Strain identifier

BacDive ID: 1604

Type strain: Yes

Species: Bacteroides uniformis

Strain history: ATCC 8492 <-- A. H. Eggerth (Bacteroides thetaiotaomicron).

NCBI tax ID(s): 411479 (strain), 820 (species)

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General

@ref: 2742

BacDive-ID: 1604

DSM-Number: 6597

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

description: Bacteroides uniformis CCUG 4942 is an anaerobe, mesophilic, rod-shaped bacterium that was isolated from human faeces.

NCBI tax id

NCBI tax idMatching level
820species
411479strain

strain history

@refhistory
2742<- ATCC <- A.H. Eggerth (Bacteroides thetaiotaomicron)
67771<- JCM <- ATCC 8492 <- AH Eggerth, Bacteroides thetaiotaomicron`
67770ATCC 8492 <-- A. H. Eggerth (Bacteroides thetaiotaomicron).

doi: 10.13145/bacdive1604.20230509.8.1

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

@ref: 2742

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Bacteroidaceae

genus: Bacteroides

species: Bacteroides uniformis

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

type strain: yes

Morphology

cell morphology

@refcell shapegram stainmotility
68367rod-shaped
68367negative
67771rod-shapedno
67771negative

colony morphology

  • @ref: 2742
  • type of hemolysis: gamma
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2742COLUMBIA 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
2742CHOPPED 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
32718MEDIUM 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)
2742FASTIDIOUS 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

culture temp

@refgrowthtypetemperaturerange
2742positivegrowth37mesophilic
32718positivegrowth37mesophilic
44812positivegrowth37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
2742anaerobe
44812anaerobe
44812microaerophile
67771anaerobe

spore formation

@refspore formation
68367no
67771no

observation

@refobservation
67770quinones: MK-10, MK-11
67771quinones: MK-10, MK-11

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836730911sorbitol-builds acid from
6836716634raffinose+builds acid from
683676731melezitose-builds acid from
6836716024D-mannose+builds acid from
6836717057cellobiose+builds acid from
6836717754glycerol-builds acid from
683674853esculin+hydrolysis
683675291gelatin-hydrolysis
6836730849L-arabinose+builds acid from
6836765327D-xylose+builds acid from
6836717814salicin+builds acid from
6836717306maltose+builds acid from
6836717992sucrose+builds acid from
6836717716lactose+builds acid from
6836716899D-mannitol-builds acid from
6836717634D-glucose+builds acid from
6836716199urea-hydrolysis
6836727897tryptophan+energy source
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
6838029985L-glutamate+degradation
6838017632nitrate-reduction
6838027897tryptophan+energy source

metabolite production

@refChebi-IDmetaboliteproduction
6836735581indoleyes
6838035581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole test
6838035581indole+
6836735581indole+

enzymes

@refvalueactivityec
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
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
68367catalase-1.11.1.6
68367beta-glucosidase+3.2.1.21
68367gelatinase-
68367urease-3.5.1.5

API 20A

@refINDUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRECATSPORGRAMCOCC
2742+-+-++++++-+-++-+-------
2742+-+-++++++-+-++-+-+/-+

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
2742--++-+++-++-++/--++--+----+--+-
2742--++-+++-++-++-++--+----+--+-
2742--++-+++-+++++-++--+----+--+-
2742--++-+++-+++++-++--+----+--+-
2742--++-+++-++-++/--++--+----+--+-
2742--++-+++-+++++-++--+----+--+-

Isolation, sampling and environmental information

isolation

@refsample type
2742human faeces
67770Human feces
67771From human faeces

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_114.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_21;96_89;97_94;98_103;99_114&stattab=map
  • Last taxonomy: Bacteroides uniformis
  • 16S sequence: AB510711
  • Sequence Identity:
  • Total samples: 385351
  • soil counts: 4816
  • aquatic counts: 15505
  • animal counts: 363541
  • plant counts: 1489

Safety information

risk assessment

  • @ref: 2742
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Bacteroides uniformis 16S-23S rDNA intergenic spacer regionAF176692485ena820
20218Bacteroides uniformis ATCC 8492 16S ribosomal RNA gene, complete sequenceL164861469ena820
2742Bacteroides uniformis gene for 16S rRNA, partial sequenceAB0501101425ena820
67770Bacteroides uniformis gene for 16S ribosomal RNA, partial sequence, strain: JCM 5828AB5107111477ena820

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bacteroides uniformis ATCC 8492 Bacteroides uniformis 82G1GCA_900896415contigncbi411479
66792Bacteroides uniformis ATCC 8492 Bacteroides uniformis 81A2GCA_900624705contigncbi411479
66792Bacteroides uniformis ATCC 8492411479.10wgspatric411479
66792Bacteroides uniformis ATCC 8492 strain Bacteroides uniformis 81A2411479.31wgspatric411479
66792Bacteroides uniformis ATCC 8492 strain Bacteroides uniformis 82G1411479.32wgspatric411479
66792Bacteroides uniformis strain DSM 6597820.37wgspatric820
66792Bacteroides uniformis strain FDAARGOS_901820.5080completepatric820
66792Bacteroides vulgatus strain ATCC 8492821.336wgspatric821
66792Bacteroides uniformis DSM 65972693429911draftimg820
66792Bacteroides uniformis ATCC 84922916274279draftimg411479
66792Bacteroides uniformis ATCC 8492641380447draftimg411479
66792Phocaeicola vulgatus ATCC 84922904834026draftimg821
67770Bacteroides uniformis DSM 6597GCA_900107315contigncbi820
67770Phocaeicola vulgatus ATCC 8492GCA_002959625contigncbi821
66792Bacteroides uniformis ATCC 8492GCA_000154205scaffoldncbi411479
66792Bacteroides uniformis ATCC 8492GCA_025147485completencbi820
66792Bacteroides uniformis strain ATCC 8492820.5953completepatric820
66792Bacteroides uniformis ATCC 8492GCA_028539285contigncbi820

GC content

@refGC-contentmethod
274246.0thermal denaturation, midpoint method (Tm)
274246.4sequence analysis
6777147.8high performance liquid chromatography (HPLC)
6777146.4genome sequence analysis
6777046thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno93.527yes
flagellatedno98.06yes
gram-positiveno96.823yes
anaerobicyes98.02no
halophileno91.434no
spore-formingno92.795yes
glucose-utilyes88.675no
aerobicno97.62yes
thermophileno99.243yes
glucose-fermentyes78.838no

External links

@ref: 2742

culture collection no.: CCUG 4942, JCM 5828, CIP 103695, KCTC 5204, DSM 6597, ATCC 8492, VPI 0061, CGMCC 1.5133, NCTC 13054

straininfo link

  • @ref: 71249
  • straininfo: 34970

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17158987Bacteroides barnesiae sp. nov., Bacteroides salanitronis sp. nov. and Bacteroides gallinarum sp. nov., isolated from chicken caecum.Lan PTN, Sakamoto M, Sakata S, Benno YInt J Syst Evol Microbiol10.1099/ijs.0.64517-02006Animals, Bacterial Typing Techniques, Bacteroides/chemistry/*classification/genetics/isolation & purification, Cecum/*microbiology, Chickens/*microbiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Phylogeny20495039Bacteroides chinchillae sp. nov. and Bacteroides rodentium sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces.Kitahara M, Tsuchida S, Kawasumi K, Amao H, Sakamoto M, Benno Y, Ohkuma MInt J Syst Evol Microbiol10.1099/ijs.0.024026-02010Anaerobiosis, Animals, Bacterial Typing Techniques, Bacteroides/*classification/genetics/*isolation & purification/physiology, Base Composition, Chinchilla/*microbiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Feces/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Enzymology23942877Cloning, expression, and characterization of the beta-glucosidase hydrolyzing secoisolariciresinol diglucoside to secoisolariciresinol from Bacteroides uniformis ZL1.Tao YL, Yang DH, Zhang YT, Zhang Y, Wang ZQ, Wang YS, Cai SQ, Liu SLAppl Microbiol Biotechnol10.1007/s00253-013-5111-72013Amino Acid Sequence, Bacteroides/*enzymology/genetics, Butylene Glycols/*metabolism, Cloning, Molecular, DNA, Bacterial/chemistry/genetics, Enzyme Stability, Escherichia coli/genetics, Gene Expression, Glucosides/*metabolism, Hydrogen-Ion Concentration, Hydrolysis, Lignans/*metabolism, Models, Molecular, Molecular Docking Simulation, Molecular Sequence Data, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Sequence Alignment, Sequence Analysis, DNA, Temperature, beta-Glucosidase/*genetics/*metabolismMetabolism
Metabolism31177942The 'in vivo lifestyle' of bile acid 7alpha-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice.Ridlon JM, Devendran S, Alves JM, Doden H, Wolf PG, Pereira GV, Ly L, Volland A, Takei H, Nittono H, Murai T, Kurosawa T, Chlipala GE, Green SJ, Hernandez AG, Fields CJ, Wright CL, Kakiyama G, Cann I, Kashyap P, McCracken V, Gaskins HRGut Microbes10.1080/19490976.2019.16181732019Animals, Bacteria, Anaerobic/*genetics/*metabolism, Bacteroides/genetics/metabolism, Bile Acids and Salts/*metabolism, Bilophila/genetics/metabolism, Cecum/*microbiology, Cholic Acids/metabolism, Clostridium/genetics/metabolism, Gene Expression Regulation, Bacterial, Genome, Bacterial, Genomics, Germ-Free Life, Humans, *Metabolome, Mice, Mice, Inbred C57BL, Microbiota, Operon, RNA-Seq, *Transcriptome, Up-RegulationGenetics
Phylogeny35657444Bacteroides humanifaecis sp. nov., isolated from faeces of healthy Korean.Kim HS, Kim JS, Suh MK, Eom MK, Lee JH, Park SH, Kang SW, Lee DH, Yoon H, Lee JH, Lee JSArch Microbiol10.1007/s00203-022-02967-x2022Bacterial Typing Techniques, *Bacteroides/genetics, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Feces/microbiology, Humans, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/chemistryPathogenicity
Phylogeny35939214Bacteroides muris sp. nov. isolated from the cecum of wild-derived house mice.Fokt H, Unni R, Repnik U, Schmitz RA, Bramkamp M, Baines JF, Unterweger DArch Microbiol10.1007/s00203-022-03148-62022Animals, Bacterial Typing Techniques, *Bacteroides/genetics, Cecum/microbiology, DNA, Bacterial/chemistry/genetics, Fatty Acids/analysis, *Gastropoda, Mice, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2742Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6597)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6597
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
32718Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15520
44812Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 4942)https://www.ccug.se/strain?id=4942
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68367Automatically annotated from API 20A
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
71249Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID34970.1StrainInfo: A central database for resolving microbial strain identifiers