Strain identifier

BacDive ID: 133402

Type strain: Yes

Species: Ruficoccus amylovorans

Strain Designation: CC-MHH0563

Strain history: C.-C. Young; Natl. Chung Hsing Univ., Taiwan; CC-MHH0563.

NCBI tax ID(s): 1804625 (species)

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General

@ref: 25264

BacDive-ID: 133402

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

description: Ruficoccus amylovorans CC-MHH0563 is an aerobe, Gram-negative, coccus-shaped bacterium that forms circular colonies and was isolated from fermenter located at a greenhouse facility.

NCBI tax id

  • NCBI tax id: 1804625
  • Matching level: species

strain history

  • @ref: 67770
  • history: C.-C. Young; Natl. Chung Hsing Univ., Taiwan; CC-MHH0563.

doi: 10.13145/bacdive133402.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/verrucomicrobiota
  • domain: Bacteria
  • phylum: Verrucomicrobiota
  • class: Opitutia
  • order: Puniceicoccales
  • family: Puniceicoccaceae
  • genus: Ruficoccus
  • species: Ruficoccus amylovorans
  • full scientific name: Ruficoccus amylovorans Lin et al. 2017

@ref: 25264

domain: Bacteria

phylum: Verrucomicrobia

class: Opitutae

order: Puniceicoccales

family: Puniceicoccaceae

genus: Ruficoccus

species: Ruficoccus amylovorans

strain designation: CC-MHH0563

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
25264negative1.2-1.5 µm1.2-1.5 µmcoccus-shapedno
69480negative99.997

colony morphology

  • @ref: 25264
  • colony color: red
  • colony shape: circular
  • incubation period: 2 days
  • medium used: nutritient agar (NA)

Culture and growth conditions

culture medium

@refnamegrowth
25264nutritient agar (NA)yes
25264tryptic soy agar (TSA)yes
25264marine agar (MA)yes
25264nitrogen-free agaryes

culture temp

@refgrowthtypetemperaturerange
25264positivegrowth15-37
67770positivegrowth25mesophilic

culture pH

  • @ref: 25264
  • ability: positive
  • type: growth
  • pH: 6.0-8.0

Physiology and metabolism

oxygen tolerance

  • @ref: 25264
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.991

halophily

  • @ref: 25264
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0.0-3.0 %(w/v)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2526453424tween 20-hydrolysis
2526453423tween 40-hydrolysis
2526453426tween 80-hydrolysis
25264167632-oxobutanoate+oxidation
25264309162-oxoglutarate+oxidation
2526417925alpha-D-glucose+oxidation
2526473706bromosuccinate+oxidation
2526417057cellobiose+oxidation
2526415824D-fructose+oxidation
2526412936D-galactose+oxidation
2526417634D-glucose+assimilation
2526416024D-mannose+assimilation
2526416024D-mannose+oxidation
2526427605D-psicose+oxidation
2526423652dextrin+oxidation
2526417754glycerol+oxidation
2526430849L-arabinose+oxidation
2526418287L-fucose+oxidation
2526429985L-glutamate+oxidation
2526462345L-rhamnose+oxidation
2526424996lactate+oxidation
2526417716lactose+oxidation
2526417306maltose+oxidation
25264320055methyl beta-D-glucopyranoside+oxidation
2526451850methyl pyruvate+oxidation
2526475146monomethyl succinate+oxidation
2526417632nitrate+reduction
2526428017starch+hydrolysis
2526430031succinate+oxidation

metabolite production

  • @ref: 25264
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
25264acid phosphatase+3.1.3.2
25264alkaline phosphatase+3.1.3.1
25264alpha-fucosidase+3.2.1.51
25264alpha-galactosidase+3.2.1.22
25264alpha-glucosidase+3.2.1.20
25264beta-glucosidase+3.2.1.21
25264catalase+1.11.1.6
25264cystine arylamidase+3.4.11.3
25264cytochrome oxidase+1.9.3.1
25264DNase-
25264esterase (C 4)+
25264esterase Lipase (C 8)+
25264leucine arylamidase+3.4.11.1
25264naphthol-AS-BI-phosphohydrolase+
25264trypsin+3.4.21.4
25264urease-3.5.1.5
25264valine arylamidase+

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    25264C13:0 anteiso1.5
    25264C15:0 anteiso35.6
    25264C17:0 anteiso1.3
    25264C12:01.1
    25264C13:01.1
    25264C14:09.1
    25264C14:0 2OH3.6
    25264C16:08.7
    25264C16:0 3OH3.4
    25264C17:05
    25264C17:1ω8c2
    25264C18:08.7
    25264C18:1ω9c8.2
    25264C14:0 iso3.6
    25264C17:1 iso ω10c2.4
  • type of FA analysis: whole cell analysis
  • incubation medium: Nutrient agar (NA)
  • agar/liquid: agar
  • incubation temperature: 30
  • incubation time: 2
  • software version: Sherlock 6.0
  • library/peak naming table: RTSBA 6
  • system: MIS MIDI
  • instrument: Agilent 7890A
  • method/protocol: Sasser 1990
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture durationenrichment culture temperatureisolation procedure
25264fermenter located at a greenhouse facilityNational Chung Hsing University, TaichungTaiwanTWNAsianutrient agar (NA; Hi-Media)3 days30standard serial dilution-plating technique
67770Liquid from a fermenter at a greenhouse facility in National Chung Hsing Univ.TaichungTaiwanTWNAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Built environment

taxonmaps

  • @ref: 69479
  • File name: preview.99_101302.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1835;96_41074;97_52419;98_69185;99_101302&stattab=map
  • Last taxonomy: Ruficoccus amylovorans subclade
  • 16S sequence: KT751307
  • Sequence Identity:
  • Total samples: 678
  • soil counts: 41
  • aquatic counts: 560
  • animal counts: 58
  • plant counts: 19

Sequence information

16S sequences

  • @ref: 25264
  • description: Cerasicoccus sp. CC-MHH0563 16S ribosomal RNA gene, partial sequence
  • accession: KT751307
  • length: 1471
  • database: nuccore
  • NCBI tax ID: 1804625

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ruficoccus amylovorans strain JCM310661804625.3wgspatric1804625
66792Ruficoccus amylovorans JCM310662914226643draftimg1804625
67770Ruficoccus amylovorans JCM31066GCA_014230085contigncbi1804625

GC content

  • @ref: 25264
  • GC-content: 57.4
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno73no
motileyes58.782yes
gram-positiveno98.816yes
anaerobicno83.828no
aerobicno54.726no
halophileno76.47no
spore-formingno93.916no
glucose-utilyes86.176yes
flagellatedno81.864no
thermophileno81.698no
glucose-fermentno69.009no

External links

@ref: 25264

culture collection no.: BCRC 80918, JCM 31066

literature

  • topic: Phylogeny
  • Pubmed-ID: 27959775
  • title: Ruficoccus amylovorans gen. nov., sp. nov., an amylolytic and nitrate-reducing diazotroph of the family Puniceicoccaceae.
  • authors: Lin SY, Hameed A, Liu YC, Hsu YH, Hung MH, Lai WA, Young CC
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001723
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, Bioreactors/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nitrates/metabolism, Phospholipids/chemistry, *Phylogeny, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Verrucomicrobia/*classification/genetics/isolation & purification, 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
25264S. Y. H. Lin, A.,Liu, Y. C.,Hsu, Y. H.,Hung, M. H.,Lai, W. A.,Young, C. C.Ruficoccus amylovorans gen. nov., sp. nov., an amylolytic and nitrate-reducing diazotroph of the family Puniceicoccaceae10.1099/ijsem.0.001723IJSEM 67: 956-962 201727959775
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes