogeny
  • Pubmed-ID: 27902335
  • title: Defluviitalea raffinosedens sp. nov., a thermophilic, anaerobic, saccharolytic bacterium isolated from an anaerobic batch digester treating animal manure and rice straw.
  • authors: Ma S, Huang Y, Wang C, Fan H, Dai L, Zhou Z, Liu X, Deng Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001664
  • year: 2017
  • mesh: Animals, Bacteria, Anaerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fermentation, Gram-Positive Bacteria/*classification/genetics/isolation & purification, Manure/*microbiology, Oryza/*microbiology, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Enzymology

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
42872Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28090Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28090)
43176Shichun Ma, Yan Huang, Cong Wang, Hui Fan, Lirong Dai, Zheng Zhou, Xing Liu, Yu DengDefluviitalea raffinosedens sp. nov., a thermophilic, anaerobic, saccharolytic bacterium isolated from an anaerobic batch digester treating animal manure and rice straw10.1099/ijsem.0.001664IJSEM 67: 1607-1612 201727902335
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
96571Reimer, 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-ID397090.1