Archive BacDiveID:10.13145/bacdive131292.20230509.8.1

Strain identifier

BacDive ID: 131292

Type strain:

Species: Paracoccus sediminis

Strain Designation: CMB17

Strain history: J. Pan CMB17.

NCBI tax ID(s): 1214787 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 22519

BacDive-ID: 131292

DSM-Number: 26170

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Paracoccus sediminis CMB17 is a mesophilic bacterium that was isolated from marine sediment.

NCBI tax id

NCBI tax id: 1214787
Matching level: species

strain history

@ref	history
22519	<- J. Pan, Zhejiang Univ., Hangzhou, China; CMB17 <- C. Sun
67770	J. Pan CMB17.

doi: 10.13145/bacdive131292.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Alphaproteobacteria
order: Rhodobacterales
family: Paracoccaceae
genus: Paracoccus
species: Paracoccus sediminis
full scientific name: Paracoccus sediminis Pan et al. 2014

@ref: 22519

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Paracoccus

species: Paracoccus sediminis

full scientific name: Paracoccus sediminis Pan et al. 2014

strain designation: CMB17

type strain: yes

Morphology

cell morphology

@ref	motility	confidence	gram stain
69480	no	96.68
69480		99.984	negative

Culture and growth conditions

culture medium

@ref: 22519
name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
growth: yes
link: https://mediadive.dsmz.de/medium/514
composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
22519	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

spore formation

@ref	spore formation	confidence
69481	no	100
69480	no	99.998

observation

@ref: 67770
observation: quinones: Q-10

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent	latitude	longitude
22519	marine sediment	East China Sea (125° 59' 24'' E 30° 58' 16'' N) at a depth of 70 m	China	CHN	Asia
67770	Marine sediment of the East China Sea (125° 59' 24" E 30° 58' 16" N) at a depth of 70 m					30.9711	125.99

isolation source categories

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

taxonmaps

@ref: 69479
File name: preview.99_63513.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_1674;97_7440;98_30411;99_63513&stattab=map
Last taxonomy: Paracoccus sediminis
16S sequence: JX126474
Sequence Identity:
Total samples: 178
soil counts: 8
aquatic counts: 56
animal counts: 51
plant counts: 63

Safety information

risk assessment

@ref: 22519
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 22519
description: Paracoccus sp. CMB17 16S ribosomal RNA gene, partial sequence
accession: JX126474
length: 1425
database: ena
NCBI tax ID: 1214787

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Paracoccus sediminis DSM 26170	GCA_900188295	contig	ncbi	1214787
66792	Paracoccus sediminis CMB17	GCA_004310385	contig	ncbi	1214787
66792	Paracoccus sediminis strain DSM 26170	1214787.3	wgs	patric	1214787
66792	Paracoccus sediminis DSM 26170	2724679705	draft	img	1214787

GC content

@ref: 22519
GC-content: 62.2
method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	no	75.163	no
gram-positive	no	97.675	no
anaerobic	no	98.623	no
aerobic	yes	87.786	no
halophile	no	79.909	no
spore-forming	no	97.166	no
thermophile	no	95.76	no
glucose-util	yes	90.036	no
flagellated	no	94.33	no
glucose-ferment	no	85.306	no

External links

@ref: 22519

culture collection no.: DSM 26170, CGMCC 1.12681, JCM 18467, BCRC 81082

straininfo link

@ref: 89734
straininfo: 405645

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	24812365	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	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Molecular Sequence Data, Pacific Ocean, Paracoccus/classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry	Genetics
Phylogeny	26296343	Paracoccus angustae sp. nov., isolated from soil.	Sun X, Luo P, Li M	Int J Syst Evol Microbiol	10.1099/ijsem.0.000440	2015	Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Paracoccus/classification/genetics/isolation & purification, Phospholipids/chemistry, Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistry	Genetics
Phylogeny	28758621	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	Air Microbiology, Bacterial Typing Techniques, Base Composition, Beijing, DNA, Bacterial/genetics, Fatty Acids/chemistry, Paracoccus/classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry	Transcriptome
Phylogeny	29722645	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	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/microbiology, Hydroxybutyrates, Natural Springs/microbiology, Nucleic Acid Hybridization, Paracoccus/classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, Pigmentation, Polyamines/chemistry, Polyesters, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Taiwan, Ubiquinone/analogs & derivatives/chemistry	Transcriptome
Phylogeny	30489238	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	Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastrodia/microbiology, Nucleic Acid Hybridization, Paracoccus/classification/isolation & purification, Phospholipids/chemistry, Phylogeny, Plant Tubers/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry	Transcriptome
Phylogeny	30888313	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	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Glycolipids/chemistry, Nucleic Acid Hybridization, Pacific Ocean, Paracoccus/classification/isolation & purification, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry	Transcriptome
Phylogeny	33388938	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	Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids, Lichens, Paracoccus/genetics, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA	Transcriptome
Phylogeny	34905098	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	Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Paracoccus/genetics, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage	Transcriptome

Reference

@id	authors	title	doi/url	catalogue
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	10.1099/ijsem.0.004332
22519	Curators of the DSMZ		https://www.dsmz.de/collection/catalogue/details/culture/DSM-26170	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (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)	https://diaspora-project.de/progress.html#genomes
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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	https://microbeatlas.org/
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)	https://diaspora-project.de/progress.html#genomes
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch	Predictions based on the model GenomeNet Sporulation v. 1	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	10.60712/SI-ID405645.1