Strain identifier

BacDive ID: 17755

Type strain: Yes

Species: Terrimonas ferruginea

Strain Designation: 3576

Strain history: CIP <- 2006, IAM

NCBI tax ID(s): 1123356 (strain), 249 (species)

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General

@ref: 9194

BacDive-ID: 17755

DSM-Number: 30193

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, Gram-negative

description: Terrimonas ferruginea 3576 is an obligate aerobe, Gram-negative bacterium of the family Chitinophagaceae.

NCBI tax id

NCBI tax idMatching level
1123356strain
249species

strain history

@refhistory
9194<- ATCC <- J.M. Coffey, 3576
374662006, IAM
67770IAM 15098 <-- NBRC 14992 <-- IFO 14992 <-- ATCC 13524 <-- J. M. Coffey.
119334CIP <- 2006, IAM

doi: 10.13145/bacdive17755.20240916.9.1

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 ferruginea
  • full scientific name: Terrimonas ferruginea (Sickles and Shaw 1934) Xie and Yokota 2006

  • synonyms

    • @ref: 20215
    • synonym: Flavobacterium ferrugineum

@ref: 9194

domain: Bacteria

phylum: Bacteroidetes

class: Chitinophagia

order: Sphingobacteriales

family: Chitinophagaceae

genus: Terrimonas

species: Terrimonas ferruginea

full scientific name: Terrimonas ferruginea (Sickles and Shaw 1934) Xie and Yokota 2006 emend. Jin et al. 2013

strain designation: 3576

type strain: yes

Morphology

cell morphology

  • @ref: 119334
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_30193_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_30193_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_30193_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_30193_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_30193_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9194NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
37466MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
119334CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperature
9194positivegrowth30
37466positivegrowth30
67770positivegrowth30

Physiology and metabolism

oxygen tolerance

  • @ref: 119334
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69481
  • spore formation: no
  • confidence: 100

compound production

  • @ref: 9194
  • compound: L carnitine

observation

  • @ref: 67770
  • observation: quinones: MK-7, MK-6

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371xylitol-builds acid from17151
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-sorbose-builds acid from17266
68371D-fructose-builds acid from15824
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371L-xylose-builds acid from65328
68371D-ribose-builds acid from16988
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
119334nitrate-reduction17632
119334nitrite-reduction16301
119334sodium thiosulfate-builds gas from132112

metabolite production

  • @ref: 119334
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 119334
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: +

enzymes

@refvalueactivityec
119334oxidase+
119334beta-galactosidase-3.2.1.23
119334catalase-1.11.1.6
119334tryptophan deaminase-
119334urease-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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    51522C14:0114
    51522C15:03.115
    51522C16:01.816
    51522C13:0 3OH/C15:1 i I/H36.814.469
    51522C13:0 iso0.912.612
    51522C15:0 ISO33.314.621
    51522C15:0 ISO 3OH1.616.135
    51522C16:0 3OH1.317.52
    51522C16:0 anteiso0.615.717
    51522C16:1 ω7c/C15:0 ISO 2OH7.815.85
    51522C17:0 iso 3OH5.818.161
    51522C18:2 ω6,9c/C18:0 ANTE217.724
    51522unknown 13.566413.566
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119334-+++-+++--++-+--+++-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119334---+/--+/--+/---+/--+/--+/----------+/--+/-+/--------+/-+/--+/-+/---------+/-

Isolation, sampling and environmental information

isolation

@refcountryorigin.countrycontinentsample type
37466JapanJPNAsia
67770Soil
119334JapanJPNAsiaEnvironment, Soil sample

taxonmaps

  • @ref: 69479
  • File name: preview.99_2195.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_185;96_1193;97_1407;98_1713;99_2195&stattab=map
  • Last taxonomy: Terrimonas ferruginea subclade
  • 16S sequence: AM230484
  • Sequence Identity:
  • Total samples: 3431
  • soil counts: 1362
  • aquatic counts: 1658
  • animal counts: 212
  • plant counts: 199

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
91941Risk group (German classification)
1193341Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218F.ferrugineum 16S ribosomal RNAM627981535nuccore249
20218Flavobacterium ferrugineum partial 16S rRNA gene, type strain DSM 30193AM2304841519nuccore249
20218Terrimonas ferruginea gene for 16S rRNA, partial sequence, strain: NBRC 14992AB6807361456nuccore249

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Terrimonas ferruginea DSM 301931123356.3wgspatric1123356
66792Terrimonas ferruginea DSM 301932523533530draftimg1123356
67770Terrimonas ferruginea DSM 30193GCA_000425585scaffoldncbi1123356

GC content

  • @ref: 67770
  • GC-content: 48.9
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno89.178no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no99.609no
69480spore-formingspore-formingAbility to form endo- or exosporesno88.773no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes86.493no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno99.163yes
69480flagellatedmotile2+Ability to perform flagellated movementno89.5no

External links

@ref: 9194

culture collection no.: DSM 30193, ATCC 13524, IAM 15098, LMG 4021, NBRC 14992, CCUG 33443, JCM 21559, BCRC 17944, IFO 14992, LMG 10403, NCIMB 11299, CIP 109225

straininfo link

  • @ref: 86746
  • straininfo: 2823

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
Phylogeny16902007Niastella koreensis gen. nov., sp. nov. and Niastella yeongjuensis sp. nov., novel members of the phylum Bacteroidetes, isolated from soil cultivated with Korean ginseng.Weon HY, Kim BY, Yoo SH, Lee SY, Kwon SW, Go SJ, Stackebrandt EInt J Syst Evol Microbiol10.1099/ijs.0.64242-02006Agriculture, Bacteroidetes/chemistry/*classification/genetics/isolation & purification, Base Composition, Cyanoacrylates/analysis, DNA, Bacterial/genetics, Fatty Acids/analysis, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Panax, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, *Soil Microbiology, Species SpecificityGenetics
Phylogeny17329780Niabella aurantiaca gen. nov., sp. nov., isolated from a greenhouse soil in Korea.Kim BY, Weon HY, Yoo SH, Hong SB, Kwon SW, Stackebrandt E, Go SJInt J Syst Evol Microbiol10.1099/ijs.0.64614-02007DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Flavobacterium/*classification/cytology/genetics/isolation & purification, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics
Phylogeny18768628Sediminibacterium salmoneum gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from sediment of a eutrophic reservoir.Qu JH, Yuan HLInt J Syst Evol Microbiol10.1099/ijs.0.65514-02008Aerobiosis, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/*isolation & purification/physiology, Base Composition, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Locomotion, Molecular Sequence Data, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidGenetics
Phylogeny20061502Terrimonas aquatica sp. nov., isolated from a freshwater spring.Sheu SY, Cho NT, Arun AB, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.020164-02010Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny20656815Flavitalea populi gen. nov., sp. nov., isolated from soil of a Euphrates poplar (Populus euphratica) forest.Wang Y, Cai F, Tang Y, Dai J, Qi H, Rahman E, Peng F, Fang CInt J Syst Evol Microbiol10.1099/ijs.0.025221-02010Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Forests, Molecular Sequence Data, *Phylogeny, *Populus, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
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
Phylogeny27412118Filimonas aurantiibacter sp. nov., an orange-pigmented bacterium isolated from lake water and emended description of the genus Filimonas.Albert RA, Waas NE, Pavlons SC, Pearson JL, Roecker J, Tewalt N, Cleeve N, Rossello-Mora R, Busse HJInt J Syst Evol Microbiol10.1099/ijsem.0.0013052016Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Lakes/*microbiology, Michigan, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spermidine/analogs & derivatives/chemistry, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny27902263Terrimonas rhizosphaerae sp. nov., isolated from ginseng rhizosphere soil.Han SI, Lee YR, Kim JO, Whang KSInt J Syst Evol Microbiol10.1099/ijsem.0.0016392017Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Panax/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
9194Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 30193)https://www.dsmz.de/collection/catalogue/details/culture/DSM-30193
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
37466Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6943
51522Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 33443)https://www.ccug.se/strain?id=33443
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
86746Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2823.1StrainInfo: A central database for resolving microbial strain identifiers
119334Curators of the CIPCollection of Institut Pasteur (CIP 109225)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109225