Strain identifier

BacDive ID: 7433

Type strain: Yes

Species: Microbacterium luticocti

Strain Designation: SC-087B

Strain history: DSM 19459 <-- C. M. Manaia SC-087B.

NCBI tax ID(s): 1122239 (strain), 451764 (species)

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General

@ref: 8101

BacDive-ID: 7433

DSM-Number: 19459

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

description: Microbacterium luticocti SC-087B is an aerobe, mesophilic, Gram-positive bacterium that was isolated from municipal sewage sludge compost.

NCBI tax id

NCBI tax idMatching level
1122239strain
451764species

strain history

@refhistory
8101<- C.M. Manaia; SC-087B
67770DSM 19459 <-- C. M. Manaia SC-087B.

doi: 10.13145/bacdive7433.20230509.8.1

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 luticocti
  • full scientific name: Microbacterium luticocti Vaz-Moreira et al. 2008

@ref: 8101

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium luticocti

full scientific name: Microbacterium luticocti Vaz-Moreira et al. 2008 emend. Nouioui et al. 2018

strain designation: SC-087B

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32437positive1.6 µm0.5 µmrod-shapedyes
69480positive100

Culture and growth conditions

culture medium

  • @ref: 8101
  • name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/92
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
8101positivegrowth28mesophilic
32437positivegrowth27-45
32437positiveoptimum36mesophilic
60221positivegrowth37mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
32437positivegrowth5.5-9.7alkaliphile
32437positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32437aerobe
60221microaerophile

spore formation

@refspore formationconfidence
32437no
69481no100
69480no99.94

halophily

@refsaltgrowthtested relationconcentration
32437NaClpositivegrowth0-10 %
32437NaClpositiveoptimum2 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3243722599arabinose+carbon source
3243717057cellobiose+carbon source
3243728757fructose+carbon source
3243733984fucose+carbon source
3243728260galactose+carbon source
3243717716lactose+carbon source
3243717306maltose+carbon source
3243729864mannitol+carbon source
3243737684mannose+carbon source
32437506227N-acetylglucosamine+carbon source
3243726546rhamnose+carbon source
3243733942ribose+carbon source
3243717814salicin+carbon source
3243727082trehalose+carbon source
324374853esculin+hydrolysis
3243717632nitrate+reduction

enzymes

@refvalueactivityec
32437gelatinase+
32437urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
8101municipal sewage sludge compostPortoPortugalPRTEurope
60221Compost,municipal sewage sludgePorto ?PortugalPRTEurope2005
67770Municipal sewage sludge compost

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Composting
#Engineered#Waste#Sewage sludge

taxonmaps

  • @ref: 69479
  • File name: preview.99_5559.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_2683;97_3295;98_4147;99_5559&stattab=map
  • Last taxonomy: Microbacterium luticocti subclade
  • 16S sequence: AM747814
  • Sequence Identity:
  • Total samples: 198
  • soil counts: 53
  • aquatic counts: 83
  • animal counts: 34
  • plant counts: 28

Safety information

risk assessment

  • @ref: 8101
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8101
  • description: Microbacterium luticocti 16S rRNA gene, type strain SC-087BT
  • accession: AM747814
  • length: 1460
  • database: ena
  • NCBI tax ID: 1122239

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium luticocti DSM 194591122239.3wgspatric1122239
66792Microbacterium luticocti DSM 194592585427556draftimg1122239
67770Microbacterium luticocti DSM 19459GCA_000422405scaffoldncbi1122239

GC content

@refGC-contentmethod
810172
6777070.7genome sequence analysis
6777071.7-72.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.955no
flagellatedno98.3no
gram-positiveyes91.959yes
anaerobicno99.17yes
aerobicyes87.906no
halophileno88.392no
spore-formingno92.009no
thermophileno94.228yes
glucose-utilyes87.295no
glucose-fermentno87.181no

External links

@ref: 8101

culture collection no.: DSM 19459, CCUG 54537, JCM 15576

straininfo link

  • @ref: 76882
  • straininfo: 408295

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18599719Microbacterium luticocti sp. nov., isolated from sewage sludge compost.Vaz-Moreira I, Lopes AR, Falsen E, Schumann P, Nunes OC, Manaia CMInt J Syst Evol Microbiol10.1099/ijs.0.65494-02008Actinomycetales/*classification/genetics/*isolation & purification, Base Composition, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sewage/*microbiology, *Soil, *Soil Microbiology, Species SpecificityGenetics
Phylogeny32053092Microbacterium protaetiae sp. nov., isolated from gut of larva of Protaetia brevitarsis seulensis.Heo J, Cho H, Kim MA, Hamada M, Tamura T, Saitou S, Kim SK, Kwon SWInt J Syst Evol Microbiol10.1099/ijsem.0.0039672020Actinobacteria/*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
8101Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19459)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19459
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
32437Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2865928776041
60221Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54537)https://www.ccug.se/strain?id=54537
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/
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
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
76882Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID408295.1StrainInfo: A central database for resolving microbial strain identifiers