Strain identifier

BacDive ID: 140716

Type strain: Yes

Species: Vagococcus martis

Strain Designation: D7T301

Strain history: <- Jin Woo Bae, Kyunghee Univ.

NCBI tax ID(s): 1768210 (species)

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General

@ref: 43491

BacDive-ID: 140716

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

description: Vagococcus martis D7T301 is a facultative aerobe, Gram-positive, coccus-shaped bacterium that forms irregular colonies and was isolated from the small intestine tract of a marten, Martes flavigula, that was killed on the road.

NCBI tax id

  • NCBI tax id: 1768210
  • Matching level: species

strain history

@refhistory
67770J.-W. Bae; Dept. of Biol., Kyung Hee Univ., South Korea; D7T301.
67771<- Jin Woo Bae, Kyunghee Univ.

doi: 10.13145/bacdive140716.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Enterococcaceae
  • genus: Vagococcus
  • species: Vagococcus martis
  • full scientific name: Vagococcus martis Tak et al. 2017

@ref: 43491

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Enterococcaceae

genus: Vagococcus

species: Vagococcus martis

strain designation: D7T301

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
43491positivecoccus-shapedno
67771coccus-shapedno
67771positive

colony morphology

  • @ref: 43491
  • colony color: creamy
  • colony shape: irregular
  • medium used: TSYA

Culture and growth conditions

culture medium

  • @ref: 43491
  • name: TSYA
  • growth: yes

culture temp

@refgrowthtypetemperaturerange
43491positivegrowth15-37
43491positiveoptimum37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
43491positivegrowth6-9alkaliphile
43491positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
43491facultative aerobe
67771facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
43491NaClpositivegrowth0-5.5 %(w/v)
43491NaClpositiveoptimum0.5 %(w/v)

observation

@refobservation
67770quinones: MK-7
67771quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4349117234glucose+assimilation
4349137684mannose+assimilation
43491506227N-acetylglucosamine+assimilation
4349117057cellobiose+builds acid from
4349115824D-fructose+builds acid from
4349112936D-galactose+builds acid from
4349117634D-glucose+builds acid from
4349162318D-lyxose+builds acid from
4349116024D-mannose+builds acid from
4349116988D-ribose+builds acid from
4349116443D-tagatose+builds acid from
43491esculin ferric citrate+builds acid from
4349117754glycerol+builds acid from
4349117266L-sorbose+builds acid from
4349117306maltose+builds acid from
43491320061methyl alpha-D-glucopyranoside+builds acid from
43491506227N-acetylglucosamine+builds acid from
43491potassium 5-dehydro-D-gluconate+builds acid from
4349117992sucrose+builds acid from
4349127082trehalose+builds acid from
4349132528turanose+builds acid from
4349117925alpha-D-glucose+respiration
4349115824D-fructose+respiration
4349116024D-mannose+respiration
4349127605D-psicose+respiration
4349116988D-ribose+respiration
4349117754glycerol+respiration
4349151850methyl pyruvate+respiration
43491506227N-acetylglucosamine+respiration
4349117992sucrose+respiration
4349127082trehalose+respiration

enzymes

@refvalueactivityec
43491catalase-1.11.1.6
43491cytochrome oxidase-1.9.3.1
43491esterase Lipase (C 8)+
43491alpha-chymotrypsin+3.4.21.1
43491acid phosphatase+3.1.3.2
43491naphthol-AS-BI-phosphohydrolase+
43491beta-glucosidase+3.2.1.21
43491alpha-fucosidase+3.2.1.51

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
43491the small intestine tract of a marten, Martes flavigula, that was killed on the roadPocheon-si, Gyeonggi-doRepublic of KoreaKORAsia
67770Small intestine of a marten, Martes flavigulaPocheon-si, Gyeonggi-doRepublic of KoreaKORAsiaMartes flavigula
67771From small intestinal tract of a marten, `Martes flavigula`Pocheon-si, Gyeonggi-doRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Host#Other#Decomposing animal
#Host#Mammals
#Host Body-Site#Gastrointestinal tract#Small intestine

taxonmaps

  • @ref: 69479
  • File name: preview.99_4559.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_1881;97_2259;98_2772;99_4559&stattab=map
  • Last taxonomy: Vagococcus
  • 16S sequence: KX881420
  • Sequence Identity:
  • Total samples: 4332
  • soil counts: 288
  • aquatic counts: 136
  • animal counts: 3833
  • plant counts: 75

Sequence information

16S sequences

  • @ref: 43491
  • description: 16S rRNA gene sequence
  • accession: KX881420
  • database: nuccore

Genome sequences

  • @ref: 67770
  • description: Vagococcus martis D7T301
  • accession: GCA_002026305
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 1768210

GC content

@refGC-contentmethod
4349133.8Thermal denaturation, fluorometry
6777133.8genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno96.788yes
gram-positiveyes93.348yes
anaerobicno94.059yes
aerobicno95.681yes
halophileyes68.322yes
spore-formingno85.179no
glucose-utilyes87.664yes
thermophileno99.186yes
motileno94.617yes
glucose-fermentyes78.8no

External links

@ref: 43491

culture collection no.: KCTC 21069, JCM 31178

literature

  • topic: Phylogeny
  • Pubmed-ID: 28857031
  • title: Vagococcus martis sp. nov., isolated from the small intestine of a marten, Martes flavigula.
  • authors: Tak EJ, Kim HS, Lee JY, Kang W, Hyun DW, Kim PS, Shin NR, Bae JW
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002131
  • year: 2017
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Enterococcaceae/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Intestine, Small/*microbiology, Mustelidae/*microbiology, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
43491Euon Jung Tak, Hyun Sik Kim, June-Young Lee, Woorim Kang, Dong-Wook Hyun, Pil Soo Kim, Na-Ri Shin, Jin-Woo BaeVagococcus martis sp. nov., isolated from the small intestine of a marten, Martes flavigula10.1099/ijsem.0.002131IJSEM 67: 3398-3402 201728857031
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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/