Strain identifier

BacDive ID: 140411

Type strain: Yes

Species: Streptococcus ruminantium

Strain Designation: GUT-187

Strain history: T. Sekizaki; Univ. of Tokyo, Japan; GUT-187.

NCBI tax ID(s): 1917441 (species)

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General

@ref: 43018

BacDive-ID: 140411

DSM-Number: 104980

keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-positive, coccus-shaped, colony-forming

description: Streptococcus ruminantium GUT-187 is an aerobe, Gram-positive, coccus-shaped bacterium that forms circular colonies and was isolated from heart of a cattle with endocarditis.

NCBI tax id

  • NCBI tax id: 1917441
  • Matching level: species

strain history

@refhistory
43018<- M. Tohya; The University of Tokyo, Tokyo, JAPAN; GUT-187<-M. Katsumi; Sendai City Institute of Public Health
67770T. Sekizaki; Univ. of Tokyo, Japan; GUT-187.

doi: 10.13145/bacdive140411.20240510.9

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Streptococcaceae
  • genus: Streptococcus
  • species: Streptococcus ruminantium
  • full scientific name: Streptococcus ruminantium Tohya et al. 2017

@ref: 43018

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Streptococcaceae

genus: Streptococcus

species: Streptococcus ruminantium

full scientific name: Streptococcus ruminantium Tohya et al. 2017

strain designation: GUT-187

type strain: yes

Morphology

cell morphology

  • @ref: 43494
  • gram stain: positive
  • cell width: 0.5-1 µm
  • cell shape: coccus-shaped
  • motility: no

colony morphology

  • @ref: 43494
  • type of hemolysis: alpha
  • hemolysis ability: 1
  • colony size: 0.5-1 mm
  • colony color: non-pigmented
  • colony shape: circular
  • medium used: Blood agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43494Blood agaryes
43018COLUMBIA 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
43018TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperature
43018positivegrowth37
67770positivegrowth37

Physiology and metabolism

oxygen tolerance

  • @ref: 43494
  • oxygen tolerance: aerobe

spore formation

  • @ref: 43494
  • spore formation: no

halophily

  • @ref: 43494
  • salt: NaCl
  • growth: no
  • tested relation: growth
  • concentration: 6.5 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4349418333D-arabitol-builds acid from
4349416899D-mannitol-builds acid from
4349428053melibiose-builds acid from
4349417924D-sorbitol-builds acid from
4349430849L-arabinose-builds acid from
434946731melezitose-builds acid from
43494320055methyl beta-D-glucopyranoside-builds acid from
4349433942ribose-builds acid from
4349433954tagatose-builds acid from
4349429016arginine-hydrolysis
43494606565hippurate-hydrolysis
4349416551D-trehalose+builds acid from
4349428087glycogen+builds acid from
4349417716lactose+builds acid from
4349417306maltose+builds acid from
4349427941pullulan+builds acid from
4349417992sucrose+builds acid from
6838129016arginine+hydrolysis
6838116988D-ribose-builds acid from
6838116899D-mannitol-builds acid from
6838130911sorbitol-builds acid from
6838117716lactose+builds acid from
6838127082trehalose+builds acid from
6838116634raffinose+builds acid from
6838117992sucrose+builds acid from
6838130849L-arabinose-builds acid from
6838118333D-arabitol-builds acid from
6838140585alpha-cyclodextrin+builds acid from
68381606565hippurate-hydrolysis
6838128087glycogen+builds acid from
6838127941pullulan+builds acid from
6838117306maltose+builds acid from
683816731melezitose-builds acid from
6838116443D-tagatose-builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
4349415688acetoinno
6838115688acetoinno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-test
4349415688acetoin-
6838115688acetoin-

enzymes

@refvalueactivityec
43494beta-glucosidase+3.2.1.21
43494esterase (C 4)+
43494leucine arylamidase+3.4.11.1
43494alpha-glucosidase+3.2.1.20
43494beta-galactosidase-3.2.1.23
43494N-acetyl-beta-glucosaminidase-3.2.1.52
43494lipase (C 14)-
43494valine arylamidase-
43494cystine arylamidase-3.4.11.3
43494trypsin-3.4.21.4
43494alpha-galactosidase-3.2.1.22
43494alpha-mannosidase-3.2.1.24
43494alpha-fucosidase-3.2.1.51
43494glycyl tryptophan arylamidase+
43494esterase Lipase (C 8)+
43494pyroglutamic acid arylamidase-
43494beta-mannosidase-3.2.1.25
43494alpha-chymotrypsin-3.4.21.1
43494acid phosphatase-3.1.3.2
43494naphthol-AS-BI-phosphohydrolase-
43494catalase-1.11.1.6
43494cytochrome oxidase-1.9.3.1
43494phenylalanine arylamidase+
43494alanine arylamidase+3.4.11.2
43494proline-arylamidase+3.4.11.5
68381beta-mannosidase+3.2.1.25
68381glycyl tryptophan arylamidase+
68381N-acetyl-beta-glucosaminidase-3.2.1.52
68381pyrrolidonyl arylamidase+3.4.19.3
68381beta-galactosidase-3.2.1.23
68381Alanyl-Phenylalanyl-Proline arylamidase+
68381alkaline phosphatase-3.1.3.1
68381alpha-galactosidase+3.2.1.22
68381beta-glucuronidase+3.2.1.31
68381beta-glucosidase+3.2.1.21
68381arginine dihydrolase+3.5.3.6

API rID32STR

@refADH Argbeta GLUbeta GARbeta GURalpha GALPALRIBMANSORLACTRERAFSACLARADARLCDEXVPAPPAbeta GALPyrAbeta NAGGTAHIPGLYGPULMALMELMLZMbeta DGTAGbeta MANURE
43018+++++----++++--+-+-+-+-++++/--+-++
43018+++++----++++--+-+-+-+-++++/----+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
43018heart of a cattle with endocarditisMiyagi PrefectureJapanJPNAsia38.2682140.869
43494heart of a cattle with endocarditis
67770Heart of a cattle with endocarditis

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host#Mammals#Bovinae (Cow, Cattle)
#Host Body-Site#Organ#Heart
#Infection#Inflammation

taxonmaps

  • @ref: 69479
  • File name: preview.99_30461.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_4;96_8;97_4465;98_5728;99_30461&stattab=map
  • Last taxonomy: Streptococcus ruminantium subclade
  • 16S sequence: LC195038
  • Sequence Identity:
  • Total samples: 85
  • soil counts: 6
  • aquatic counts: 7
  • animal counts: 72

Sequence information

16S sequences

  • @ref: 43018
  • description: Streptococcus ruminantium GUT-187 gene for 16S ribosomal RNA, partial sequence
  • accession: LC195038
  • length: 1546
  • database: nuccore
  • NCBI tax ID: 1917441

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptococcus ruminantium GUT-1872880287480completeimg1917441
67770Streptococcus ruminantium GUT-187GCA_003609975completencbi1917441

GC content

  • @ref: 43018
  • GC-content: 41.4
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 43018

culture collection no.: DSM 104980, JCM 31869

straininfo link

  • @ref: 96687
  • straininfo: 405087

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28840807Defining the taxonomic status of Streptococcus suis serotype 33: the proposal for Streptococcus ruminantium sp. nov.Tohya M, Arai S, Tomida J, Watanabe T, Kawamura Y, Katsumi M, Ushimizu M, Ishida-Kuroki K, Yoshizumi M, Uzawa Y, Iguchi S, Yoshida A, Kikuchi K, Sekizaki TInt J Syst Evol Microbiol10.1099/ijsem.0.0022042017Animals, Bacterial Typing Techniques, Cattle, DNA, Bacterial/genetics, Genes, Bacterial, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Serogroup, Streptococcus suis/*classificationTranscriptome
Genetics29659811Complete Genome Sequence of Streptococcus ruminantium sp. nov. GUT-187T (=DSM 104980T =JCM 31869T), the Type Strain of S. ruminantium, and Comparison with Genome Sequences of Streptococcus suis Strains.Tohya M, Sekizaki T, Miyoshi-Akiyama TGenome Biol Evol10.1093/gbe/evy0782018Animals, Base Sequence, Genome/genetics, *Molecular Sequence Annotation, Phylogeny, Sequence Analysis, DNA, Streptococcal Infections/*genetics/microbiology, Streptococcus/*genetics, Streptococcus suis/genetics, *Whole Genome SequencingPhylogeny

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
43018Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104980Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104980)
43494Mari Tohya, Sakura Arai, Junko Tomida, Takayasu Watanabe, Yoshiaki Kawamura, Masanori Katsumi, Mariko Ushimizu, Kasumi Ishida-Kuroki, Mina Yoshizumi, Yutaka Uzawa, Shigekazu Iguchi, Atsushi Yoshida, Ken Kikuchi, Tsutomu SekizakiDefining the taxonomic status of Streptococcus suis serotype 33: the proposal for Streptococcus ruminantium sp. nov.10.1099/ijsem.0.002204IJSEM 67: 3660-3665 201728840807
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68381Automatically annotated from API rID32STR
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
96687Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID405087.1