Strain identifier

BacDive ID: 17742

Type strain: Yes

Species: Chitinophaga arvensicola

Strain Designation: M64

Strain history: CIP <- 1996, IFO <- 1989, IAM <- H. Oyaizu, Tokyo Univ., Tokyo, Japan <- T. Harada, Osaka Univ., Osaka, Japan: strain M64

NCBI tax ID(s): 29529 (species)

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General

@ref: 1457

BacDive-ID: 17742

DSM-Number: 3695

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

description: Chitinophaga arvensicola M64 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 29529
  • Matching level: species

strain history

@refhistory
1457<- JCM <- H. Oyaizu, M64
67770H. Oyaizu M64 <-- T. Harada.
116514CIP <- 1996, IFO <- 1989, IAM <- H. Oyaizu, Tokyo Univ., Tokyo, Japan <- T. Harada, Osaka Univ., Osaka, Japan: strain M64

doi: 10.13145/bacdive17742.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Chitinophagia
  • order: Chitinophagales
  • family: Chitinophagaceae
  • genus: Chitinophaga
  • species: Chitinophaga arvensicola
  • full scientific name: Chitinophaga arvensicola (Oyaizu et al. 1983) Kämpfer et al. 2006

  • synonyms

    • @ref: 20215
    • synonym: Cytophaga arvensicola

@ref: 1457

domain: Bacteria

phylum: Bacteroidetes

class: Chitinophagia

order: Sphingobacteriales

family: Chitinophagaceae

genus: Chitinophaga

species: Chitinophaga arvensicola

full scientific name: Chitinophaga arvensicola (Oyaizu et al. 1983) Kämpfer et al. 2006 emend. Pankratov et al. 2006

strain designation: M64

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
125438negative97.139
125439negative98.7
116514negativerod-shapedno

colony morphology

  • @ref: 116514

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1457CY-AGAR (DSMZ Medium 67)yeshttps://mediadive.dsmz.de/medium/67Name: CY-AGAR (DSMZ Medium 67) Composition: Agar 15.0 g/l Casitone 3.0 g/l CaCl2 x 2 H2O 1.36 g/l Yeast extract 1.0 g/l Distilled water
39104MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116514CIP Medium 251yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=251
116514CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
116514CIP Medium 99yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=99

culture temp

@refgrowthtypetemperature
1457positivegrowth30
39104positivegrowth30
67770positivegrowth30
116514positivegrowth5-37
116514nogrowth41
116514nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
116514obligate aerobe
125439obligate aerobe90.2

spore formation

  • @ref: 125439
  • spore formation: no
  • confidence: 98.7

compound production

  • @ref: 1457
  • compound: succinoglucan depolymerase

halophily

@refsaltgrowthtested relationconcentration
116514NaClpositivegrowth0-2 %
116514NaClnogrowth4 %
116514NaClnogrowth6 %
116514NaClnogrowth8 %
116514NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1165144853esculin+hydrolysis
116514606565hippurate-hydrolysis
11651417632nitrate+reduction
11651416301nitrite-reduction
11651415792malonate-assimilation
11651417632nitrate-respiration

antibiotic resistance

  • @ref: 116514
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 116514
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11651415688acetoin-
11651417234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382beta-galactosidase+3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382lipase (C 14)+
68382esterase lipase (C 8)+
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
116514oxidase+
116514beta-galactosidase+3.2.1.23
116514alcohol dehydrogenase-1.1.1.1
116514gelatinase-
116514amylase-
116514DNase-
116514caseinase-3.4.21.50
116514catalase+1.11.1.6
116514tween esterase-
116514gamma-glutamyltransferase+2.3.2.2
116514lecithinase-
116514lipase-
116514lysine decarboxylase-4.1.1.18
116514ornithine decarboxylase-4.1.1.17
116514tryptophan deaminase-
116514urease-3.5.1.5
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116514-++++++++-++-+-+++--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116514+-+++-++-++++++++++++++++------+--++---+-+-------+----++---+-------------------++-----+--++--------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
1457soilJapanJPNAsia
67770Soil
116514Environment, SoilJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_9002.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_334;96_4254;97_5197;98_6597;99_9002&stattab=map
  • Last taxonomy: Chitinophaga arvensicola
  • 16S sequence: AM237311
  • Sequence Identity:
  • Total samples: 25
  • soil counts: 24
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
14571Risk group (German classification)
1165141Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Cytophaga arvensicola partial 16S rRNA gene, type strain DSM 3695TAM2373111424nuccore29529
20218Cytophaga arvensicola gene for 16S ribosomal RNA, partial sequenceD126571263nuccore29529
20218Chitinophaga arvensicola gene for 16S rRNA, partial sequence, strain: NBRC 14973AB6807281452nuccore29529

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chitinophaga arvensicola strain DSM 369529529.11wgspatric29529
66792Chitinophaga arvensicola DSM 36952636416040draftimg29529
67770Chitinophaga arvensicola DSM 3695GCA_900110835scaffoldncbi29529

GC content

@refGC-contentmethod
145746.0
6777046thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno97.139no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.72no
125438spore-formingspore-formingAbility to form endo- or exosporesno83.891no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes89.338yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno96.99no
125438motile2+flagellatedAbility to perform flagellated movementno85no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno98.7
125439BacteriaNetmotilityAbility to perform movementyes58.1
125439BacteriaNetgram_stainReaction to gram-stainingnegative98.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe90.2

External links

@ref: 1457

culture collection no.: DSM 3695, ATCC 51264, IAM 12650, JCM 2836, NCIB 11855, CECT 358, CIP 104804, IFO 14973, IFO 16136, KCTC 2943, NBRC 14973, NBRC 16136, NCIMB 11855

straininfo link

  • @ref: 86732
  • straininfo: 10826

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17158974Isolation of aerobic, gliding, xylanolytic and laminarinolytic bacteria from acidic Sphagnum peatlands and emended description of Chitinophaga arvensicola Kampfer et al. 2006.Pankratov TA, Kulichevskaya IS, Liesack W, Dedysh SNInt J Syst Evol Microbiol10.1099/ijs.0.64451-02006Bacteria, Aerobic/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Bacteroidetes/*classification, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Glucans, Hydrogen-Ion Concentration, Molecular Sequence Data, *Movement, Nitrates/metabolism, Phylogeny, Pigmentation, Polysaccharides/*metabolism, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA, Sphagnopsida/*microbiology, Wetlands, Xylans/*metabolismMetabolism
Phylogeny19684320Chitinophaga vermicomposti sp. nov., with antifungal activity, isolated from vermicompost.Yasir M, Aslam Z, Song GC, Bibi F, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.013425-02009
Phylogeny21057055Chitinophaga eiseniae sp. nov., isolated from vermicompost.Yasir M, Chung EJ, Song GC, Bibi F, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.023028-02010Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/*isolation & purification/physiology, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, *Soil Microbiology, Temperature, Vitamin K 2/analysisGenetics
Phylogeny35482508Chitinophaga hostae sp. nov., isolated from the rhizosphere soil of Hosta plantaginea.He SW, Ma R, Zhao YY, An L, Huang JH, Zhang Q, Han JG, Zhang XXInt J Syst Evol Microbiol10.1099/ijsem.0.0053352022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Gammaproteobacteria/genetics, *Hosta/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, Soil, Soil Microbiology, Vitamin K 2Pathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1457Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 3695)https://www.dsmz.de/collection/catalogue/details/culture/DSM-3695
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
39104Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16752
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
86732Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10826.1StrainInfo: A central database for resolving microbial strain identifiers
116514Curators of the CIPCollection of Institut Pasteur (CIP 104804)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104804
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1