Strain identifier

BacDive ID: 12610

Type strain: Yes

Species: Xylanimonas pachnodae

Strain Designation: VPCX2

Strain history: DSM 12657 <-- A. E. Cazemier VPCX2.

NCBI tax ID(s): 101489 (species)

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General

@ref: 4785

BacDive-ID: 12610

DSM-Number: 12657

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-positive

description: Xylanimonas pachnodae VPCX2 is a mesophilic, Gram-positive bacterium that was isolated from hindgut of Pachnoda marginata larvae.

NCBI tax id

  • NCBI tax id: 101489
  • Matching level: species

strain history

@refhistory
4785<- A.E. Cazemier; VPCX2
67770DSM 12657 <-- A. E. Cazemier VPCX2.

doi: 10.13145/bacdive12610.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Promicromonosporaceae
  • genus: Xylanimonas
  • species: Xylanimonas pachnodae
  • full scientific name: Xylanimonas pachnodae (Cazemier et al. 2004) Heo et al. 2020

  • synonyms

    @refsynonym
    20215Cellulomonas pachnodae
    20215Xylanimicrobium pachnodae
    20215Promicromonospora pachnodae

@ref: 4785

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Promicromonosporaceae

genus: Xylanimonas

species: Xylanimonas pachnodae

full scientific name: Xylanimonas pachnodae (Cazemier et al. 2004) Heo et al. 2020

strain designation: VPCX2

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colorincubation periodmedium used
18502Ivory (1014)10-14 daysISP 2
18502Ivory (1014)10-14 daysISP 3
18502Ivory (1014)10-14 daysISP 4
18502Ivory (1014)10-14 daysISP 5
18502Ivory (1014)10-14 daysISP 6
18502Ivory (1014)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18502noISP 2
18502noISP 3
18502noISP 4
18502noISP 5
18502noISP 6
18502noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4785TRYPTICASE 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
18502ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18502ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18502ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18502ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18502ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18502ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
4785positivegrowth28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.957

murein

  • @ref: 4785
  • murein short key: A11.48
  • type: A4alpha L-Lys-L-Ser-D-Glu

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1850262968cellulose+
1850216634raffinose+
1850226546rhamnose+
1850228757fructose+
1850229864mannitol+
1850217268myo-inositol+
1850218222xylose+
1850217992sucrose+
1850222599arabinose+
1850217234glucose+
6837917632nitrate+reduction
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose-fermentation
6837965327D-xylose+fermentation
6837916899D-mannitol-fermentation
6837917306maltose+fermentation
6837917716lactose+fermentation
6837917992sucrose+fermentation
6837928087glycogen+fermentation

enzymes

@refvalueactivityec
68379gelatinase+
68379urease-3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18502+----++++-++-+-++++

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18502-++-++---+-++-++++-

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
4785hindgut of Pachnoda marginata larvaePachnoda marginataNetherlandsNLDEurope
67770Hindgut of larvae of the scarab beetle (Pachnoda marginata)Pachnoda marginata

isolation source categories

Cat1Cat2Cat3
#Host#Arthropoda#Insecta
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_69051.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1778;97_2128;98_2941;99_69051&stattab=map
  • Last taxonomy: Xylanimicrobium pachnodae
  • 16S sequence: AF105422
  • Sequence Identity:
  • Total samples: 173
  • soil counts: 95
  • aquatic counts: 29
  • animal counts: 29
  • plant counts: 20

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
185021German classification
47851Risk group (German classification)

Sequence information

16S sequences

  • @ref: 4785
  • description: Promicromonospora pachnodae 16S ribosomal RNA gene, partial sequence
  • accession: AF105422
  • length: 1467
  • database: ena
  • NCBI tax ID: 101489

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xylanimicrobium pachnodae JCM 13526 = NBRC 107786GCA_001314005contigncbi1305855
66792Xylanimicrobium pachnodae JCM 13526 = NBRC 1077861305855.6wgspatric1305855
66792Xylanimicrobium pachnodae JCM 13526 = NBRC 1077861305855.5wgspatric1305855
66792Xylanimicrobium pachnodae JCM 13526, NBRC 1077862731957681draftimg1305855
66792Xylanimicrobium pachnodae JCM 13526, NBRC 1077862734481968draftimg1305855
67770Xylanimicrobium pachnodae JCM 13526 = NBRC 107786GCA_001592145contigncbi1305855

GC content

@refGC-contentmethod
6777071.9genome sequence analysis
6777070

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes52no
motileno90.751no
gram-positiveyes86.922no
anaerobicno94.472no
halophileno91.189no
spore-formingno92.985no
thermophileno98.797yes
glucose-utilyes89.92yes
aerobicyes56.337no
flagellatedno98.14no
glucose-fermentyes62.349yes

External links

@ref: 4785

culture collection no.: DSM 12657, JCM 13526, NBRC 107786, NCCB 100020

straininfo link

  • @ref: 81824
  • straininfo: 49336

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15143008Reclassification of Cellulosimicrobium variabile Bakalidou et al. 2002 as Isoptericola variabilis gen. nov., comb. nov.Stackebrandt E, Schumann P, Cui XLInt J Syst Evol Microbiol10.1099/ijs.0.02878-02004Actinomycetales/*classification/genetics/metabolism, Amino Acid Sequence, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Peptidoglycan/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Terminology as TopicMetabolism
Phylogeny31532356Antribacter gilvus gen. nov., sp. nov., a new member of the family Promicromonosporaceae from a karstic cavern.Zhang LY, Fang BZ, Jiao JY, Zhang XT, Liu L, Meng XL, Ming H, Nie GX, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0036822019Actinobacteria/*classification/isolation & purification, Actinomycetales/classification, Bacterial Typing Techniques, Base Composition, Caves/*microbiology, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny31976851Xylanimonas allomyrinae sp. nov. isolated from the gut of larva of Allomyrina dichotoma, reclassification of Xylanibacterium ulmi as Xylanimonas ulmi comb. nov. and Xylanimicrobium pachnodae as Xylanimonas pachnodae comb. nov., and emendation of the genus Xylanimonas.Heo J, Cho H, Hamada M, Kim JS, Hong SB, Kim SJ, Kwon SWInt J Syst Evol Microbiol10.1099/ijsem.0.0040012020Actinobacteria/*classification/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, Coleoptera/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Tract/*microbiology, Larva/microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNATranscriptome
Phylogeny32306134Lactococcus protaetiae sp. nov. and Xylanimonas protaetiae sp. nov., isolated from gut of larvae of Protaetia brevitarsis seulensis.Heo J, Kim SJ, Kim MA, Tamura T, Saitou S, Hamada M, Kim JS, Hong SB, Kwon SWAntonie Van Leeuwenhoek10.1007/s10482-020-01413-62020Actinobacteria/*classification/genetics/*isolation & purification, Actinomycetales/classification, Animals, Bacterial Typing Techniques, Base Composition, Coleoptera/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, *Gastrointestinal Microbiome, Lactococcus/*classification/genetics/*isolation & purification, Larva/*microbiology, Peptidoglycan, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAEnzymology

Reference

@idauthorscataloguedoi/urltitle
4785Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12657)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12657
18502Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM12657.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
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/
68379Automatically annotated from API Coryne
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)
81824Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49336.1StrainInfo: A central database for resolving microbial strain identifiers