Pseudonocardia sediminis (DSM 45779, JCM 18540, YIM M13141)

Name: Pseudonocardia sediminis (DSM 45779, JCM 18540, YIM M13141)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24446

Type strain

Culture col. no. DSM 45779 JCM 18540 YIM M13141

NCBI tax ID(s) 1397368

Special Collections DSMZ JCM

History <- S.-K. Tang, Yunnan Univ., Yunnan Inst. Microbiol. (YIM), Kunming, China; YIM M13141 <- D.-F. Zhang, YIM S.-K. Tang YIM M13141.

Links

Pseudonocardia sediminis DSM 45779 is a bacterium that was isolated from marine sediment.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 404135

JCM 18540,DSM 45779

@ref 20215

Last LPSN update 2026-02-09 11:23:58

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Pseudonocardia

Species Pseudonocardia sediminis

Full scientific name Pseudonocardia sediminis Zhang et al. 2014

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	positive	93.093
125439	positive	97.8

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
20748	GPHF-MEDIUM (DSMZ Medium 553)		Medium recipe at MediaDive	Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
20748	positive	growth	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	aerobe	92.424
125439	obligate aerobe	98.9

Observation

67770

Observationquinones: MK-8(H₄)

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	threonine metabolism	100	10 of 10
66794	ethanol fermentation	100	2 of 2
66794	octane oxidation	100	3 of 3
66794	enterobactin biosynthesis	100	3 of 3
66794	acetate fermentation	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	IAA biosynthesis	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	resorcinol degradation	100	2 of 2
66794	3-chlorocatechol degradation	100	5 of 5
66794	starch degradation	100	10 of 10
66794	biotin biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	Entner Doudoroff pathway	100	10 of 10
66794	ethylmalonyl-CoA pathway	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	taurine degradation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	glycine betaine biosynthesis	100	5 of 5
66794	cyanate degradation	100	3 of 3
66794	ribulose monophosphate pathway	100	2 of 2
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	glycolate and glyoxylate degradation	100	6 of 6
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	aminopropanol phosphate biosynthesis	100	2 of 2
66794	pentose phosphate pathway	100	11 of 11
66794	adipate degradation	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	vitamin K metabolism	100	5 of 5
66794	glycogen metabolism	100	5 of 5
66794	phenol degradation	95	19 of 20
66794	phenylalanine metabolism	92.31	12 of 13
66794	leucine metabolism	92.31	12 of 13
66794	propionate fermentation	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	dTDPLrhamnose biosynthesis	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	heme metabolism	85.71	12 of 14
66794	citric acid cycle	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	vitamin B12 metabolism	85.29	29 of 34
66794	tryptophan metabolism	84.21	32 of 38
66794	purine metabolism	82.98	78 of 94
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	3-phenylpropionate degradation	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	glutathione metabolism	78.57	11 of 14
66794	d-mannose degradation	77.78	7 of 9
66794	methionine metabolism	76.92	20 of 26
66794	vitamin B1 metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	isoleucine metabolism	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	cyclohexanol degradation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	degradation of aromatic, nitrogen containing compounds	75	9 of 12
66794	glycogen biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	non-pathway related	73.68	28 of 38
66794	proline metabolism	72.73	8 of 11
66794	metabolism of disaccharids	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	aclacinomycin biosynthesis	71.43	5 of 7
66794	tyrosine metabolism	71.43	10 of 14
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	pyrimidine metabolism	71.11	32 of 45
66794	ascorbate metabolism	68.18	15 of 22
66794	oxidative phosphorylation	68.13	62 of 91
66794	lipid metabolism	67.74	21 of 31
66794	methane metabolism	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	sphingosine metabolism	66.67	4 of 6
66794	daunorubicin biosynthesis	66.67	6 of 9
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	cysteine metabolism	66.67	12 of 18
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	carotenoid biosynthesis	63.64	14 of 22
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	degradation of sugar alcohols	62.5	10 of 16
66794	carnitine metabolism	62.5	5 of 8
66794	alanine metabolism	62.07	18 of 29
66794	sulfate reduction	61.54	8 of 13
66794	urea cycle	61.54	8 of 13
66794	hydrogen production	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	bile acid biosynthesis, neutral pathway	58.82	10 of 17
66794	arginine metabolism	58.33	14 of 24
66794	propanol degradation	57.14	4 of 7
66794	degradation of sugar acids	56	14 of 25
66794	lysine metabolism	54.76	23 of 42
66794	phenylpropanoid biosynthesis	53.85	7 of 13
66794	pantothenate biosynthesis	50	3 of 6
66794	quinate degradation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	vitamin E metabolism	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	degradation of pentoses	50	14 of 28
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	degradation of hexoses	44.44	8 of 18
66794	lipid A biosynthesis	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	creatinine degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	coenzyme M biosynthesis	40	4 of 10
66794	vitamin B6 metabolism	36.36	4 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	allantoin degradation	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	polyamine pathway	30.43	7 of 23
66794	arachidonic acid metabolism	27.78	5 of 18
66794	cholesterol biosynthesis	27.27	3 of 11
66794	alginate biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	chlorophyll metabolism	22.22	4 of 18

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
20748	marine sediment	South China Sea (21° 23.2029 N 117° 37.2089 E) at a depth of 652 m	China	CHN	Asia	21.3867	117.62 21.3867/117.62
67770	Marine sediment from the South China Sea

Taxonmaps

69479

Global distribution of 16S sequence KF564279 (>99% sequence identity) for Pseudonocardia sediminis subclade from Microbeatlas

Aquatic Samples	32
Soil Samples	90
Animal Samples	278
Plant Samples	542
Total Samples	942

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
20748	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM421718v1 assembly for Pseudonocardia sediminis DSM 45779	contig	GCA_004217185	1397368.3	2806310546	1397368	72.29

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20748	Pseudonocardia sediminis strain YIM M13141 16S ribosomal RNA gene, complete sequence	KF564279	1541		1397368

GC content

@ref	GC-content (mol%)	Method
20748	73.1	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: Pseudonocardia sediminis DSM 45779
NCBI: GCA_004217185

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	51.80	no
125439	motility	BacteriaNetⓘ	no	73.60	no
125439	gram_stain	BacteriaNetⓘ	positive	97.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudonocardia sediminis strain DSM 45779
PATRIC: 1397368.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	93.09	no
125438	anaerobic	anaerobicⓘ	no	97.47	no
125438	spore-forming	spore-formingⓘ	yes	68.11	no
125438	aerobic	aerobicⓘ	yes	92.42	no
125438	thermophilic	thermophileⓘ	no	96.00	yes
125438	flagellated	motile2+ⓘ	no	85.97	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Advances in actinomycete research: an ActinoBase review of 2019.	Prudence SMM, Addington E, Castano-Espriu L, Mark DR, Pintor-Escobar L, Russell AH, McLean TC.	Microbiology (Reading)	10.1099/mic.0.000944	2020
Phylogeny	Pseudonocardia sediminis sp. nov., isolated from marine sediment.	Zhang DF, Jiang Z, Li L, Liu BB, Zhang XM, Tian XP, Zhang S, Li WJ	Int J Syst Evol Microbiol	10.1099/ijs.0.057844-0	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 )
#20748	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45779
#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 )
#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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Pseudonocardia sediminis (DSM 45779, JCM 18540, YIM M13141)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Observation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004217185

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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