Strain identifier

BacDive ID: 13484

Type strain: Yes

Species: Saccharothrix texasensis

Strain history: IFO 14971 <-- NRRL B-16134 <-- M. P. Lechevalier LLR-37U-77.

NCBI tax ID(s): 103734 (species)

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General

@ref: 11493

BacDive-ID: 13484

DSM-Number: 44231

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, Gram-positive

description: Saccharothrix texasensis DSM 44231 is a spore-forming, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 103734
  • Matching level: species

strain history

@refhistory
11493<- NRRL <- M. P. Lechevalier, IMRU, LLR-37U-77
67770IFO 14971 <-- NRRL B-16134 <-- M. P. Lechevalier LLR-37U-77.

doi: 10.13145/bacdive13484.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Saccharothrix
  • species: Saccharothrix texasensis
  • full scientific name: Saccharothrix texasensis Labeda and Lyons 1989

@ref: 11493

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Saccharothrix

species: Saccharothrix texasensis

full scientific name: Saccharothrix texasensis Labeda and Lyons 1989

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colorincubation periodmedium used
20025Golden yellow (1004)10-14 daysISP 2
20025Bright yellow10-14 daysISP 3
20025Colorless10-14 daysISP 4
20025Yellow orange (1037)10-14 daysISP 5
20025Yellow orange (1037)10-14 daysISP 6
20025Yellow orange (1037)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20025yesAerial MyceliumSparse/ whiteISP 2
20025yesAerial MyceliumWhiteISP 3
20025yesAerial MyceliumWhiteISP 4
20025yesAerial MyceliumWhiteISP 5
20025noISP 6
20025yesAerial MyceliumWhiteISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11493GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
20025ISP 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
20025ISP 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:
20025ISP 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
20025ISP 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
20025ISP 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
20025ISP 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
11493positivegrowth28mesophilic
20025positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481yes100
69480yes100

halophily

  • @ref: 20025
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 2.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea+hydrolysis
6836816947citrate+assimilation
6836818257ornithine+degradation
6836825094lysine+degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-test
6836935581indole-
6836815688acetoin-
6836835581indole-

enzymes

@refvalueactivityec
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease+3.5.1.5
68368ornithine decarboxylase+4.1.1.17
68368lysine decarboxylase+4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)-
68382lipase (C 14)-
68382valine arylamidase-
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
20025+-+---++++-++-+++--
11493+---+/------+/-+/-+/--++/-+---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
20025+++++-+---+

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
11493+----++++++/-+/-+/--+--+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11493soilDallasUSAUSANorth America
67770SoilDallas, TXUSAUSANorth America

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
114931Risk group (German classification)
200251German classification

Sequence information

16S sequences

  • @ref: 20218
  • description: Saccharothrix texasensis strain NRRL B-16134 16S ribosomal RNA gene, partial sequence
  • accession: AF114814
  • length: 1512
  • database: ena
  • NCBI tax ID: 103734

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Saccharothrix texasensis strain DSM 44231103734.3wgspatric103734
66792Saccharothrix texasensis DSM 442312784132178draftimg103734
67770Saccharothrix texasensis DSM 44231GCA_003752005contigncbi103734

GC content

  • @ref: 11493
  • GC-content: 74.9
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno90.994no
flagellatedno96.956no
gram-positiveyes89.239no
anaerobicno99.091no
aerobicyes93.969no
halophileno86.326no
spore-formingyes95.654no
thermophileno98.644no
glucose-utilyes88.539yes
glucose-fermentno92.216yes

External links

@ref: 11493

culture collection no.: DSM 44231, ATCC 51593, IFO 14971, JCM 9113, NBRC 14971, NCIMB 13186, NRRL B-16134, CGMCC 4.1713, IMSNU 21343, KCTC 9399, VKM Ac-1968

straininfo link

  • @ref: 82676
  • straininfo: 43068

literature

topicPubmed-IDtitleauthorsjournalyearmeshtopic2DOI
Phylogeny12557341[Study on the reclassification of two deposited strains AS4.1186 and AS4.1187 of Nocardia].Zhang J, Zhang Y, Liu ZWei Sheng Wu Xue Bao2002Actinomycetales/chemistry/*classification/genetics, DNA, Bacterial/genetics, Nocardia/chemistry/*classification/genetics, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodococcus/chemistry/*classification/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidTranscriptome
Phylogeny23645017Saccharothrix saharensis sp. nov., an actinomycete isolated from Algerian Saharan soil.Boubetra D, Zitouni A, Bouras N, Mathieu F, Lebrihi A, Schumann P, Sproer C, Klenk HP, Sabaou NInt J Syst Evol Microbiol2013Actinomycetales/*classification/genetics/isolation & purification, Algeria, Bacterial Typing Techniques, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/analysisGenetics10.1099/ijs.0.051839-0
Phylogeny27915411Saccharothrix ghardaiensis sp. nov., an actinobacterium isolated from Saharan soil.Bouznada K, Bouras N, Mokrane S, Chaabane Chaouch F, Zitouni A, Potter G, Sproer C, Klenk HP, Sabaou NAntonie Van Leeuwenhoek2016Actinomycetales/*classification/genetics/*isolation & purification/physiology, Africa, Northern, Algeria, Cell Wall/chemistry, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Micromonosporaceae/genetics, Phenotype, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sodium Chloride/metabolism, Soil/chemistry, *Soil Microbiology, Species Specificity, Temperature, Vitamin K 2/analogs & derivatives/analysisPhenotype10.1007/s10482-016-0812-4
Phylogeny36268867Saccharothrix luteola sp. nov., a novel cellulose-degrading actinobacterium isolated from soil and emended description of the genus Saccharothrix.He C, Sun X, Huang Z, Wang Z, Luo X, Song J, Wang X, Zhao J, Xiang WInt J Syst Evol Microbiol2022RNA, Ribosomal, 16S/genetics, *Soil, *Phosphatidylethanolamines, Soil Microbiology, Vitamin K 2, Cellulose, Cardiolipins, Congo Red, Galactose, Mannose, Ribose, Base Composition, Phylogeny, Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Sequence Analysis, DNA, Phosphatidylinositols, PhospholipidsTranscriptome10.1099/ijsem.0.005572

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11493Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44231)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44231
20025Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44231.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
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
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/
68368Automatically annotated from API 20E
68369Automatically annotated from API 20NE
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)
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
82676Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43068.1StrainInfo: A central database for resolving microbial strain identifiers