Strain identifier

BacDive ID: 17557

Type strain: Yes

Species: Stenotrophomonas acidaminiphila

Strain history: CIP <- 2000, H. Macarie, U.A.M.I., Mexico: strain AMX 19

NCBI tax ID(s): 128780 (species)

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General

@ref: 4909

BacDive-ID: 17557

DSM-Number: 13117

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

description: Stenotrophomonas acidaminiphila DSM 13117 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from industrial waste water.

NCBI tax id

  • NCBI tax id: 128780
  • Matching level: species

strain history

@refhistory
4909<- A. S. Ouattara <- S. Thierry, Laboratoire de Microbiologie IRD, UAM, Iztapalapa, Mexico; AMX 19
395322000, H. Macarie, U.A.M.I., Mexico: strain AMX 19
67770CIP 106456 <-- H. Macarie AMX 19.
115994CIP <- 2000, H. Macarie, U.A.M.I., Mexico: strain AMX 19

doi: 10.13145/bacdive17557.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Stenotrophomonas
  • species: Stenotrophomonas acidaminiphila
  • full scientific name: Stenotrophomonas acidaminiphila Assih et al. 2002

@ref: 4909

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Lysobacteraceae

genus: Stenotrophomonas

species: Stenotrophomonas acidaminiphila

full scientific name: Stenotrophomonas acidaminiphila Assih et al. 2002

type strain: yes

Morphology

cell morphology

  • @ref: 115994
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 115994
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4909TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)yeshttps://mediadive.dsmz.de/medium/545Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
4909NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
39532MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
115994CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
4909positivegrowth35mesophilic
39532positivegrowth30mesophilic
57384positivegrowth30-37mesophilic
67770positivegrowth30mesophilic
115994positivegrowth10-41
115994nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
57384aerobe
115994obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
115994NaClpositivegrowth0-4 %
115994NaClnogrowth6 %
115994NaClnogrowth8 %
115994NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
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
68371trehalose-builds acid from27082
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
68371myo-inositol-builds acid from17268
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
68371glycerol-builds acid from17754
68369malate-assimilation25115
68369adipate-assimilation17128
68369decanoate-assimilation27689
68369gluconate-assimilation24265
68369maltose+assimilation17306
68369N-acetylglucosamine+assimilation59640
68369D-mannitol-assimilation16899
68369D-mannose+assimilation16024
68369L-arabinose-assimilation30849
68369D-glucose-assimilation17634
68369gelatin+hydrolysis5291
68369esculin+hydrolysis4853
68369urea-hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate+reduction17632
115994citrate-carbon source16947
115994esculin+hydrolysis4853
115994nitrate+reduction17632
115994nitrite+reduction16301
115994glucose+/-degradation17234

antibiotic resistance

  • @ref: 115994
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11599435581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
115994oxidase+
115994beta-galactosidase-3.2.1.23
115994alcohol dehydrogenase-1.1.1.1
115994gelatinase+/-
115994amylase-
115994DNase-
115994caseinase-3.4.21.50
115994catalase+1.11.1.6
115994tween esterase+
115994lecithinase-
115994lipase-
115994lysine decarboxylase-4.1.1.18
115994ornithine decarboxylase-4.1.1.17
115994protease-
115994tryptophan deaminase-
115994urease-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
115994-+++-++-++++---+-+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
4909+----++---+-++------+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
115994----------+/-+/-+/---------+/---+/---+/----------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
115994++--+----++------------------------------------------------+---------------+--+-------+-+-+++++-+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dateisolation date
4909industrial waste waterMexicoMEXNorth America
57384MudMexicoMEXNorth America1999
67770Anaerobic sludge of a lab-scale UASB reactor
115994Environment, MudMexicoMEXNorth America1999

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Industrial wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_4737.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17;96_26;97_288;98_321;99_4737&stattab=map
  • Last taxonomy: Stenotrophomonas sp.
  • 16S sequence: AF273080
  • Sequence Identity:
  • Total samples: 7580
  • soil counts: 1383
  • aquatic counts: 3113
  • animal counts: 2568
  • plant counts: 516

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
49091Risk group (German classification)
1159941Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Stenotrophomonas acidaminiphila 16S ribosomal RNA gene, partial sequence
  • accession: AF273080
  • length: 1542
  • database: ena
  • NCBI tax ID: 128780

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Stenotrophomonas acidaminiphila strain JCM 13310128780.7wgspatric128780
66792Stenotrophomonas acidaminiphila JCM 133102713896760draftimg128780
67770Stenotrophomonas acidaminiphila JCM 13310GCA_001431595contigncbi128780
66792Stenotrophomonas acidaminiphila DSM 13117GCA_024221815contigncbi128780

GC content

  • @ref: 67770
  • GC-content: 66.4-67.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes91.157no
gram-positiveno98.564no
anaerobicno98.547yes
aerobicyes92.253no
halophileno95.14no
spore-formingno94.429no
glucose-utilyes84.896yes
flagellatedno74.428no
thermophileno98.354yes
glucose-fermentno91.423yes

External links

@ref: 4909

culture collection no.: DSM 13117, ATCC 700916, CIP 106456, CCUG 46887, LMG 22073, AMX 19, JCM 13310

straininfo link

  • @ref: 86553
  • straininfo: 311033

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11931169Stenotrophomonas acidaminiphila sp. nov., a strictly aerobic bacterium isolated from an upflow anaerobic sludge blanket (UASB) reactor.Assih EA, Ouattara AS, Thierry S, Cayol JL, Labat M, Macarie HInt J Syst Evol Microbiol10.1099/00207713-52-2-5592002Anaerobiosis, Anti-Bacterial Agents/pharmacology, DNA, Bacterial/chemistry, Environmental Microbiology, Industrial Waste, Microbial Sensitivity Tests, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/chemistry, Sequence Homology, Nucleic Acid, Sewage/*microbiology, Stenotrophomonas/*classification/drug effects/physiologyGenetics
Phylogeny20400671Stenotrophomonas daejeonensis sp. nov., isolated from sewage.Lee M, Woo SG, Chae M, Shin MC, Jung HM, Ten LNInt J Syst Evol Microbiol10.1099/ijs.0.017780-02010Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Stenotrophomonas/*classification/genetics/*isolation & purification/physiologyGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4909Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13117)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13117
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
39532Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18588
57384Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 46887)https://www.ccug.se/strain?id=46887
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/
68369Automatically annotated from API 20NE
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
86553Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID311033.1StrainInfo: A central database for resolving microbial strain identifiers
115994Curators of the CIPCollection of Institut Pasteur (CIP 106456)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106456