Strain identifier
BacDive ID: 1626
Type strain:
Species: Bacteroides xylanisolvens
Strain Designation: XB1A
Strain history: CCUG 53782 <-- A. Bernalier-Donadille XB1A.
NCBI tax ID(s): 371601 (species)
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
@ref | history |
---|---|
7732 | <- A. Bernalier-Donadille; XB1A {2006} |
67770 | CCUG 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
@ref | gram stain | cell length | cell width | cell shape | motility |
---|---|---|---|---|---|
32442 | negative | 2.15 µm | 0.25 µm | rod-shaped | no |
28664 | negative | 1.8-2.5 µm | 0.2-0.3 µm | rod-shaped | no |
68367 | rod-shaped | ||||
68367 | negative |
colony morphology
- @ref: 7732
- type of hemolysis: gamma
- incubation period: 1-2 days
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7732 | FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) | yes | https://mediadive.dsmz.de/medium/1203a | Name: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water |
7732 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
7732 | CHOPPED MEAT MEDIUM (DSMZ Medium 78) | yes | https://mediadive.dsmz.de/medium/78 | Name: 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
7732 | positive | growth | 37 | mesophilic |
32442 | positive | growth | 25-42 | |
32442 | positive | optimum | 38 | mesophilic |
28664 | positive | optimum | 38 | mesophilic |
28664 | positive | growth | 25-42 | |
60012 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
32442 | positive | growth | 6-7.2 |
32442 | positive | optimum | 6.8 |
28664 | positive | growth | 6.0-7.2 |
28664 | positive | optimum | 6.8 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
7732 | anaerobe |
32442 | anaerobe |
28664 | obligate anaerobe |
60012 | anaerobe |
spore formation
@ref | spore formation |
---|---|
32442 | no |
68367 | no |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32442 | 22599 | arabinose | + | carbon source |
32442 | 17057 | cellobiose | + | carbon source |
32442 | 17234 | glucose | + | carbon source |
32442 | 17754 | glycerol | + | carbon source |
32442 | 17716 | lactose | + | carbon source |
32442 | 17306 | maltose | + | carbon source |
32442 | 29864 | mannitol | + | carbon source |
32442 | 37684 | mannose | + | carbon source |
32442 | 16634 | raffinose | + | carbon source |
32442 | 26546 | rhamnose | + | carbon source |
32442 | 17814 | salicin | + | carbon source |
32442 | 30911 | sorbitol | + | carbon source |
32442 | 17992 | sucrose | + | carbon source |
32442 | 27082 | trehalose | + | carbon source |
32442 | 18222 | xylose | + | carbon source |
32442 | 4853 | esculin | + | hydrolysis |
28664 | 22599 | arabinose | + | builds acid from |
28664 | 28427 | arabinoxylan | +/- | growth |
28664 | 17057 | cellobiose | + | builds acid from |
28664 | 62968 | cellulose | - | growth |
28664 | 4853 | esculin | + | hydrolysis |
28664 | 28757 | fructose | + | fermentation |
28664 | 28260 | galactose | + | fermentation |
28664 | 24175 | galacturonate | +/- | growth |
28664 | 5291 | gelatin | - | hydrolysis |
28664 | 17234 | glucose | + | builds acid from |
28664 | 17754 | glycerol | + | builds acid from |
28664 | 35581 | indole | - | |
28664 | 17716 | lactose | + | builds acid from |
28664 | 17306 | maltose | + | builds acid from |
28664 | 29864 | mannitol | + | builds acid from |
28664 | 37684 | mannose | + | builds acid from |
28664 | 6731 | melezitose | + | builds acid from |
28664 | 28053 | melibiose | + | fermentation |
28664 | 17632 | nitrate | - | reduction |
28664 | 17309 | pectin | +/- | growth |
28664 | 16634 | raffinose | + | builds acid from |
28664 | 26546 | rhamnose | + | builds acid from |
28664 | 33942 | ribose | + | fermentation |
28664 | rumen extract | - | required for growth | |
28664 | 17814 | salicin | + | builds acid from |
28664 | 30911 | sorbitol | + | builds acid from |
28664 | 28017 | starch | - | growth |
28664 | 17992 | sucrose | + | builds acid from |
28664 | 27082 | trehalose | + | builds acid from |
28664 | 27897 | tryptophan | - | energy source |
28664 | 37166 | xylan | + | degradation |
28664 | 18222 | xylose | + | builds acid from |
68367 | 62345 | L-rhamnose | + | builds acid from |
68367 | 16634 | raffinose | + | builds acid from |
68367 | 16024 | D-mannose | + | builds acid from |
68367 | 17057 | cellobiose | + | builds acid from |
68367 | 4853 | esculin | + | hydrolysis |
68367 | 30849 | L-arabinose | + | builds acid from |
68367 | 65327 | D-xylose | + | builds acid from |
68367 | 17306 | maltose | + | builds acid from |
68367 | 17992 | sucrose | + | builds acid from |
68367 | 17716 | lactose | + | builds acid from |
68367 | 17634 | D-glucose | + | builds acid from |
68367 | 16199 | urea | - | hydrolysis |
68367 | 27897 | tryptophan | + | energy source |
68380 | 16199 | urea | - | hydrolysis |
68380 | 29016 | arginine | - | hydrolysis |
68380 | 16024 | D-mannose | + | fermentation |
68380 | 16634 | raffinose | + | fermentation |
68380 | 29985 | L-glutamate | + | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | + | energy source |
68381 | 29016 | arginine | - | hydrolysis |
68381 | 16988 | D-ribose | + | builds acid from |
68381 | 16899 | D-mannitol | - | builds acid from |
68381 | 30911 | sorbitol | - | builds acid from |
68381 | 17716 | lactose | + | builds acid from |
68381 | 27082 | trehalose | + | builds acid from |
68381 | 16634 | raffinose | + | builds acid from |
68381 | 17992 | sucrose | + | builds acid from |
68381 | 30849 | L-arabinose | + | builds acid from |
68381 | 18333 | D-arabitol | - | builds acid from |
68381 | 40585 | alpha-cyclodextrin | - | builds acid from |
68381 | 606565 | hippurate | - | hydrolysis |
68381 | 28087 | glycogen | + | builds acid from |
68381 | 27941 | pullulan | + | builds acid from |
68381 | 17306 | maltose | + | builds acid from |
68381 | 28053 | melibiose | + | builds acid from |
68381 | 6731 | melezitose | + | builds acid from |
68381 | 320055 | methyl beta-D-glucopyranoside | - | builds acid from |
68381 | 16443 | D-tagatose | - | builds acid from |
68381 | 16199 | urea | - | hydrolysis |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
28664 | 30089 | acetate | yes |
28664 | 17272 | propionate | yes |
28664 | 30031 | succinate | yes |
28664 | 35581 | indole | no |
68367 | 35581 | indole | yes |
68380 | 35581 | indole | yes |
68381 | 15688 | acetoin | no |
metabolite tests
@ref | Chebi-ID | metabolite | indole test | voges-proskauer-test |
---|---|---|---|---|
28664 | 35581 | indole | - | |
68381 | 15688 | acetoin | - | |
68380 | 35581 | indole | + | |
68367 | 35581 | indole | + |
enzymes
@ref | value | activity | ec |
---|---|---|---|
32442 | alkaline phosphatase | + | 3.1.3.1 |
32442 | alpha-galactosidase | + | 3.2.1.22 |
28664 | cytochrome oxidase | - | 1.9.3.1 |
28664 | catalase | - | 1.11.1.6 |
28664 | tryptophan deaminase | - | 4.1.99.1 |
28664 | urease | - | 3.5.1.5 |
28664 | alpha-galactosidase | + | 3.2.1.22 |
28664 | beta-galactosidase | + | 3.2.1.23 |
28664 | alpha-glucosidase | + | 3.2.1.20 |
28664 | beta-glucosidase | + | 3.2.1.21 |
28664 | alpha-arabinosidase | + | 3.2.1.55 |
28664 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
28664 | glutamate decarboxylase | + | 4.1.1.15 |
28664 | alpha-fucosidase | + | 3.2.1.51 |
28664 | alkaline phosphatase | + | 3.1.3.1 |
28664 | leucyl glycin arylamidase | + | 3.4.11.1 |
28664 | phenylalanine arylamidase | + | |
28664 | glutamyl-glutamate arylamidase | + | |
28664 | arginine dihydrolase | - | 3.5.3.6 |
28664 | 6-phospho-beta-galactosidase | - | 3.2.1.85 |
28664 | beta-glucuronidase | - | 3.2.1.31 |
28664 | arginine arylamidase | - | |
28664 | proline-arylamidase | - | 3.4.11.5 |
28664 | phenylalanine arylamidase | - | |
28664 | leucine arylamidase | - | 3.4.11.1 |
28664 | pyroglutamic acid arylamidase | - | |
28664 | tyrosine arylamidase | - | |
28664 | glycin arylamidase | - | |
28664 | histidine arylamidase | - | |
28664 | serine arylamidase | - | |
68381 | urease | - | 3.5.1.5 |
68381 | beta-mannosidase | - | 3.2.1.25 |
68381 | glycyl tryptophan arylamidase | + | |
68381 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68381 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68381 | beta-galactosidase | + | 3.2.1.23 |
68381 | Alanyl-Phenylalanyl-Proline arylamidase | + | |
68381 | alkaline phosphatase | + | 3.1.3.1 |
68381 | alpha-galactosidase | + | 3.2.1.22 |
68381 | beta-glucuronidase | - | 3.2.1.31 |
68381 | beta-glucosidase | + | 3.2.1.21 |
68381 | arginine dihydrolase | - | 3.5.3.6 |
68380 | serine arylamidase | - | |
68380 | glutamyl-glutamate arylamidase | + | |
68380 | histidine arylamidase | - | |
68380 | glycin arylamidase | - | |
68380 | alanine arylamidase | + | 3.4.11.2 |
68380 | tyrosine arylamidase | - | |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | leucine arylamidase | - | 3.4.11.1 |
68380 | phenylalanine arylamidase | - | |
68380 | leucyl glycin arylamidase | + | 3.4.11.1 |
68380 | proline-arylamidase | - | 3.4.11.5 |
68380 | L-arginine arylamidase | - | |
68380 | alkaline phosphatase | + | 3.1.3.1 |
68380 | tryptophan deaminase | + | 4.1.99.1 |
68380 | alpha-fucosidase | + | 3.2.1.51 |
68380 | glutamate decarboxylase | + | 4.1.1.15 |
68380 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | beta-glucosidase | + | 3.2.1.21 |
68380 | alpha-glucosidase | + | 3.2.1.20 |
68380 | beta-galactosidase | + | 3.2.1.23 |
68380 | alpha-galactosidase | + | 3.2.1.22 |
68380 | arginine dihydrolase | - | 3.5.3.6 |
68380 | urease | - | 3.5.1.5 |
68367 | beta-glucosidase | + | 3.2.1.21 |
68367 | urease | - | 3.5.1.5 |
API 20A
@ref | IND | URE | GLU | MAN | LAC | SAC | MAL | SAL | XYL | ARA | GEL | ESC | GLY | CEL | MNE | MLZ | RAF | SOR | RHA | TRE | SPOR | GRAM | COCC |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
7732 | + | - | + | + | + | + | + | + | + | + | +/- | + | + | + | + | + | + | + | + | + | - | - | - |
7732 | + | - | + | - | + | + | + | - | + | + | - | + | - | + | + | - | + | - | + | - |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
7732 | - | - | + | + | - | + | + | + | - | + | + | + | + | + | - | + | + | - | - | + | - | - | - | - | + | - | - | + | - |
7732 | - | - | + | + | +/- | + | + | +/- | - | + | + | + | + | + | - | + | + | - | - | + | - | - | - | - | + | - | - | + | - |
7732 | - | - | + | + | +/- | + | + | + | - | + | + | + | + | + | - | + | + | - | - | + | - | - | - | - | + | - | - | + | - |
API rID32STR
@ref | ADH Arg | beta GLU | beta GAR | beta GUR | alpha GAL | PAL | RIB | MAN | SOR | LAC | TRE | RAF | SAC | LARA | DARL | CDEX | VP | APPA | beta GAL | PyrA | beta NAG | GTA | HIP | GLYG | PUL | MAL | MEL | MLZ | Mbeta DG | TAG | beta MAN | URE |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
7732 | - | + | + | - | + | + | + | - | - | + | + | + | + | + | - | - | - | + | + | - | + | + | - | + | + | + | + | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | sampling date | geographic location |
---|---|---|---|---|---|---|
7732 | human faeces | France | FRA | Europe | ||
28664 | human faeces of a healthy, non-methane excreting individual | |||||
60012 | Human feces,31-yr-old male,healthy volunteer | France | FRA | Europe | 2004 | Clermont/Theix,INRA |
67770 | Human feces |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
7732 | Bacteroides xylanisolvens partial 16S rRNA gene, type strain XB1AT | AM230650 | 1368 | ena | 657309 |
67770 | Bacteroides xylanisolvens gene for 16S ribosomal RNA, partial sequence, strain: JCM 15633 | AB510713 | 1465 | ena | 657309 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bacteroides xylanisolvens XB1A | GCA_000210075 | chromosome | ncbi | 657309 |
66792 | Bacteroides xylanisolvens XB1A | 657309.4 | complete | patric | 657309 |
66792 | Bacteroides xylanisolvens XB1A | 650377911 | complete | img | 657309 |
GC content
@ref | GC-content | method |
---|---|---|
7732 | 42.8 | high performance liquid chromatography (HPLC) |
32442 | 42.8 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
gram-positive | no | 97.387 | yes |
anaerobic | yes | 94.611 | yes |
halophile | no | 90.728 | no |
spore-forming | no | 94.852 | yes |
glucose-util | yes | 92.014 | yes |
thermophile | no | 99.065 | yes |
flagellated | no | 97.576 | yes |
aerobic | no | 96.168 | yes |
glucose-ferment | yes | 75.515 | no |
motile | no | 92.555 | yes |
External links
@ref: 7732
culture collection no.: DSM 18836, CCUG 53782, JCM 15633
straininfo link
- @ref: 71272
- straininfo: 396613
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 18398210 | Bacteroides xylanisolvens sp. nov., a xylan-degrading bacterium isolated from human faeces. | Chassard C, Delmas E, Lawson PA, Bernalier-Donadille A | Int J Syst Evol Microbiol | 10.1099/ijs.0.65504-0 | 2008 | Bacteroides/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/metabolism | Metabolism |
Phylogeny | 22544795 | Bacteroides reticulotermitis sp. nov., isolated from the gut of a subterranean termite (Reticulitermes speratus). | Sakamoto M, Ohkuma M | Int J Syst Evol Microbiol | 10.1099/ijs.0.040931-0 | 2012 | Animals, 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/analysis | Genetics |
Pathogenicity | 27987846 | Differential 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 IM | Carbohydr Polym | 10.1016/j.carbpol.2016.11.017 | 2016 | Bacteroides/*growth & development, Dysbiosis, Flax/*chemistry, Humans, Intestines/microbiology, Polysaccharides, Prebiotics, Symbiosis, Xylans/*chemistry |
Reference
@id | authors | catalogue | doi/url | title | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|
7732 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18836) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18836 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
28664 | 10.1099/ijs.0.65504-0 | 18398210 | ||||
32442 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28776041 | 28664 | |
60012 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 53782) | https://www.ccug.se/strain?id=53782 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68367 | Automatically annotated from API 20A | |||||
68380 | Automatically annotated from API rID32A | |||||
68381 | Automatically annotated from API rID32STR | |||||
69479 | João 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 | |||
71272 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID396613.1 | StrainInfo: A central database for resolving microbial strain identifiers |