Hoyosella subflava (DSM 45089, CGMCC 4.3532, JCM 17490)

Name: Hoyosella subflava (DSM 45089, CGMCC 4.3532, JCM 17490)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 8593

Type strain

Strain Designation DQS3-9A1

Culture col. no. DSM 45089 CGMCC 4.3532 JCM 17490 NBRC 109087 DQS3-9A1

NCBI tax ID(s) 639313

Special Collections DSMZ JCM Literature strains

History <- X.-L. Wu; DQS3-9A1 <- Y.-N. Wang <- Z.-Y. Lou CGMCC 4.3532 <-- Y.-N. Wang et al. DQS3-9A1.

Links

Hoyosella subflava DQS3-9A1 is an aerobe, Gram-positive, coccus-shaped bacterium that forms circular colonies and was isolated from oil-polluted saline soil.

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

Name and taxonomic classification

SI-ID 406859

NBRC 109087,JCM 17490,DSM 45089

@ref 20215

Last LPSN update 2026-02-09 11:19:44

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Mycobacteriales

Family Nocardiaceae

Genus Hoyosella

Species Hoyosella subflava

Full scientific name Hoyosella subflava (Wang et al. 2010) Hamada et al. 2016

Synonyms (1)

Amycolicicoccus subflavus

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
24974	positive	1.1-1.2 µm		coccus-shaped
29301	positive	0.975 µm	0.8 µm	coccus-shaped
125439	positive				91.3
125438					93

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
24974	cream	circular	2 days	BHI agar plate

Pigmentation

29301

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
12331	PEPTONE MEAT EXTRACT GLYCEROL AGAR (DSMZ Medium 250)	Medium recipe at MediaDive	Name: PEPTONE MEAT EXTRACT GLYCEROL AGAR (DSMZ Medium 250) Composition: Agar 20.0 g/l Proteose peptone no. 3 5.0 g/l Meat extract 3.0 g/l Glycerol Distilled water
12331	MYCOBACTERIUM MEDIUM (DSMZ Medium 219)	Medium recipe at MediaDive	Name: MYCOBACTERIUM MEDIUM (DSMZ Medium 219) Composition: Agar 20.0 g/l Na2HPO4 x 12 H2O 2.5 g/l Yeast extract 2.0 g/l Proteose peptone no. 3 2.0 g/l Casein peptone 2.0 g/l Sodium citrate 1.5 g/l KH2PO4 1.0 g/l MgSO4 x 7 H2O 0.6 g/l Tween 0.5 g/l Glycerol Distilled water
24974	BHI agar plate

Culture temp

@ref	Growth	Type	Temperature (°C)
12331	positive	growth	28
24974	positive	growth	20.0-37.0
24974	negative	growth	5.0-15.0
24974	negative	growth	45
24974	negative	growth	60
24974	positive	optimum	28.0-37.0
29301	positive	growth	15-42
29301	positive	optimum	37
67770	positive	growth	37

Culture pH

@ref	Ability	Type	PH	PH range
24974	positive	optimum	7.0-9.0
29301	positive	optimum	8
24974	positive	growth	7.0-11.0	alkaliphile
29301	positive	growth	06-11

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
24974	aerobe
29301	aerobe
125438	aerobe	90.837
125439	obligate aerobe	98.3

Spore formation

@ref	Spore formation
24974
29301

Halophily

@ref	Salt	Growth	Tested relation	Concentration
24974	NaCl	positive	growth	0.0-7.0 %(w/v)
24974	NaCl	positive	growth	10 %(w/v)
24974	NaCl		growth	15 %(w/v)
29301	NaCl	positive	growth	01-12 %
29301	NaCl	positive	optimum	8 %

Murein

@ref	Murein short key	Type
24974	A31	A1gamma m-Dpm-direct

Observation

67770

Observationquinones: MK-8, MK-7, MK-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29301	17057 ChEBI	cellobiose	+	carbon source
24974	15824 ChEBI	D-fructose	+	assimilation
24974	17634 ChEBI	D-glucose	-	assimilation
24974	16899 ChEBI	D-mannitol	-	assimilation
29301	23652 ChEBI	dextrin	+	carbon source
29301	33984 ChEBI	fucose	+	carbon source
29301	17234 ChEBI	glucose	+	carbon source
24974	30849 ChEBI	L-arabinose	-	assimilation
29301	25115 ChEBI	malate	+	carbon source
29301	17306 ChEBI	maltose	+	carbon source
29301	29864 ChEBI	mannitol	+	carbon source
29301	37684 ChEBI	mannose	+	carbon source
24974	17268 ChEBI	myo-inositol	-	assimilation
29301	17632 ChEBI	nitrate	+	reduction
29301	26271 ChEBI	proline	+	carbon source
29301	30911 ChEBI	sorbitol	+	carbon source
29301	30031 ChEBI	succinate	+	carbon source
29301	17992 ChEBI	sucrose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
29301	16136 ChEBI	hydrogen sulfide

Enzymes

@ref	Value	Activity	Ec
24974	acid phosphatase	+	3.1.3.2
24974	alkaline phosphatase	+	3.1.3.1
24974	alpha-chymotrypsin	-	3.4.21.1
24974	alpha-fucosidase	-	3.2.1.51
24974	alpha-galactosidase	-	3.2.1.22
24974	alpha-glucosidase	+	3.2.1.20
24974	alpha-mannosidase	-	3.2.1.24
24974	beta-galactosidase	-	3.2.1.23
24974	beta-glucosidase	+	3.2.1.21
24974	beta-glucuronidase	-	3.2.1.31
24974	catalase	+	1.11.1.6
24974	cystine arylamidase	-	3.4.11.3
24974	cytochrome oxidase	-	1.9.3.1
24974	esterase (C 4)	+
24974	esterase Lipase (C 8)	+
24974	leucine arylamidase	+	3.4.11.1
24974	lipase (C 14)	-
24974	N-acetyl-beta-glucosaminidase	-	3.2.1.52
24974	naphthol-AS-BI-phosphohydrolase	+
24974	trypsin	-	3.4.21.4
24974	valine arylamidase	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Contamination	#Oil (Fuel)
#Environmental	#Terrestrial	#Soil
#Condition	#Saline	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
12331	oil-polluted saline soil	Shengli Oilfield	China	CHN	Asia
67770	Saline soil contaminated with crude oil in the Daqing Oilfield		China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence EF564379 (>99% sequence identity) for Hoyosella from Microbeatlas

Aquatic Samples	567
Soil Samples	948
Animal Samples	1015
Plant Samples	155
Total Samples	2685

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
12331	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM21417v1 assembly for Hoyosella subflava DQS3-9A1	complete	GCA_000214175	443218.3	650716009	443218	91.54

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
12331	Amycolicicoccus subflavus DQS3-9A1 16S ribosomal RNA gene, partial sequence	EF564379	1486		443218

GC content

@ref	GC-content (mol%)	Method
12331	62.2
24974	62.2	genome sequence analysis
29301	60.04
67770	60.04	thermal denaturation, midpoint method (Tm)
67770	62.24	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Hoyosella subflava DQS3-9A1
IMG: 650716009

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	53.30	no
125439	motility	BacteriaNetⓘ	no	80.90	no
125439	gram_stain	BacteriaNetⓘ	positive	91.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Hoyosella subflava DQS3-9A1 DQS3-9A1
NCBI: GCA_000214175.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	88.63	yes
125438	anaerobic	anaerobicⓘ	no	99.32	yes
125438	aerobic	aerobicⓘ	yes	90.84	no
125438	spore-forming	spore-formingⓘ	no	60.54	yes
125438	thermophilic	thermophileⓘ	no	96.97	no
125438	flagellated	motile2+ⓘ	no	93.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Bioemulsification and Microbial Community Reconstruction in Thermally Processed Crude Oil.	Hu B, Zhao JY, Nie Y, Qin XY, Zhang KD, Xing JM, Wu XL	Microorganisms	10.3390/microorganisms9102054	2021
Phylogeny	Reclassification of Amycolicicoccus subflavus as Hoyosella subflava comb. nov. and emended descriptions of the genus Hoyosella and Hoyosella altamirensis.	Hamada M, Shibata C, Sakurai K, Hosoyama A, Oji S, Teramoto K, Tamura T	Int J Syst Evol Microbiol	10.1099/ijsem.0.001415	2016
Genetics	The genome of the moderate halophile Amycolicicoccus subflavus DQS3-9A1(T) reveals four alkane hydroxylation systems and provides some clues on the genetic basis for its adaptation to a petroleum environment.	Nie Y, Fang H, Li Y, Chi CQ, Tang YQ, Wu XL	PLoS One	10.1371/journal.pone.0070986	2013
Genetics	Complete genome sequence of Amycolicicoccus subflavus DQS3-9A1T, an actinomycete isolated from crude oil-polluted soil.	Cai M, Chen WM, Nie Y, Chi CQ, Wang YN, Tang YQ, Li GY, Wu XL	J Bacteriol	10.1128/JB.05388-11	2011
Phylogeny	Hoyosella suaedae sp. nov., a novel bacterium isolated from rhizosphere soil of Suaeda aralocaspica (Bunge) Freitag & Schutze.	Liu DF, Chen SQ, Wang HF, Xie YG, Gao R, Song JQ, Gao YL, Xiao M, Li QL, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.005117	2021
Phylogeny	Hoyosella rhizosphaerae sp. nov., a halotolerant actinobacterium isolated from rhizosphere soil of Suaeda salsa, and emended description of the genus Hoyosella.	Li XJ, Liu SW, Jiang ZK, Wu G, Sun CH	Int J Syst Evol Microbiol	10.1099/ijsem.0.001416	2016
Phylogeny	Amycolicicoccus subflavus gen. nov., sp. nov., an actinomycete isolated from a saline soil contaminated by crude oil.	Wang YN, Chi CQ, Cai M, Lou ZY, Tang YQ, Zhi XY, Li WJ, Wu XL, Du X	Int J Syst Evol Microbiol	10.1099/ijs.0.010546-0	2009

References

#12331	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45089
#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 )
#24974	M. S. Hamada, Chiyo,Sakurai, Kenta,Hosoyama, Akira,Oji, Syoko,Teramoto, Kanae,Tamura, Tomohiko: Reclassification of Amycolicicoccus subflavus as Hoyosella subflava comb. nov. and emended descriptions of the genus Hoyosella and Hoyosella altamirensis. IJSEM 66: 4711 - 4715 2016 ( DOI 10.1099/ijsem.0.001415 , PubMed 27514929 )
#25715	IJSEM 638 2010 ( DOI 10.1099/ijs.0.010546-0 , PubMed 19654348 )
#29301	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25715
#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 .
#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 )

Rate our new design

Content

About us

Hoyosella subflava (DSM 45089, CGMCC 4.3532, JCM 17490)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Murein

Observation

Metabolite utilization

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000214175

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media