Strain identifier

BacDive ID: 13432

Type strain: Yes

Species: Saccharomonospora halophila

Strain Designation: 8

Strain history: CIP <- 2002, DSMZ <- S. Al-Zarban, Univ. Kuwait: strain 8

NCBI tax ID(s): 129922 (species)

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General

@ref: 11536

BacDive-ID: 13432

DSM-Number: 44411

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

description: Saccharomonospora halophila 8 is a mesophilic, Gram-positive, rod-shaped bacterium that builds an aerial mycelium and was isolated from high salinity soil.

NCBI tax id

  • NCBI tax id: 129922
  • Matching level: species

strain history

@refhistory
11536<- S. Al-Zarban, Univ. of Kuwait; 8
67770DSM 44411 <-- S. Al-Zarban 8.
119810CIP <- 2002, DSMZ <- S. Al-Zarban, Univ. Kuwait: strain 8

doi: 10.13145/bacdive13432.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Saccharomonospora
  • species: Saccharomonospora halophila
  • full scientific name: Saccharomonospora halophila Al-Zarban et al. 2002

@ref: 11536

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Saccharomonospora

species: Saccharomonospora halophila

full scientific name: Saccharomonospora halophila Al-Zarban et al. 2002 emend. Nouioui et al. 2018

strain designation: 8

type strain: yes

Morphology

cell morphology

  • @ref: 119810
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
19666Brown beige10-14 daysISP 2
19666Brown beige10-14 daysISP 3
19666Beige10-14 daysISP 4
19666Beige10-14 daysISP 5
19666Lemon yellow10-14 daysISP 6
19666Brown beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namemedium namecomplex color
19666yesAerial MyceliumISP 2
19666yesAerial MyceliumISP 3White
19666yesAerial MyceliumISP 4White
19666noISP 5
19666yesAerial MyceliumISP 6White
19666yesAerial MyceliumISP 7White

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11536STARCH NITRATE MEDIUM (DSMZ Medium 856)yeshttps://mediadive.dsmz.de/medium/856Name: STARCH NITRATE MEDIUM (DSMZ Medium 856) Composition: NaCl 100.0 g/l Agar 20.0 g/l Starch 20.0 g/l CaCO3 3.0 g/l KNO3 2.0 g/l K2HPO4 1.0 g/l MgSO4 0.5 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
19666ISP 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
19666ISP 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:
19666ISP 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
19666ISP 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
19666ISP 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
19666ISP 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
11536positivegrowth28mesophilic
19666positiveoptimum30mesophilic
67770positivegrowth28mesophilic
119810positivegrowth25-41
119810nogrowth10psychrophilic
119810nogrowth45thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
119810NaClnogrowth0 %
119810NaClnogrowth2 %
119810NaClnogrowth4 %
119810NaClnogrowth6 %
119810NaClnogrowth8 %
119810NaClnogrowth10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1966617234glucose+
1966622599arabinose-
1966617992sucrose-
1966618222xylose-
1966617268myo-inositol-
1966629864mannitol-
1966628757fructose-
1966626546rhamnose+
1966616634raffinose-
1966662968cellulose+
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
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
6837115443inulin-builds acid from
6837128053melibiose-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
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
1198104853esculin-hydrolysis
119810606565hippurate-hydrolysis
11981017632nitrate-reduction
11981016301nitrite-reduction
11981017632nitrate-respiration
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

antibiotic resistance

  • @ref: 119810
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 119810
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11981015688acetoin-
11981017234glucose-

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
119810oxidase-
119810beta-galactosidase+3.2.1.23
119810alcohol dehydrogenase-1.1.1.1
119810gelatinase+/-
119810amylase-
119810DNase-
119810caseinase+3.4.21.50
119810catalase+1.11.1.6
119810tween esterase+
119810gamma-glutamyltransferase-2.3.2.2
119810lecithinase-
119810lipase+
119810lysine decarboxylase-4.1.1.18
119810ornithine decarboxylase-4.1.1.17
119810phenylalanine ammonia-lyase-4.3.1.24
119810tryptophan deaminase-
119810urease-3.5.1.5
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382alpha-galactosidase-3.2.1.22
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19666-+++-++++----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19666+++-+++++++-+++++--
119810-++-----------------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119810+/----+/-----+/-+/-+/----------------+/-+/--+/-+/--+/------+/---------+/-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11536high salinity soilDesert areaKuwaitKWTAsia
67770Marsh soilKuwaitKWTAsia
119810Environment, High salinity soilKuwaitKWTAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_767.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_466;97_533;98_613;99_767&stattab=map
  • Last taxonomy: Saccharomonospora
  • 16S sequence: AJ278497
  • Sequence Identity:
  • Total samples: 1665
  • soil counts: 719
  • aquatic counts: 120
  • animal counts: 716
  • plant counts: 110

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
115361Risk group (German classification)
196661Risk group (German classification)
1198101Risk group (French classification)

Sequence information

16S sequences

  • @ref: 11536
  • description: Saccharomonospora halophila 16S rRNA gene, strain DSM 44411T
  • accession: AJ278497
  • length: 1506
  • database: ena
  • NCBI tax ID: 928729

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Saccharomonospora halophila 8928729.3wgspatric928729
66792Saccharomonospora halophila 82517093017draftimg928729
67770Saccharomonospora halophila 8GCA_000383775scaffoldncbi928729

GC content

  • @ref: 67770
  • GC-content: 70.9
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno87.914no
flagellatedno97.394no
gram-positiveyes88.873no
anaerobicno97.977no
halophileyes61.87no
spore-formingyes52.229no
thermophileno92.692yes
glucose-utilyes88.096yes
aerobicyes90.44no
glucose-fermentno93.965no

External links

@ref: 11536

culture collection no.: DSM 44411, JCM 11761, NRRL B-24125, BCRC 16373, CIP 107429, CPCC 203285

straininfo link

  • @ref: 82625
  • straininfo: 87959

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11931168Saccharomonospora halophila sp. nov., a novel halophilic actinomycete isolated from marsh soil in Kuwait.Al-Zarban SS, Al-Musallam AA, Abbas I, Stackebrandt E, Kroppenstedt RMInt J Syst Evol Microbiol10.1099/00207713-52-2-5552002Actinomycetales/chemistry/*classification/physiology, Arabinose/analysis, DNA, Bacterial/chemistry, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Galactose/analysis, Kuwait, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/chemistry, Sequence Homology, Nucleic Acid, *Soil MicrobiologyGenetics
Phylogeny13130053Saccharomonospora paurometabolica sp. nov., a moderately halophilic actinomycete isolated from soil in China.Li WJ, Tang SK, Stackebrandt E, Kroppenstedt RM, Schumann P, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.02633-02003Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Base Composition, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Microscopy, Electron, Scanning, Molecular Sequence Data, Phenotype, Phospholipids/analysis, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sodium Chloride, Soil MicrobiologyGenetics
Phylogeny18319456Saccharomonospora saliphila sp. nov., a halophilic actinomycete from an Indian soil.Syed DG, Tang SK, Cai M, Zhi XY, Agasar D, Lee JC, Kim CJ, Jiang CL, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.65449-02008Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, *Soil Microbiology, Species SpecificityGenetics
Phylogeny19666793Prauserella marina sp. nov., isolated from ocean sediment of the South China Sea.Wang J, Li Y, Bian J, Tang SK, Ren B, Chen M, Li WJ, Zhang LXInt J Syst Evol Microbiol10.1099/ijs.0.013862-02009Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, China, DNA, Ribosomal/analysis/genetics, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitle
11536Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44411)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44411
19666Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44411.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/
68371Automatically annotated from API 50CH acid
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
82625Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87959.1StrainInfo: A central database for resolving microbial strain identifiers
119810Curators of the CIPCollection of Institut Pasteur (CIP 107429)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107429