Strain identifier

BacDive ID: 1626

Type strain: Yes

Species: Bacteroides xylanisolvens

Strain Designation: XB1A

Strain history: CCUG 53782 <-- A. Bernalier-Donadille XB1A.

NCBI tax ID(s): 371601 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 7732

BacDive-ID: 1626

DSM-Number: 18836

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

description: Bacteroides xylanisolvens XB1A is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human faeces.

NCBI tax id

  • NCBI tax id: 371601
  • Matching level: species

strain history

@refhistory
7732<- A. Bernalier-Donadille; XB1A {2006}
67770CCUG 53782 <-- A. Bernalier-Donadille XB1A.

doi: 10.13145/bacdive1626.20230509.8.1

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 xylanisolvens
  • full scientific name: Bacteroides xylanisolvens Chassard et al. 2008

@ref: 7732

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Bacteroidaceae

genus: Bacteroides

species: Bacteroides xylanisolvens

full scientific name: Bacteroides xylanisolvens Chassard et al. 2008

strain designation: XB1A

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32442negative2.15 µm0.25 µmrod-shapedno
28664negative1.8-2.5 µm0.2-0.3 µmrod-shapedno
68367rod-shaped
68367negative

colony morphology

  • @ref: 7732
  • type of hemolysis: gamma
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7732FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)yeshttps://mediadive.dsmz.de/medium/1203aName: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water
7732COLUMBIA 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
7732CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water

culture temp

@refgrowthtypetemperaturerange
7732positivegrowth37mesophilic
32442positivegrowth25-42
32442positiveoptimum38mesophilic
28664positiveoptimum38mesophilic
28664positivegrowth25-42
60012positivegrowth37mesophilic
67770positivegrowth37mesophilic

culture pH

@refabilitytypepH
32442positivegrowth6-7.2
32442positiveoptimum6.8
28664positivegrowth6.0-7.2
28664positiveoptimum6.8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
7732anaerobe
32442anaerobe
28664obligate anaerobe
60012anaerobe

spore formation

@refspore formation
32442no
68367no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3244222599arabinose+carbon source
3244217057cellobiose+carbon source
3244217234glucose+carbon source
3244217754glycerol+carbon source
3244217716lactose+carbon source
3244217306maltose+carbon source
3244229864mannitol+carbon source
3244237684mannose+carbon source
3244216634raffinose+carbon source
3244226546rhamnose+carbon source
3244217814salicin+carbon source
3244230911sorbitol+carbon source
3244217992sucrose+carbon source
3244227082trehalose+carbon source
3244218222xylose+carbon source
324424853esculin+hydrolysis
2866422599arabinose+builds acid from
2866428427arabinoxylan+/-growth
2866417057cellobiose+builds acid from
2866462968cellulose-growth
286644853esculin+hydrolysis
2866428757fructose+fermentation
2866428260galactose+fermentation
2866424175galacturonate+/-growth
286645291gelatin-hydrolysis
2866417234glucose+builds acid from
2866417754glycerol+builds acid from
2866435581indole-
2866417716lactose+builds acid from
2866417306maltose+builds acid from
2866429864mannitol+builds acid from
2866437684mannose+builds acid from
286646731melezitose+builds acid from
2866428053melibiose+fermentation
2866417632nitrate-reduction
2866417309pectin+/-growth
2866416634raffinose+builds acid from
2866426546rhamnose+builds acid from
2866433942ribose+fermentation
28664rumen extract-required for growth
2866417814salicin+builds acid from
2866430911sorbitol+builds acid from
2866428017starch-growth
2866417992sucrose+builds acid from
2866427082trehalose+builds acid from
2866427897tryptophan-energy source
2866437166xylan+degradation
2866418222xylose+builds acid from
6836762345L-rhamnose+builds acid from
6836716634raffinose+builds acid from
6836716024D-mannose+builds acid from
6836717057cellobiose+builds acid from
683674853esculin+hydrolysis
6836730849L-arabinose+builds acid from
6836765327D-xylose+builds acid from
6836717306maltose+builds acid from
6836717992sucrose+builds acid from
6836717716lactose+builds acid from
6836717634D-glucose+builds acid from
6836716199urea-hydrolysis
6836727897tryptophan+energy source
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
6838016634raffinose+fermentation
6838029985L-glutamate+degradation
6838017632nitrate-reduction
6838027897tryptophan+energy source
6838129016arginine-hydrolysis
6838116988D-ribose+builds acid from
6838116899D-mannitol-builds acid from
6838130911sorbitol-builds acid from
6838117716lactose+builds acid from
6838127082trehalose+builds acid from
6838116634raffinose+builds acid from
6838117992sucrose+builds acid from
6838130849L-arabinose+builds acid from
6838118333D-arabitol-builds acid from
6838140585alpha-cyclodextrin-builds acid from
68381606565hippurate-hydrolysis
6838128087glycogen+builds acid from
6838127941pullulan+builds acid from
6838117306maltose+builds acid from
6838128053melibiose+builds acid from
683816731melezitose+builds acid from
68381320055methyl beta-D-glucopyranoside-builds acid from
6838116443D-tagatose-builds acid from
6838116199urea-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
2866430089acetateyes
2866417272propionateyes
2866430031succinateyes
2866435581indoleno
6836735581indoleyes
6838035581indoleyes
6838115688acetoinno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
2866435581indole-
6838115688acetoin-
6838035581indole+
6836735581indole+

enzymes

@refvalueactivityec
32442alkaline phosphatase+3.1.3.1
32442alpha-galactosidase+3.2.1.22
28664cytochrome oxidase-1.9.3.1
28664catalase-1.11.1.6
28664tryptophan deaminase-4.1.99.1
28664urease-3.5.1.5
28664alpha-galactosidase+3.2.1.22
28664beta-galactosidase+3.2.1.23
28664alpha-glucosidase+3.2.1.20
28664beta-glucosidase+3.2.1.21
28664alpha-arabinosidase+3.2.1.55
28664N-acetyl-beta-glucosaminidase+3.2.1.52
28664glutamate decarboxylase+4.1.1.15
28664alpha-fucosidase+3.2.1.51
28664alkaline phosphatase+3.1.3.1
28664leucyl glycin arylamidase+3.4.11.1
28664phenylalanine arylamidase+
28664glutamyl-glutamate arylamidase+
28664arginine dihydrolase-3.5.3.6
286646-phospho-beta-galactosidase-3.2.1.85
28664beta-glucuronidase-3.2.1.31
28664arginine arylamidase-
28664proline-arylamidase-3.4.11.5
28664phenylalanine arylamidase-
28664leucine arylamidase-3.4.11.1
28664pyroglutamic acid arylamidase-
28664tyrosine arylamidase-
28664glycin arylamidase-
28664histidine arylamidase-
28664serine arylamidase-
68381urease-3.5.1.5
68381beta-mannosidase-3.2.1.25
68381glycyl tryptophan arylamidase+
68381N-acetyl-beta-glucosaminidase+3.2.1.52
68381pyrrolidonyl arylamidase-3.4.19.3
68381beta-galactosidase+3.2.1.23
68381Alanyl-Phenylalanyl-Proline arylamidase+
68381alkaline phosphatase+3.1.3.1
68381alpha-galactosidase+3.2.1.22
68381beta-glucuronidase-3.2.1.31
68381beta-glucosidase+3.2.1.21
68381arginine dihydrolase-3.5.3.6
68380serine arylamidase-
68380glutamyl-glutamate 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
68380beta-glucosidase+3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
68367beta-glucosidase+3.2.1.21
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRESPORGRAMCOCC
7732+-+++++++++/-+++++++++---
7732+-+-+++-++-+-++-+-+-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
7732--++-+++-+++++-++--+----+--+-
7732--+++/-+++/--+++++-++--+----+--+-
7732--+++/-+++-+++++-++--+----+--+-

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
7732-++-+++--+++++---++-++-+++++----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic location
7732human faecesFranceFRAEurope
28664human faeces of a healthy, non-methane excreting individual
60012Human feces,31-yr-old male,healthy volunteerFranceFRAEurope2004Clermont/Theix,INRA
67770Human feces

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1462.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_21;96_684;97_978;98_1153;99_1462&stattab=map
  • Last taxonomy: Bacteroides xylanisolvens
  • 16S sequence: AM230650
  • Sequence Identity:
  • Total samples: 219481
  • soil counts: 1755
  • aquatic counts: 4947
  • animal counts: 212224
  • plant counts: 555

Safety information

risk assessment

  • @ref: 7732
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
7732Bacteroides xylanisolvens partial 16S rRNA gene, type strain XB1ATAM2306501368ena657309
67770Bacteroides xylanisolvens gene for 16S ribosomal RNA, partial sequence, strain: JCM 15633AB5107131465ena657309

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides xylanisolvens XB1AGCA_000210075chromosomencbi657309
66792Bacteroides xylanisolvens XB1A657309.4completepatric657309
66792Bacteroides xylanisolvens XB1A650377911completeimg657309

GC content

@refGC-contentmethod
773242.8high performance liquid chromatography (HPLC)
3244242.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno97.387yes
anaerobicyes94.611yes
halophileno90.728no
spore-formingno94.852yes
glucose-utilyes92.014yes
thermophileno99.065yes
flagellatedno97.576yes
aerobicno96.168yes
glucose-fermentyes75.515no
motileno92.555yes

External links

@ref: 7732

culture collection no.: DSM 18836, CCUG 53782, JCM 15633

straininfo link

  • @ref: 71272
  • straininfo: 396613

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18398210Bacteroides xylanisolvens sp. nov., a xylan-degrading bacterium isolated from human faeces.Chassard C, Delmas E, Lawson PA, Bernalier-Donadille AInt J Syst Evol Microbiol10.1099/ijs.0.65504-02008Bacteroides/classification/genetics/*isolation & purification/*metabolism, Base Composition, Base Sequence, Biotransformation, Carbohydrate Metabolism, DNA Primers/genetics, DNA, Bacterial/chemistry/genetics, Feces/microbiology, Genes, Bacterial, Humans, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, Terminology as Topic, Xylans/metabolismMetabolism
Phylogeny22544795Bacteroides reticulotermitis sp. nov., isolated from the gut of a subterranean termite (Reticulitermes speratus).Sakamoto M, Ohkuma MInt J Syst Evol Microbiol10.1099/ijs.0.040931-02012Animals, Bacterial Typing Techniques, Bacteroides/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Gastrointestinal Tract/*microbiology, Isoptera/*microbiology, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Pathogenicity27987846Differential growth of bowel commensal Bacteroides species on plant xylans of differing structural complexity.Centanni M, Hutchison JC, Carnachan SM, Daines AM, Kelly WJ, Tannock GW, Sims IMCarbohydr Polym10.1016/j.carbpol.2016.11.0172016Bacteroides/*growth & development, Dysbiosis, Flax/*chemistry, Humans, Intestines/microbiology, Polysaccharides, Prebiotics, Symbiosis, Xylans/*chemistry

Reference

@idauthorscataloguedoi/urltitlepubmedID_cross_reference
7732Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18836)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18836
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
2866410.1099/ijs.0.65504-018398210
32442Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128664
60012Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53782)https://www.ccug.se/strain?id=53782
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68367Automatically annotated from API 20A
68380Automatically annotated from API rID32A
68381Automatically annotated from API rID32STR
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
71272Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID396613.1StrainInfo: A central database for resolving microbial strain identifiers