Strain identifier

BacDive ID: 12499

Type strain: Yes

Species: Parabacteroides merdae

Strain Designation: T4-1

Strain history: CIP <- 1994, ATCC <- L.V. Moore, VPI: strain T4-1 <- W.E.C. Moore

NCBI tax ID(s): 411477 (strain), 46503 (species)

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General

@ref: 8118

BacDive-ID: 12499

DSM-Number: 19495

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

description: Parabacteroides merdae T4-1 is an anaerobe, mesophilic, Gram-negative human pathogen that was isolated from human faeces.

NCBI tax id

NCBI tax idMatching level
46503species
411477strain

strain history

@refhistory
8118<- JCM <- ATCC <- L. V. Moore; VPI T4-1 <- W. E. C. Moore
67770ATCC 43184 <-- L. V. Moore VPI T4-1 <-- W. E. C. Moore.
120896CIP <- 1994, ATCC <- L.V. Moore, VPI: strain T4-1 <- W.E.C. Moore

doi: 10.13145/bacdive12499.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Tannerellaceae
  • genus: Parabacteroides
  • species: Parabacteroides merdae
  • full scientific name: Parabacteroides merdae (Johnson et al. 1986) Sakamoto and Benno 2006

  • synonyms

    • @ref: 20215
    • synonym: Bacteroides merdae

@ref: 8118

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Tannerellaceae

genus: Parabacteroides

species: Parabacteroides merdae

full scientific name: Parabacteroides merdae (Johnson et al. 1986) Sakamoto and Benno 2006 emend. Hahnke et al. 2016

strain designation: T4-1

type strain: yes

Morphology

cell morphology

  • @ref: 120896
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 8118
  • incubation period: 1-2 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8118COLUMBIA 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
8118CHOPPED 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
34044MEDIUM 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)
120896CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperaturerange
8118positivegrowth37mesophilic
34044positivegrowth37mesophilic
54425positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
8118anaerobe
54425anaerobe

observation

  • @ref: 67770
  • observation: quinones: MK-9, MK-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12089617632nitrate-reduction
12089616301nitrite-reduction
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
6838016634raffinose+fermentation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
12089635581indoleno
6838035581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase+
68380histidine arylamidase+
68380alanine arylamidase+3.4.11.2
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
68380N-acetyl-beta-glucosaminidase+3.2.1.52
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
120896oxidase-
120896catalase-1.11.1.6
120896urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase-3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120896-+---+-----+-+---+--

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
8118--++-++++/-+++----++-+++-+++++-
8118--++-++/-+/--++++---++-+++-+/-++/-++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
8118human faecesUSAUSANorth America
54425Human fecesUSAUSANorth AmericaTexas
67770Human feces
120896Human, FecesUnited States of AmericaUSANorth AmericaTexas1972

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1709.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_126;96_972;97_1132;98_1349;99_1709&stattab=map
  • Last taxonomy: Parabacteroides merdae subclade
  • 16S sequence: EU136685
  • Sequence Identity:
  • Total samples: 300697
  • soil counts: 3196
  • aquatic counts: 11747
  • animal counts: 284785
  • plant counts: 969

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
8118yes, in single cases1Risk group (German classification)
1208962Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Parabacteroides merdae gene for 16S ribosomal RNA, partial sequence, strain: JCM 9497AB2389281492ena46503
20218Bacteroides merdae 16S-23S ribosomal RNA intergenic spacer region, partial sequenceAY153427431ena411477
20218Parabacteroides merdae strain JCM9497 16S ribosomal RNA gene, partial sequenceEU1366852023ena46503
20218Bacteroides merdae 16S ribosomal RNA gene, partial sequenceU5041662ena411477
8118B.merdae 16S rRNA (ATCC 43184T)X839541405ena411477
8118Parabacteroides merdae ATCC 43184 16S ribosomal RNA, partial sequenceNR_1191661405nuccore411477

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Parabacteroides merdae NCTC13052GCA_900445495contigncbi46503
66792Parabacteroides merdae ATCC 43184411477.4wgspatric411477
66792Parabacteroides merdae strain NCTC1305246503.89wgspatric46503
66792Parabacteroides merdae NCTC 130522811995281draftimg46503
66792Parabacteroides merdae ATCC 43184640963016draftimg411477
66792Parabacteroides merdae ATCC 43184GCA_000154105scaffoldncbi411477
66792Parabacteroides merdae ATCC 43184GCA_025151215completencbi411477
66792Parabacteroides merdae ATCC 43184411477.87completepatric411477

GC content

@refGC-contentmethod
811844
811845.3sequence analysis
6777044thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno90.994no
flagellatedno98.143no
gram-positiveno97.108no
anaerobicyes98.405yes
aerobicno97.661no
halophileno89.128no
spore-formingno95.577no
glucose-fermentyes64.407no
thermophileno97.606yes
glucose-utilyes91.719no

External links

@ref: 8118

culture collection no.: DSM 19495, ATCC 43184, CCUG 38734, CIP 104202, JCM 9497, VPI T4-1, NCTC 13052

straininfo link

  • @ref: 81718
  • straininfo: 41698

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology7549766Detection of Bacteroides fragilis in clinical specimens by polymerase chain reaction amplification of the neuraminidase gene.Jotwani R, Kato N, Kato H, Watanabe K, Ueno KCurr Microbiol10.1007/BF002983761995Bacterial Infections/*microbiology, Bacterial Proteins/*analysis/genetics, Bacteroides fragilis/enzymology/*isolation & purification, Base Sequence, Humans, Molecular Sequence Data, Neuraminidase/*analysis/genetics, Polymerase Chain ReactionPathogenicity
Phylogeny16145101"Bacteroides goldsteinii sp. nov." isolated from clinical specimens of human intestinal origin.Song Y, Liu C, Lee J, Bolanos M, Vaisanen ML, Finegold SMJ Clin Microbiol10.1128/JCM.43.9.4522-4527.20052005Bacterial Typing Techniques, Bacteroides/*classification/genetics/*isolation & purification/physiology, Bacteroides Infections/*microbiology, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Humans, Intestines/*microbiology, Molecular Sequence Data, Phenotype, *Phylogeny, RNA, Ribosomal, 16S/*genetics, Sequence Analysis, DNAPathogenicity
Phylogeny16825636Reclassification of Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae as Parabacteroides distasonis gen. nov., comb. nov., Parabacteroides goldsteinii comb. nov. and Parabacteroides merdae comb. nov.Sakamoto M, Benno YInt J Syst Evol Microbiol10.1099/ijs.0.64192-02006Bacterial Typing Techniques, Bacteroides/chemistry/*classification/genetics/physiology, Bacteroidetes/chemistry/*classification/genetics/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA/genetics, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Vitamin K 2/analysis/chemistryGenetics
Phylogeny17267966Parabacteroides johnsonii sp. nov., isolated from human faeces.Sakamoto M, Kitahara M, Benno YInt J Syst Evol Microbiol10.1099/ijs.0.64588-02007Anaerobiosis, Bacterial Typing Techniques, Bacteroidetes/*classification/cytology/*isolation & purification/physiology, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Feces/*microbiology, Genes, rRNA, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis/chemistry, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidPathogenicity
Phylogeny22199215Parabacteroides chartae sp. nov., an obligately anaerobic species from wastewater of a paper mill.Tan HQ, Li TT, Zhu C, Zhang XQ, Wu M, Zhu XFInt J Syst Evol Microbiol10.1099/ijs.0.038000-02011Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, Carbohydrate Metabolism, DNA, Bacterial/genetics, Fatty Acids/analysis, Fermentation, Molecular Sequence Data, *Paper, *Phylogeny, Quinones/analysis, Sequence Analysis, DNA, Waste Water/*microbiologyGenetics
Phylogeny23563230Parabacteroides chinchillae sp. nov., isolated from chinchilla (Chincilla lanigera) faeces.Kitahara M, Sakamoto M, Tsuchida S, Kawasumi K, Amao H, Benno Y, Ohkuma MInt J Syst Evol Microbiol10.1099/ijs.0.050146-02013Animals, Bacterial Typing Techniques, Bacteroides/*classification/genetics/isolation & purification, Base Composition, Chaperonin 60/genetics, Chinchilla/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, Feces/microbiology, Genes, Bacterial, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Phylogeny31641517Parabacteroides massiliensis sp. nov., a new bacterium isolated from a fresh human stool specimen.Bellali S, Lo CI, Naud S, Fonkou MDM, Armstrong N, Raoult D, Fournier PE, Fenollar FNew Microbes New Infect10.1016/j.nmni.2019.1006022019
Phylogeny35496671Parabacteroides pekinense sp. nov.: a new bacterium isolated from the stool of a healthy man living in China.Li Z, Zhou X, Xu W, Chen R, Zhao B, Wu CNew Microbes New Infect10.1016/j.nmni.2022.1009732022

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8118Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19495)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19495
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
34044Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16084
54425Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 38734)https://www.ccug.se/strain?id=38734
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
81718Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID41698.1StrainInfo: A central database for resolving microbial strain identifiers
120896Curators of the CIPCollection of Institut Pasteur (CIP 104202)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104202