Strain identifier

BacDive ID: 12498

Type strain: Yes

Species: Parabacteroides johnsonii

Strain Designation: M-165

Strain history: CIP <- 2007, DSMZ <- M. Sakamoto, Bioresources Cent., Saitama, Japan: strain M-165

NCBI tax ID(s): 537006 (strain), 387661 (species)

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General

@ref: 7499

BacDive-ID: 12498

DSM-Number: 18315

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

description: Parabacteroides johnsonii M-165 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human faeces.

NCBI tax id

NCBI tax idMatching level
537006strain
387661species

strain history

@refhistory
7499<- M. Sakamoto; M-165 <- M. Kitahara
67770M. Sakamoto <-- M. Kitahara M-165.
120361CIP <- 2007, DSMZ <- M. Sakamoto, Bioresources Cent., Saitama, Japan: strain M-165

doi: 10.13145/bacdive12498.20250331.9.3

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 johnsonii
  • full scientific name: Parabacteroides johnsonii Sakamoto et al. 2007

@ref: 7499

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Tannerellaceae

genus: Parabacteroides

species: Parabacteroides johnsonii

full scientific name: Parabacteroides johnsonii Sakamoto et al. 2007 emend. Hahnke et al. 2016

strain designation: M-165

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31881negative1.7-2.5 µm0.8 µmrod-shapedno
120361negativerod-shapedno
125439negative98.6
125438negative93.023

colony morphology

@refincubation period
74991-2 days
604032 days

pigmentation

  • @ref: 31881
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7499COLUMBIA 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
7499PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
34705MEDIUM 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)
120361CIP Medium 137yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=137
120361CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperature
7499positivegrowth37
34705positivegrowth37
60403positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
7499anaerobe
31881anaerobe
60403anaerobe
120361anaerobe
125439obligate anaerobe99.5

spore formation

@refspore formationconfidence
31881no
125439no99.3
125438no93.243

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3188122599arabinose+carbon source
3188117234glucose+carbon source
3188117716lactose+carbon source
3188117306maltose+carbon source
3188137684mannose+carbon source
3188116634raffinose+carbon source
3188126546rhamnose+carbon source
3188117992sucrose+carbon source
3188127082trehalose+carbon source
3188118222xylose+carbon source
318814853esculin+hydrolysis
6838017632nitrate-reduction
6838027897tryptophan-energy source
6838029016arginine-hydrolysis
6838016199urea-hydrolysis
12036117632nitrate-reduction
12036116301nitrite-reduction
6838029985L-glutamate+degradation
6838016024D-mannose+fermentation
6836730911sorbitol-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
6836717992sucrose+builds acid from
6836717716lactose+builds acid from
6836716899D-mannitol-builds acid from
6836717634D-glucose+builds acid from
6836716199urea-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6838035581indoleno
12036135581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
31881alkaline phosphatase+3.1.3.1
31881alpha-galactosidase+3.2.1.22
31881catalase+1.11.1.6
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
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase+3.2.1.22
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-
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
120361oxidase-
120361catalase+1.11.1.6
120361urease-3.5.1.5
68380glutamate decarboxylase+4.1.1.15
68380beta-glucosidase+3.2.1.21
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380histidine arylamidase+
68380glycin arylamidase+
68380alanine arylamidase+3.4.11.2
68380leucine arylamidase+3.4.11.1
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-arabinosidase+3.2.1.55
68380alpha-glucosidase+3.2.1.20
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
68367beta-glucosidase+3.2.1.21
68367gelatinase-
68367urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120361-+---+---++-++---+--

API 20A

@refUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRE
7499-+-+++/--++-+--+++/--+/-+/-

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
7499--++-++++/-++++---++-++/-+-+/-++++/-+/-
7499--++-+++-+++/-+---++-++++++++++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7499human faecesJapanJPNAsia
60403Human feces
67770Human feces
120361Human, FaecesJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4981.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_126;96_972;97_1132;98_3725;99_4981&stattab=map
  • Last taxonomy: Parabacteroides johnsonii subclade
  • 16S sequence: AB261128
  • Sequence Identity:
  • Total samples: 70244
  • soil counts: 461
  • aquatic counts: 2276
  • animal counts: 67348
  • plant counts: 159

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
74991Risk group (German classification)
1203612Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7499
  • description: Parabacteroides johnsonii gene for 16S ribosomal RNA, partial sequence
  • accession: AB261128
  • length: 1492
  • database: nuccore
  • NCBI tax ID: 537006

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Parabacteroides johnsonii DSM 18315537006.5wgspatric537006
66792Parabacteroides johnsonii DSM 18315642979358draftimg537006
67770Parabacteroides johnsonii DSM 18315GCA_000156495scaffoldncbi537006
66792Parabacteroides johnsonii DSM 18315GCA_025151045completencbi537006
66792Parabacteroides johnsonii DSM 18315537006.36completepatric537006

GC content

@refGC-contentmethod
749947.6
749945.2sequence analysis
6777047.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno93.023yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes86.448no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no90.835yes
125438spore-formingspore-formingAbility to form endo- or exosporesno93.243yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno92.87no
125438motile2+flagellatedAbility to perform flagellated movementno89.5yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesno99.3
125439BacteriaNetmotilityAbility to perform movementno76.9
125439BacteriaNetgram_stainReaction to gram-stainingnegative98.6
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate anaerobe99.5

External links

@ref: 7499

culture collection no.: DSM 18315, CIP 109537, JCM 13406, CCUG 54943

straininfo link

  • @ref: 81717
  • straininfo: 293991

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
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
Phylogeny30652964Parabacteroides acidifaciens sp. nov., isolated from human faeces.Wang YJ, Xu XJ, Zhou N, Sun Y, Liu C, Liu SJ, You XInt J Syst Evol Microbiol10.1099/ijsem.0.0032302019Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Fermentation, Humans, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryPathogenicity
30687968A 2.08 A resolution structure of HLB5, a novel cellulase from the anaerobic gut bacterium Parabacteroides johnsonii DSM 18315.Chang C, Brooke C, Piao H, Mack J, Babnigg G, Joachimiak A, Hess MProtein Sci10.1002/pro.35822019Bacterial Proteins/*chemistry, Bacteroidetes/*chemistry, Binding Sites, Cellulase/*chemistry, Crystallography, X-Ray, Hydrolysis, Models, Molecular, Protein Conformation

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7499Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18315)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18315
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
31881Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2814128776041
34705Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7291
60403Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54943)https://www.ccug.se/strain?id=54943
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
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
81717Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID293991.1StrainInfo: A central database for resolving microbial strain identifiers
120361Curators of the CIPCollection of Institut Pasteur (CIP 109537)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109537
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1