Strain identifier

BacDive ID: 3935

Type strain: Yes

Species: Barrientosiimonas humi

Strain Designation: 39

Strain history: CGMCC 4.6864 <-- L.-H. Lee 39.

NCBI tax ID(s): 999931 (species)

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

@ref: 17717

BacDive-ID: 3935

DSM-Number: 24617

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

description: Barrientosiimonas humi 39 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from Antarctic soil, upper top soil layer.

NCBI tax id

  • NCBI tax id: 999931
  • Matching level: species

strain history

@refhistory
17717<- L.-H. Lee, Universiti Putra Malaysia, Dept. Biomedical Science, Faculty Medicine and Health Scs.; strain 39
67770CGMCC 4.6864 <-- L.-H. Lee 39.

doi: 10.13145/bacdive3935.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Dermacoccaceae
  • genus: Barrientosiimonas
  • species: Barrientosiimonas humi
  • full scientific name: Barrientosiimonas humi Lee et al. 2013

@ref: 17717

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dermacoccaceae

genus: Barrientosiimonas

species: Barrientosiimonas humi

full scientific name: Barrientosiimonas humi Lee et al. 2013

strain designation: 39

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30533positive1.25 µm0.315 µmcoccus-shapedno
69480no97.517
69480positive100

pigmentation

  • @ref: 30533
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17717
  • name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/65
  • composition: Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
17717positivegrowth28mesophilic
30533positivegrowth24-40
30533positiveoptimum32mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
30533positivegrowth06-10alkaliphile
30533positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 30533
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30533no
69480no99.967

halophily

@refsaltgrowthtested relationconcentration
30533NaClpositivegrowth0-14 %
30533NaClpositiveoptimum2 %

murein

  • @ref: 17717
  • murein short key: A11.36
  • type: A4alpha L-Lys-L-Ser-D-Asp

observation

@refobservation
30533aggregates in chains
67770quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3053330089acetate+carbon source
3053316449alanine+carbon source
3053322599arabinose+carbon source
3053329016arginine+carbon source
3053323652dextrin+carbon source
3053328757fructose+carbon source
3053328260galactose+carbon source
3053324265gluconate+carbon source
3053317234glucose+carbon source
3053329987glutamate+carbon source
3053317754glycerol+carbon source
3053327570histidine+carbon source
3053317306maltose+carbon source
3053337684mannose+carbon source
3053328053melibiose+carbon source
3053328044phenylalanine+carbon source
3053351850methyl pyruvate+carbon source
3053316634raffinose+carbon source
3053333942ribose+carbon source
3053317814salicin+carbon source
3053317822serine+carbon source
3053317992sucrose+carbon source
3053316296D-tryptophan+carbon source
3053353423tween 40+carbon source
3053353426tween 80+carbon source
305334853esculin+hydrolysis

enzymes

@refvalueactivityec
30533catalase+1.11.1.6
30533gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentlatitudelongitude
17717Antarctic soil, upper top soil layerBarrientos Island (62°24' 26.0'' S 59° 44' 49.1'' W)Australia and Oceania-62.4072-59.747
67770Soil from Barrientos Island in the Antarctic

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Psychrophilic (<10°C)
#Climate#Cold#Polar

taxonmaps

  • @ref: 69479
  • File name: preview.99_11725.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_844;97_986;98_8794;99_11725&stattab=map
  • Last taxonomy: Barrientosiimonas
  • 16S sequence: JF346171
  • Sequence Identity:
  • Total samples: 1666
  • soil counts: 161
  • aquatic counts: 155
  • animal counts: 1304
  • plant counts: 46

Safety information

risk assessment

  • @ref: 17717
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17717
  • description: Barrientosiimonas humi strain 39 16S ribosomal RNA gene, partial sequence
  • accession: JF346171
  • length: 1495
  • database: ena
  • NCBI tax ID: 999931

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Barrientosiimonas humi strain DSM 24617999931.3wgspatric999931
66792Barrientosiimonas humi DSM 246172814122977draftimg999931
67770Barrientosiimonas humi DSM 24617GCA_006716095contigncbi999931

GC content

@refGC-contentmethod
1771768.4high performance liquid chromatography (HPLC)
3053368.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno57no
motileno94.402yes
flagellatedno97.427yes
gram-positiveyes91.538yes
anaerobicno98.852no
halophileno88.842no
spore-formingno84.953yes
thermophileno98.064no
glucose-utilyes88.86yes
aerobicyes93.763no
glucose-fermentno89.62no

External links

@ref: 17717

culture collection no.: DSM 24617, CGMCC 4.6864, JCM 19663

straininfo link

  • @ref: 73444
  • straininfo: 401745

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22389286Barrientosiimonas humi gen. nov., sp. nov., an actinobacterium of the family Dermacoccaceae.Lee LH, Cheah YK, Sidik SM, Xie QY, Tang YL, Lin HP, Mutalib NA, Hong KInt J Syst Evol Microbiol10.1099/ijs.0.038232-02012Actinomycetales/*classification/genetics/isolation & purification, Antarctic Regions, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Peptidoglycan/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny26060216Barrientosiimonas endolithica sp. nov., isolated from pebbles, reclassification of the only species of the genus Tamlicoccus, Tamlicoccus marinus Lee 2013, as Barrientosiimonas marina comb. nov. and emended description of the genus Barrientosiimonas.Parag B, Sasikala C, Ramana CVInt J Syst Evol Microbiol10.1099/ijs.0.0003742015*Actinomycetales/classification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Lysine, Molecular Sequence Data, Nucleic Acid Hybridization/genetics, Peptidoglycan/chemistry, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
17717Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24617)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24617
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
30533Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2686528776041
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
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)
73444Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID401745.1StrainInfo: A central database for resolving microbial strain identifiers