Cite this strain

"Paracoccus siganidrum" (DSM 26381, CCTCC AB 2012865, M26)

BacDive ID 24492

Type strain

Strain Designation M26

Culture col. no. DSM 26381 CCTCC AB 2012865 M26

NCBI tax ID(s) 1276757

Special Collections DSMZ

History <- Y. Liu, Guangdong Ocean Univ., College of Food Science and Technol., China; M26 <- W. Shi

Links

"Paracoccus siganidrum" M26 is a mesophilic prokaryote that was isolated from gastrointestinal tract of the fish Siganus fuscescens.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 404292

DSM 26381

@ref 20215

Last LPSN update 2026-02-09 11:23:59

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Paracoccaceae

Genus Paracoccus

Species "Paracoccus siganidrum"

Full scientific name Paracoccus siganidrum Liu et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	98
125439	negative	96.3

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20720	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)		Medium recipe at MediaDive	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
20720	CASO AGAR (MERCK 105458) (DSMZ Medium 220)		Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
20720	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.1

Spore formation

@ref	Spore formation	Confidence
125438		90.65
125439		96.1

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	quinate degradation	100	2 of 2
66794	glycogen biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	allantoin degradation	100	9 of 9
66794	octane oxidation	100	3 of 3
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	ethanol fermentation	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	sulfopterin metabolism	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	Entner Doudoroff pathway	100	10 of 10
66794	enterobactin biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	acetate fermentation	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	aerobactin biosynthesis	100	1 of 1
66794	photosynthesis	100	14 of 14
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	biotin biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	vitamin B1 metabolism	92.31	12 of 13
66794	leucine metabolism	92.31	12 of 13
66794	phenylalanine metabolism	92.31	12 of 13
66794	proline metabolism	90.91	10 of 11
66794	pentose phosphate pathway	90.91	10 of 11
66794	propionate fermentation	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	vitamin B12 metabolism	88.24	30 of 34
66794	citric acid cycle	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	glutathione metabolism	85.71	12 of 14
66794	urea cycle	84.62	11 of 13
66794	NAD metabolism	83.33	15 of 18
66794	purine metabolism	82.98	78 of 94
66794	alanine metabolism	82.76	24 of 29
66794	pyrimidine metabolism	82.22	37 of 45
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	gallate degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	3-chlorocatechol degradation	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	d-mannose degradation	77.78	7 of 9
66794	methionine metabolism	76.92	20 of 26
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	butanoate fermentation	75	3 of 4
66794	arginine metabolism	75	18 of 24
66794	ketogluconate metabolism	75	6 of 8
66794	degradation of sugar alcohols	75	12 of 16
66794	CMP-KDO biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	tryptophan metabolism	73.68	28 of 38
66794	flavin biosynthesis	73.33	11 of 15
66794	vitamin B6 metabolism	72.73	8 of 11
66794	oxidative phosphorylation	72.53	66 of 91
66794	histidine metabolism	72.41	21 of 29
66794	tyrosine metabolism	71.43	10 of 14
66794	lysine metabolism	71.43	30 of 42
66794	heme metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	sulfate reduction	69.23	9 of 13
66794	degradation of sugar acids	68	17 of 25
66794	degradation of pentoses	67.86	19 of 28
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	methane metabolism	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	3-phenylpropionate degradation	66.67	10 of 15
66794	phenol degradation	65	13 of 20
66794	non-pathway related	63.16	24 of 38
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	lipid metabolism	61.29	19 of 31
66794	degradation of hexoses	61.11	11 of 18
66794	cysteine metabolism	61.11	11 of 18
66794	myo-inositol biosynthesis	60	6 of 10
66794	creatinine degradation	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	vitamin K metabolism	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	isoprenoid biosynthesis	57.69	15 of 26
66794	propanol degradation	57.14	4 of 7
66794	metabolism of disaccharids	54.55	6 of 11
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	glycine metabolism	50	5 of 10
66794	kanosamine biosynthesis II	50	1 of 2
66794	coenzyme M biosynthesis	50	5 of 10
66794	toluene degradation	50	2 of 4
66794	ascorbate metabolism	50	11 of 22
66794	lactate fermentation	50	2 of 4
66794	androgen and estrogen metabolism	50	8 of 16
66794	resorcinol degradation	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	polyamine pathway	47.83	11 of 23
66794	nitrate assimilation	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	starch degradation	40	4 of 10
66794	lipoate biosynthesis	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	cellulose degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	carnitine metabolism	37.5	3 of 8
66794	d-xylose degradation	36.36	4 of 11
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	alginate biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	daunorubicin biosynthesis	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Host	#Fishes
#Host Body-Site	#Gastrointestinal tract

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
20720	gastrointestinal tract of the fish Siganus fuscescens	Siganus fuscescens	Guangdong province, Zhanjiang port (N21° 9', E110°17')	China	CHN	Asia	21.15	110.283 21.15/110.283

Taxonmaps

69479

Global distribution of 16S sequence JX398976 (>99% sequence identity) for Paracoccus siganidrum from Microbeatlas

Aquatic Samples	66
Soil Samples	15
Animal Samples	37
Plant Samples	2
Total Samples	120

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM370956v1 assembly for Paracoccus siganidrum M26	contig	GCA_003709565	1276757.4	2834594880	1276757	55.28
66792	ASM359483v1 assembly for Paracoccus siganidrum DSM 26381	contig	GCA_003594835	1276757.3		1276757	21.88

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20720	Paracoccus siganidrum strain M26 16S ribosomal RNA gene, partial sequence	JX398976	1422		1276757

GC content

@ref	GC-content (mol%)	Method
20720	64.3	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: Paracoccus siganidrum M26
NCBI: GCA_003709565

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.10	no
125439	gram_stain	BacteriaNetⓘ	negative	96.30	no
125439	motility	BacteriaNetⓘ	yes	56.70	no
125439	spore_formation	BacteriaNetⓘ	no	96.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paracoccus siganidrum strain DSM 26381
PATRIC: 1276757.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.00	no
125438	anaerobic	anaerobicⓘ	no	94.85	no
125438	spore-forming	spore-formingⓘ	no	90.65	no
125438	aerobic	aerobicⓘ	yes	84.82	no
125438	thermophilic	thermophileⓘ	no	98.00	yes
125438	flagellated	motile2+ⓘ	no	54.75	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Paracoccus siganidrum sp. nov., isolated from fish gastrointestinal tract.	Liu Y, Xie QY, Hong K, Li L, Zhao YM, Tang YL, An JY, Zhu PP, Xu CH	Antonie Van Leeuwenhoek	10.1007/s10482-013-9894-4	2013

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 )
#20720	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26381
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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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"Paracoccus siganidrum" (DSM 26381, CCTCC AB 2012865, M26)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_003709565

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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