Strain identifier

BacDive ID: 7493

Type strain: Yes

Species: Microcella alkaliphila

Strain Designation: Ac4r

Strain history: CIP <- 2004, I. Tiago, Coimbra Univ., Coimbra, Portugal: strain AC4r

NCBI tax ID(s): 279828 (species)

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General

@ref: 7742

BacDive-ID: 7493

DSM-Number: 18851

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

description: Microcella alkaliphila Ac4r is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from alkaline groundwater.

NCBI tax id

  • NCBI tax id: 279828
  • Matching level: species

strain history

@refhistory
7742<- CIP <- I. Tiago
382782004, I. Tiago, Coimbra Univ., Coimbra, Portugal: strain AC4r
116242CIP <- 2004, I. Tiago, Coimbra Univ., Coimbra, Portugal: strain AC4r

doi: 10.13145/bacdive7493.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Microcella
  • species: Microcella alkaliphila
  • full scientific name: Microcella alkaliphila Tiago et al. 2006

@ref: 7742

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Microcella

species: Microcella alkaliphila

full scientific name: Microcella alkaliphila Tiago et al. 2006

strain designation: Ac4r

type strain: yes

Morphology

cell morphology

  • @ref: 116242
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 116242

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7742MICROCELLA ALKALIPHILA MEDIUM (DSMZ Medium 1063)yeshttps://mediadive.dsmz.de/medium/1063Name: MICROCELLA ALKALIPHILA MEDIUM (DSMZ Medium 1063) Composition: Trypticase soy broth 30.0 g/l Yeast extract 3.0 g/l KH2PO4 0.5 g/l NaCl 0.4 g/l NH4Cl 0.4 g/l MgCl2 x 6 H2O 0.33 g/l Na2CO3 anhydrous 0.053 g/l CaCl2 x 2 H2O 0.05 g/l NaHCO3 0.042 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l Pyridoxine hydrochloride 0.0015 g/l Thiamine-HCl x 2 H2O 0.001 g/l Nicotinic acid 0.001 g/l Calcium pantothenate 0.0005 g/l Vitamin B12 0.0005 g/l p-Aminobenzoic acid 0.0004 g/l CoCl2 x 6 H2O 0.00019 g/l D-(+)-biotin 0.0001 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l H3BO3 6e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water
38278MEDIUM 591 - for No nameyesDistilled water make up to (690.000 ml);Agar (15.000 g);Yeast extract (5.000 g);Tryptone (5.000 g);Ketoglutaric acid (1.000 g);Thermus macronutrients 10X solution - M00976 (100.000 ml);Thermus micronutrients 100X solution - M00975 (10.000 ml);Carbonatebic
116242CIP Medium 591yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=591

culture temp

@refgrowthtypetemperaturerange
7742positivegrowth35mesophilic
38278positivegrowth37mesophilic
116242positivegrowth18-41
116242nogrowth10psychrophilic
116242nogrowth45thermophilic

culture pH

  • @ref: 116242
  • ability: no
  • type: growth
  • pH: 6

Physiology and metabolism

oxygen tolerance

  • @ref: 116242
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
116242NaClpositivegrowth0-6 %
116242NaClnogrowth8 %
116242NaClnogrowth10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate-builds acid from
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
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
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
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
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
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
116242citrate-carbon source16947
116242esculin-hydrolysis4853
116242glucose-fermentation17234
116242hippurate-hydrolysis606565
116242lactose-fermentation17716
116242nitrate-reduction17632
116242nitrite-reduction16301
116242malonate+assimilation15792
116242sodium thiosulfate-builds gas from132112

antibiotic resistance

  • @ref: 116242
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 116242
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11624215688acetoin-
11624217234glucose-

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
116242oxidase-
116242beta-galactosidase+/-3.2.1.23
116242alcohol dehydrogenase-1.1.1.1
116242amylase-
116242DNase-
116242caseinase-3.4.21.50
116242catalase+1.11.1.6
116242tween esterase-
116242gamma-glutamyltransferase+2.3.2.2
116242lecithinase-
116242lipase-
116242lysine decarboxylase-4.1.1.18
116242ornithine decarboxylase-4.1.1.17
116242phenylalanine ammonia-lyase-4.3.1.24
116242protease-
116242tryptophan deaminase-
116242urease+3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116242--++-+---------+--+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116242--+/-+++----+/-+/---+/---+/---------++/---+/-+/--------+---+--+/--+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116242---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
7742alkaline groundwaterCabeco de VidePortugalPRTEurope
116242Environment, Alkaline ground waterCabeco de VidePortugalPRTEurope2000

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Groundwater
#Condition#Alkaline

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
77421Risk group (German classification)
1162421Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7742
  • description: Microcella alkaliphila AC4r 16S rRNA gene, type strain AC4rT
  • accession: AJ717385
  • length: 1505
  • database: ena
  • NCBI tax ID: 279828

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Microcella alkaliphila AC4rGCA_004216855contigncbi279828
66792Microcella alkaliphila AC4r2802428807draftimg279828

GC content

  • @ref: 7742
  • GC-content: 67.1

External links

@ref: 7742

culture collection no.: DSM 18851, CIP 108473, LMG 22690, KCTC 19624

straininfo link

  • @ref: 76939
  • straininfo: 135984

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17012553Microcella alkaliphila sp. nov., a novel member of the family Microbacteriaceae isolated from a non-saline alkaline groundwater, and emended description of the genus Microcella.Tiago I, Morais PV, da Costa MS, Verissimo AInt J Syst Evol Microbiol10.1099/ijs.0.64320-02006Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fresh Water/*microbiology, Genes, rRNA, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride, Species SpecificityGenetics
Phylogeny34628559Microcella flavibacter sp. nov., isolated from marine sediment, and reclassification of Chryseoglobus frigidaquae, Chryseoglobus indicus, and Yonghaparkia alkaliphila as Microcella frigidaquae comb. nov., Microcella indica nom. nov., and Microcella alkalica nom. nov.Xie F, Pei S, Huang X, Wang L, Kou J, Zhang GAntonie Van Leeuwenhoek10.1007/s10482-021-01668-72021Actinobacteria, Bacterial Typing Techniques, DNA, Bacterial/genetics, *Fatty Acids/analysis, *Geologic Sediments, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7742Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18851)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18851
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
38278Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6099
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
76939Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID135984.1StrainInfo: A central database for resolving microbial strain identifiers
116242Curators of the CIPCollection of Institut Pasteur (CIP 108473)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108473