Strain identifier

BacDive ID: 3036

Type strain: Yes

Species: Conexibacter woesei

Strain Designation: ID131577

Strain history: CIP <- 2003, DSMZ <- P. Monciardini <- L. Cavaletti: strain ID131577

NCBI tax ID(s): 469383 (strain), 191495 (species)

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General

@ref: 5480

BacDive-ID: 3036

DSM-Number: 14684

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic

description: Conexibacter woesei ID131577 is an obligate aerobe, mesophilic bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
469383strain
191495species

strain history

@refhistory
5480<- P. Monciardini <- L. Cavaletti; ID131577
67770P. Monciardini ID131577.
123954CIP <- 2003, DSMZ <- P. Monciardini <- L. Cavaletti: strain ID131577

doi: 10.13145/bacdive3036.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Thermoleophilia
  • order: Solirubrobacterales
  • family: Conexibacteraceae
  • genus: Conexibacter
  • species: Conexibacter woesei
  • full scientific name: Conexibacter woesei Monciardini et al. 2003

@ref: 5480

domain: Bacteria

phylum: Actinobacteria

class: Thermoleophilia

order: Solirubrobacterales

family: Conexibacteraceae

genus: Conexibacter

species: Conexibacter woesei

full scientific name: Conexibacter woesei Monciardini et al. 2003 emend. Nouioui et al. 2018

strain designation: ID131577

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no95.657
6948099.999positive
123954yespositiverod-shaped

colony morphology

  • @ref: 123954

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_14684_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5480TRYPTICASE 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
33883MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123954CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
5480positivegrowth28mesophilic
33883positivegrowth30mesophilic
67770positivegrowth28mesophilic
123954positivegrowth25-30mesophilic
123954nogrowth10psychrophilic
123954nogrowth15psychrophilic
123954nogrowth37mesophilic
123954nogrowth41thermophilic
123954nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123954
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.847

halophily

@refsaltgrowthtested relationconcentration
123954NaClpositivegrowth0-2 %
123954NaClnogrowth4 %
123954NaClnogrowth6 %
123954NaClnogrowth8 %
123954NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-7(H4)

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate+builds acid from
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
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
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
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin+builds acid from4853
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-rhamnose+builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose+builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
123954citrate-carbon source16947
123954esculin+hydrolysis4853
123954hippurate+hydrolysis606565
123954nitrate+reduction17632
123954nitrite-reduction16301

antibiotic resistance

  • @ref: 123954
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 123954
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12395415688acetoin-
12395417234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
123954oxidase+
123954beta-galactosidase+3.2.1.23
123954alcohol dehydrogenase-1.1.1.1
123954gelatinase+/-
123954amylase-
123954DNase-
123954caseinase-3.4.21.50
123954catalase+1.11.1.6
123954tween esterase+
123954gamma-glutamyltransferase+2.3.2.2
123954lecithinase-
123954lipase-
123954lysine decarboxylase-4.1.1.18
123954ornithine decarboxylase-4.1.1.17
123954phenylalanine ammonia-lyase-4.3.1.24
123954protease-
123954tryptophan deaminase-
123954urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123954--++-+-+--++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123954+-+-++----+---+---------+-----------------+-----+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic locationisolation date
5480soilItalyITAEurope
67770Soil from a wooded areaItalyITAEuropeGerenzano
123954Environment, SoilItalyITAEurope2003

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_3862.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_373;96_1982;97_2383;98_2943;99_3862&stattab=map
  • Last taxonomy: Conexibacter woesei subclade
  • 16S sequence: AJ440237
  • Sequence Identity:
  • Total samples: 5850
  • soil counts: 4181
  • aquatic counts: 1103
  • animal counts: 280
  • plant counts: 286

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
54801Risk group (German classification)
1239541Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Conexibacter woesei partial 16S rRNA gene, type strain DSM 14684T
  • accession: AJ440237
  • length: 1470
  • database: ena
  • NCBI tax ID: 469383

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Conexibacter woesei DSM 14684GCA_000025265completencbi469383
66792Conexibacter woesei DSM 14684469383.5completepatric469383
66792Conexibacter woesei ID131577, DSM 14684646311917completeimg469383

GC content

@refGC-contentmethod
548071.0
6777071high performance liquid chromatography (HPLC)
6777072.73genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes66no
motileyes64.513no
flagellatedno93.349no
gram-positiveyes82.874no
anaerobicno96.667no
aerobicyes82.176no
halophileno91.233no
spore-formingno86.935no
thermophileno95.702no
glucose-utilyes86.589no
glucose-fermentno90.871no

External links

@ref: 5480

culture collection no.: DSM 14684, JCM 11494, CCUG 47730, CIP 108061, KCTC 19437, KCTC 9949, NBRC 100937

straininfo link

  • @ref: 72556
  • straininfo: 97656

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12710628Conexibacter woesei gen. nov., sp. nov., a novel representative of a deep evolutionary line of descent within the class Actinobacteria.Monciardini P, Cavaletti L, Schumann P, Rohde M, Donadio SInt J Syst Evol Microbiol10.1099/ijs.0.02400-02003Actinobacteria/chemistry/*classification/genetics/physiology, Biological Evolution, Cell Wall/*chemistry, DNA, Bacterial/chemistry/genetics, Diaminopimelic Acid/*metabolism, Fatty Acids/analysis, Microscopy, Electron, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/analysis, *Soil MicrobiologyGenetics
Phylogeny16449447Patulibacter minatonensis gen. nov., sp. nov., a novel actinobacterium isolated using an agar medium supplemented with superoxide dismutase, and proposal of Patulibacteraceae fam. nov.Takahashi Y, Matsumoto A, Morisaki K, Omura SInt J Syst Evol Microbiol10.1099/ijs.0.63796-02006Actinobacteria/*classification/genetics/*isolation & purification/physiology, *Agar, Bacterial Typing Techniques, Bacteriological Techniques, Base Composition, *Culture Media, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Superoxide Dismutase/*metabolismGenetics
Phylogeny17625174Solirubrobacter soli sp. nov., isolated from soil of a ginseng field.Kim MK, Na JR, Lee TH, Im WT, Soung NK, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.64715-02007Actinobacteria/chemistry/*classification/*isolation & purification/physiology, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Korea, Locomotion, Molecular Sequence Data, Panax, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Spores, Bacterial, Vitamin K 2/analysisGenetics
Genetics21304704Complete genome sequence of Conexibacter woesei type strain (ID131577).Pukall R, Lapidus A, Glavina Del Rio T, Copeland A, Tice H, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Mavromatis K, Ivanova N, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Meincke L, Sims D, Brettin T, Detter JC, Rohde M, Goker M, Bristow J, Eisen JA, Markowitz V, Kyrpides NC, Klenk HP, Hugenholtz PStand Genomic Sci10.4056/sigs.7513392010
Phylogeny22140169Conexibacter arvalis sp. nov., isolated from a cultivated field soil sample.Seki T, Matsumoto A, Shimada R, Inahashi Y, Omura S, Takahashi YInt J Syst Evol Microbiol10.1099/ijs.0.036095-02011Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/analysis, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny29299847Baekduia soli gen. nov., sp. nov., a novel bacterium isolated from the soil of Baekdu Mountain and proposal of a novel family name, Baekduiaceae fam. nov.An DS, Siddiqi MZ, Kim KH, Yu HS, Im WTJ Microbiol10.1007/s12275-018-7107-62018Bacteria/*classification/genetics/*isolation & purification/metabolism, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Panax/growth & development, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5480Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14684)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14684
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
33883Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5642
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
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
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)
72556Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID97656.1StrainInfo: A central database for resolving microbial strain identifiers
123954Curators of the CIPCollection of Institut Pasteur (CIP 108061)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108061