Strain identifier

BacDive ID: 7406

Type strain: Yes

Species: Microbacterium hominis

Strain history: CIP <- 1998, IFO <- D.A. de Briel, Lab. Bacteriol., Univ. Louis Pasteur <- LCDC

NCBI tax ID(s): 1348634 (strain), 162426 (species)

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General

@ref: 4754

BacDive-ID: 7406

DSM-Number: 12509

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

description: Microbacterium hominis DSM 12509 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from lung aspirate.

NCBI tax id

NCBI tax idMatching level
1348634strain
162426species

strain history

@refhistory
4754<- IFO <- D.A. de Briel <- LCDC, 84-209
67770NBRC 15708 <-- IFO 15708 <-- D. A. de Briel <-- LCDC 84-209.
119949CIP <- 1998, IFO <- D.A. de Briel, Lab. Bacteriol., Univ. Louis Pasteur <- LCDC

doi: 10.13145/bacdive7406.20230509.8.1

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 hominis
  • full scientific name: Microbacterium hominis Takeuchi and Hatano 1998

@ref: 4754

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microbacterium

species: Microbacterium hominis

full scientific name: Microbacterium hominis Takeuchi and Hatano 1998

type strain: yes

Morphology

cell morphology

  • @ref: 119949
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium usedhemolysis ability
18366Lemon yellow (1012)10-14 daysISP 2
18366Lemon yellow (1012)10-14 daysISP 3
18366Lemon yellow (1012)10-14 daysISP 4
18366Lemon yellow (1012)10-14 daysISP 5
18366Lemon yellow (1012)10-14 daysISP 6
18366Lemon yellow (1012)10-14 daysISP 7
1199491

multicellular morphology

@refforms multicellular complexmedium name
18366noISP 2
18366noISP 3
18366noISP 4
18366noISP 5
18366noISP 6
18366noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4754TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: 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
18366ISP 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
18366ISP 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:
18366ISP 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
18366ISP 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
18366ISP 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
18366ISP 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
39349MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
119949CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
18366positiveoptimum28mesophilic
4754positivegrowth30mesophilic
39349positivegrowth30mesophilic
59517positivegrowth37mesophilic
67770positivegrowth28mesophilic
119949positivegrowth15-41
119949nogrowth10psychrophilic
119949nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59517aerobe
119949facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
119949NaClpositivegrowth0-6 %
119949NaClnogrowth8 %
119949NaClnogrowth10 %

murein

  • @ref: 4754
  • murein short key: B01
  • type: B1alpha {Gly} [L-Lys] D-Glu(Hyg)-Gly-L-Lys

observation

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

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate+builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose+builds acid from32528
68371xylitol-builds acid from17151
68371raffinose+builds acid from16634
68371melezitose+builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin+builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose+builds acid from65327
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
119949esculin+hydrolysis4853
119949hippurate+hydrolysis606565
119949nitrate-reduction17632
119949nitrite-reduction16301
119949nitrate+respiration17632
68379esculin+hydrolysis4853
68379gelatin-hydrolysis5291
68379D-glucose+fermentation17634
68379D-ribose-fermentation16988
68379glycogen-fermentation28087

metabolite production

  • @ref: 119949
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11994915688acetoin+
11994917234glucose+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase+3.2.1.22
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68379catalase-1.11.1.6
68379gelatinase-
68379beta-glucosidase+3.2.1.21
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379pyrrolidonyl arylamidase-3.4.19.3
119949oxidase-
119949beta-galactosidase+3.2.1.23
119949alcohol dehydrogenase-1.1.1.1
119949gelatinase-
119949amylase-
119949DNase+
119949caseinase-3.4.21.50
119949catalase+1.11.1.6
119949tween esterase-
119949gamma-glutamyltransferase-2.3.2.2
119949lecithinase-
119949lipase-
119949lysine decarboxylase-4.1.1.18
119949ornithine decarboxylase-4.1.1.17
119949phenylalanine ammonia-lyase+4.3.1.24
119949protease-
119949tryptophan deaminase-
119949urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControlCAT
18366+----++-++-+-------
59517-+-+-++++--+-+++++---

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18366-++-+------++-++---
59517--+-+----++++-+++---
119949+++-++---++++-+++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119949+--++/-+---++++----+---+++++++++++-+++/-+/--+/-+------+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119949+++++--+++++++-+++++++-+-+-----+-+++-----+-------+---+--++-++---+---+---+-----+++-----+-+----+--+--

Isolation, sampling and environmental information

isolation

@refsample type
4754lung aspirate
59517Human lung aspirate
67770Lung aspirate
119949Human, Lung aspirate

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Oral cavity and airways#Lung
#Host Body Product#Fluids#Aspirate

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
47541Risk group (German classification)
1199491Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Microbacterium hominis partial 16S rRNA gene, type strain DSM 12509AM1815041512ena162426
4754Microbacterium hominis gene for 16S rRNA, partial sequenceAB0047271503ena162426

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microbacterium hominis NBRC 157081348634.3wgspatric1348634
66792Microbacterium hominis NBRC 157082731957680draftimg1348634
67770Microbacterium hominis NBRC 15708GCA_001592125contigncbi1348634
67770Microbacterium hominis LCDC 84-0209GCA_001553805contigncbi162426

GC content

@refGC-contentmethod
475471.2
6777071.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno89.638no
gram-positiveyes94.647no
anaerobicno99.448yes
halophileno90.834no
spore-formingno92.924no
thermophileno99.44yes
glucose-utilyes86.011no
aerobicyes90.938no
flagellatedno98.12no
glucose-fermentno87.783yes

External links

@ref: 4754

culture collection no.: DSM 12509, IFO 15708, NBRC 15708, NRRL B-24220, CCUG 52344 A, CIP 105731, JCM 12413, LCDC 84-209, CCUG 52344, IAM 15210, LMG 22182, VKM Ac-2081

straininfo link

  • @ref: 76855
  • straininfo: 49310

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9734054Proposal of six new species in the genus Microbacterium and transfer of Flavobacterium marinotypicum ZoBell and Upham to the genus Microbacterium as Microbacterium maritypicum comb. nov.Takeuchi M, Hatano KInt J Syst Bacteriol10.1099/00207713-48-3-9731998Actinomycetales/chemistry/*classification/genetics, DNA, Bacterial/analysis, Flavobacterium/*classification, Nucleic Acid Hybridization
Phylogeny16166712Microbacterium xylanilyticum sp. nov., a xylan-degrading bacterium isolated from a biofilm.Kim KK, Park HY, Park W, Kim IS, Lee STInt J Syst Evol Microbiol10.1099/ijs.0.63706-02005Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Biodegradation, Environmental, Biofilms/*growth & development, *Bioreactors, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Waste Disposal, Fluid/*methods, Xylans/*metabolismGenetics
Phylogeny20305059Microbacterium mitrae sp. nov., isolated from salted turban shell.Kim YJ, Roh SW, Jung MJ, Kim MS, Park EJ, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.021519-02010Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Fermentation, *Food Microbiology, Molecular Sequence Data, Ornithine/analysis, *Phylogeny, Pigments, Biological/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sodium ChlorideBiotechnology
Phylogeny20656817Microbacterium arthrosphaerae sp. nov., isolated from the faeces of the pill millipede Arthrosphaera magna Attems.Kampfer P, Rekha PD, Schumann P, Arun AB, Young CC, Chen WM, Sridhar KRInt J Syst Evol Microbiol10.1099/ijs.0.026401-02010Actinomycetales/*classification/genetics/*isolation & purification, Amino Acids/analysis, Animals, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Feces/*microbiology, India, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisGenetics
Phylogeny22280899Microbacterium marinum sp. nov., isolated from deep-sea water.Zhang L, Xi L, Ruan J, Huang YSyst Appl Microbiol10.1016/j.syapm.2011.11.0042012Actinomycetales/*classification/*genetics/isolation & purification, Aquatic Organisms/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition/genetics, Base Sequence, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis/genetics, Indian Ocean, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Seawater/*microbiology, Sequence Alignment, Sequence Analysis, DNAEnzymology
Phylogeny25744585Microbacterium proteolyticum sp. nov. isolated from roots of Halimione portulacoides.Alves A, Riesco R, Correia A, Trujillo MEInt J Syst Evol Microbiol10.1099/ijs.0.0001772015Actinomycetales/*classification/genetics/isolation & purification, Amaranthaceae/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, Plant Roots/*microbiology, Portugal, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryGenetics
Phylogeny25829331Microbacterium enclense sp. nov., isolated from sediment sample.Mawlankar RR, Mual P, Sonalkar VV, Thorat MN, Verma A, Srinivasan K, Dastager SGInt J Syst Evol Microbiol10.1099/ijs.0.0002212015Actinomycetales/*classification/genetics/isolation & purification, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, India, Islands, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4754Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12509)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12509
18366Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM12509.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
39349Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17783
59517Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 52344 A)https://www.ccug.se/strain?id=52344
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/
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
76855Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49310.1StrainInfo: A central database for resolving microbial strain identifiers
119949Curators of the CIPCollection of Institut Pasteur (CIP 105731)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105731