Strain identifier

BacDive ID: 7270

Type strain: Yes

Species: Agromyces ulmi

Strain Designation: XIL01

Strain history: CIP <- 2004, DSMZ <- E.V. Perez <- R. Rivas, Spain: strain XIL01

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6097

BacDive-ID: 7270

DSM-Number: 15747

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

description: Agromyces ulmi XIL01 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from sawdust of Ulmus nigra.

NCBI tax id

NCBI tax idMatching level
248902species
1302723strain

strain history

@refhistory
6097<- E. V. Perez; XIL01 <- R. Rivas
67770LMG 21954 <-- E. Velázquez XIL01 <-- R. Rivas.
123714CIP <- 2004, DSMZ <- E.V. Perez <- R. Rivas, Spain: strain XIL01

doi: 10.13145/bacdive7270.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Agromyces
  • species: Agromyces ulmi
  • full scientific name: Agromyces ulmi Rivas et al. 2004

@ref: 6097

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Agromyces

species: Agromyces ulmi

full scientific name: Agromyces ulmi Rivas et al. 2004

strain designation: XIL01

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31213positiverod-shapedno
69480positive99.643
123714positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18395Clear10-14 daysISP 2
1839510-14 daysISP 3
18395Clear10-14 daysISP 4
1839510-14 daysISP 5
18395Beige (1001)10-14 daysISP 6
1839510-14 daysISP 7
123714

multicellular morphology

@refforms multicellular complexmedium name
18395noISP 2
18395noISP 3
18395noISP 4
18395noISP 5
18395noISP 6
18395noISP 7

pigmentation

  • @ref: 31213
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6097TRYPTICASE 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
18395ISP 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
18395ISP 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:
18395ISP 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
18395ISP 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
18395ISP 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
18395ISP 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
40031MEDIUM 338 - for Sanguibacter keddieiiyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (3.000 g);Trypto casein soy agar (30.000 g)
123714CIP Medium 338yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=338

culture temp

@refgrowthtypetemperaturerange
18395positiveoptimum28mesophilic
6097positivegrowth28mesophilic
31213positivegrowth15-37
31213positiveoptimum28mesophilic
40031positivegrowth30mesophilic
67770positivegrowth28mesophilic
123714positivegrowth25-37mesophilic
123714nogrowth10psychrophilic
123714nogrowth41thermophilic
123714nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31213aerobe
123714obligate aerobe

spore formation

@refspore formationconfidence
31213no
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
123714NaClpositivegrowth0-6 %
123714NaClnogrowth8 %
123714NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: MK-12, MK-11, MK-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1839517234glucose+
1839522599arabinose-
1839517992sucrose+
1839518222xylose-
1839517268myo-inositol-
1839529864mannitol+
1839528757fructose+
1839526546rhamnose+
1839516634raffinose-
1839562968cellulose+
3121322599arabinose+carbon source
3121317057cellobiose+carbon source
3121328260galactose+carbon source
3121317234glucose+carbon source
3121317754glycerol+carbon source
3121317716lactose+carbon source
3121317306maltose+carbon source
3121337684mannose+carbon source
3121328053melibiose+carbon source
31213506227N-acetylglucosamine+carbon source
3121316634raffinose+carbon source
3121326546rhamnose+carbon source
3121333942ribose+carbon source
3121317814salicin+carbon source
3121317992sucrose+carbon source
3121318222xylose+carbon source
312134853esculin+hydrolysis
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-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
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin-builds acid from
683714853esculin+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
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+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
12371416947citrate-carbon source
1237144853esculin+hydrolysis
123714606565hippurate+hydrolysis
12371417632nitrate-reduction
12371416301nitrite-reduction
12371417632nitrate-respiration
683794853esculin+hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917992sucrose-fermentation

antibiotic resistance

  • @ref: 123714
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 123714
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12371415688acetoin+
12371417234glucose-

enzymes

@refvalueactivityec
31213gelatinase+
68382alpha-fucosidase-3.2.1.51
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
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase+3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
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
123714oxidase-
123714beta-galactosidase+3.2.1.23
123714alcohol dehydrogenase-1.1.1.1
123714gelatinase-
123714amylase+
123714DNase+
123714caseinase-3.4.21.50
123714catalase-1.11.1.6
123714tween esterase-
123714gamma-glutamyltransferase-2.3.2.2
123714lecithinase-
123714lipase-
123714lysine decarboxylase-4.1.1.18
123714ornithine decarboxylase-4.1.1.17
123714phenylalanine ammonia-lyase-4.3.1.24
123714tryptophan deaminase-
123714urease-3.5.1.5

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
18395++---+++---

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18395-++-++++------++++-
123714-++-+-+--++---+++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123714-----+---++++-+/----------+-++--+/-+/-------+/-+/----+/-----+/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123714+++-+----++----+--+--+---------+---+---------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
6097sawdust of Ulmus nigraUlmus nigraSalamancaSpainESPEurope
67770Decayed stump of an elm tree (Ulmus nigra)Ulmus nigraSpainESPEurope
123714Sawdust of Ulmus nigraSpainESPEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Dust (Ash)
#Host#Plants#Tree

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
60971Risk group (German classification)
1237141Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31213
  • description: Agromyces ulmi strain XIL01 16S ribosomal RNA gene, complete sequence
  • accession: AY427830
  • length: 1519
  • database: nuccore
  • NCBI tax ID: 248902

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Agromyces ulmi JCM 13315GCA_001313305contigncbi1302723
66792Agromyces ulmi JCM 133151302723.3wgspatric1302723
66792Agromyces ulmi JCM 133152734481940draftimg1302723

GC content

@refGC-contentmethod
609772
6777072thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno81no
motileno89.932no
gram-positiveyes94.015yes
anaerobicno99.12no
halophileno95.665no
spore-formingno96.693yes
thermophileno98.251yes
glucose-utilyes88.15no
aerobicyes95.294yes
flagellatedno97.499yes
glucose-fermentno85.682no

External links

@ref: 6097

culture collection no.: DSM 15747, CIP 108592, LMG 21954, NBRC 109083, JCM 13315, IAM 15233

straininfo link

  • @ref: 76721
  • straininfo: 100241

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15545422Agromyces ulmi sp. nov., a xylanolytic bacterium isolated from Ulmus nigra in Spain.Rivas R, Trujillo ME, Mateos PF, Martinez-Molina E, Velazquez EInt J Syst Evol Microbiol10.1099/ijs.0.63058-02004Actinomycetales/*classification/cytology/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, Catalase/analysis, Cell Wall/chemistry, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Gentian Violet, Molecular Sequence Data, Movement, Nitrate Reductase, Nitrate Reductases/analysis, Peptidoglycan/chemistry/isolation & purification, Phenazines, Phospholipids/analysis/isolation & purification, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spain, Ulmus/*microbiology, Urease/analysis, Vitamin K 2/analysis/isolation & purification, Xylans/*metabolismEnzymology
Phylogeny20639226Agromyces soli sp. nov., isolated from farm soil.Lee M, Ten LN, Woo SG, Park JInt J Syst Evol Microbiol10.1099/ijs.0.021568-02010Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Amino Acids/analysis, Base Composition, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny31851604Agromyces protaetiae sp. nov., isolated from gut of larva of Protaetia brevitarsis seulensis.Heo J, Hamada M, Tamura T, Saito S, Lee SD, Kim JS, Hong SB, Kwon SW, Kim SJInt J Syst Evol Microbiol10.1099/ijsem.0.0039082020Actinobacteria/*classification/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, Coleoptera/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrointestinal Tract/*microbiology, Glycolipids/chemistry, Larva/microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6097Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15747)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15747
18395Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM15747.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
31213Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2753928776041
40031Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6237
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
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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)
76721Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100241.1StrainInfo: A central database for resolving microbial strain identifiers
123714Curators of the CIPCollection of Institut Pasteur (CIP 108592)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108592