Strain identifier

BacDive ID: 17504

Type strain: Yes

Species: Pseudoxanthomonas mexicana

Strain Designation: AMX26B

Strain history: CIP <- 2000, S. Thierry, U.A.M.I., Mexico: strain AMX 26B

NCBI tax ID(s): 128785 (species)

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General

@ref: 6768

BacDive-ID: 17504

DSM-Number: 17121

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

description: Pseudoxanthomonas mexicana AMX26B is an aerobe, mesophilic, Gram-negative bacterium that was isolated from biomass slugde of an anaerobic reactor treating cheese waste water.

NCBI tax id

  • NCBI tax id: 128785
  • Matching level: species

strain history

@refhistory
6768<- S. Thierry; AMX 26B
403892000, S. Thierry, U.A.M.I., Mexico: strain AMX 26B
67770T. Iizuka AMX 26B <-- H. Macarie AMX 26B <-- S. Thierry AMX 26B.
120929CIP <- 2000, S. Thierry, U.A.M.I., Mexico: strain AMX 26B

doi: 10.13145/bacdive17504.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Pseudoxanthomonas
  • species: Pseudoxanthomonas mexicana
  • full scientific name: Pseudoxanthomonas mexicana Thierry et al. 2004

@ref: 6768

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Pseudoxanthomonas

species: Pseudoxanthomonas mexicana

full scientific name: Pseudoxanthomonas mexicana Thierry et al. 2004

strain designation: AMX26B

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
29999negative1.2 µm0.6 µmrod-shapedyes
120929negativerod-shapedyes

colony morphology

  • @ref: 58565
  • incubation period: 1-2 days

pigmentation

  • @ref: 120929
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6768NUTRIENT AGAR (DSMZ Medium 1)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1.pdf
40389MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
120929CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
6768positivegrowth30mesophilic
29999positivegrowth10-37
29999positiveoptimum33.5mesophilic
40389positivegrowth30mesophilic
58565positivegrowth30-42
67770positivegrowth30mesophilic
120929positivegrowth25-41
120929nogrowth5psychrophilic
120929nogrowth10psychrophilic

culture pH

@refabilitytypepHPH range
29999positivegrowth6.5-9.5alkaliphile
29999positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29999aerobe
58565aerobe
120929obligate aerobe

spore formation

  • @ref: 29999
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
29999NaClpositivegrowth0-4 %
29999NaClpositiveoptimum2 %
120929NaClpositivegrowth0-2 %
120929NaClnogrowth4 %
120929NaClnogrowth6 %
120929NaClnogrowth8 %
120929NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2999935391aspartate+carbon source
2999917057cellobiose+carbon source
2999928757fructose+carbon source
2999917234glucose+carbon source
2999929987glutamate+carbon source
2999927570histidine+carbon source
2999917306maltose+carbon source
2999937684mannose+carbon source
2999926271proline+carbon source
2999917822serine+carbon source
2999927082trehalose+carbon source
299994853esculin+hydrolysis
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12092916947citrate-carbon source
1209294853esculin+hydrolysis
12092917632nitrate+reduction
12092916301nitrite+reduction
12092917234glucose+/-degradation
12092917632nitrate-respiration

antibiotic resistance

  • @ref: 120929
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 120929
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29999catalase+1.11.1.6
29999cytochrome oxidase+1.9.3.1
120929oxidase+
120929beta-galactosidase-3.2.1.23
120929alcohol dehydrogenase-1.1.1.1
120929gelatinase+
120929amylase-
120929caseinase+3.4.21.50
120929catalase+1.11.1.6
120929tween esterase+
120929lecithinase-
120929lipase+
120929lysine decarboxylase-4.1.1.18
120929ornithine decarboxylase-4.1.1.17
120929protease+
120929tryptophan deaminase-
120929urease-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
120929-+++-+++++++---++-+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
120929----------+/-+/-+/------------+/---+/-----------+/-----------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120929++-++----++----++-+----------------------------------------+-------------+-+--+---------++++--+-+-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
6768biomass slugde of an anaerobic reactor treating cheese waste waterMexico CityMexicoMEXNorth America
58565Sludge of a lab-scale reactor/cheese waste water1999-09-01
67770Sludge of an anaerobic reactor treating the wastewater of a cheese factoryMexicoMEXNorth America
120929Environment, MudMexicoMEXNorth America1999

isolation source categories

Cat1Cat2Cat3
#Engineered#Bioreactor
#Engineered#Waste#Industrial wastewater
#Condition#Anoxic (anaerobic)

taxonmaps

  • @ref: 69479
  • File name: preview.99_4236.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_856;97_2573;98_3190;99_4236&stattab=map
  • Last taxonomy: Pseudoxanthomonas
  • 16S sequence: AF273082
  • Sequence Identity:
  • Total samples: 20716
  • soil counts: 5760
  • aquatic counts: 7508
  • animal counts: 5790
  • plant counts: 1658

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
67681Risk group (German classification)
1209291Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6768
  • description: Pseudoxanthomonas mexicana strain AMX 26B 16S ribosomal RNA gene, partial sequence
  • accession: AF273082
  • length: 1540
  • database: ena
  • NCBI tax ID: 128785

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudoxanthomonas mexicana strain DSM 17121128785.15wgspatric128785
67770Pseudoxanthomonas mexicana DSM 17121GCA_010093385contigncbi128785

GC content

@refGC-contentmethod
2999967.8
6777065.8-69.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes89.361yes
gram-positiveno98.592no
anaerobicno98.758no
aerobicyes96.243yes
halophileno95.967no
spore-formingno96.937no
thermophileno99.323yes
glucose-utilyes86.46yes
flagellatedno80.594no
glucose-fermentno92.91no

External links

@ref: 6768

culture collection no.: DSM 17121, CCUG 49454, CIP 106674, JCM 11524, ATCC 700993, AMX 26B

straininfo link

  • @ref: 86501
  • straininfo: 44244

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15545466Pseudoxanthomonas mexicana sp. nov. and Pseudoxanthomonas japonensis sp. nov., isolated from diverse environments, and emended descriptions of the genus Pseudoxanthomonas Finkmann et al. 2000 and of its type species.Thierry S, Macarie H, Iizuka T, Geissdorfer W, Assih EA, Spanevello M, Verhe F, Thomas P, Fudou R, Monroy O, Labat M, Ouattara ASInt J Syst Evol Microbiol10.1099/ijs.0.02810-02004Aerobiosis, Anti-Bacterial Agents/pharmacology, Bacterial Typing Techniques, Base Composition, Bioreactors/*microbiology, Carbohydrate Metabolism, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Flagella, Genes, rRNA, Gentian Violet, Humans, Molecular Sequence Data, Movement, Nitrites/metabolism, Nucleic Acid Hybridization, Oxygen/metabolism, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spores, Bacterial/cytology, Stenotrophomonas/genetics, Ubiquinone/analysis/isolation & purification, Urine/*microbiology, Xanthomonadaceae/*classification/cytology/*isolation & purification/physiology, Xanthomonas/geneticsEnzymology
Phylogeny20870889Pseudoxanthomonas indica sp. nov., isolated from a hexachlorocyclohexane dumpsite.Kumari K, Sharma P, Tyagi K, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.017624-02010Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Environmental Pollutants/*metabolism, Fatty Acids/analysis, Hexachlorocyclohexane/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Xanthomonadaceae/*classification/*isolation & purification/metabolismMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6768Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17121)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17121
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
29999Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2636428776041
40389Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18830
58565Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 49454)https://www.ccug.se/strain?id=49454
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/
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
86501Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44244.1StrainInfo: A central database for resolving microbial strain identifiers
120929Curators of the CIPCollection of Institut Pasteur (CIP 106674)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106674