Strain identifier

BacDive ID: 24189

Type strain: Yes

Species: Humibacter antri

Strain Designation: D7-27

Strain history: <- Soon Dong Lee, 제주대학교 과학교육과

NCBI tax ID(s): 1280375 (species)

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General

@ref: 21183

BacDive-ID: 24189

DSM-Number: 25738

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

description: Humibacter antri D7-27 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from clay soil from inside a natural cave.

NCBI tax id

  • NCBI tax id: 1280375
  • Matching level: species

strain history

@refhistory
21183<- S. D. Lee, Jeju National Univ., Rep. of Korea; D7-27
67770DSM 25738 <-- S. D. Lee; Jeju Natl. Univ., South Korea; D7-27.
67771<- Soon Dong Lee, 제주대학교 과학교육과

doi: 10.13145/bacdive24189.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Humibacter
  • species: Humibacter antri
  • full scientific name: Humibacter antri Lee 2013

@ref: 21183

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Humibacter

species: Humibacter antri

full scientific name: Humibacter antri Lee 2013

strain designation: D7-27

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31046positive1.33 µm0.485 µmrod-shapedno
67771positive

pigmentation

  • @ref: 31046
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21183
  • 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
21183positivegrowth28mesophilic
31046positivegrowth20-30
31046positiveoptimum29mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
31046positivegrowth5.0-8.0
31046positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31046aerobe
67771aerobe

halophily

  • @ref: 31046
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 1 %

observation

@refobservation
31046aggregates in clumps
67770quinones: MK-12, MK-11, MK-10
67771quinones: MK-12, MK-11, MK-10(minor)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3104617234glucose+carbon source
3104625115malate+carbon source
3104617306maltose+carbon source
3104637684mannose+carbon source
31046506227N-acetylglucosamine+carbon source
310464853esculin+hydrolysis
3104617632nitrate+reduction

enzymes

@refvalueactivityec
31046acid phosphatase+3.1.3.2
31046alpha-galactosidase+3.2.1.22
31046catalase+1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
21183clay soil from inside a natural caveJejuRepublic of KoreaKORAsia
67770Clay soils inside a natural cave in JejuRepublic of KoreaKORAsia
67771From Natural cave soilRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_160584.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_2066;97_2857;98_65628;99_160584&stattab=map
  • Last taxonomy: Humibacter
  • 16S sequence: HF570028
  • Sequence Identity:
  • Total samples: 139
  • soil counts: 71
  • aquatic counts: 7
  • animal counts: 32
  • plant counts: 29

Safety information

risk assessment

  • @ref: 21183
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21183
  • description: Humibacter antri partial 16S rRNA gene, type strain D7-27T
  • accession: HF570028
  • length: 1412
  • database: ena
  • NCBI tax ID: 1280375

GC content

@refGC-contentmethod
2118366.3high performance liquid chromatography (HPLC)
3104666.3

External links

@ref: 21183

culture collection no.: DSM 25738, JCM 31974, KCTC 33009

straininfo link

  • @ref: 88142
  • straininfo: 402829

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23838446Humibacter antri sp. nov., an actinobacterium isolated from a natural cave, and emended description of the genus Humibacter.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.050708-02013Actinomycetales/*classification/genetics/isolation & purification, Antineoplastic Combined Chemotherapy Protocols, Base Composition, Caves/*microbiology, Cell Wall/chemistry, Cyclophosphamide, DNA, Bacterial/genetics, Doxorubicin, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, Podophyllotoxin, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Soil Microbiology, Vincristine, Vitamin K 2/chemistryGenetics
Phylogeny25977283Humibacter ginsengiterrae sp. nov., and Humibacter ginsengisoli sp. nov., isolated from soil of a ginseng field.Kim EK, Hoang VA, Kim YJ, Nguyen NL, Sukweenadhi J, Kang JP, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.0003352015Actinomycetales/*classification/genetics/isolation & purification, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Panax/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryGenetics
Phylogeny26582590Cnuibacter physcomitrellae gen. nov., sp. nov., a novel member of the family Microbacteriaceae isolated from the moss of Physcomitrella patens.Zhou X, Nan Guo G, Qi Wang L, Lan Bai S, Hong Li YInt J Syst Evol Microbiol10.1099/ijsem.0.0007752015
Phylogeny27983468Humibacter aquilariae sp. nov., an actinobacterium isolated from an agarwood chip.Lin SY, Hameed A, Liu YC, Hsu YH, Hsieh YT, Lai WA, Young CCInt J Syst Evol Microbiol10.1099/ijsem.0.0017402017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Thymelaeaceae/*microbiology, Vitamin K 2/chemistry, Wood/*microbiologyTranscriptome

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
21183Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-25738Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25738)
31046Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172737628776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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/
88142Reimer, 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-ID402829.1