Hyphococcus luteus (MCCC 1K03432, KCTC 62156, SY-3-19)

Name: Hyphococcus luteus (MCCC 1K03432, KCTC 62156, SY-3-19)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159701

Type strain

Strain Designation SY-3-19

Culture col. no. MCCC 1K03432 KCTC 62156 SY-3-19

NCBI tax ID(s) 2058213

Special Collections KCTC Literature strains

History <- Xiao- Yun Yu, Zhejiang Univ.

Links

Hyphococcus luteus SY-3-19 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from surface water sample.

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

Name and taxonomic classification

SI-ID 27848

KCTC 62156

@ref 20215

Last LPSN update 2026-02-09 11:38:43

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order "Parvularculales"

Family "Parvularculaceae"

Genus Hyphococcus

Species Hyphococcus luteus

Full scientific name Hyphococcus luteus Ye et al. 2025

Synonyms (1)

Marinicaulis flavus

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
66565	negative	0.5-1 µm		coccus-shaped
66565	negative			ovoid-shaped
66565	negative	0.5-0.8 µm	0.3-0.7 µm	rod-shaped
66565	negative	2-5 µm		spiral-shaped
66565	negative	2-5 µm		curved-shaped
125439	negative				99.5

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
66565	0.5-1 mm	yellow	circular	5 days	Marine agar (MA) 2216

Culture and growth conditions

Culture medium

@ref	Name	Growth
66565	Marine agar (MA) 2216

Culture temp

@ref	Growth	Type	Temperature (°C)
66565	positive	optimum	28
66565	positive	growth	4-40
67771	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
66565	positive	optimum	6.5-7.5
66565	positive	growth	5-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
66565	aerobe
67771	aerobe

Spore formation

@ref	Spore formation	Confidence
66565
125439		98.8

Halophily

@ref	Salt	Growth	Tested relation	Concentration
66565	NaCl	positive	growth	0.5-16 %(w/v)
66565	NaCl	positive	optimum	4 %(w/v)

Observation

@ref	Observation
66565	Cells have three different morphologies with one to three flagella including: (1) coccoid-shaped or ovoid-shaped with one to six prosthecates; (2) short rod- or rod-shaped with no to one prosthecate; (3) spiral-shaped or curved rod-shaped with no prosthecate
66565	Cells are flocculated in marine broth 2216

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
66565	62064 ChEBI	2,3-butanediol	+	respiration
66565	64552 ChEBI	2-hydroxybutyrate	+	respiration
66565	16763 ChEBI	2-oxobutanoate	+	respiration
66565	16810 ChEBI	2-oxoglutarate	-	respiration
66565	28644 ChEBI	2-oxopentanoate	+	respiration
66565	37054 ChEBI	3-hydroxybutyrate	+	respiration
66565	18240 ChEBI	4-hydroxy-L-proline	+	respiration
66565	16724 ChEBI	4-hydroxybutyrate	-	respiration
66565	18101 ChEBI	4-hydroxyphenylacetic acid	-	respiration
66565	16411 ChEBI	acetic acid	+	respiration
66565	40585 ChEBI	alpha-cyclodextrin	-	respiration
66565	17925 ChEBI	alpha-D-glucose	+	respiration
66565	73706 ChEBI	bromosuccinate	+	respiration
66565	85146 ChEBI	carboxymethylcellulose	-	hydrolysis
66565	17057 ChEBI	cellobiose	+	respiration
66565	16383 ChEBI	cis-aconitate	-	respiration
66565	53258 ChEBI	citric acid	+	respiration
66565	15570 ChEBI	D-alanine	-	respiration
66565	18333 ChEBI	D-arabitol	-	respiration
66565	15824 ChEBI	D-fructose	+	respiration
66565	15895 ChEBI	D-galactonic acid lactone	+	respiration
66565	12936 ChEBI	D-galactose	-	respiration
66565	18024 ChEBI	D-galacturonic acid	+	respiration
66565	30612 ChEBI	D-glucarate	+	respiration
66565	8391 ChEBI	D-gluconate	-	respiration
66565	17784 ChEBI	D-glucosaminic acid	+	respiration
66565	14314 ChEBI	D-glucose 6-phosphate	-	respiration
66565	15748 ChEBI	D-glucuronate	+	respiration
66565	16899 ChEBI	D-mannitol	-	respiration
66565	16024 ChEBI	D-mannose	+	respiration
66565	27605 ChEBI	D-psicose	+	respiration
66565	16523 ChEBI	D-serine	+	respiration
66565	17924 ChEBI	D-sorbitol	-	respiration
66565	23652 ChEBI	dextrin	-	respiration
66565	17126 ChEBI	DL-carnitine	-	respiration
66565	17113 ChEBI	erythritol	-	respiration
66565	16000 ChEBI	ethanolamine	+	respiration
66565	15740 ChEBI	formate	+	respiration
66565	16865 ChEBI	gamma-aminobutyric acid	+	respiration
66565	5291 ChEBI	gelatin	-	hydrolysis
66565	28066 ChEBI	gentiobiose	-	respiration
66565	17234 ChEBI	glucose	-	fermentation
66565	17234 ChEBI	glucose	+	fermentation
66565	29042 ChEBI	glucose 1-phosphate	+	respiration
66565	32323 ChEBI	glucuronamide	+	respiration
66565	17754 ChEBI	glycerol	+	respiration
66565	14336 ChEBI	glycerol 1-phosphate	+	respiration
66565	28087 ChEBI	glycogen	+	respiration
66565	73804 ChEBI	glycyl L-aspartic acid	+	respiration
66565	73784 ChEBI	glycyl-L-glutamate	-	respiration
66565	17596 ChEBI	inosine	-	respiration
66565	17240 ChEBI	itaconate	+	respiration
66565	21217 ChEBI	L-alaninamide	-	respiration
66565	16977 ChEBI	L-alanine	+	respiration
66565	73786 ChEBI	L-alanylglycine	+	respiration
66565	30849 ChEBI	L-arabinose	+	respiration
66565	17196 ChEBI	L-asparagine	+	respiration
66565	29991 ChEBI	L-aspartate	+	respiration
66565	18287 ChEBI	L-fucose	-	respiration
66565	29985 ChEBI	L-glutamate	+	respiration
66565	15971 ChEBI	L-histidine	+	respiration
66565	15603 ChEBI	L-leucine	+	respiration
66565	15729 ChEBI	L-ornithine	+	respiration
66565	17295 ChEBI	L-phenylalanine	-	respiration
66565	17203 ChEBI	L-proline	+	respiration
66565	18183 ChEBI	L-pyroglutamic acid	+	respiration
66565	62345 ChEBI	L-rhamnose	+	respiration
66565	17115 ChEBI	L-serine	+	respiration
66565	16857 ChEBI	L-threonine	+	respiration
66565	24996 ChEBI	lactate	+	respiration
66565	17716 ChEBI	lactose	-	respiration
66565	6359 ChEBI	lactulose	-	respiration
66565	15792 ChEBI	malonate	+	respiration
66565	17306 ChEBI	maltose	+	respiration
66565	28053 ChEBI	melibiose	-	respiration
66565	320055 ChEBI	methyl beta-D-glucopyranoside	-	respiration
66565	51850 ChEBI	methyl pyruvate	+	respiration
66565	75146 ChEBI	monomethyl succinate	+	respiration
66565	17268 ChEBI	myo-inositol	-	respiration
66565	28800 ChEBI	N-acetylgalactosamine	+	respiration
66565	59640 ChEBI	N-acetylglucosamine	+	respiration
66565	17632 ChEBI	nitrate	+	reduction
66565	50048 ChEBI	phenylethylamine	+	respiration
66565	17272 ChEBI	propionate	+	respiration
66565	17148 ChEBI	putrescine	+	respiration
66565	26490 ChEBI	quinate	+	respiration
66565	16634 ChEBI	raffinose	+	respiration
66565	15963 ChEBI	ribitol	-	respiration
66565	41865 ChEBI	sebacic acid	+	respiration
66565		skimmed milk	-	hydrolysis
66565	26710 ChEBI	sodium chloride	+	required for growth
66565	28017 ChEBI	starch	-	hydrolysis
66565	143136 ChEBI	succinamate	+	respiration
66565	30031 ChEBI	succinate	+	respiration
66565	17992 ChEBI	sucrose	+	respiration
66565	17748 ChEBI	thymidine	-	respiration
66565	27082 ChEBI	trehalose	+	respiration
66565	32528 ChEBI	turanose	+	respiration
66565	53424 ChEBI	tween 20	+	hydrolysis
66565	53423 ChEBI	tween 40	+	hydrolysis
66565	53423 ChEBI	tween 40	+	respiration
66565	53425 ChEBI	tween 60	+	hydrolysis
66565	53426 ChEBI	tween 80	+	hydrolysis
66565	53426 ChEBI	tween 80	+	respiration
66565	16704 ChEBI	uridine	+	respiration
66565	27248 ChEBI	urocanic acid	-	respiration
66565	17151 ChEBI	xylitol	-	respiration

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.	Resistance conc.
66565	17698	chloramphenicol	30 µg (disc)
66565	48923	erythromycin		15 µg (disc)
66565	17833	gentamicin	10 µg (disc)
66565	6104	kanamycin	30 µg (disc)
66565	28077	rifampicin	5 µg (disc)
66565	17076	streptomycin	10 µg (disc)
66565	28001	vancomycin	30 µg (disc)

Metabolite production

@ref	Chebi-ID	Metabolite
66565	15688 ChEBI	acetoin
66565	16136 ChEBI	hydrogen sulfide
66565	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
66565	15688 ChEBI	acetoin	-
66565	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
66565	alpha-fucosidase	-	3.2.1.51
66565	alpha-galactosidase	-	3.2.1.22
66565	alpha-glucosidase	+	3.2.1.20
66565	alpha-mannosidase	-	3.2.1.24
66565	arginine dihydrolase	-	3.5.3.6
66565	beta-galactosidase	-	3.2.1.23
66565	beta-glucosidase	-	3.2.1.21
66565	beta-glucuronidase	-	3.2.1.31
66565	catalase	+	1.11.1.6
66565	chymotrypsin	-	3.4.4.5
66565	cystine arylamidase	-	3.4.11.3
66565	cytochrome oxidase	+	1.9.3.1
66565	esterase (C 4)	+
66565	lipase (C 14)	+
66565	N-acetyl-beta-glucosaminidase	-	3.2.1.52
66565	trypsin	+	3.4.21.4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Surface water

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture temperature	Isolation date	Isolation procedure
66565	surface water sample	2012-09-22	South China Sea	China	CHN	Asia	modified marine agar 2216	20	2016-01-12	standard dilution technique
67771	From sea water		Pacific Mariana Trench	China	CHN	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM294356v1 assembly for Hyphococcus luteus SY-3-19	contig	GCA_002943565	2058213.3	2786546860	2058213	74.68

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66565	Marinicaulis flavus strain SY-3-19 16S ribosomal RNA gene, partial sequence	KY861741	1424		2058213

GC content

@ref	GC-content (mol%)	Method
66565	60.9	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Marinicaulis flavus SY-3-19
NCBI: GCA_002943565

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.80	no
125439	motility	BacteriaNetⓘ	yes	53.10	no
125439	gram_stain	BacteriaNetⓘ	negative	99.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	71.90	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Validation List no. 223. Valid publication of new names and new combinations effectively published outside the IJSEM.	Oren A, Goker M.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006699	2025
Phylogeny	Marinicaulis aureum sp. nov., isolated from a culture of the green alga Ulva prolifera, and emended description of the genus Marinicaulis.	Wang Z, Zhang Z, Li C, Hu Z, Zhao H, Zhang Y	Antonie Van Leeuwenhoek	10.1007/s10482-018-1139-0	2018
Phylogeny	Marinicaulis flavus gen. nov., sp. nov., a novel stalked bacterium of the family Parvularculaceae.	Yu XY, Yu XD, Fu GY, Zhao Z, Shen X, Sun C, Wu M	Int J Syst Evol Microbiol	10.1099/ijsem.0.002795	2018

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 )
#66565	Xiao-Yun Yu, Xiao-Dong Yu, Ge-Yi Fu, Zhe Zhao, Xia Shen, Cong Sun, Min Wu: Marinicaulis flavus gen. nov., sp. nov., a novel stalked bacterium of the family Parvularculaceae. IJSEM 68: 2061 - 2067 2018 ( DOI 10.1099/ijsem.0.002795 , PubMed 29701576 )
#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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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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Hyphococcus luteus (MCCC 1K03432, KCTC 62156, SY-3-19)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_002943565

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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