Strain identifier

BacDive ID: 17740

Type strain: Yes

Species: Chitinophaga pinensis

Strain history: CIP <- 2002, ACM <- 1979, V. Sangtkhobol

NCBI tax ID(s): 485918 (strain), 79329 (species)

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General

@ref: 1142

BacDive-ID: 17740

DSM-Number: 2588

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

description: Chitinophaga pinensis DSM 2588 is an obligate aerobe, spore-forming, Gram-negative bacterium that was isolated from pine litter.

NCBI tax id

NCBI tax idMatching level
79329species
485918strain

strain history

@refhistory
1142<- UQM <- V. Sangkhobol
121834CIP <- 2002, ACM <- 1979, V. Sangtkhobol

doi: 10.13145/bacdive17740.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Chitinophagia
  • order: Chitinophagales
  • family: Chitinophagaceae
  • genus: Chitinophaga
  • species: Chitinophaga pinensis
  • full scientific name: Chitinophaga pinensis Sangkhobol and Skerman 1981

@ref: 1142

domain: Bacteria

phylum: Bacteroidetes

class: Chitinophagia

order: Sphingobacteriales

family: Chitinophagaceae

genus: Chitinophaga

species: Chitinophaga pinensis

full scientific name: Chitinophaga pinensis Sangkhobol and Skerman 1981 emend. Hahnke et al. 2016

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43362negative40 µm0.5-0.8 µmrod-shaped
121834negativerod-shapedno
69480negative92.565

colony morphology

  • @ref: 121834

pigmentation

@refproductioncolorname
43362yesYellowishUnknown
121834noFlexirubin

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_2588_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1142CY-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
33117MEDIUM 342 - for Flexibacter filiformisyesDistilled water make up to (1000.000 ml);Calcium chloride dihydrate (1.360g);Agar (15.000 g);Casitone (3.000 g)
121834CIP Medium 35yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=35

culture temp

@refgrowthtypetemperature
1142positivegrowth22
33117positivegrowth22
43362positiveoptimum24
43425positivegrowth12-37
121834positivegrowth22-30
121834nogrowth5
121834nogrowth15
121834nogrowth37
121834nogrowth41
121834nogrowth45

culture pH

@refabilitytypepHPH range
43362positiveoptimum7
43362positivegrowth4-10alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 121834
  • oxygen tolerance: obligate aerobe

spore formation

  • @ref: 43425
  • spore description: Diameter of 0.8-0.9 µm, formed upon aging
  • type of spore: myxospore
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
43362NaClpositivegrowth0-1.5 %
121834NaClpositivegrowth0 %
121834NaClnogrowth2 %
121834NaClnogrowth4 %
121834NaClnogrowth6 %
121834NaClnogrowth8 %
121834NaClnogrowth10 %

observation

  • @ref: 43425
  • observation: Resistant to 0.01 but not 0.1% sodium lauryl sulfate

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
434252509agar-hydrolysis
4336258187alginate-hydrolysis
43362casein+hydrolysis
4336262968cellulose-hydrolysis
4336217029chitin+hydrolysis
4342516991dna-hydrolysis
433625291gelatin+hydrolysis
4336217234glucose+builds acid from
4336217716lactose+builds acid from
4336217632nitrate-reduction
4336228017starch-hydrolysis
4336217992sucrose+builds acid from
1218344853esculin+hydrolysis
121834606565hippurate+hydrolysis
12183417632nitrate-reduction
12183416301nitrite-reduction
12183415792malonate-assimilation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
4336217698chloramphenicolyesyes25 µg (disc)
4336217076streptomycinyesyes10 µg (disc)
4336227902tetracyclineyesyes10 µg (disc)
433626104kanamycinyesyes30 µg (disc)
433627507neomycinyesyes10 µg (disc)
4336248923erythromycinyesyes5 µg (disc)
4336218208penicillin gyesyes4 Unit (disc)
1218340129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)yesyesno

metabolite production

@refChebi-IDmetaboliteproduction
4342516136hydrogen sulfideno
4342535581indoleno
12183435581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12183415688acetoin-
12183417234glucose-

enzymes

@refvalueactivityec
43362urease+3.5.1.5
43362catalase+1.11.1.6
43362cytochrome oxidase+1.9.3.1
43425phenylalanine deaminase-4.3.1.5
43425tryptophan deaminase-4.1.99.1
43425lipase (Tween 80)+
43425lipase+
121834oxidase-
121834beta-galactosidase+3.2.1.23
121834alcohol dehydrogenase-1.1.1.1
121834gelatinase-
121834amylase-
121834DNase-
121834caseinase-3.4.21.50
121834catalase+1.11.1.6
121834tween esterase-
121834gamma-glutamyltransferase-2.3.2.2
121834lecithinase-
121834lipase-
121834lysine decarboxylase-4.1.1.18
121834ornithine decarboxylase-4.1.1.17
121834phenylalanine ammonia-lyase-4.3.1.24
121834tryptophan deaminase-
121834urease-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
121834-++--++-+-++++-+++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121834+-+++-++-++++--++++-++++-+---------+-----+-----------------+--+--+--------------------+------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeisolation date
1142pine litterBrisbane, AlderleyAustraliaAUSAustralia and Oceania
43362from an infusion of litter from the base of a pine treeAlderley, BrisbaneAustraliaAUSAustralia and Oceania-27153
121834Pine needlesAdlerly, QueenslandAustraliaAUSAustralia and Oceania1979

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host#Plants#Decomposing plant

taxonmaps

  • @ref: 69479
  • File name: preview.99_6479.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_334;96_3064;97_3763;98_4777;99_6479&stattab=map
  • Last taxonomy: Chitinophaga pinensis subclade
  • 16S sequence: AB681008
  • Sequence Identity:
  • Total samples: 6789
  • soil counts: 4418
  • aquatic counts: 723
  • animal counts: 378
  • plant counts: 1270

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
11421Risk group (German classification)
434251
1218341Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Chitinophaga pinensis gene for 16S rRNA, partial sequence, strain: NBRC 15968AB6810081451nuccore79329
124043Chitinophaga pinensis 16S ribosomal RNA gene, partial sequence.AF0787751458nuccore485918

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chitinophaga pinensis DSM 2588GCA_000024005completencbi485918
66792Chitinophaga pinensis DSM 2588485918.6completepatric485918
66792Chitinophaga pinensis UQM 2034, DSM 2588644736340completeimg485918

GC content

@refGC-contentmethod
114244.6
4342544.58thermal denaturation, midpoint method (Tm)
114245.2sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno78no
69480gram-positivegram-positivePositive reaction to Gram-stainingno92.565no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.308no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes88.584yes
69480spore-formingspore-formingAbility to form endo- or exosporesno63.051yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98.49no
69480flagellatedmotile2+Ability to perform flagellated movementno87.75no

External links

@ref: 1142

culture collection no.: DSM 2588, ATCC 43595, IFO 15968, NBRC 15968, UQM 2034, CIP 107364, ACM 2034, NCIMB 11800

straininfo link

  • @ref: 86730
  • straininfo: 7622

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Genetics21304681Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034).Glavina Del Rio T, Abt B, Spring S, Lapidus A, Nolan M, Tice H, Copeland A, Cheng JF, Chen F, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Chain P, Saunders E, Detter JC, Brettin T, Rohde M, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Lucas SStand Genomic Sci10.4056/sigs.6611992010
Phylogeny22307507Chitinophaga oryziterrae sp. nov., isolated from the rhizosphere soil of rice (Oryza sativa L.).Chung EJ, Park TS, Jeon CO, Chung YRInt J Syst Evol Microbiol10.1099/ijs.0.036442-02012Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Oryza/*microbiology, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analysis, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny24425740Thermoflavifilum aggregans gen. nov., sp. nov., a thermophilic and slightly halophilic filamentous bacterium from the phylum Bacteroidetes.Anders H, Dunfield PF, Lagutin K, Houghton KM, Power JF, MacKenzie AD, Vyssotski M, Ryan JLJ, Hanssen EG, Moreau JW, Stott MBInt J Syst Evol Microbiol10.1099/ijs.0.057463-02014Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hot Temperature, Molecular Sequence Data, New Zealand, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryStress
Phylogeny26476525Filobacterium rodentium gen. nov., sp. nov., a member of Filobacteriaceae fam. nov. within the phylum Bacteroidetes; includes a microaerobic filamentous bacterium isolated from specimens from diseased rodent respiratory tracts.Ike F, Sakamoto M, Ohkuma M, Kajita A, Matsushita S, Kokubo TInt J Syst Evol Microbiol10.1099/ijsem.0.0006852015Animals, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rats, Rats, Wistar, Respiratory System/*microbiology, Sequence Analysis, DNAGenetics
Metabolism31793783Functional Analysis of a Gene Cluster from Chitinophaga pinensis Involved in Biosynthesis of the Pyrrolidine Azasugar DAB-1.Nunez C, Horenstein NAJ Nat Prod10.1021/acs.jnatprod.9b007582019Aza Compounds/*metabolism, Bacterial Proteins/metabolism, Bacteroidetes/*metabolism, *Genes, Bacterial, *Multigene Family, Proton Magnetic Resonance Spectroscopy, Pyrrolidines/chemistry/*metabolism, Sugars/*metabolism
Phylogeny32409863In Silico Characterization of a Unique Plant-Like "Loopful" GH19 Chitinase from Newly Isolated Chitinophaga sp. YS-16.Sharma S, Singh R, Kaur RCurr Microbiol10.1007/s00284-020-02022-22020Bacteroidetes, Chitin, *Chitinases/genetics, Computer Simulation, Phylogeny, RNA, Ribosomal, 16S
Phylogeny33063169Chitinophaga agri sp. nov., a bacterium isolated from soil of reclaimed land.Lee SA, Heo J, Kim TW, Sang MK, Song J, Kwon SW, Weon HYArch Microbiol10.1007/s00203-020-02066-92020Bacteroidetes/classification/genetics, Base Composition, Gammaproteobacteria/*classification/genetics, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species Specificity
Phylogeny34846287Chitinophaga rhizophila sp. nov., isolated from rhizosphere soil of banana.Zhang XJ, Feng GD, Yang F, Zhu H, Yao QInt J Syst Evol Microbiol10.1099/ijsem.0.0051182021Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, *Musa/microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
36073872Fixed-target serial crystallography at the Structural Biology Center.Sherrell DA, Lavens A, Wilamowski M, Kim Y, Chard R, Lazarski K, Rosenbaum G, Vescovi R, Johnson JL, Akins C, Chang C, Michalska K, Babnigg G, Foster I, Joachimiak AJ Synchrotron Radiat10.1107/S16005775220078952022Biology, Crystallography, Proteins, *Stenotrophomonas maltophilia

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1142Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2588)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2588
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
33117Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4791
43362Tijana Glavina Del Rio, Birte Abt, Stefan Spring, Alla Lapidus, Matt Nolan, Hope Tice, Alex Copeland, Jan-Fang Cheng, Feng Chen, David Bruce, Lynne Goodwin, Sam Pitluck, Natalia Ivanova, Konstantinos Mavromatis, Natalia Mikhailova, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Patrick Chain, Elizabeth Saunders, John C. Detter, Thomas Brettin, Manfred Rohde, Markus Göker, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C. Kyrpides, Hans-Peter Klenk, Susan Lucas10.1099/00207713-31-3-285Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034)Stand Genomic Sci 2: 87-95 2010
43425Vullapa Sangkhobol, V. B. D. Skerman10.4056/sigs.661199Chitinophaga, a New Genus of Chitinolytic MyxobacteriaIJSEM 31: 285-293 198121304681
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
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
86730Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID7622.1StrainInfo: A central database for resolving microbial strain identifiers
121834Curators of the CIPCollection of Institut Pasteur (CIP 107364)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107364
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy