Strain identifier

BacDive ID: 12501

Type strain: Yes

Species: Parabacteroides gordonii

Strain Designation: MS-1

Strain history: M. Sakamoto MS-1 <-- N. Matsunaga strain 1.

NCBI tax ID(s): 1203610 (strain), 574930 (species)

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General

@ref: 16712

BacDive-ID: 12501

DSM-Number: 23371

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

description: Parabacteroides gordonii MS-1 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human blood cultures.

NCBI tax id

NCBI tax idMatching level
1203610strain
574930species

strain history

@refhistory
16712<- CCUG <- M. Sakamoto, JCM/RIKEN <- N. Matsunaga, Tokyo Med. Univ. Hospital, Japan; MS-1
67770M. Sakamoto MS-1 <-- N. Matsunaga strain 1.

doi: 10.13145/bacdive12501.20250331.9.3

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 gordonii
  • full scientific name: Parabacteroides gordonii Sakamoto et al. 2009

@ref: 16712

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Tannerellaceae

genus: Parabacteroides

species: Parabacteroides gordonii

full scientific name: Parabacteroides gordonii Sakamoto et al. 2009

strain designation: MS-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29308negative2.1 µm0.8 µmrod-shapedno
125438negative92.385

colony morphology

@reftype of hemolysisincubation period
16712gamma
613422 days

pigmentation

  • @ref: 29308
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16712COLUMBIA 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
16712CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78; with strain-specific modifications) 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 Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water

culture temp

@refgrowthtypetemperature
16712positivegrowth37
61342positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
16712anaerobe
29308anaerobe
61342anaerobe

spore formation

@refspore formationconfidence
29308no
125438no91.379
125439no97

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2930822599arabinose+carbon source
2930817234glucose+carbon source
2930817716lactose+carbon source
2930817306maltose+carbon source
2930837684mannose+carbon source
2930816634raffinose+carbon source
2930817992sucrose+carbon source
2930818222xylose+carbon source
6838017632nitrate-reduction
6838027897tryptophan-energy source
6838016024D-mannose+fermentation
6838016634raffinose+fermentation
6838029985L-glutamate-degradation
6838029016arginine-hydrolysis
6838016199urea-hydrolysis
6836727082trehalose-builds acid from
6836762345L-rhamnose+builds acid from
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

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

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

enzymes

@refvalueactivityec
16712catalase+1.11.1.6
16712cytochrome-c oxidase-1.9.3.1
29308alkaline phosphatase+3.1.3.1
29308catalase+1.11.1.6
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase+3.4.19.3
68380leucine arylamidase+3.4.11.1
68380phenylalanine arylamidase+
68380N-acetyl-beta-glucosaminidase+3.2.1.52
68380beta-glucosidase-3.2.1.21
68380glutamyl-glutamate arylamidase+
68380histidine arylamidase+
68380glycin arylamidase+
68380alanine arylamidase+3.4.11.2
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
68380glutamate decarboxylase-4.1.1.15
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase+3.2.1.55
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

@refUREGLUMANLACSACMALSALXYLARAGELESCGLYCELMNEMLZRAFSORRHATRECAT
16712-+-+++-++----+-+-+-+

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
16712--++---+-+++----++-+++++++++-
16712--++-+-+-+++----++-++++++++++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
16712human blood cultures
61342Human bloodJapanJPNAsia
67770Human blood cultures

isolation source categories

Cat1Cat2Cat3
#Infection#Patient#Blood culture
#Host#Human
#Host Body Product#Fluids#Blood

taxonmaps

  • @ref: 69479
  • File name: preview.99_3935.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_126;96_2004;97_2413;98_2983;99_3935&stattab=map
  • Last taxonomy: Parabacteroides gordonii subclade
  • 16S sequence: AB470343
  • Sequence Identity:
  • Total samples: 17375
  • soil counts: 84
  • aquatic counts: 362
  • animal counts: 16868
  • plant counts: 61

Safety information

risk assessment

  • @ref: 16712
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16712
  • description: Parabacteroides gordonii gene for 16S ribosomal RNA, partial sequence, strain: JCM 15724
  • accession: AB470343
  • length: 1485
  • database: nuccore
  • NCBI tax ID: 1203610

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Parabacteroides gordonii DSM 233711122931.3wgspatric1203610
66792Parabacteroides gordonii MS-11203610.3wgspatric1203610
66792Parabacteroides gordonii DSM 233712524614557draftimg1203610
66792Parabacteroides gordonii MS-12619619297draftimg1203610
67770Parabacteroides gordonii MS-1 = DSM 23371GCA_000969825scaffoldncbi1203610
67770Parabacteroides gordonii MS-1 = DSM 23371GCA_000428565scaffoldncbi1203610

GC content

@refGC-contentmethod
1671244.6
6777044.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate anaerobe85.1
125439BacteriaNetgram_stainReaction to gram-stainingnegative88.7
125439BacteriaNetmotilityAbility to perform movementno63.1
125439BacteriaNetspore_formationAbility to form endo- or exosporesno97
125438gram-positivegram-positivePositive reaction to Gram-stainingno92.385no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes87.14no
125438spore-formingspore-formingAbility to form endo- or exosporesno91.379yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no90.11yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno94.403yes
125438motile2+flagellatedAbility to perform flagellated movementno86no

External links

@ref: 16712

culture collection no.: DSM 23371, CCUG 57478, JCM 15724, KCTC 15149

straininfo link

  • @ref: 81720
  • straininfo: 398651

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19628614Parabacteroides gordonii sp. nov., isolated from human blood cultures.Sakamoto M, Suzuki N, Matsunaga N, Koshihara K, Seki M, Komiya H, Benno YInt J Syst Evol Microbiol10.1099/ijs.0.010611-02009Aged, Bacteroidetes/*classification/genetics/*isolation & purification/metabolism, Blood/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Humans, Male, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny25667391Parabacteroides faecis sp. nov., isolated from human faeces.Sakamoto M, Tanaka Y, Benno Y, Ohkuma MInt J Syst Evol Microbiol10.1099/ijs.0.0001092015Bacterial Proteins/genetics, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, Bile, Chaperonin 60/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Humans, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryPathogenicity
Phylogeny30267315Parabacteroides chongii sp. nov., isolated from blood of a patient with peritonitis.Kim H, Im WT, Kim M, Kim D, Seo YH, Yong D, Jeong SH, Lee KJ Microbiol10.1007/s12275-018-8122-32018Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Gram-Negative Bacterial Infections/*blood, Humans, Male, Middle Aged, Peritonitis/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisPathogenicity
Phylogeny32071723Parabacteroides pacaensis sp. nov. and Parabacteroides provencensis sp. nov., two new species identified from human gut microbiota.Benabdelkader S, Naud S, Lo CI, Fadlane A, Traore SI, Aboudharam G, La Scola BNew Microbes New Infect10.1016/j.nmni.2019.1006422020

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16712Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23371)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23371
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
29308Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2572128776041
61342Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 57478)https://www.ccug.se/strain?id=57478
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
81720Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID398651.1StrainInfo: A central database for resolving microbial strain identifiers
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