Strain identifier

BacDive ID: 1592

Type strain: Yes

Species: Bacteroides ovatus

Strain Designation: LRA 044 07 88

Strain history: CIP <- 1993, R. Mercier, bioMérieux, La Balme-les-Grottes, France: strain LRA 044 07 88 <- 1985, Analytab, Plainview, USA

NCBI tax ID(s): 411476 (strain), 28116 (species)

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

@ref: 918

BacDive-ID: 1592

DSM-Number: 1896

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

description: Bacteroides ovatus LRA 044 07 88 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from Human feces.

NCBI tax id

NCBI tax idMatching level
28116species
411476strain

strain history

@refhistory
918<- ATCC; ATCC 8483 <- A. H. Eggerth;
67770ATCC 8483 <-- A. H. Eggerth.
121472CIP <- 1993, R. Mercier, bioMérieux, La Balme-les-Grottes, France: strain LRA 044 07 88 <- 1985, Analytab, Plainview, USA

doi: 10.13145/bacdive1592.20230509.8.1

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 ovatus
  • full scientific name: Bacteroides ovatus Eggerth and Gagnon 1933 (Approved Lists 1980)

@ref: 918

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Bacteroidaceae

genus: Bacteroides

species: Bacteroides ovatus

full scientific name: Bacteroides ovatus Eggerth and Gagnon 1933 emend. Hahnke et al. 2016

strain designation: LRA 044 07 88

type strain: yes

Morphology

cell morphology

  • @ref: 121472
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

@reftype of hemolysisincubation period
918gamma1-2 days
121472

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
918COLUMBIA 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
918CHOPPED 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
32784MEDIUM 20 - for Anaerobic bacteriayesAgar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
918FASTIDIOUS 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
121472CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
918positivegrowth37mesophilic
32784positivegrowth37mesophilic
44813positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
918anaerobe
44813anaerobe
44813obligate anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1214724853esculin+hydrolysis
12147217632nitrate-reduction
12147216301nitrite-reduction
12147217632nitrate+respiration
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
6838016634raffinose+fermentation
6838029985L-glutamate+degradation
6838017632nitrate-reduction

metabolite production

  • @ref: 121472
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
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
68380glutamate decarboxylase+4.1.1.15
68380N-acetyl-beta-glucosaminidase+3.2.1.52
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
121472oxidase-
121472beta-galactosidase+3.2.1.23
121472gelatinase-
121472amylase+
121472DNase-
121472caseinase+3.4.21.50
121472catalase+1.11.1.6
121472tween esterase-
121472lecithinase-
121472lipase-
121472protease-
121472urease-3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    44813C14:02.214
    44813C15:09.715
    44813C16:04.416
    44813C13:0 ANTEISO0.812.701
    44813C13:0 iso0.812.612
    44813C14:0 ISO2.313.618
    44813C15:0 2OH0.516.217
    44813C15:0 3OH3.716.504
    44813C15:0 ANTEISO39.514.711
    44813C15:0 ISO9.314.621
    44813C15:0 ISO 3OH0.516.135
    44813C16:0 3OH6.317.52
    44813C16:0 iso0.315.626
    44813C16:0 iso 3OH0.917.145
    44813C17:0 2OH2.918.249
    44813C17:0 3OH1.518.535
    44813C17:0 iso 3OH10.718.161
    44813C18:2 ω6,9c/C18:0 ANTE1.417.724
    44813unknown 13.5662.313.566
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121472-+--------++-+------

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
918--++-+++-+++++/--++--+----+--+/--
918--++-+++-++++--++--+----+--+/--
918--++-+++-++++--++--+----+----
918--++-++++/-+++++/--++--+----+--+/--
918--++-+++-++++--++--+----+--+-
918--++-+++-++++--+/-+--+----+--+/--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121472---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

  • @ref: 67770
  • sample type: Human feces

taxonmaps

  • @ref: 69479
  • File name: preview.99_1176.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_21;96_684;97_799;98_926;99_1176&stattab=map
  • Last taxonomy: Bacteroides ovatus
  • 16S sequence: AB510705
  • Sequence Identity:
  • Total samples: 79597
  • soil counts: 195
  • aquatic counts: 1522
  • animal counts: 77814
  • plant counts: 66

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
9182Risk group (German classification)
1214722Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacteroides ovatus 16S-23S rDNA intergenic spacer regionAF176691551ena28116
20218Bacteroides ovatus ATCC:8483 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceFJ4103833455ena28116
20218Bacteroides ovatus NCTC 11153 16S ribosomal RNA gene, complete sequenceL164841468ena28116
20218B.ovatus 16S rRNA (ATCC 8483T)X839521395ena28116
918Bacteroides ovatus strain JCM5824 16S ribosomal RNA gene, partial sequenceEU1366821435ena28116
67770Bacteroides ovatus gene for 16S ribosomal RNA, partial sequence, strain: JCM 5824AB5107051459ena28116

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides ovatus ATCC 8483GCA_001314995completencbi28116
66792Bacteroides ovatus ATCC 8483411476.11wgspatric411476
66792Bacteroides ovatus strain ATCC 848328116.7completepatric28116
66792Bacteroides ovatus strain ATCC 848328116.125wgspatric28116
66792Bacteroides ovatus strain DSM 189628116.16wgspatric28116
66792Bacteroides ovatus strain NCTC1115328116.197wgspatric28116
66792Bacteroides ovatus ATCC 8483641380449draftimg411476
66792Bacteroides ovatus DSM 18962693429857draftimg28116
66792Bacteroides ovatus ATCC 84832684623200completeimg411476
67770Bacteroides ovatus DSM 1896GCA_900107475scaffoldncbi28116
67770Bacteroides ovatus ATCC 8483GCA_002959635contigncbi28116
67770Bacteroides ovatus NCTC11153GCA_900445505contigncbi28116
66792Bacteroides ovatus ATCC 8483GCA_000154125scaffoldncbi411476
66792Bacteroides ovatus ATCC 8483GCA_025146775completencbi28116
66792Bacteroides ovatus strain ATCC 848328116.1884completepatric28116

GC content

@refGC-contentmethod
91840.0thermal denaturation, midpoint method (Tm)
91841.9sequence analysis
6777040thermal denaturation, midpoint method (Tm)

External links

@ref: 918

culture collection no.: DSM 1896, ATCC 8483, NCTC 11153, CCUG 4943, CIP 103756, JCM 5824, KCTC 5011, BCRC 10623

straininfo link

  • @ref: 71237
  • straininfo: 92789

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism2036001Co-utilization of polymerized carbon sources by Bacteroides ovatus grown in a two-stage continuous culture system.MacFarlane GT, Gibson GRAppl Environ Microbiol10.1128/aem.57.1.1-6.19911991Bacteroides/growth & development/*metabolism, Colony Count, Microbial, Enzymes/metabolism, Fermentation, Polysaccharides/*metabolismEnzymology
Enzymology2418781Immunochemical investigations of antigens isolated from Bacteroides ovatus strain ATCC 8483.Beckmann I, Paelinck J, Zuijderduijn J, Sawicka-Grzelak A, Meisel-Mikolajczyk FAntonie Van Leeuwenhoek10.1007/BF024399361985Antigens, Bacterial/*analysis, Bacteroides/*immunology, Carbohydrates/analysis, Epitopes/analysis, Hemagglutination Tests, Immune Sera, Immunoelectrophoresis
Pathogenicity2579527Properties of Bacteroides fragilis antigens with specificity B.Sawicka-Grzelak A, Meisel-Mikolajczyk FActa Microbiol Pol1985Animals, Antigens, Bacterial/*immunology, Bacteroides fragilis/*immunology, Endotoxins/immunology, Hemagglutination Tests, Immunodiffusion, Rabbits, Serotyping
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
Enzymology22051376Properties of BoAGE2, a second N-acetyl-D-glucosamine 2-epimerase from Bacteroides ovatus ATCC 8483.Sola-Carvajal A, Sanchez-Carron G, Garcia-Garcia MI, Garcia-Carmona F, Sanchez-Ferrer ABiochimie10.1016/j.biochi.2011.10.0122011Amino Acid Sequence, Bacteroides/*enzymology, Base Sequence, Carbohydrate Epimerases/chemistry/*metabolism, Carrier Proteins/chemistry/*metabolism, DNA Primers, Electrophoresis, Polyacrylamide Gel, Kinetics, Models, Molecular, Molecular Sequence Data, Polymerase Chain Reaction, Renin/metabolism, Sequence Homology, Amino AcidMetabolism
Metabolism27872187Galactomannan Catabolism Conferred by a Polysaccharide Utilization Locus of Bacteroides ovatus: ENZYME SYNERGY AND CRYSTAL STRUCTURE OF A beta-MANNANASE.Bagenholm V, Reddy SK, Bouraoui H, Morrill J, Kulcinskaja E, Bahr CM, Aurelius O, Rogers T, Xiao Y, Logan DT, Martens EC, Koropatkin NM, Stalbrand HJ Biol Chem10.1074/jbc.M116.7464382016Bacteroides/*enzymology, Catalysis, Crystallography, X-Ray, Galactose/analogs & derivatives, Hydrolysis, Mannans/*metabolism, Polysaccharides/*metabolism, Protein Conformation, Substrate Specificity, beta-Mannosidase/*chemistry/*metabolismEnzymology
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
Phylogeny30663928Bacteroides ovatus ATCC 8483 monotherapy is superior to traditional fecal transplant and multi-strain bacteriotherapy in a murine colitis model.Ihekweazu FD, Fofanova TY, Queliza K, Nagy-Szakal D, Stewart CJ, Engevik MA, Hulten KG, Tatevian N, Graham DY, Versalovic J, Petrosino JF, Kellermayer RGut Microbes10.1080/19490976.2018.15607532019Animals, Bacteria/classification/growth & development, Bacteroides/classification/growth & development/*physiology, Colitis/chemically induced/pathology/*therapy, Dextran Sulfate/toxicity, Disease Models, Animal, *Fecal Microbiota Transplantation, Feces/microbiology, Gastrointestinal Tract/microbiology/pathology, Inflammation/prevention & control, Male, Mice, Inbred C57BL, RNA, Ribosomal, 16S/genetics, Survival Analysis, Treatment OutcomePathogenicity
Phylogeny33881983Bacteroides luhongzhouii sp. nov. and Bacteroides zhangwenhongii sp. nov., isolated from human faeces.Ge Y, Zhang G, Yang J, Lai XH, Jin D, Lu S, Pu J, Huang Y, Luo X, Zheng H, Zhang X, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0047722021Bacterial Typing Techniques, Bacteroides/*classification/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Humans, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryPathogenicity
35087500Biochemical Characterization of Two Rhamnogalacturonan Lyases From Bacteroides ovatus ATCC 8483 With Preference for RG-I Substrates.Wang W, Wang Y, Yi H, Liu Y, Zhang G, Zhang L, Mayo KH, Yuan Y, Zhou YFront Microbiol10.3389/fmicb.2021.7998752022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
918Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1896)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1896
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
32784Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15588
44813Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 4943)https://www.ccug.se/strain?id=4943
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/
68380Automatically annotated from API rID32A
68382Automatically annotated from API zym
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
71237Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92789.1StrainInfo: A central database for resolving microbial strain identifiers
121472Curators of the CIPCollection of Institut Pasteur (CIP 103756)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103756