Ruficoccus amylovorans (BCRC 80918, JCM 31066, CC-MHH0563)

Name: Ruficoccus amylovorans (BCRC 80918, JCM 31066, CC-MHH0563)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133402

Type strain

Strain Designation CC-MHH0563

Culture col. no. BCRC 80918 JCM 31066 CC-MHH0563

NCBI tax ID(s) 1804625

Special Collections JCM Literature strains

History C.-C. Young; Natl. Chung Hsing Univ., Taiwan; CC-MHH0563.

Links

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

Gram-negative coccus-shaped colony-forming aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 27253

BCRC 80918,JCM 31066

@ref 20215

Last LPSN update 2026-02-09 11:31:56

Domain Bacteria

Phylum Verrucomicrobiota

Class Opitutia

Order Puniceicoccales

Family Cerasicoccaceae

Genus Ruficoccus

Species Ruficoccus amylovorans

Full scientific name Ruficoccus amylovorans Lin et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
25264	negative	1.2-1.5 µm	1.2-1.5 µm	coccus-shaped
125438	negative					94

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
25264	red	circular	2 days	nutritient agar (NA)

Culture and growth conditions

Culture medium

@ref	Name	Growth
25264	nutritient agar (NA)
25264	tryptic soy agar (TSA)
25264	marine agar (MA)
25264	nitrogen-free agar

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
25264	positive	growth	15-37
67770	positive	growth	25	mesophilic

Culture pH

@ref	Ability	Type	PH
25264	positive	growth	6.0-8.0

Physiology and metabolism

Oxygen tolerance

25264

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		95.1

Halophily

@ref	Salt	Growth	Tested relation	Concentration
25264	NaCl	positive	growth	0.0-3.0 %(w/v)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
25264	16763 ChEBI	2-oxobutanoate	+	oxidation
25264	30916 ChEBI	2-oxoglutarate	+	oxidation
25264	17925 ChEBI	alpha-D-glucose	+	oxidation
25264	73706 ChEBI	bromosuccinate	+	oxidation
25264	17057 ChEBI	cellobiose	+	oxidation
25264	15824 ChEBI	D-fructose	+	oxidation
25264	12936 ChEBI	D-galactose	+	oxidation
25264	17634 ChEBI	D-glucose	+	assimilation
25264	16024 ChEBI	D-mannose	+	assimilation
25264	16024 ChEBI	D-mannose	+	oxidation
25264	27605 ChEBI	D-psicose	+	oxidation
25264	23652 ChEBI	dextrin	+	oxidation
25264	17754 ChEBI	glycerol	+	oxidation
25264	30849 ChEBI	L-arabinose	+	oxidation
25264	18287 ChEBI	L-fucose	+	oxidation
25264	29985 ChEBI	L-glutamate	+	oxidation
25264	62345 ChEBI	L-rhamnose	+	oxidation
25264	24996 ChEBI	lactate	+	oxidation
25264	17716 ChEBI	lactose	+	oxidation
25264	17306 ChEBI	maltose	+	oxidation
25264	320055 ChEBI	methyl beta-D-glucopyranoside	+	oxidation
25264	51850 ChEBI	methyl pyruvate	+	oxidation
25264	75146 ChEBI	monomethyl succinate	+	oxidation
25264	17632 ChEBI	nitrate	+	reduction
25264	28017 ChEBI	starch	+	hydrolysis
25264	30031 ChEBI	succinate	+	oxidation
25264	53424 ChEBI	tween 20	-	hydrolysis
25264	53423 ChEBI	tween 40	-	hydrolysis
25264	53426 ChEBI	tween 80	-	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite	Production
25264	35581 ChEBI	indole

Enzymes

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

Fatty acid profile

Metadata FA analysis

@ref

25264

Fatty acid	Percentage
C15:0 anteiso	35.6
C14:0	9.1
C16:0	8.7
C18:0	8.7
C18:1ω9c	8.2
C17:0	5
C14:0 iso	3.6
C14:0 2OH	3.6
C16:0 3OH	3.4
C17:1 iso ω10c	2.4
C17:1ω8c	2
C13:0 anteiso	1.5
C17:0 anteiso	1.3
C13:0	1.1
C12:0	1.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Engineered	#Built environment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture duration	Enrichment culture temperature	Isolation procedure
25264	fermenter located at a greenhouse facility	National Chung Hsing University, Taichung	Taiwan, Province of China	TWN	Asia	nutrient agar (NA; Hi-Media)	3 days	30	standard serial dilution-plating technique
67770	Liquid from a fermenter at a greenhouse facility in National Chung Hsing Univ.	Taichung	Taiwan, Province of China	TWN	Asia

Taxonmaps

69479

Global distribution of 16S sequence KT751307 (>99% sequence identity) for Ruficoccus amylovorans subclade from Microbeatlas

Aquatic Samples	560
Soil Samples	41
Animal Samples	58
Plant Samples	19
Total Samples	678

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM1423008v1 assembly for Ruficoccus amylovorans JCM31066	contig	GCA_014230085	1804625.3	2914226643	1804625	60.14

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
25264	Ruficoccus amylovorans strain CC-MHH0563 16S ribosomal RNA gene, partial sequence	KT751307	1471		1804625

GC content

@ref	GC-content (mol%)	Method
25264	57.4	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Ruficoccus amylovorans JCM31066
NCBI: GCA_014230085

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.10	no
125439	motility	BacteriaNetⓘ	yes	64.40	no
125439	gram_stain	BacteriaNetⓘ	negative	87.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative aerobe	62.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Ruficoccus amylovorans strain JCM31066
PATRIC: 1804625.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.00	yes
125438	anaerobic	anaerobicⓘ	no	79.23	yes
125438	spore-forming	spore-formingⓘ	no	85.62	no
125438	aerobic	aerobicⓘ	yes	65.69	yes
125438	thermophilic	thermophileⓘ	no	90.32	yes
125438	flagellated	motile2+ⓘ	yes	50.34	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Rubellicoccus peritrichatus gen. nov., sp. nov., isolated from crustose coralline algae in a coral aquarium.	Luo J, Li J, Wang C, Li M, Hu S, Lu K, Wang G.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006325	2024
Phylogeny	Ruficoccus amylovorans gen. nov., sp. nov., an amylolytic and nitrate-reducing diazotroph of the family Puniceicoccaceae.	Lin SY, Hameed A, Liu YC, Hsu YH, Hung MH, Lai WA, Young CC	Int J Syst Evol Microbiol	10.1099/ijsem.0.001723	2017

References

#20215	Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#25264	S. 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 Puniceicoccaceae. IJSEM 67: 956 - 962 2017 ( DOI 10.1099/ijsem.0.001723 , PubMed 27959775 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#69479	João 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 beta .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Ruficoccus amylovorans (BCRC 80918, JCM 31066, CC-MHH0563)

Name and taxonomic classification