Strain identifier

BacDive ID: 17737

Type strain: Yes

Species: Iamia majanohamensis

Strain Designation: F12

Strain history: <- Y. Fukunaga; F12

NCBI tax ID(s): 467976 (species)

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General

@ref: 8408

BacDive-ID: 17737

DSM-Number: 19957

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

description: Iamia majanohamensis F12 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from sea cucumber .

NCBI tax id

  • NCBI tax id: 467976
  • Matching level: species

strain history

  • @ref: 8408
  • history: <- Y. Fukunaga; F12

doi: 10.13145/bacdive17737.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Acidimicrobiia
  • order: Acidimicrobiales
  • family: Iamiaceae
  • genus: Iamia
  • species: Iamia majanohamensis
  • full scientific name: Iamia majanohamensis Kurahashi et al. 2009

@ref: 8408

domain: Bacteria

phylum: Actinobacteria

class: Acidimicrobiia

order: Acidimicrobiales

family: Iamiaceae

genus: Iamia

species: Iamia majanohamensis

full scientific name: Iamia majanohamensis Kurahashi et al. 2009

strain designation: F12

type strain: yes

Morphology

cell morphology

  • @ref: 29077
  • gram stain: positive
  • cell length: 1.45 µm
  • cell width: 0.4 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18618Golden yellow (1004)10-14 daysISP 2
18618Lemon yellow (1012)10-14 daysISP 3
1861810-14 daysISP 4
1861810-14 daysISP 5
1861810-14 daysISP 6
1861810-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18618noISP 2
18618noISP 3
18618noISP 4
18618noISP 5
18618noISP 6
18618noISP 7

multimedia

  • @ref: 8408
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_19957.jpg
  • caption: Medium 514 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8408BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
18618ISP 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
18618ISP 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:
18618ISP 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
18618ISP 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
18618ISP 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
18618ISP 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
8408positivegrowth28mesophilic
18618positiveoptimum28mesophilic
29077positivegrowth15-40
29077positiveoptimum29mesophilic

culture pH

@refabilitytypepHPH range
29077positivegrowth06-09alkaliphile
29077positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29077
  • oxygen tolerance: aerobe

spore formation

  • @ref: 29077
  • spore formation: no

observation

  • @ref: 29077
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2907722599arabinose+carbon source
2907729016arginine+carbon source
2907728260galactose+carbon source
290775291gelatin+carbon source
2907737684mannose+carbon source
2907718257ornithine+carbon source
2907726546rhamnose+carbon source
2907718222xylose+carbon source
2907717632nitrate+reduction
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

enzymes

@refvalueactivityec
29077catalase+1.11.1.6
29077gelatinase+
29077cytochrome oxidase+1.9.3.1
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
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18618-+/--+-++++++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18618++++++++++-++++++++

Isolation, sampling and environmental information

isolation

  • @ref: 8408
  • sample type: sea cucumber (Holothuria edulis)
  • host species: Holothuria edulis
  • geographic location: Aka Island, Okinawa
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Echinodermata

taxonmaps

  • @ref: 69479
  • File name: preview.99_98880.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1007;96_40231;97_51327;98_67668;99_98880&stattab=map
  • Last taxonomy: Iamia majanohamensis subclade
  • 16S sequence: AB360448
  • Sequence Identity:
  • Total samples: 7537
  • soil counts: 3777
  • aquatic counts: 1490
  • animal counts: 783
  • plant counts: 1487

Safety information

risk assessment

  • @ref: 8408
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8408
  • description: Iamia majanohamensis gene for 16S rRNA, partial sequence
  • accession: AB360448
  • length: 1474
  • database: ena
  • NCBI tax ID: 467976

Genome sequences

  • @ref: 66792
  • description: Iamia majanohamensis DSM 19957
  • accession: GCA_028532485
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 467976

GC content

  • @ref: 8408
  • GC-content: 74.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno91.726no
flagellatedno98.488yes
gram-positiveyes81.758no
anaerobicno98.576yes
aerobicyes94.138yes
halophileno85.3no
spore-formingno86.906yes
glucose-fermentno92.98yes
thermophileno98.985yes
glucose-utilyes82.802no

External links

@ref: 8408

culture collection no.: DSM 19957, KCTC 19879, NBRC 102561

straininfo link

  • @ref: 86727
  • straininfo: 408187

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19329622Iamia majanohamensis gen. nov., sp. nov., an actinobacterium isolated from sea cucumber Holothuria edulis, and proposal of Iamiaceae fam. nov.Kurahashi M, Fukunaga Y, Sakiyama Y, Harayama S, Yokota AInt J Syst Evol Microbiol10.1099/ijs.0.005611-02009Actinobacteria/chemistry/*classification/genetics/*isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Holothuria/*microbiology, Japan, Molecular Sequence Data, Peptidoglycan/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Vitamin K 2/analysisGenetics
Phylogeny32501198Actinomarinicola tropica gen. nov. sp. nov., a new marine actinobacterium of the family Iamiaceae, isolated from South China Sea sediment environments.He YQ, Chen RW, Li C, Shi SB, Cui LQ, Long LJ, Tian XPInt J Syst Evol Microbiol10.1099/ijsem.0.0042512020Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
8408Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19957)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19957
18618Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM19957.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
29077Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2550728776041
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)
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
86727Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID408187.1StrainInfo: A central database for resolving microbial strain identifiers