Name: Lacisediminihabitans profunda CHu50b-6-2
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 164320

Type strain:

Species: Lacisediminihabitans profunda

Strain Designation: CHu50b-6-2

Culture col. no.: JCM 32673, KCTC 49081

Strain history: S.-R. Ko; KRIBB, South Korea; CHu50b-6-2.

NCBI tax ID(s): 2594790 (species)

Section

Lacisediminihabitans profunda CHu50b-6-2 is a mesophilic, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from Sediment core from the Daechung Reservoir at a water depth of 17 m.

colony-forming
Gram-positive
rod-shaped
mesophilic
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	*Lacisediminihabitans*
	Species	**Lacisediminihabitans profunda**
	Full Scientific Name (LPSN)	Lacisediminihabitans profunda Zhuo et al. 2020

Information on morphological and physiological properties Morphology

[Ref.: #68083]	Gram stain	positive

[Ref.: #68083]	Cell shape	rod-shaped

[Ref.: #68083]	Motility	no

[Ref.: #68083]	Colony color	yellow
[Ref.: #68083]	Colony shape	circular
[Ref.: #68083]	Cultivation medium used	Reasoner's 2A agar (R2A)

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #67770]	growth	28 °C
[Ref.: #68083]	growth	4-30 °C
[Ref.: #68083]	optimum	25-30 °C

[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #68083]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #68083]			optimum	7
[Ref.: #68083]			growth	6.0-10.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #68083]

Ability of spore formation

[Ref.: #67770]	Observation	quinones: MK-10
[Ref.: #68083]	Observation	The predominant respiratory menaquinone is MK-10
[Ref.: #68083]	Observation	The major polar lipids are diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), and an unidentified glycolipid (GL)
[Ref.: #68083]	Observation	The cell-wall peptidoglycan is B1alpha contains 2, 4-diaminobutyric acid as the diagnostic diamino acid

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68083]	2,3-butanediol	+	assimilation
[Ref.: #68083]	alpha-hydroxybutyrate ChEBI	+	assimilation
[Ref.: #68083]	cellobiose ChEBI	+	assimilation
[Ref.: #68083]	D-fructose ChEBI	+	assimilation
[Ref.: #68083]	D-galactose ChEBI	+	assimilation
[Ref.: #68083]	D-gluconate ChEBI	+	assimilation
[Ref.: #68083]	D-glucose ChEBI	+	assimilation
[Ref.: #68083]	D-ribose ChEBI	+	assimilation
[Ref.: #68083]	D-sorbitol ChEBI	+	assimilation
[Ref.: #68083]	dextrin ChEBI	+	assimilation
[Ref.: #68083]	esculin ChEBI	-	hydrolysis
[Ref.: #68083]	gelatin ChEBI	-	hydrolysis
[Ref.: #68083]	glucose ChEBI	-	fermentation
[Ref.: #68083]	glycerol ChEBI	+	assimilation
[Ref.: #68083]	inosine ChEBI	+	assimilation
[Ref.: #68083]	L-arabinose ChEBI	+	assimilation
[Ref.: #68083]	L-lactate	+	assimilation
[Ref.: #68083]	lactulose ChEBI	+	assimilation
[Ref.: #68083]	mannitol ChEBI	+	assimilation
[Ref.: #68083]	melibiose ChEBI	+	assimilation
[Ref.: #68083]	methyl pyruvate ChEBI	+	assimilation
[Ref.: #68083]	myo-inositol ChEBI	+	assimilation
[Ref.: #68083]	N-acetyl-D-glucosamine ChEBI	+	assimilation
[Ref.: #68083]	N-acetylgalactosamine ChEBI	+	assimilation
[Ref.: #68083]	nitrate ChEBI	+	reduction
[Ref.: #68083]	raffinose ChEBI	+	assimilation
[Ref.: #68083]	rhamnose ChEBI	+	assimilation
[Ref.: #68083]	sucrose ChEBI	+	assimilation
[Ref.: #68083]	thymidine ChEBI	+	assimilation
[Ref.: #68083]	turanose ChEBI	+	assimilation
[Ref.: #68083]	uridine ChEBI	+	assimilation
[Ref.: #68083]	xylitol ChEBI	+	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #68083]	amikacin ChEBI	yes	30	µg/mL
[Ref.: #68083]	chloramphenicol ChEBI	yes	30	µg/mL
[Ref.: #68083]	erythromycin ChEBI	yes	30	µg/mL
[Ref.: #68083]	gentamicin ChEBI				yes	30	µg/mL
[Ref.: #68083]	kanamycin ChEBI	yes	30	µg/mL
[Ref.: #68083]	lincomycin ChEBI	yes	15	µg/mL
[Ref.: #68083]	nalidixic acid ChEBI				yes	30	µg/mL
[Ref.: #68083]	rifampicin ChEBI	yes	30	µg/mL
[Ref.: #68083]	spectinomycin ChEBI	yes	25	µg/mL
[Ref.: #68083]	streptomycin ChEBI	yes	25	µg/mL
[Ref.: #68083]	teicoplanin ChEBI	yes	30	µg/mL
[Ref.: #68083]	tetracycline ChEBI				yes	30	µg/mL
[Ref.: #68083]	vancomycin ChEBI	yes	30	µg/mL
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Group ID of combined antibiotics	Metabolite	Antibiotic resistance	Concentration
[Ref.: #68083]		20	ampicillin ChEBI	yes	20	µg/mL
[Ref.: #68083]		20	sulbactam ChEBI	yes	20	µg/mL

	Metabolite production	Metabolite	Production
[Ref.: #68083]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68083]	acid phosphatase	+	3.1.3.2
[Ref.: #68083]	alkaline phosphatase	-	3.1.3.1
[Ref.: #68083]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #68083]	alpha-fucosidase	-	3.2.1.51
[Ref.: #68083]	alpha-galactosidase	+	3.2.1.22
[Ref.: #68083]	alpha-glucosidase	+	3.2.1.20
[Ref.: #68083]	alpha-mannosidase	-	3.2.1.24
[Ref.: #68083]	arginine dihydrolase	-	3.5.3.6
[Ref.: #68083]	beta-galactosidase	+	3.2.1.23
[Ref.: #68083]	beta-glucosidase	+	3.2.1.21
[Ref.: #68083]	beta-glucuronidase	-	3.2.1.31
[Ref.: #68083]	catalase	+	1.11.1.6
[Ref.: #68083]	cystine arylamidase	+	3.4.11.3
[Ref.: #68083]	cytochrome oxidase	-	1.9.3.1
[Ref.: #68083]	esterase (C 4)	+
[Ref.: #68083]	esterase Lipase (C 8)	+
[Ref.: #68083]	leucine arylamidase	+	3.4.11.1
[Ref.: #68083]	lipase (C 14)	-
[Ref.: #68083]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #68083]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #68083]	trypsin	-	3.4.21.4
[Ref.: #68083]	urease	-	3.5.1.5
[Ref.: #68083]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #67770]	Sample type/isolated from	Sediment core from the Daechung Reservoir at a water depth of 17 m
[Ref.: #67770]	Geographic location (country and/or sea, region)	Daejeon
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #68083]	Sample type/isolated from	67-cm-long sediment core, depth of 17 m
[Ref.: #68083]	Geographic location (country and/or sea, region)	Daechung Reservoir, Daejeon
[Ref.: #68083]	Country	Republic of Korea
[Ref.: #68083]	Country ISO 3 Code	KOR
[Ref.: #68083]	Continent	Asia
[Ref.: #68083]	Geographic location	36.3750°/127.5660°
* marker position based on {}

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.: #68083]	Lacisediminihabitans profunda 16S ribosomal RNA gene, partial sequence	MF770244	1461	ENA	2594790 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Lacisediminihabitans profunda CHu50b-6-2	GCA_008040105	contig	GenBank	2594790 tax ID

[Ref.: #68083]

GC-content

67.3 mol%

genome sequence analysis

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Lacisediminihabitans profunda CHu50b-6-2 NCBI: GCA_008040105.1
[Ref.: #69480]	motile	yes	56.961	no
[Ref.: #69480]	flagellated	no	95.068	no
[Ref.: #69480]	gram-positive	yes	89.168	yes
[Ref.: #69480]	anaerobic	no	99.354	no
[Ref.: #69480]	aerobic	yes	90.432	no
[Ref.: #69480]	halophile	no	96.41	no
[Ref.: #69480]	spore-forming	no	87.762	yes
[Ref.: #69480]	glucose-util	yes	86.546	no
[Ref.: #69480]	thermophile	no	97.696	yes
[Ref.: #69480]	glucose-ferment	no	90.65	yes

Availability in culture collections External links

[Ref.: #67770]

Culture collection no.

JCM 32673, KCTC 49081

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lacisediminihabitans profunda gen. nov., sp. nov., a member of the family Microbacteriaceae isolated from freshwater sediment.	Zhuo Y, Jin CZ, Jin FJ, Li T, Kang DH, Oh HM, Lee HG, Jin L	Antonie Van Leeuwenhoek	10.1007/s10482-019-01347-8	2019	*
Phylogeny	Lacisediminihabitans changchengi sp. nov., an actinobacterium isolated from Antarctic swamplands mud.	Liang Y, Jiang P, Yao B, Jiao Y, Li J	Arch Microbiol	10.1007/s00203-021-02531-z	2021	*

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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68083

Ye Zhuo, Chun-Zhi Jin, Feng-Jie Jin, Taihua Li, Dong Hyo Kang, Hee-Mock Oh, Hyung-Gwan Lee, Long Jin: Lacisediminihabitans profunda gen. nov., sp. nov., a member of the family Microbacteriaceae isolated from freshwater sediment. Antonie Van Leeuwenhoek 113: 365 - 375 2020 ( DOI 10.1007/s10482-019-01347-8 )

#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) .

* These data were automatically processed and therefore are not curated

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