Strain identifier

BacDive ID: 133102

Type strain: Yes

Species: Humibacter aquilariae

Strain Designation: CC-YTH161

Strain history: C.-C. Young; Natl. Chung Hsing Univ., Taiwan; CC-YTH161.

NCBI tax ID(s): 1848970 (species)

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General

@ref: 25295

BacDive-ID: 133102

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

description: Humibacter aquilariae CC-YTH161 is an aerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from agarwood sample collected at Nantou County.

NCBI tax id

  • NCBI tax id: 1848970
  • Matching level: species

strain history

  • @ref: 67770
  • history: C.-C. Young; Natl. Chung Hsing Univ., Taiwan; CC-YTH161.

doi: 10.13145/bacdive133102.20230509.8.1

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 aquilariae
  • full scientific name: Humibacter aquilariae Lin et al. 2017

@ref: 25295

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Micrococcales

family: Microbacteriaceae

genus: Humibacter

species: Humibacter aquilariae

strain designation: CC-YTH161

type strain: yes

Morphology

cell morphology

  • @ref: 25295
  • gram stain: positive
  • cell length: 1.0-1.4 µm
  • cell width: 0.5-0.6 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 25295
  • colony size: 1-2 mm
  • colony color: yellowish
  • colony shape: circular
  • incubation period: 2 days
  • medium used: NA

Culture and growth conditions

culture medium

@refnamegrowth
25295Nutrient agar (NA)yes
25295Trypticase Soy Agar (TSA)yes
25295Reasoner's 2A agar (R2A)yes

culture temp

@refgrowthtypetemperaturerange
25295positivegrowth20-40
25295positiveoptimum25mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
25295positivegrowth5.0-9.0alkaliphile
25295positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 25295
  • oxygen tolerance: aerobe

halophily

@refsalttested relationconcentrationgrowth
25295NaCloptimum1 %
25295NaClgrowth0-5 %(w/v)positive

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2529530849L-arabinose-assimilation
25295506227N-acetylglucosamine-assimilation
2529517632nitrate-reduction
2529517925alpha-D-glucose+carbon source
2529573706bromosuccinate+carbon source
2529517057cellobiose+carbon source
2529515824D-fructose+carbon source
252958391D-gluconate+carbon source
2529517634D-glucose+assimilation
2529516899D-mannitol+carbon source
2529516899D-mannitol+assimilation
2529516024D-mannose+carbon source
2529516024D-mannose+assimilation
2529523652dextrin+carbon source
252955291gelatin+hydrolysis
2529528066gentiobiose+carbon source
2529517754glycerol+carbon source
2529514336glycerol 1-phosphate+carbon source
2529530849L-arabinose+carbon source
2529525115malate+assimilation
2529517306maltose+carbon source
2529517306maltose+assimilation
2529551850methyl pyruvate+carbon source
2529532032potassium gluconate+assimilation
2529517148putrescine+carbon source
2529517992sucrose+carbon source
2529527082trehalose+carbon source
2529532528turanose+carbon source
2529553423tween 40+carbon source
2529553426tween 80+carbon source

enzymes

@refvalueactivityec
25295acid phosphatase+3.1.3.2
25295alkaline phosphatase+3.1.3.1
25295alpha-chymotrypsin-3.4.21.1
25295alpha-galactosidase-3.2.1.22
25295alpha-glucosidase+3.2.1.20
25295alpha-mannosidase-3.2.1.24
25295beta-galactosidase-3.2.1.23
25295beta-glucosidase+3.2.1.21
25295beta-glucuronidase+3.2.1.31
25295catalase+1.11.1.6
25295cystine arylamidase+3.4.11.3
25295cytochrome oxidase+1.9.3.1
25295esterase (C 4)+
25295esterase Lipase (C 8)+
25295leucine arylamidase+3.4.11.1
25295lipase (C 14)+
25295N-acetyl-beta-glucosaminidase-3.2.1.52
25295naphthol-AS-BI-phosphohydrolase+
25295trypsin+3.4.21.4
25295urease-3.5.1.5
25295valine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25295C15:0 anteiso51.1
    25295C17:0 anteiso16.1
    25295C15:1ω5c1.1
    25295C16:01.7
    25295C18:1ω7c / C18:1ω6c8.2
    25295C14:0 iso1
    25295C16:0 iso14.3
    25295C17:0 iso1.3
    25295C17:1 iso ω10c2.1
  • type of FA analysis: whole cell analysis
  • incubation medium: Nutrient agar (NA)
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation pH: 6.00
  • software version: Sherlock 6.0
  • library/peak naming table: RTSBA 6
  • system: MIS MIDI
  • method/protocol: Sasser 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
25295agarwood sample collected at Nantou CountyNantou County, TaiwanTaiwanTWNAsia24.077121.066
67770Agarwood chip

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site

taxonmaps

  • @ref: 69479
  • File name: preview.99_4072.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_2066;97_2491;98_3083;99_4072&stattab=map
  • Last taxonomy: Microbacteriaceae
  • 16S sequence: KU248164
  • Sequence Identity:
  • Total samples: 325
  • soil counts: 45
  • aquatic counts: 59
  • animal counts: 160
  • plant counts: 61

Sequence information

16S sequences

  • @ref: 25295
  • description: 16S rRNA gene sequences
  • accession: KU248164
  • length: 1410
  • database: ena
  • NCBI tax ID: 1848970

GC content

  • @ref: 25295
  • GC-content: 67
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 25295

culture collection no.: BCRC 80936, JCM 31199

literature

  • topic: Phylogeny
  • Pubmed-ID: 27983468
  • title: Humibacter aquilariae sp. nov., an actinobacterium isolated from an agarwood chip.
  • authors: Lin SY, Hameed A, Liu YC, Hsu YH, Hsieh YT, Lai WA, Young CC
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001740
  • year: 2017
  • mesh: Actinomycetales/*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/*microbiology
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
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
25295S. Y. H. Lin, A.,Liu, Y. C.,Hsu, Y. H.,Hsieh, Y. T.,Lai, W. A.,Young, C. C.Humibacter aquilariae sp. nov., an actinobacterium isolated from an agarwood chip10.1099/ijsem.0.001740IJSEM 67: 1468-1472 201727983468
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/