Strain identifier

BacDive ID: 140688

Type strain: Yes

Species: Domibacillus epiphyticus

Strain history: S. Krishnamurthi; MTCC, India; SAB 38.

NCBI tax ID(s): 1714355 (species)

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General

@ref: 43455

BacDive-ID: 140688

DSM-Number: 100929

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, spore-forming, Gram-positive, motile, rod-shaped, colony-forming

description: Domibacillus epiphyticus KCTC 33830 is an obligate aerobe, spore-forming, Gram-positive bacterium that forms circular colonies and was isolated from surface of an intertidal macroalga growing in Anjuna Beach.

NCBI tax id

  • NCBI tax id: 1714355
  • Matching level: species

strain history

  • @ref: 67770
  • history: S. Krishnamurthi; MTCC, India; SAB 38.

doi: 10.13145/bacdive140688.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Domibacillus
  • species: Domibacillus epiphyticus
  • full scientific name: Domibacillus epiphyticus Verma et al. 2017

@ref: 43455

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Caryophanales

family: Bacillaceae

genus: Domibacillus

species: Domibacillus epiphyticus

type strain: yes

Morphology

cell morphology

  • @ref: 43455
  • gram stain: positive
  • cell length: 2.2 µm
  • cell width: 0.8 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 43455
  • colony color: Ivory
  • colony shape: circular
  • incubation period: 1 day
  • medium used: TSBA

Culture and growth conditions

culture medium

  • @ref: 43455
  • name: TSBA
  • growth: yes

culture temp

@refgrowthtypetemperature
43455positivegrowth20-45
43455positiveoptimum35-40
67770positivegrowth28

culture pH

@refabilitytypepHPH range
43455positivegrowth5-9alkaliphile
43455positiveoptimum7-7.5

Physiology and metabolism

oxygen tolerance

  • @ref: 43455
  • oxygen tolerance: obligate aerobe

spore formation

@refspore descriptiontype of sporespore formationconfidence
43455central position, spherical or ellipsoidal in swollen sporangiaendosporeyes
125438yes91.401

halophily

@refsaltgrowthtested relationconcentration
43455NaClpositivegrowth0-4 %(w/v)
43455NaClpositiveoptimum1 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4345517128adipate-assimilation
4345516899D-mannitol-assimilation
4345516024D-mannose-assimilation
434554853esculin-assimilation
434555291gelatin-assimilation
4345530849L-arabinose-assimilation
43455506227N-acetylglucosamine-assimilation
4345518401phenylacetate-assimilation
4345532032potassium gluconate-assimilation
4345553258sodium citrate-assimilation
4345522599arabinose-builds acid from
4345517057cellobiose-builds acid from
4345516813galactitol-builds acid from
4345528757fructose-builds acid from
4345528260galactose-builds acid from
4345517268myo-inositol-builds acid from
4345515443inulin-builds acid from
4345517716lactose-builds acid from
4345517306maltose-builds acid from
4345537684mannose-builds acid from
4345528053melibiose-builds acid from
4345516634raffinose-builds acid from
4345526546rhamnose-builds acid from
4345517814salicin-builds acid from
4345530911sorbitol-builds acid from
4345518222xylose-builds acid from
4345517234glucose-fermentation
43455casein-hydrolysis
434554853esculin-hydrolysis
434555291gelatin-hydrolysis
4345528017starch-hydrolysis
4345516199urea-hydrolysis
4345517632nitrate-reduction
4345527689decanoate+assimilation
4345517234glucose+assimilation
4345525115malate+assimilation
4345517306maltose+assimilation
4345529864mannitol+builds acid from
4345517992sucrose+builds acid from
4345527082trehalose+builds acid from
4345517128adipate+growth
4345517234glucose+growth
4345525115malate+growth
4345517306maltose+growth
4345529864mannitol+growth
4345518401phenylacetate+growth
4345532032potassium gluconate+growth
4345530089acetate+oxidation
4345524996lactate+oxidation
4345525115malate+oxidation
4345517634D-glucose+/-builds acid from
4345513705acetoacetate+/-oxidation
4345573706bromosuccinate+/-oxidation
4345523652dextrin+/-oxidation
4345515740formate+/-oxidation
4345517309pectin+/-oxidation
4345517272propionate+/-oxidation
4345517992sucrose+/-oxidation
4345527082trehalose+/-oxidation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
434552637amikacinyesyes30 µg (disc)
4345528971ampicillinyesyes10 µg (disc)
434552676amoxicillinyesyes10 µg (disc)
434553479cefadroxilyesyes30 µg (disc)
434553493cefoperazoneyesyes75 µg (disc)
434553508ceftazidimeyesyes30 µg (disc)
4345529007ceftriaxoneyesyes30 µg (disc)
4345517698chloramphenicolyesyes30 µg (disc)
43455100241ciprofloxacinyesyes5 µg (disc)
4345549566cloxacillinyesyes1 µg (disc)
434553770co-trimoxazoleyesyes25 µg (disc)
4345548923erythromycinyesyes15 µg (disc)
4345517833gentamicinyesyes10 µg (disc)
434557528netilmycinyesyes10 µg (disc)
4345571415nitrofurantoinyesyes300 µg (disc)
43455100246norfloxacinyesyes10 µg (disc)
4345517334penicillinyesyes60 µg (disc)
4345528864tobramycinyesyes10 µg (disc)
4345528001vancomycinyesyes30 µg (disc)
43455100147nalidixic acidyesyes10 µg (disc)
4345548607lithium chlorideyesyes
4345575248potassium telluriteyesyes
4345526710sodium chlorideyesyes
4345564103sodium butyrateyesyes
434551 % sodium lactateyesyes

metabolite production

@refChebi-IDmetaboliteproduction
4345515688acetoinno
4345535581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
4345517234glucose-
4345515688acetoin-

enzymes

@refvalueactivityec
43455catalase+1.11.1.6
43455cytochrome oxidase+1.9.3.1
43455alkaline phosphatase+3.1.3.1
43455esterase (C 4)+
43455esterase Lipase (C 8)+
43455beta-galactosidase-3.2.1.23
43455leucine arylamidase-3.4.11.1
43455valine arylamidase-
43455cystine arylamidase-3.4.11.3
43455trypsin-3.4.21.4
43455alpha-chymotrypsin-3.4.21.1
43455acid phosphatase-3.1.3.2
43455naphthol-AS-BI-phosphohydrolase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43455C15:0 anteiso10.2
    43455C17:0 anteiso1.7
    43455C14:06.6
    43455C16:014
    43455C16:1ω11c8
    43455C16:1ω7c / C16:1ω7c8.6
    43455C17:1isol / anteiso B5.7
    43455C14:0 iso1.9
    43455C15:0 iso32
    43455C16:0 iso2.1
    43455C17:0 iso2.1
  • type of FA analysis: whole cell analysis
  • incubation medium: TSBA
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 2
  • incubation_oxygen: aerobic
  • software version: Sherlock 6.1
  • library/peak naming table: TSBA 6.0
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
43455surface of an intertidal macroalga (Dictyota) growing in Anjuna BeachState of GoaIndiaINDAsia15.56773.733
67770Surface of a macroalga from Anjuna beachGoaIndiaINDAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Coast
#Environmental#Terrestrial#Tidal flat
#Host#Algae

taxonmaps

  • @ref: 69479
  • File name: preview.99_2557.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_3;96_1025;97_1195;98_1431;99_2557&stattab=map
  • Last taxonomy: Domibacillus
  • 16S sequence: LN879432
  • Sequence Identity:
  • Total samples: 159
  • soil counts: 89
  • aquatic counts: 22
  • animal counts: 22
  • plant counts: 26

Sequence information

16S sequences

  • @ref: 43455
  • description: Domibacillus sp. SAB 38 partial 16S rRNA gene, isolate SAB 38
  • accession: LN879432
  • database: nuccore

Genome sequences

  • @ref: 67770
  • description: Domibacillus epiphyticus SAB 38
  • accession: GCA_001975785
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 1714355

GC content

  • @ref: 43455
  • GC-content: 41.5
  • method: genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes80.921no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no92.622no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes80.091yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes91.401yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno83.76yes
125438motile2+flagellatedAbility to perform flagellated movementyes85.109no

External links

@ref: 43455

culture collection no.: KCTC 33830, MTCC 12575, DSM 100929, SAB 38, JCM 32632

literature

  • topic: Phylogeny
  • Pubmed-ID: 28829034
  • title: Domibacillus mangrovi sp. nov. and Domibacillus epiphyticus sp. nov., isolated from marine habitats of the central west coast of India.
  • authors: Verma A, Ojha AK, Dastager SG, Natarajan R, Mayilraj S, Krishnamurthi S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002085
  • year: 2017
  • mesh: Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry
  • 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
43455Ashish Verma, Anup Kumar Ojha, Syed G. Dastager, Rameshkumar Natarajan, Shanmugam Mayilraj, Srinivasan KrishnamurthiDomibacillus mangrovi sp. nov. and Domibacillus epiphyticus sp. nov., isolated from marine habitats of the central west coast of India10.1099/ijsem.0.002085IJSEM 67: 3063-3070 201728829034
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
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/
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695