Strain identifier

BacDive ID: 158536

Type strain: Yes

Species: Floricoccus penangensis

Strain Designation: HibF3

Strain history: G. Rusul; Univ. Sains Malaysia, Malaysia; HibF3.

NCBI tax ID(s): 1859475 (species)

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General

@ref: 65224

BacDive-ID: 158536

keywords: genome sequence, 16S sequence, Bacteria, Gram-positive, coccus-shaped, colony-forming

description: Floricoccus penangensis HibF3 is a Gram-positive, coccus-shaped bacterium that forms circular colonies and was isolated from fresh flowers of Hibiscus .

NCBI tax id

  • NCBI tax id: 1859475
  • Matching level: species

strain history

  • @ref: 67770
  • history: G. Rusul; Univ. Sains Malaysia, Malaysia; HibF3.

doi: 10.13145/bacdive158536.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Lactobacillales
  • family: Streptococcaceae
  • genus: Floricoccus
  • species: Floricoccus penangensis
  • full scientific name: Floricoccus penangensis Chuah et al. 2017

@ref: 65224

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Streptococcaceae

genus: Floricoccus

species: Floricoccus penangensis

strain designation: HibF3

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
65224positivecoccus-shapedno
125438no94.5
125438positive92.73

colony morphology

  • @ref: 65224
  • type of hemolysis: alpha
  • hemolysis ability: 1
  • colony size: 1-2 mm
  • colony color: cream-white
  • colony shape: circular
  • incubation period: 1-2 days
  • medium used: all purpose Tween medium

Culture and growth conditions

culture medium

@refnamegrowthcomposition
65224all purpose Tween mediumyeswith 1 % (w/v) sodium pyruvate
65224brain-heart infusion brothyeswith 0.1 % (w/v) bromocresol purple
65224bile aesculin agaryes
65224MRSno
65224M17 lactose agarno
65224brain-heart infusion agaryes
65224blood agar baseyeswith 5 % (v/v) sheep blood

culture temp

@refgrowthtypetemperature
65224positivegrowth15-40
65224positiveoptimum30-37
65224nogrowth7
65224nogrowth45
67770positivegrowth30

culture pH

@refabilitytypepHPH range
65224positivegrowth5
65224positivegrowth6
65224positivegrowth7.5
65224positivegrowth9alkaliphile
65224nogrowth3

Physiology and metabolism

oxygen tolerance

  • @ref: 125439
  • oxygen tolerance: microaerophile
  • confidence: 93.3

spore formation

  • @ref: 65224
  • type of spore: endospore
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
65224NaClnogrowth4 %
65224NaClnogrowth5 %
65224NaClnogrowth6.5 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
652242-oxogluconate-builds acid from
652245-dehydro-D-gluconate-builds acid from58143
65224ribitol-builds acid from15963
65224amygdalin-builds acid from27613
65224arbutin+builds acid from18305
65224arginine+hydrolysis29016
65224beta-gentiobiose-builds acid from71422
65224cellobiose+builds acid from17057
65224citrate-assimilation16947
65224D-arabinose-builds acid from17108
65224D-arabitol-builds acid from18333
65224D-fructose+builds acid from15824
65224D-fucose-builds acid from28847
65224D-glucose+builds acid from17634
65224D-lyxose-builds acid from62318
65224D-mannose+builds acid from16024
65224D-tagatose-builds acid from16443
65224D-xylose-builds acid from65327
65224galactitol-builds acid from16813
65224erythritol-builds acid from17113
65224esculin+builds acid from4853
65224galactose-builds acid from28260
65224gelatin+hydrolysis5291
65224gluconate-builds acid from24265
65224glucose+builds acid from17234
65224glucose+builds gas from17234
65224glucose+fermentation17234
65224glycerol-builds acid from17754
65224glycogen+builds acid from28087
65224hippurate-hydrolysis606565
65224myo-inositol-builds acid from17268
65224inulin-builds acid from15443
65224L-arabinose-builds acid from30849
65224L-arabitol-builds acid from18403
65224L-fucose-builds acid from18287
65224L-sorbose-builds acid from17266
65224L-xylose-builds acid from65328
65224lactose-builds acid from17716
65224maltose+builds acid from17306
65224mannitol+builds acid from29864
65224melezitose+builds acid from6731
65224melibiose-builds acid from28053
65224methyl alpha-D-glucopyranoside-builds acid from320061
65224methyl alpha-D-mannoside-builds acid from43943
65224methyl beta-D-xylopyranoside-builds acid from74863
65224milk-builds acid from
65224N-acetylglucosamine+builds acid from506227
65224raffinose-builds acid from16634
65224rhamnose-builds acid from26546
65224ribose-builds acid from33942
65224salicin+builds acid from17814
65224sorbitol-builds acid from30911
65224sucrose+builds acid from17992
65224trehalose+builds acid from27082
65224turanose-builds acid from32528
65224xylitol-builds acid from17151

metabolite production

  • @ref: 65224
  • Chebi-ID: 15688
  • metabolite: acetoin
  • production: yes

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
6522417234glucose+
6522415688acetoin+

enzymes

@refvalueactivityec
65224catalase-1.11.1.6
65224cytochrome oxidase-1.9.3.1
65224naphthol-AS-BI-phosphohydrolase+
65224alpha-galactosidase+3.2.1.22
65224valine arylamidase+
65224alkaline phosphatase-3.1.3.1
65224esterase (C 4)-
65224esterase Lipase (C 8)-
65224lipase (C 14)-
65224leucine arylamidase-3.4.11.1
65224leucine aminopeptidase-3.4.1.1
65224cystine arylamidase-3.4.11.3
65224alpha-chymotrypsin-3.4.21.1
65224trypsin-3.4.21.4
65224acid phosphatase-3.1.3.2
65224beta-galactosidase-3.2.1.23
65224beta-glucosidase-3.2.1.21
65224beta-glucuronidase-3.2.1.31
65224alpha-glucosidase-3.2.1.20
65224N-acetyl-beta-glucosaminidase-3.2.1.52
65224alpha-mannosidase-3.2.1.24
65224alpha-fucosidase-3.2.1.51
65224pyrrolidonyl arylamidase-3.4.19.3
65224arginine dihydrolase-3.5.3.6

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperaturehost species
65224fresh flowers of Hibiscus (Hibiscus rosa-sinensis L.)2014-12-16campus ground of Universiti Sains Malaysia, in PenangMalaysiaMYSAsiaall purpose Tween mediawith 1 % sodium pyruvate1-2 days30
67770Fresh flowers of durian (Durio zibethinus) in an orchard in Teluk BahangPenangMalaysiaMYSAsiaDurio zibethinus

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Plant#Flower
#Host#Plants#Shrub (Scrub)
#Host#Plants#Tree

taxonmaps

  • @ref: 69479
  • File name: preview.99_3464.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_58;96_1809;97_2168;98_2659;99_3464&stattab=map
  • Last taxonomy: Floricoccus
  • 16S sequence: KX185708
  • Sequence Identity:
  • Total samples: 9166
  • soil counts: 203
  • aquatic counts: 684
  • animal counts: 8061
  • plant counts: 218

Sequence information

16S sequences

  • @ref: 65224
  • description: Floricoccus penangensis strain HibF3 16S ribosomal RNA gene, partial sequence
  • accession: KX185708
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Floricoccus penangensis strain HibF31859475.4wgspatric1859475
66792Floricoccus penangensis HibF32788500174draftimg1859475
67770Floricoccus penangensis HibF3GCA_001832885contigncbi1859475

GC content

  • @ref: 67770
  • GC-content: 33.1
  • method: genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes92.73yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no85.111no
125438spore-formingspore-formingAbility to form endo- or exosporesno84.557yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no94.46no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno93.666no
125438motile2+flagellatedAbility to perform flagellated movementno94.5yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes50.5
125439BacteriaNetmotilityAbility to perform movementyes56.1
125439BacteriaNetgram_stainReaction to gram-stainingpositive84
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthmicroaerophile93.3

External links

@ref: 65224

culture collection no.: LMG 29831, JCM 31735

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29034853Floricoccus tropicus gen. nov., sp. nov. and Floricoccus penangensis sp. nov. isolated from fresh flowers of durian tree and hibiscus.Chuah LO, Yap KP, Shamila-Syuhada AK, Thong KL, Ahmad R, Liong MT, Rusul GInt J Syst Evol Microbiol10.1099/ijsem.0.0023862017Bacterial Typing Techniques, Bombacaceae/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flowers/*microbiology, Genes, Bacterial, Hibiscus/*microbiology, Malaysia, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptococcaceae/*classification/genetics/isolation & purificationTranscriptome
Phylogeny31719601Partial rpoB Gene Sequencing Identification and Probiotic Potential of Floricoccus penangensis ML061-4 Isolated from Assam Tea (Camellia sinensis var. assamica).Rungsirivanich P, Inta A, Tragoolpua Y, Thongwai NSci Rep10.1038/s41598-019-52979-92019Bacterial Adhesion/drug effects, Bacterial Proteins/*genetics, Camellia sinensis/*microbiology, *Genes, Bacterial, Hydrophobic and Hydrophilic Interactions, Lactic Acid/metabolism, Microbial Sensitivity Tests, Phylogeny, Probiotics/*pharmacology, *Sequence Analysis, DNA, Streptococcaceae/drug effects/*genetics/isolation & purification/ultrastructurePathogenicity

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
65224Li-Oon Chuah, Kien-Pong Yap, Ahamed Kamal Shamila-Syuhada, Kwai Lin Thong, Rosma Ahmad, Min Tze Liong, Gulam RusulFloricoccus tropicus gen. nov., sp. nov. and Floricoccus penangensis sp. nov. isolated from fresh flowers of durian tree and hibiscus10.1099/ijsem.0.002386IJSEM 67: 4979-4985 201729034853
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG