Strain identifier

BacDive ID: 7464

Type strain: Yes

Species: Microbacterium amylolyticum

Strain Designation: N5

Strain history: CIP <- 2013, DSMZ <- R. Lal, Delhi Univ., India: strain N5

NCBI tax ID(s): 936337 (species)

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General

@ref: 17564

BacDive-ID: 7464

DSM-Number: 24221

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

description: Microbacterium amylolyticum N5 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from soil from an industrial waste site.

NCBI tax id

  • NCBI tax id: 936337
  • Matching level: species

strain history

@refhistory
17564<- R. Lal, Univ. Delhi, Dept. Zoology, India; N5
67770CCM 7881 <-- R. Lal; Univ. of Delhi, India; N5.
116353CIP <- 2013, DSMZ <- R. Lal, Delhi Univ., India: strain N5

doi: 10.13145/bacdive7464.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Microbacterium
  • species: Microbacterium amylolyticum
  • full scientific name: Microbacterium amylolyticum Anand et al. 2012

@ref: 17564

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium amylolyticum

full scientific name: Microbacterium amylolyticum Anand et al. 2012

strain designation: N5

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30363positive2 µm1.1 µmrod-shapedno
69480no95.657
69480positive100
116353positiverod-shapedno

pigmentation

  • @ref: 30363
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
41597MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116353CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
30363positivegrowth10-37
30363positiveoptimum28mesophilic
41597positivegrowth30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
30363positivegrowth07-10alkaliphile
30363positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30363
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30363no
69481no100
69480no99.999

murein

  • @ref: 17564
  • murein short key: B06
  • type: B2ß {Gly} [L-Hsr] D-Glu(Hyg)-Gly-D-Orn

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
303634853esculin+hydrolysis
3036317632nitrate+reduction

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17564soil from an industrial waste siteUttar Pradesh, Noida (Delhi NCR)IndiaINDAsia
67770Soil from an industrial waste site on the outskirts of DelhiIndiaINDAsia
116353Environment, Soil from an industrial waste siteUttar Pradesh, Noida (Delhi NCR), IndiaIndiaINDAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial
#Engineered#Waste
#Environmental#Terrestrial#Soil

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
175641Risk group (German classification)
1163531Risk group (French classification)

Sequence information

16S sequences

  • @ref: 17564
  • description: Microbacterium amylolyticum strain N5 16S ribosomal RNA gene, partial sequence
  • accession: HQ605925
  • length: 1420
  • database: ena
  • NCBI tax ID: 936337

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium amylolyticum DSM 24221GCA_011046975completencbi936337
66792Microbacterium amylolyticum DSM 24221GCA_017876695contigncbi936337
66792Microbacterium amylolyticum strain DSM 24221936337.3completepatric936337
66792Microbacterium amylolyticum strain DSM 24221936337.4wgspatric936337
66792Microbacterium amylolyticum DSM 242212918397618draftimg936337

GC content

@refGC-contentmethod
1756468.0fluorimetric
3036368
6777068thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno93.03no
flagellatedno96.426no
gram-positiveyes95.847yes
anaerobicno99.6yes
aerobicyes90.457yes
halophileyes52.522no
spore-formingno92.822no
thermophileno98.877yes
glucose-utilyes89.043no
glucose-fermentno84.484no

External links

@ref: 17564

culture collection no.: DSM 24221, CCM 7881, CIP 110689, JCM 30491

straininfo link

  • @ref: 76909
  • straininfo: 413280

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22039005Microbacterium amylolyticum sp. nov., isolated from soil from an industrial waste site.Anand S, Bala K, Saxena A, Schumann P, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.034439-02011Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, India, *Industrial Waste, Molecular Sequence Data, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/analysis, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny26220793Microbacterium nanhaiense sp. nov., an actinobacterium isolated from sea sediment.Yan L, Wang J, Chen Z, Guan Y, Li JInt J Syst Evol Microbiol10.1099/ijsem.0.0004802015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Ornithine/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistryGenetics
Phylogeny33064070Microbacterium excoecariae sp. nov., a novel endophytic actinobacterium isolated from bark of Excoecaria agallocha Linn.Chen MS, Li F, Yan XR, Tuo LInt J Syst Evol Microbiol10.1099/ijsem.0.0045232020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Euphorbiaceae/*microbiology, Fatty Acids/chemistry, Microbacterium/*classification/isolation & purification, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Pigmentation, Plant Bark/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17564Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24221)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24221
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
30363Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2670328776041
41597Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/30494
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/
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
76909Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID413280.1StrainInfo: A central database for resolving microbial strain identifiers
116353Curators of the CIPCollection of Institut Pasteur (CIP 110689)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110689