Strain identifier

BacDive ID: 5194

Type strain: Yes

Species: Xenorhabdus indica

Strain Designation: 28

Strain history: CIP <- 2005, DSMZ <- V.S. Somvanshi, India: strain 28

NCBI tax ID(s): 333964 (species)

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General

@ref: 6939

BacDive-ID: 5194

DSM-Number: 17382

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, motile, animal pathogen

description: Xenorhabdus indica 28 is a facultative anaerobe, mesophilic, motile animal pathogen that was isolated from entomopathogenic nematode Steinernema thermophilum.

NCBI tax id

  • NCBI tax id: 333964
  • Matching level: species

strain history

@refhistory
6939<- V.S. Somvanshi
120077CIP <- 2005, DSMZ <- V.S. Somvanshi, India: strain 28

doi: 10.13145/bacdive5194.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Morganellaceae
  • genus: Xenorhabdus
  • species: Xenorhabdus indica
  • full scientific name: Xenorhabdus indica Somvanshi et al. 2009

@ref: 6939

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Morganellaceae

genus: Xenorhabdus

species: Xenorhabdus indica

full scientific name: Xenorhabdus indica Somvanshi et al. 2009

strain designation: 28

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.512
6948099.905negative
120077yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6939REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b)yeshttps://mediadive.dsmz.de/medium/535bName: REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b) Composition: Trypticase soy broth 30.0 g/l Casein peptone 17.0 g/l Agar 15.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l K2HPO4 2.5 g/l D(+)-Glucose 2.5 g/l Distilled water
38328MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120077CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6939positivegrowth30mesophilic
38328positivegrowth30mesophilic
120077positivegrowth30-37mesophilic
120077nogrowth5psychrophilic
120077nogrowth10psychrophilic
120077nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120077
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.98

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 2-ketogluconate-builds acid from
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
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
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
68369adipate-assimilation17128
68369decanoate-assimilation27689
68369N-acetylglucosamine+assimilation59640
68369D-mannitol-assimilation16899
68369L-arabinose-assimilation30849
68369D-glucose+assimilation17634
68369gelatin+hydrolysis5291
68369urea-hydrolysis16199
68369tryptophan+energy source27897
68369nitrate-reduction17632
120077mannitol-fermentation29864
120077citrate-carbon source16947
120077glucose+fermentation17234
120077lactose+fermentation17716
120077nitrate-reduction17632
120077nitrite-reduction16301
120077malonate-assimilation15792
120077sodium thiosulfate-builds gas from132112
68372glycerol+assimilation17754
68372erythritol-assimilation17113
68372D-arabinose-assimilation17108
68372L-arabinose-assimilation30849
68372D-ribose-assimilation16988
68372D-xylose-assimilation65327
68372L-xylose-assimilation65328
68372ribitol-assimilation15963
68372methyl beta-D-xylopyranoside-assimilation74863
68372D-galactose-assimilation12936
68372D-glucose+assimilation17634
68372D-fructose+assimilation15824
68372D-mannose+assimilation16024
68372L-sorbose-assimilation17266
68372L-rhamnose-assimilation62345
68372galactitol-assimilation16813
68372myo-inositol+assimilation17268
68372D-mannitol-assimilation16899
68372sorbitol-assimilation30911
68372methyl alpha-D-mannoside-assimilation43943
68372methyl alpha-D-glucopyranoside-assimilation320061
68372N-acetylglucosamine+assimilation59640
68372amygdalin-assimilation27613
68372arbutin-assimilation18305
68372esculin+assimilation4853
68372salicin-assimilation17814
68372cellobiose-assimilation17057
68372maltose-assimilation17306
68372lactose-assimilation17716
68372melibiose-assimilation28053
68372sucrose-assimilation17992
68372trehalose-assimilation27082
68372inulin-assimilation15443
68372melezitose-assimilation6731
68372raffinose-assimilation16634
68372starch-assimilation28017
68372glycogen-assimilation28087
68372xylitol-assimilation17151
68372gentiobiose-assimilation28066
68372turanose-assimilation32528
68372D-lyxose-assimilation62318
68372D-tagatose-assimilation16443
68372D-fucose-assimilation28847
68372L-fucose-assimilation18287
68372D-arabitol-assimilation18333
68372L-arabitol-assimilation18403
68372gluconate+assimilation24265
68372Potassium 2-ketogluconate-assimilation
68372Potassium 5-ketogluconate-assimilation

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleyes
12007735581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole+
12007715688acetoin-
12007717234glucose-

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
68369cytochrome oxidase-1.9.3.1
68369gelatinase+
68369urease-3.5.1.5
120077oxidase-
120077beta-galactosidase-3.2.1.23
120077alcohol dehydrogenase-1.1.1.1
120077gelatinase-
120077catalase-1.11.1.6
120077lysine decarboxylase-4.1.1.18
120077ornithine decarboxylase-4.1.1.17
120077phenylalanine ammonia-lyase+4.3.1.24
120077tryptophan deaminase-
120077urease-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
120077-+---+-----------+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6939-+++-++-+-+-+-+--+---
6939-++/-+/--+/-+-+-+/--++/-+/---+/----

API 50CHac

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
6939-+----------++--------+--+------+--------------+-+
120077+/----------+/-+/-+/----+/-----+/------+/----------------------

API 50CHas

@refQGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
6939-+---------+++---+----+--+---------------------+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120077+---+--------------------------++----------------+---------++------------------++-----+--++---+--+-

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentisolation date
6939entomopathogenic nematode Steinernema thermophilumSteinernema thermophilumIndiaINDAsia
120077Animal, Entomopathogenic nematode, Steinernema thermophilumIndiaINDAsia2005

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Nematoda

taxonmaps

  • @ref: 69479
  • File name: preview.99_15321.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_27;97_9436;98_11591;99_15321&stattab=map
  • Last taxonomy: Xenorhabdus indica subclade
  • 16S sequence: AM040494
  • Sequence Identity:
  • Total samples: 113
  • soil counts: 7
  • aquatic counts: 15
  • animal counts: 90
  • plant counts: 1

Safety information

risk assessment

@refpathogenicity animalbiosafety levelbiosafety level comment
6939yes1Risk group (German classification)
1200771Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6939
  • description: Xenorhabdus sp. 28 16S rRNA gene, type strain 28T
  • accession: AM040494
  • length: 1530
  • database: ena
  • NCBI tax ID: 333964

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Xenorhabdus indica DSM 17382GCA_014467235scaffoldncbi333964
66792Xenorhabdus indica strain DSM 17382333964.4wgspatric333964

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes51.787no
gram-positiveno97.914no
anaerobicno97.181no
aerobicyes83.669no
halophileno86.229no
spore-formingno94.623no
thermophileno97.158no
glucose-utilyes89.423no
motileyes85.18no
glucose-fermentyes80.628no

External links

@ref: 6939

culture collection no.: DSM 17382, CIP 108830, CCM 7375

straininfo link

  • @ref: 74686
  • straininfo: 297621

literature

  • topic: Phylogeny
  • Pubmed-ID: 16459045
  • title: A novel species of Xenorhabdus, family Enterobacteriaceae: Xenorhabdus indica sp. nov., symbiotically associated with entomopathogenic nematode Steinernema thermophilum Ganguly and Singh, 2000.
  • authors: Somvanshi VS, Lang E, Ganguly S, Swiderski J, Saxena AK, Stackebrandt E
  • journal: Syst Appl Microbiol
  • DOI: 10.1016/j.syapm.2006.01.004
  • year: 2006
  • mesh: Animals, Base Sequence, DNA, Bacterial/chemistry/genetics, India, Microbial Sensitivity Tests, Molecular Sequence Data, Nematoda/*microbiology, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/chemistry/genetics, Sequence Analysis, DNA, Xenorhabdus/*classification/genetics/growth & development/metabolism
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitle
6939Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17382)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17382
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
38328Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6503
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)
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
68372Automatically annotated from API 50CH assim
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
74686Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297621.1StrainInfo: A central database for resolving microbial strain identifiers
120077Curators of the CIPCollection of Institut Pasteur (CIP 108830)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108830