Strain identifier

BacDive ID: 3918

Type strain: Yes

Species: Dermabacter hominis

Strain Designation: S69, S-69

Strain history: CIP <- 1997, G. Funke, Inst. Med. Mikrobiol., Zürich, Switzerland <- NCFB <- D. Jones: strain S-69

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General

@ref: 2893

BacDive-ID: 3918

DSM-Number: 7083

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, rod-shaped, human pathogen

description: Dermabacter hominis S69 is a facultative anaerobe, mesophilic, Gram-positive human pathogen that was isolated from human skin.

NCBI tax id

NCBI tax idMatching level
36740species
1349750strain

strain history

@refhistory
2893<- NCFB <- D. Jones, S69
67770NCFB 2769 <-- D. Jones and M. D. Collins S69.
119947CIP <- 1997, G. Funke, Inst. Med. Mikrobiol., Zürich, Switzerland <- NCFB <- D. Jones: strain S-69

doi: 10.13145/bacdive3918.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Dermabacteraceae
  • genus: Dermabacter
  • species: Dermabacter hominis
  • full scientific name: Dermabacter hominis corrig. Jones and Collins 1989
  • synonyms

    • @ref: 20215
    • synonym: Dermabacter hominus

@ref: 2893

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dermabacteraceae

genus: Dermabacter

species: Dermabacter hominis

full scientific name: Dermabacter hominis Jones and Collins 1989 emend. Nouioui et al. 2018

strain designation: S69, S-69

type strain: yes

Morphology

cell morphology

  • @ref: 119947
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
19723Ivory10-14 daysISP 2
19723Light ivory10-14 daysISP 3
19723Light ivory10-14 daysISP 4
19723Ivory10-14 daysISP 6
19723Light ivory10-14 daysISP 7
119947

multicellular morphology

@refforms multicellular complexmedium name
19723noISP 2
19723noISP 3
19723noISP 4
19723noISP 6
19723noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2893TRYPTICASE 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
19723ISP 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
19723ISP 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:
19723ISP 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
19723ISP 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
19723ISP 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
34667MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
40521MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
119947CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
19723positiveoptimum28mesophilic
2893positivegrowth37mesophilic
34667positivegrowth37mesophilic
40521positivegrowth37mesophilic
67770positivegrowth28mesophilic
119947positivegrowth15-41
119947nogrowth10psychrophilic
119947nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119947
  • oxygen tolerance: facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
19723NaClpositivemaximum10 %
119947NaClpositivegrowth0-6 %
119947NaClnogrowth8 %
119947NaClnogrowth10 %

murein

  • @ref: 2893
  • murein short key: A31.03
  • type: A4gamma m-Dpm-D-Asp-D-Glu; alpha-carboxyl group of D-Glu substituted by glycine

observation

  • @ref: 67770
  • observation: quinones: MK-9 (MK-8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1972317234glucose+
1972322599arabinose-
1972317992sucrose-
1972318222xylose-
1972317268myo-inositol-
1972329864mannitol-
1972328757fructose-
1972326546rhamnose-
1972316634raffinose-
1972362968cellulose-
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128017starch+builds acid from
6837116634raffinose+builds acid from
683716731melezitose+builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
11994716947citrate-carbon source
1199474853esculin+hydrolysis
119947606565hippurate-hydrolysis
11994717632nitrate-reduction
11994716301nitrite-reduction
11994717632nitrate+respiration
6837917632nitrate+reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin-hydrolysis
6837917634D-glucose+fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose+fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen+fermentation

antibiotic resistance

  • @ref: 119947
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11994735581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
11994715688acetoin-
11994717234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382N-acetyl-beta-glucosaminidase+3.2.1.52
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
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
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
68379pyrazinamidase-3.5.1.B15
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
119947oxidase-
119947beta-galactosidase+3.2.1.23
119947alcohol dehydrogenase-1.1.1.1
119947gelatinase+/-
119947amylase+
119947DNase+
119947caseinase-3.4.21.50
119947catalase+1.11.1.6
119947tween esterase-
119947gamma-glutamyltransferase-2.3.2.2
119947lecithinase-
119947lipase-
119947lysine decarboxylase+4.1.1.18
119947ornithine decarboxylase+4.1.1.17
119947phenylalanine ammonia-lyase-4.3.1.24
119947protease-
119947tryptophan deaminase-
119947urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19723+-++--+----++/---+-++

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119947-+++-+----+-++-++++-

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19723---------+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119947+/----+----++++------+/-+++++/-+/-++++++-++++/--++---------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119947--------------------------------------------------------------------------------------------------+

Isolation, sampling and environmental information

isolation

@refsample type
2893human skin
51307Human skin,forearm of healthy adult
67770Forearm of a healthy adult
119947Human, Forearm

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Limb#Arm
#Host#Human
#Host Body-Site#Organ#Skin, Nail, Hair

taxonmaps

  • @ref: 69479
  • File name: preview.99_2911.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_737;97_860;98_1003;99_2911&stattab=map
  • Last taxonomy: Dermabacter
  • 16S sequence: LC144978
  • Sequence Identity:
  • Total samples: 37762
  • soil counts: 2427
  • aquatic counts: 1910
  • animal counts: 32727
  • plant counts: 698

Safety information

risk assessment

@refpathogenicity humanbiosafety levelbiosafety level comment
2893yes, in single cases1Risk group (German classification)
197231Risk group (German classification)
1199471Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218D.hominis (NCFB 2769) gene for 16S ribosomal RNAX767281481ena36740
2893D.hominis 16S ribosomal RNA geneX910341511ena36740
67770Dermabacter hominis gene for 16S ribosomal RNA, partial sequence, strain: JCM 7448LC1449781456ena36740

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dermabacter hominis NBRC 1061571349750.9wgspatric1349750
66792Dermabacter hominis NBRC 1061572731957604draftimg1349750
67770Dermabacter hominis NBRC 106157GCA_001570785contigncbi1349750

GC content

@refGC-contentmethod
289362.0thermal denaturation, midpoint method (Tm)
6777062thermal denaturation, midpoint method (Tm)
6777063.2genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno91.448no
gram-positiveyes92.499no
anaerobicno97.671no
halophileno78.767no
spore-formingno93.709no
glucose-utilyes85.565yes
aerobicno64.188no
flagellatedno96.791no
thermophileno95.62no
glucose-fermentyes51.704no

External links

@ref: 2893

culture collection no.: DSM 7083, ATCC 49369, NCFB 2769, CCUG 32998, JCM 7448, CCM 4122, CECT 4165, CIP 105144, IFM 10528, IMSNU 21318, NBRC 106157, NCIMB 13131

straininfo link

  • @ref: 73427
  • straininfo: 42442

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny7989543Recognition of Dermabacter hominis, formerly CDC fermentative coryneform group 3 and group 5, as a potential human pathogen.Gruner E, Steigerwalt AG, Hollis DG, Weyant RS, Weaver RE, Moss CW, Daneshvar M, Brenner DJJ Clin Microbiol10.1128/jcm.32.8.1918-1922.19941994Actinomycetales/*classification/enzymology/*pathogenicity, Actinomycetales Infections/microbiology, Adult, Aged, Bacterial Typing Techniques, Centers for Disease Control and Prevention, U.S., DNA, Bacterial/genetics, Fatty Acids/analysis, Female, Humans, Infant, Infant, Newborn, Male, Middle Aged, Nucleic Acid Hybridization, United StatesPathogenicity
Phylogeny18768630Devriesea agamarum gen. nov., sp. nov., a novel actinobacterium associated with dermatitis and septicaemia in agamid lizards.Martel A, Pasmans F, Hellebuyck T, Haesebrouck F, Vandamme PInt J Syst Evol Microbiol10.1099/ijs.0.65478-02008Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Animals, Base Composition, Catalase/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Dermatitis/microbiology/*veterinary, Fatty Acids/analysis, Genes, rRNA, Lizards/*microbiology, Locomotion, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sepsis/microbiology/*veterinary, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Temperature, Vitamin K 2/analysisGenetics
Phylogeny26867728Dermabacter vaginalis sp. nov., isolated from human vaginal fluid.Chang DH, Rhee MS, Kim BCInt J Syst Evol Microbiol10.1099/ijsem.0.0009602016Actinomycetales/*classification/genetics/isolation & purification, Asians, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Female, Glycolipids/chemistry, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vagina/*microbiology, Vitamin K 2/chemistryPathogenicity
Phylogeny27088668Dermabacter jinjuensis sp. nov., a novel species of the genus Dermabacter isolated from a clinical specimen.Park YK, Lee KM, Lee WK, Cho MJ, Lee HS, Cho YG, Lee YC, Lee WK, Seong WK, Hwang KJInt J Syst Evol Microbiol10.1099/ijsem.0.0010922016Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fingers/*microbiology/pathology, Humans, Necrosis, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Suppuration/*microbiology, Vitamin K 2/chemistryPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2893Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7083)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7083
19723Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM7083.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
34667Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17131
40521Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14891
51307Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32998)https://www.ccug.se/strain?id=32998
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/
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
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
73427Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID42442.1StrainInfo: A central database for resolving microbial strain identifiers
119947Curators of the CIPCollection of Institut Pasteur (CIP 105144)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105144