Strain identifier

BacDive ID: 134180

Type strain: Yes

Species: Terrimonas lutea

Strain Designation: DY

Strain history: CIP <- 2006, IAM

NCBI tax ID(s): 296052 (species)

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General

@ref: 31718

BacDive-ID: 134180

keywords: 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped

description: Terrimonas lutea DY is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from Garden soil.

NCBI tax id

  • NCBI tax id: 296052
  • Matching level: species

strain history

@refhistory
327852006, IAM
67770IAM 15284 <-- C.-H. Xie strain DY.
120685CIP <- 2006, IAM

doi: 10.13145/bacdive134180.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Chitinophagia
  • order: Chitinophagales
  • family: Chitinophagaceae
  • genus: Terrimonas
  • species: Terrimonas lutea
  • full scientific name: Terrimonas lutea Xie and Yokota 2006

@ref: 31718

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Chitinophagales

family: Chitinophagaceae

genus: Terrimonas

species: Terrimonas lutea

strain designation: DY

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31718negative01-03 µm0.3-0.5 µmrod-shapedno
120685negativerod-shapedno

pigmentation

  • @ref: 31718
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
32785MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
120685CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
31718positivegrowth10-37
31718positiveoptimum25-32mesophilic
32785positivegrowth30mesophilic
67770positivegrowth27mesophilic

culture pH

@refabilitytypepH
31718positivegrowth7
31718positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31718aerobe
120685obligate aerobe

spore formation

  • @ref: 31718
  • spore formation: no

halophily

  • @ref: 31718
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %

observation

@refobservation
31718aggregates in chains
67770quinones: MK-7, MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31718581435-dehydro-D-gluconate+carbon source
3171822599arabinose+carbon source
3171817057cellobiose+carbon source
3171828757fructose+carbon source
3171828260galactose+carbon source
3171817234glucose+carbon source
3171817716lactose+carbon source
3171817306maltose+carbon source
3171837684mannose+carbon source
3171828053melibiose+carbon source
31718506227N-acetylglucosamine+carbon source
3171816634raffinose+carbon source
3171817992sucrose+carbon source
3171817632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose+builds acid from
683716731melezitose-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837117634D-glucose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12068517632nitrate-reduction
12068516301nitrite-reduction

metabolite production

  • @ref: 120685
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31718catalase+1.11.1.6
31718cytochrome oxidase+1.9.3.1
120685oxidase+
120685catalase+1.11.1.6
120685urease-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
120685-+++-+++++++++++++++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120685---+/-+/-+/----+/-++/-+----+---+/-++++++/-+/-+/-+-+/--+---+/-----------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
67770Garden soilJapanJPNAsia
120685Environment, Soil, gardenJapanJPNAsiaTokyo

taxonmaps

  • @ref: 69479
  • File name: preview.99_39829.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_185;96_18648;97_23074;98_29105;99_39829&stattab=map
  • Last taxonomy: Terrimonas lutea subclade
  • 16S sequence: AB192292
  • Sequence Identity:
  • Total samples: 1461
  • soil counts: 537
  • aquatic counts: 412
  • animal counts: 296
  • plant counts: 216

Safety information

risk assessment

  • @ref: 120685
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31718
  • description: Terrimonas lutea gene for 16S rRNA, partial sequence
  • accession: AB192292
  • length: 1431
  • database: nuccore
  • NCBI tax ID: 296052

GC content

@refGC-contentmethod
3171847.2
6777047.2high performance liquid chromatography (HPLC)

External links

@ref: 31718

culture collection no.: IAM 15284, CCTCC AB 205006, JCM 21735, BCRC 17943, CIP 109226

straininfo link

  • @ref: 91778
  • straininfo: 291136

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16627664Reclassification of [Flavobacterium] ferrugineum as Terrimonas ferruginea gen. nov., comb. nov., and description of Terrimonas lutea sp. nov., isolated from soil.Xie CH, Yokota AInt J Syst Evol Microbiol10.1099/ijs.0.64115-02006Bacterial Typing Techniques, Base Composition, DNA Gyrase/genetics, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/isolation & purification, Flavobacteriaceae/*classification/cytology/*isolation & purification/physiology, Genes, rRNA/genetics, Japan, Molecular Sequence Data, Phylogeny, Quinones/analysis/isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil MicrobiologyEnzymology
Phylogeny22904230Terrimonas pekingensis sp. nov., isolated from bulking sludge, and emended descriptions of the genus Terrimonas, Terrimonas ferruginea, Terrimonas lutea and Terrimonas aquatica.Jin D, Wang P, Bai Z, Jin B, Yu Z, Wang X, Zhuang G, Zhang HInt J Syst Evol Microbiol10.1099/ijs.0.036848-02012Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
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
31718Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172799428776041
32785Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6944
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
91778Reimer, 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-ID291136.1
120685Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109226Collection of Institut Pasteur (CIP 109226)