Strain identifier

BacDive ID: 1624

Type strain: Yes

Species: Bacteroides graminisolvens

Strain Designation: XDT-1

Strain history: A. Ueki XDT-1.

NCBI tax ID(s): 1121097 (strain), 477666 (species)

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General

@ref: 8354

BacDive-ID: 1624

DSM-Number: 19988

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, rod-shaped

description: Bacteroides graminisolvens XDT-1 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from rice straw residue from a methanogenic reactor.

NCBI tax id

NCBI tax idMatching level
1121097strain
477666species

strain history

@refhistory
8354<- A. Ueki; XDT-1
67770A. Ueki XDT-1.

doi: 10.13145/bacdive1624.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Bacteroidaceae
  • genus: Bacteroides
  • species: Bacteroides graminisolvens
  • full scientific name: Bacteroides graminisolvens Nishiyama et al. 2009

@ref: 8354

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Bacteroidaceae

genus: Bacteroides

species: Bacteroides graminisolvens

full scientific name: Bacteroides graminisolvens Nishiyama et al. 2009 emend. Hahnke et al. 2016

strain designation: XDT-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29190negative2.85 µm0.5 µmrod-shapedno
69480negative99.998

colony morphology

@refincubation period
83541-2 days
624931 day

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8354COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
8354CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperaturerange
8354positivegrowth35mesophilic
8354positivegrowth30-37mesophilic
29190positivegrowth05-40
29190positiveoptimum33mesophilic
62493positivegrowth37mesophilic
67770positivegrowth30mesophilic

culture pH

  • @ref: 29190
  • ability: positive
  • type: optimum
  • pH: 7.2

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
8354anaerobe
29190anaerobe
62493anaerobe
69480anaerobe99.527

spore formation

@refspore formationconfidence
29190no
69481no100
69480no99.997

halophily

  • @ref: 29190
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-4 %

observation

  • @ref: 67770
  • observation: quinones: MK-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2919030089acetate+carbon source
2919022599arabinose+carbon source
2919017057cellobiose+carbon source
2919023652dextrin+carbon source
2919028757fructose+carbon source
2919028260galactose+carbon source
2919017234glucose+carbon source
2919028087glycogen+carbon source
2919017716lactose+carbon source
2919017306maltose+carbon source
2919037684mannose+carbon source
2919028053melibiose+carbon source
2919017272propionate+carbon source
2919016634raffinose+carbon source
2919026546rhamnose+carbon source
2919033942ribose+carbon source
2919017814salicin+carbon source
2919017992sucrose+carbon source
2919018222xylose+carbon source
291904853esculin+hydrolysis
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380serine arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase+3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase+3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase+3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase+3.2.1.55
68380beta-glucosidase+3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8354---+-+++--+-----+--+----+--+/--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
8354rice straw residue from a methanogenic reactorHokkaido, Betsukai-machiJapanJPNAsia
62493Rice straw residue from methanogenic reactorJapanJPNAsia2000
67770Rice-straw residue in a methanogenic reacter treating waste from cattle farms

isolation source categories

Cat1Cat2Cat3
#Engineered#Bioreactor
#Host#Plants#Herbaceous plants (Grass,Crops)
#Condition#Anoxic (anaerobic)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1411.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_21;96_816;97_950;98_1117;99_1411&stattab=map
  • Last taxonomy: Bacteroides graminisolvens subclade
  • 16S sequence: AB547643
  • Sequence Identity:
  • Total samples: 68859
  • soil counts: 2465
  • aquatic counts: 21442
  • animal counts: 44247
  • plant counts: 705

Safety information

risk assessment

  • @ref: 8354
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacteroides graminisolvens gene for 16S ribosomal RNA, partial sequence, strain: JCM 15093AB5476431486ena477666
8354Bacteroides graminisolvens gene for 16S ribosomal RNA, partial sequenceAB3639731415ena477666

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides graminisolvens DSM 199881121097.3wgspatric1121097
66792Bacteroides graminisolvens JCM 150931236499.3wgspatric1121097
66792Bacteroides graminisolvens DSM 199882524614553draftimg1121097
66792Bacteroides graminisolvens JCM 150932585427863draftimg1121097
67770Bacteroides graminisolvens DSM 19988 = JCM 15093GCA_000428125scaffoldncbi1121097
67770Bacteroides graminisolvens DSM 19988 = JCM 15093GCA_000613825contigncbi1121097

GC content

@refGC-contentmethod
835438.0high performance liquid chromatography (HPLC)
2919038
835441.5sequence analysis
6777038high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.074yes
flagellatedno97.531yes
gram-positiveno98.258yes
anaerobicyes98.32yes
aerobicno98.217no
halophileno90.553no
spore-formingno93.423yes
glucose-utilyes90.38yes
thermophileno98.708yes
glucose-fermentyes66.739no

External links

@ref: 8354

culture collection no.: CCUG 60910, DSM 19988, JCM 15093, KCTC 15146

straininfo link

  • @ref: 71270
  • straininfo: 404109

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19567576Bacteroides graminisolvens sp. nov., a xylanolytic anaerobe isolated from a methanogenic reactor treating cattle waste.Nishiyama T, Ueki A, Kaku N, Watanabe K, Ueki KInt J Syst Evol Microbiol10.1099/ijs.0.008268-02009Anaerobiosis, Animals, Bacterial Typing Techniques, Bacteroides/*classification/genetics/*isolation & purification/metabolism, Base Composition, Benzoquinones/analysis, Bioreactors/*microbiology, Carbohydrate Metabolism, Cattle, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hemin/metabolism, Hydrogen-Ion Concentration, Industrial Waste, Locomotion, Microscopy/methods, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Temperature, Xylans/*metabolismMetabolism
Genetics25736980Distribution and evolution of nitrogen fixation genes in the phylum Bacteroidetes.Inoue J, Oshima K, Suda W, Sakamoto M, Iino T, Noda S, Hongoh Y, Hattori M, Ohkuma MMicrobes Environ10.1264/jsme2.ME141422015Acetylene/metabolism, Bacteroidetes/classification/*genetics/*metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, *Evolution, Molecular, Genome, Bacterial, Metabolic Networks and Pathways/*genetics, Molecular Sequence Data, *Nitrogen Fixation, Oxidation-Reduction, Phylogeny, Sequence Analysis, DNA, Sequence HomologyPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
8354Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19988)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19988
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
29190Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604125614
62493Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 60910)https://www.ccug.se/strain?id=60910
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68380Automatically annotated from API rID32A
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
71270Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404109.1StrainInfo: A central database for resolving microbial strain identifiers