Name: Pseudoclavibacter caeni MJ28
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 7481

Type strain:

Species: Pseudoclavibacter caeni

Strain Designation: MJ28, H17-1

Culture col. no.: DSM 26484, JCM 16921, KCTC 19773

Strain history: <- MK Kim, Seoul Women's Univ.

NCBI tax ID(s): 908846 (species)

SI-ID 398768

DSM 26484

Special Collections

Section

Pseudoclavibacter caeni MJ28 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from sludge of sewage disposal plant.

Gram-positive
rod-shaped
aerobe
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Microbacteriaceae*
	Genus	*Pseudoclavibacter*
	Species	**Pseudoclavibacter caeni**
	Full Scientific Name (LPSN)	Pseudoclavibacter caeni Srinivasan et al. 2012

Synonym

"Caespitibacter caeni"

Information on morphological and physiological properties Morphology

[Ref.: #30063]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %90.438

[Ref.: #30063]	Cell length	0.3-0.7 µm

[Ref.: #30063]	Cell width	0.2-0.3 µm

[Ref.: #30063]	Cell shape	rod-shaped

[Ref.: #30063]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %94.375

[Ref.: #18244]

Incubation period

2-3 days

[Ref.: #30063]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #18244]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #18244]

Culture medium growth

[Ref.: #18244]

Culture medium link

Medium recipe at MediaDive

[Ref.: #18244]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #18244]	growth	28 °C
[Ref.: #30063]	growth	20-42 °C
[Ref.: #30063]	optimum	30 °C
[Ref.: #67770]	growth	28 °C
[Ref.: #67771]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #30063]			optimum	7-7.5
[Ref.: #30063]			growth	4-8.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30063]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #30063]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30063]		NaCl		growth	0-6	%

[Ref.: #67770]

Observation

quinones: MK-9

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30063]	arabinose ChEBI	+	carbon source
[Ref.: #30063]	malate ChEBI	+	carbon source
[Ref.: #30063]	malonate ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30063]		acid phosphatase	+	3.1.3.2
[Ref.: #30063]		catalase	+	1.11.1.6

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

[Ref.: #18244]	Sample type/isolated from	sludge of sewage disposal plant
[Ref.: #18244]	Geographic location (country and/or sea, region)	Daejeon
[Ref.: #18244]	Country	Republic of Korea
[Ref.: #18244]	Country ISO 3 Code	KOR
[Ref.: #18244]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Sludge at the Daejeon sewage disposal plant
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From sludge, Daejeon sewage disposal plant
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Waste	#Water treatment plant
#Environmental	#Terrestrial	#Mud (Sludge)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HQ266601 (>99% sequence identity) for Pseudoclavibacter caeni subclade from Microbeatlas

Aquatic Samples	382
Soil Samples	97
Animal Samples	317
Plant Samples	58
Total Samples	854

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

[Ref.: #18244]

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.: #18244]	Pseudoclavibacter caeni strain MJ28 16S ribosomal RNA gene, partial sequence	HQ266601	1376	GenBank ENA	908846 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Pseudoclavibacter caeni DSM 26484	GCA_013410595	contig	GenBank ENA	908846 tax ID
[Ref.: #67770]	Pseudoclavibacter caeni JCM 16921	GCA_008831125	scaffold	GenBank ENA	908846 tax ID
[Ref.: #66792]	Pseudoclavibacter caeni strain DSM 26484	908846.4	wgs	PATRIC	908846 tax ID	*
[Ref.: #66792]	Pseudoclavibacter caeni strain JCM 16921	908846.3	wgs	PATRIC	908846 tax ID	*
[Ref.: #66792]	Pseudoclavibacter caeni DSM 26484	2857411303	draft	JGI IMG/M	908846 tax ID	*

[Ref.: #18244]	GC-content	65.8 mol%
[Ref.: #67770]	GC-content	65.8 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: Pseudoclavibacter caeni JCM 16921 NCBI: GCA_008831125.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	82	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudoclavibacter caeni strain DSM 26484 PATRIC: 908846.4
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	90.438	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	89.973	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	78.335	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	87.299	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	91.134	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	94.375	no

Availability in culture collections External links

[Ref.: #18244]

Culture collection no.

DSM 26484, JCM 16921, KCTC 19773

[Ref.: #76926]

SI-ID 398768

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudoclavibacter caeni sp. nov., isolated from sludge of a sewage disposal plant.	Srinivasan S, Kim HS, Kim MK, Lee M	Int J Syst Evol Microbiol	10.1099/ijs.0.028951-0	2011	*

References

#18244

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26484

#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 )

#30063

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 #26423 (see below)

#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;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

#76926

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-ID398768.1 )

#26423

IJSEM 786 2012 ( DOI 10.1099/ijs.0.028951-0 , PubMed 21571937 )

* These data were automatically processed and therefore are not curated

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Pseudoclavibacter caeni JCM 16921

Pseudoclavibacter caeni strain DSM 26484

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