Name: Ruficoccus amylovorans CC-MHH0563
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133402

Type strain:

Species: Ruficoccus amylovorans

Strain Designation: CC-MHH0563

Culture col. no.: BCRC 80918, JCM 31066

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

NCBI tax ID(s): 1804625 (species)

Section

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.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Verrucomicrobiota*
	Class	*Opitutia*
	Order	*Puniceicoccales*
	Family	*Puniceicoccaceae*
	Genus	*Ruficoccus*
	Species	**Ruficoccus amylovorans**
	Full Scientific Name (LPSN)	Ruficoccus amylovorans Lin et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #25264]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.997

[Ref.: #25264]	Cell length	1.2-1.5 µm

[Ref.: #25264]	Cell width	1.2-1.5 µm

[Ref.: #25264]	Cell shape	coccus-shaped

[Ref.: #25264]	Motility	no

[Ref.: #25264]	Colony color	red
[Ref.: #25264]	Colony shape	circular
[Ref.: #25264]	Incubation period	2 days
[Ref.: #25264]	Cultivation medium used	nutritient agar (NA)

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25264]

Culture medium

nutritient agar (NA)

[Ref.: #25264]

Culture medium growth

[Ref.: #25264]

Culture medium

tryptic soy agar (TSA)

[Ref.: #25264]

Culture medium growth

[Ref.: #25264]

Culture medium

marine agar (MA)

[Ref.: #25264]

Culture medium growth

[Ref.: #25264]

Culture medium

nitrogen-free agar

[Ref.: #25264]

Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #25264]			growth	15-37 °C
[Ref.: #67770]			growth	25 °C

[Ref.: #67770]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #25264]			growth	6.0-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25264]

Oxygen tolerance

aerobe

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.991

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25264]		NaCl		growth	0.0-3.0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25264]	2-oxobutanoate ChEBI	+	oxidation
[Ref.: #25264]	2-oxoglutarate ChEBI	+	oxidation
[Ref.: #25264]	alpha-D-glucose ChEBI	+	oxidation
[Ref.: #25264]	bromosuccinate ChEBI	+	oxidation
[Ref.: #25264]	cellobiose ChEBI	+	oxidation
[Ref.: #25264]	D-fructose ChEBI	+	oxidation
[Ref.: #25264]	D-galactose ChEBI	+	oxidation
[Ref.: #25264]	D-glucose ChEBI	+	assimilation
[Ref.: #25264]	D-mannose ChEBI	+	assimilation
[Ref.: #25264]	D-mannose ChEBI	+	oxidation
[Ref.: #25264]	D-psicose ChEBI	+	oxidation
[Ref.: #25264]	dextrin ChEBI	+	oxidation
[Ref.: #25264]	glycerol ChEBI	+	oxidation
[Ref.: #25264]	L-arabinose ChEBI	+	oxidation
[Ref.: #25264]	L-fucose ChEBI	+	oxidation
[Ref.: #25264]	L-glutamate ChEBI	+	oxidation
[Ref.: #25264]	L-rhamnose ChEBI	+	oxidation
[Ref.: #25264]	lactate ChEBI	+	oxidation
[Ref.: #25264]	lactose ChEBI	+	oxidation
[Ref.: #25264]	maltose ChEBI	+	oxidation
[Ref.: #25264]	methyl beta-D-glucopyranoside ChEBI	+	oxidation
[Ref.: #25264]	methyl pyruvate ChEBI	+	oxidation
[Ref.: #25264]	monomethyl succinate ChEBI	+	oxidation
[Ref.: #25264]	nitrate ChEBI	+	reduction
[Ref.: #25264]	starch ChEBI	+	hydrolysis
[Ref.: #25264]	succinate ChEBI	+	oxidation
[Ref.: #25264]	tween 20 ChEBI	-	hydrolysis
[Ref.: #25264]	tween 40 ChEBI	-	hydrolysis
[Ref.: #25264]	tween 80 ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #25264]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #25264]	acid phosphatase	+	3.1.3.2
[Ref.: #25264]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25264]	alpha-fucosidase	+	3.2.1.51
[Ref.: #25264]	alpha-galactosidase	+	3.2.1.22
[Ref.: #25264]	alpha-glucosidase	+	3.2.1.20
[Ref.: #25264]	beta-glucosidase	+	3.2.1.21
[Ref.: #25264]	catalase	+	1.11.1.6
[Ref.: #25264]	cystine arylamidase	+	3.4.11.3
[Ref.: #25264]	cytochrome oxidase	+	1.9.3.1
[Ref.: #25264]	DNase	-
[Ref.: #25264]	esterase (C 4)	+
[Ref.: #25264]	esterase Lipase (C 8)	+
[Ref.: #25264]	leucine arylamidase	+	3.4.11.1
[Ref.: #25264]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #25264]	trypsin	+	3.4.21.4
[Ref.: #25264]	urease	-	3.5.1.5
[Ref.: #25264]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[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

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #25264]	Sample type/isolated from	fermenter located at a greenhouse facility
[Ref.: #25264]	Geographic location (country and/or sea, region)	National Chung Hsing University, Taichung
[Ref.: #25264]	Country	Taiwan
[Ref.: #25264]	Country ISO 3 Code	TWN
[Ref.: #25264]	Continent	Asia
[Ref.: #25264]	Enrichment culture	nutrient agar (NA; Hi-Media)
[Ref.: #25264]	Enrichment culture duration	3 days
[Ref.: #25264]	Enrichment culture temperature	30 ̊C
[Ref.: #25264]	Isolation/enrichment procedure	standard serial dilution-plating technique

[Ref.: #67770]	Sample type/isolated from	Liquid from a fermenter at a greenhouse facility in National Chung Hsing Univ.
[Ref.: #67770]	Geographic location (country and/or sea, region)	Taichung
[Ref.: #67770]	Country	Taiwan
[Ref.: #67770]	Country ISO 3 Code	TWN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered

#Built environment

What are isolation sources categories?

[Ref.: #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

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #25264]	Cerasicoccus sp. CC-MHH0563 16S ribosomal RNA gene, partial sequence	KT751307	1471	GenBank	1804625 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Ruficoccus amylovorans JCM31066	GCA_014230085	contig	GenBank	1804625 tax ID
[Ref.: #66792]	Ruficoccus amylovorans strain JCM31066	1804625.3	wgs	PATRIC	1804625 tax ID	*
[Ref.: #66792]	Ruficoccus amylovorans JCM31066	2914226643	draft	JGI IMG/M	1804625 tax ID	*

[Ref.: #25264]

GC-content

57.4 mol%

high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Ruficoccus amylovorans strain JCM31066 PATRIC: 1804625.3
[Ref.: #69481]	spore-forming	no	73	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Ruficoccus amylovorans strain JCM31066 PATRIC: 1804625.3
[Ref.: #69480]	motile	yes	58.782	yes
[Ref.: #69480]	gram-positive	no	98.816	yes
[Ref.: #69480]	anaerobic	no	83.828	no
[Ref.: #69480]	aerobic	no	54.726	no
[Ref.: #69480]	halophile	no	76.47	no
[Ref.: #69480]	spore-forming	no	93.916	no
[Ref.: #69480]	glucose-util	yes	86.176	yes
[Ref.: #69480]	flagellated	no	81.864	no
[Ref.: #69480]	thermophile	no	81.698	no
[Ref.: #69480]	glucose-ferment	no	69.009	no

Availability in culture collections External links

[Ref.: #25264]

Culture collection no.

BCRC 80918, JCM 31066

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

* These data were automatically processed and therefore are not curated

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Ruficoccus amylovorans strain JCM31066

Ruficoccus amylovorans strain JCM31066

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