Strain identifier

BacDive ID: 133022

Type strain: Yes

Species: Microbacterium sorbitolivorans

Strain Designation: SZDIS-1-1

Strain history: <- M. Cai, Institute Of Microbiology, Chinese Academy of Sciences, Beijing, China; SZDIS-1-1

NCBI tax ID(s): 1867410 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 24810

BacDive-ID: 133022

DSM-Number: 103422

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-positive, rod-shaped, colony-forming

description: Microbacterium sorbitolivorans SZDIS-1-1 is a facultative anaerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from fermentation bed of a pigpen.

NCBI tax id

  • NCBI tax id: 1867410
  • Matching level: species

strain history

  • @ref: 24810
  • history: <- M. Cai, Institute Of Microbiology, Chinese Academy of Sciences, Beijing, China; SZDIS-1-1

doi: 10.13145/bacdive133022.20230509.8.1

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 sorbitolivorans
  • full scientific name: Microbacterium sorbitolivorans Meng et al. 2016

@ref: 24810

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium sorbitolivorans

full scientific name: Microbacterium sorbitolivorans Meng et al. 2016

strain designation: SZDIS-1-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25049positive1.52-1.83 µm0.65-1.1 µmrod-shapedno
69480positive100

colony morphology

  • @ref: 25049
  • colony color: pale yellow
  • colony shape: circular

Culture and growth conditions

culture medium

  • @ref: 24810
  • 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
25049positivegrowth10-40
25049positiveoptimum30mesophilic
24810positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
25049positivegrowth6.0-9.0alkaliphile
25049positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 25049
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.997

halophily

@refsalttested relationconcentrationgrowth
25049NaCloptimum0 %
25049NaClgrowth0-11.0 %(w/v)positive

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
25049168082-dehydro-D-gluconate-builds acid from
25049174265-dehydro-D-gluconate-builds acid from
2504917924D-sorbitol-builds acid from
2504916443D-tagatose-builds acid from
2504933984fucose-builds acid from
2504916813galactitol-builds acid from
2504917268myo-inositol-builds acid from
2504918403L-arabitol-builds acid from
2504917266L-sorbose-builds acid from
2504917632nitrate-reduction
2504932032potassium gluconate-builds acid from
2504927897tryptophan-energy source
2504916199urea-hydrolysis
2504916651(S)-lactate+carbon source
2504916651(S)-lactate+nitrogen source
25049645522-hydroxybutyrate+carbon source
25049645522-hydroxybutyrate+nitrogen source
2504930089acetate+carbon source
2504930089acetate+nitrogen source
2504913705acetoacetate+carbon source
2504913705acetoacetate+nitrogen source
2504917925alpha-D-glucose+carbon source
2504917925alpha-D-glucose+nitrogen source
2504927613amygdalin+builds acid from
2504918305arbutin+builds acid from
2504917057cellobiose+builds acid from
2504917057cellobiose+carbon source
2504917057cellobiose+nitrogen source
2504916947citrate+carbon source
2504916947citrate+nitrogen source
2504918333D-arabitol+carbon source
2504918333D-arabitol+nitrogen source
2504915824D-fructose+builds acid from
2504915824D-fructose+carbon source
2504915824D-fructose+nitrogen source
2504978697D-fructose 6-phosphate+carbon source
2504978697D-fructose 6-phosphate+nitrogen source
2504912936D-galactose+builds acid from
2504912936D-galactose+carbon source
2504912936D-galactose+nitrogen source
250498391D-gluconate+carbon source
250498391D-gluconate+nitrogen source
2504917634D-glucose+builds acid from
2504962318D-lyxose+builds acid from
2504916899D-mannitol+builds acid from
2504916899D-mannitol+carbon source
2504916899D-mannitol+nitrogen source
2504916024D-mannose+builds acid from
2504916024D-mannose+carbon source
2504916024D-mannose+nitrogen source
2504916988D-ribose+builds acid from
2504917924D-sorbitol+carbon source
2504917924D-sorbitol+nitrogen source
2504965327D-xylose+builds acid from
2504923652dextrin+carbon source
2504923652dextrin+nitrogen source
2504917113erythritol+builds acid from
250494853esculin+degradation
250494853esculin+builds acid from
25049esculin ferric citrate+builds acid from
2504928066gentiobiose+builds acid from
2504928066gentiobiose+carbon source
2504928066gentiobiose+nitrogen source
2504917754glycerol+builds acid from
2504917754glycerol+carbon source
2504917754glycerol+nitrogen source
2504928087glycogen+builds acid from
2504917596inosine+carbon source
2504917596inosine+nitrogen source
2504930849L-arabinose+builds acid from
2504929991L-aspartate+carbon source
2504929991L-aspartate+nitrogen source
2504918287L-fucose+carbon source
2504918287L-fucose+nitrogen source
2504929985L-glutamate+carbon source
2504929985L-glutamate+nitrogen source
2504962345L-rhamnose+builds acid from
2504962345L-rhamnose+carbon source
2504962345L-rhamnose+nitrogen source
2504917716lactose+builds acid from
2504917716lactose+carbon source
2504917716lactose+nitrogen source
2504917306maltose+builds acid from
2504917306maltose+carbon source
2504917306maltose+nitrogen source
250496731melezitose+builds acid from
2504928053melibiose+builds acid from
2504928053melibiose+carbon source
2504928053melibiose+nitrogen source
25049320055methyl beta-D-glucopyranoside+carbon source
25049320055methyl beta-D-glucopyranoside+nitrogen source
25049506227N-acetylglucosamine+builds acid from
25049506227N-acetylglucosamine+carbon source
25049506227N-acetylglucosamine+nitrogen source
2504917309pectin+carbon source
2504917309pectin+nitrogen source
2504916634raffinose+builds acid from
2504916634raffinose+carbon source
2504916634raffinose+nitrogen source
2504917814salicin+builds acid from
2504917814salicin+carbon source
2504917814salicin+nitrogen source
2504917164stachyose+carbon source
2504917164stachyose+nitrogen source
2504928017starch+builds acid from
2504917992sucrose+builds acid from
2504917992sucrose+carbon source
2504917992sucrose+nitrogen source
2504927082trehalose+builds acid from
2504927082trehalose+carbon source
2504927082trehalose+nitrogen source
2504932528turanose+builds acid from
2504932528turanose+carbon source
2504932528turanose+nitrogen source
2504953423tween 40+carbon source
2504953423tween 40+nitrogen source
2504917151xylitol+builds acid from

antibiotic resistance

@refChEBImetaboliteis antibioticis resistant
2504931810fleroxacinyesyes
25049116278lomefloxacinyesyes
2504917698chloramphenicolyesyes
250492955azithromycinyesyes
250493745clindamycinyesyes
2504927902tetracyclineyesyes
250499332sulfamethoxazoleyesyes
250493508ceftazidimeyesyes
250497809oxacillinyesyes
2504971415nitrofurantoinyesyes

metabolite production

@refChebi-IDmetaboliteproduction
2504935581indoleno
2504915688acetoinyes

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
2504915688acetoin+
2504935581indole-

enzymes

@refvalueactivityec
25049acid phosphatase-3.1.3.2
25049alkaline phosphatase-3.1.3.1
25049alpha-chymotrypsin-3.4.21.1
25049alpha-fucosidase-3.2.1.51
25049alpha-galactosidase-3.2.1.22
25049alpha-glucosidase+3.2.1.20
25049alpha-mannosidase-3.2.1.24
25049arginine dihydrolase-3.5.3.6
25049beta-glucosidase+3.2.1.21
25049beta-glucuronidase-3.2.1.31
25049catalase+1.11.1.6
25049cystine arylamidase+3.4.11.3
25049esterase lipase (C 8)+
25049leucine arylamidase+3.4.11.1
25049lipase-
25049lysine decarboxylase-4.1.1.18
25049N-acetyl-beta-glucosaminidase+3.2.1.52
25049naphthol-AS-BI-phosphohydrolase-
25049ornithine decarboxylase-4.1.1.17
25049tryptophan deaminase-4.1.99.1
25049valine arylamidase-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
24810fermentation bed of a pigpenFujian Province, XiamenChinaCHNAsia
25049dextran-inorganic salt agar plates1/l: 10g dextran, 2g KNO3, 0.05g MgSO4.7H2O, 2g K2HPO4.3H2O, 0.02g CaCO3, 0.01g FeSO4.7H2O, 10g NaCl, 2g KCl, 3g MgSO4.6H2O7 days30

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Livestock (Husbandry)
#Host#Mammals#Suidae (Pig,Swine)

taxonmaps

  • @ref: 69479
  • File name: preview.99_31908.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1340;97_1590;98_23679;99_31908&stattab=map
  • Last taxonomy: Microbacterium
  • 16S sequence: KX250270
  • Sequence Identity:
  • Total samples: 655
  • soil counts: 83
  • aquatic counts: 62
  • animal counts: 474
  • plant counts: 36

Safety information

risk assessment

  • @ref: 24810
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24810
  • description: Microbacterium sorbitolivorans strain SZDIS-1-1 16S ribosomal RNA gene, partial sequence
  • accession: KX250270
  • length: 1445
  • database: ena
  • NCBI tax ID: 1867410

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium sorbitolivorans CGMCC 1.15228GCA_003327285scaffoldncbi1867410
66792Microbacterium sorbitolivorans CGMCC 1.15228GCA_014641475scaffoldncbi1867410
66792Microbacterium sorbitolivorans strain CGMCC 1.152281867410.4wgspatric1867410

GC content

  • @ref: 24810
  • GC-content: 67.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno93.654yes
flagellatedno97.307yes
gram-positiveyes92.939yes
anaerobicno99.561yes
aerobicyes82.642no
halophileno72.652no
spore-formingno93.604no
glucose-utilyes85.723yes
thermophileno99.081yes
glucose-fermentno72.982no

External links

@ref: 24810

culture collection no.: DSM 103422, CGMCC 1.15228

straininfo link

  • @ref: 91296
  • straininfo: 400044

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny27902249Microbacterium sorbitolivorans sp. nov., a novel member of Microbacteriaceae isolated from fermentation bed in pigpen.Meng YC, Liu HC, Yang LL, Kang YQ, Zhou YG, Cai MInt J Syst Evol Microbiol10.1099/ijsem.0.0015562016Actinomycetales/*classification/genetics/isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Fermentation, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Swine, Vitamin K 2/chemistryTranscriptome
Phylogeny30547854Microbacterium suaedae sp. nov., isolated from Suaeda aralocaspica.Zhu ZN, Li YR, Li YQ, Xiao M, Han MX, Wadaan MAM, Hozzein WN, An DD, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0031622018Actinobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Chenopodiaceae/*microbiology, China, DNA, Bacterial/genetics, *Desert Climate, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salt-Tolerant Plants/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
24810Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103422Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103422)
25049Y. C. L. Meng, H. C.,Yang, L. L.,Kang, Y. Q.,Zhou, Y. G.,Cai, M.Microbacterium sorbitolivorans sp. nov., a novel member of Microbacteriaceae isolated from fermentation bed in pigpen10.1099/ijsem.0.001556IJSEM 66: 5556-5561 201627902249
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91296Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID400044.1