Name: Paracoccus sediminis CMB17
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 131292

Type strain:

Species: Paracoccus sediminis

Strain Designation: CMB17

Culture col. no.: DSM 26170, CGMCC 1.12681, JCM 18467, BCRC 81082

Strain history: J. Pan CMB17.

NCBI tax ID(s): 1214787 (species)

SI-ID 405645

DSM 26170

Special Collections

DSMZ
JCM

Section

Paracoccus sediminis CMB17 is a Gram-negative bacterium that was isolated from marine sediment.

Gram-negative
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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Rhodobacterales*
	Family	*Paracoccaceae*
	Genus	*Paracoccus*
	Species	**Paracoccus sediminis**
	Full Scientific Name (LPSN)	Paracoccus sediminis Pan et al. 2014

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %98.494

Information on culture and growth conditions Culture and growth conditions

[Ref.: #22519]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #22519]

Culture medium growth

[Ref.: #22519]

Culture medium link

Medium recipe at MediaDive

[Ref.: #22519]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #22519]			growth	30 °C
[Ref.: #67770]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]

Ability of spore formation

no Confidence in %100

[Ref.: #67770]

Observation

quinones: Q-10

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

[Ref.: #22519]	Sample type/isolated from	marine sediment
[Ref.: #22519]	Geographic location (country and/or sea, region)	East China Sea (125° 59' 24'' E 30° 58' 16'' N) at a depth of 70 m
[Ref.: #22519]	Country	China
[Ref.: #22519]	Country ISO 3 Code	CHN
[Ref.: #22519]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Marine sediment of the East China Sea (125° 59' 24" E 30° 58' 16" N) at a depth of 70 m
[Ref.: #67770]	Geographic location	30.9711°/125.9900°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JX126474 (>99% sequence identity) for Paracoccus sediminis from Microbeatlas

Aquatic Samples	56
Soil Samples	8
Animal Samples	51
Plant Samples	63
Total Samples	178

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #22519]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #22519]	Paracoccus sp. CMB17 16S ribosomal RNA gene, partial sequence	JX126474	1425	GenBank ENA	1214787 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paracoccus sediminis DSM 26170	GCA_900188295	contig	GenBank ENA	1214787 tax ID	*
[Ref.: #66792]	Paracoccus sediminis CMB17	GCA_004310385	contig	GenBank ENA	1214787 tax ID	*
[Ref.: #66792]	Paracoccus sediminis strain DSM 26170	1214787.3	wgs	PATRIC	1214787 tax ID	*
[Ref.: #66792]	Paracoccus sediminis DSM 26170	2724679705	draft	JGI IMG/M	1214787 tax ID	*

[Ref.: #22519]

GC-content

62.2 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Paracoccus sediminis strain DSM 26170 PATRIC: 1214787.3
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paracoccus sediminis strain DSM 26170 PATRIC: 1214787.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98.494	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	98.287	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	88.349	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	84.722	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	97.94	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	59.095	no

Availability in culture collections External links

[Ref.: #22519]

Culture collection no.

DSM 26170, CGMCC 1.12681, JCM 18467, BCRC 81082

[Ref.: #89734]

SI-ID 405645

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Description of Paracoccus endophyticus sp. nov., isolated from Gastrodia elata Blume.	Zhang H, Li YQ, Xiao M, Fang BZ, Alkhalifah DHM, Hozzein WN, Rao MPN, Li WJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003142	2018	*
Phylogeny	Paracoccus aerius sp. nov., isolated from air.	Xue H, Piao CG, Guo MW, Wang LF, Li Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.001976	2017	*
Phylogeny	Paracoccus shandongensis sp. nov., Isolated from Activated Sludge.	Gong XF, Wang F, Meng D, Liu YL, Gu PF, Fan XY, Huang ZS, Du ZJ, Li Q	Curr Microbiol	10.1007/s00284-021-02705-4	2021	*
Phylogeny	Paracoccus lichenicola sp. nov., Isolated from Lichen.	Lang L, An DF, Jiang LQ, Li GD, Wang LS, Wang XY, Li QY, Jiang CL, Jiang Y	Curr Microbiol	10.1007/s00284-020-02321-8	2021	*
Phylogeny	Paracoccus subflavus sp. nov., isolated from Pacific Ocean sediment.	Zhang G, Jiao K, Xie F, Pei S, Jiang L	Int J Syst Evol Microbiol	10.1099/ijsem.0.003344	2019	*
Phylogeny	Paracoccus fontiphilus sp. nov., isolated from a freshwater spring.	Sheu SY, Hsieh TY, Young CC, Chen WM	Int J Syst Evol Microbiol	10.1099/ijsem.0.002793	2018	*
Phylogeny	Paracoccus angustae sp. nov., isolated from soil.	Sun X, Luo P, Li M	Int J Syst Evol Microbiol	10.1099/ijsem.0.000440	2015	*
Phylogeny	Paracoccus sediminis sp. nov., isolated from Pacific Ocean marine sediment.	Pan J, Sun C, Zhang XQ, Huo YY, Zhu XF, Wu M	Int J Syst Evol Microbiol	10.1099/ijs.0.051318-0	2014	*

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 )

#22519

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26170

#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 )

#89734

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID405645.1 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Paracoccus sediminis in external resources:
SILVA
BRENDA
PANGAEA
GBIF

Paracoccus sediminis strain DSM 26170

Paracoccus sediminis strain DSM 26170

Change proposal

Change proposal