Lacisediminimonas profundi (KCTC 62287, JCM 32676, CHu64-6-4)

Name: Lacisediminimonas profundi (KCTC 62287, JCM 32676, CHu64-6-4)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 164323

Type strain

Strain Designation CHu64-6-4

Culture col. no. KCTC 62287 JCM 32676 CHu64-6-4

NCBI tax ID(s) 2603856

Special Collections JCM KCTC Literature strains

History S.-R. Ko; KRIBB, South Korea; CHu64-6-4.

Links

Lacisediminimonas profundi CHu64-6-4 is a mesophilic, Gram-negative, rod-shaped prokaryote that forms circular colonies and was isolated from Sediment core from the Daechung Reservoir at a water depth of 17 m in Daejeon.

Gram-negative rod-shaped colony-forming mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 26904

KCTC 62287,JCM 32676

@ref 20215

Last LPSN update 2026-02-09 11:39:49

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Oxalobacteraceae

Genus Lacisediminimonas

Species Lacisediminimonas profundi

Full scientific name Lacisediminimonas profundi Wu et al. 2020

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
68077	negative	rod-shaped
125439	negative			98

Colony morphology

@ref	Colony color	Colony shape	Medium used
68077	colorless	circular	Reasoner's 2A agar (R2A)

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
67770	positive	growth	30	mesophilic
68077	positive	growth	4-37
68077	positive	optimum	25-30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
68077	positive	optimum	7
68077	positive	growth	7.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	95.4

Spore formation

@ref	Spore formation	Confidence
68077
125439		95.2

Observation

@ref	Observation
67770	quinones: Q-8
68077	The predominant respiratory ubiquinone is Q-8
68077	The major polar lipids are phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylethnolamine

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68077	37054 ChEBI	3-hydroxybutyrate	+	assimilation
68077	4853 ChEBI	esculin	-	hydrolysis
68077	5291 ChEBI	gelatin	-	hydrolysis
68077	17234 ChEBI	glucose	-	fermentation
68077	17240 ChEBI	itaconate	+	assimilation
68077		L-lactate	+	assimilation
68077	25115 ChEBI	malate	+	assimilation
68077	17632 ChEBI	nitrate	+	hydrolysis

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.	Group ID	Resistance conc.
68077	2637	amikacin	30 µg/mL
68077	28971	ampicillin		20
68077	17698	chloramphenicol	30 µg/mL
68077	48923	erythromycin			30 µg/mL
68077	17833	gentamicin	30 µg/mL
68077	6104	kanamycin	30 µg/mL
68077	6472	lincomycin	15 µg/mL
68077	100147	nalidixic acid	30 µg/mL
68077	28077	rifampicin	30 µg/mL
68077	9215	spectinomycin	25 µg/mL
68077	17076	streptomycin	25 µg/mL
68077	9321	sulbactam		20
68077	29687	teicoplanin	30 µg/mL
68077	27902	tetracycline	30 µg/mL
68077	28001	vancomycin	30 µg/mL

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68077	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68077	acid phosphatase	+	3.1.3.2
68077	alkaline phosphatase	+	3.1.3.1
68077	alpha-chymotrypsin	-	3.4.21.1
68077	alpha-fucosidase	-	3.2.1.51
68077	alpha-galactosidase	-	3.2.1.22
68077	alpha-glucosidase	+	3.2.1.20
68077	alpha-mannosidase	-	3.2.1.24
68077	arginine dihydrolase	-	3.5.3.6
68077	beta-galactosidase	-	3.2.1.23
68077	beta-glucosidase	-	3.2.1.21
68077	beta-glucuronidase	-	3.2.1.31
68077	cystine arylamidase	-	3.4.11.3
68077	esterase (C 4)	+
68077	esterase Lipase (C 8)	+
68077	leucine arylamidase	+	3.4.11.1
68077	lipase (C 14)	-
68077	N-acetyl-beta-glucosaminidase	-	3.2.1.52
68077	naphthol-AS-BI-phosphohydrolase	+
68077	trypsin	-	3.4.21.4
68077	urease	-	3.5.1.5
68077	valine arylamidase	-

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
67770	Sediment core from the Daechung Reservoir at a water depth of 17 m in Daejeon		Republic of Korea	KOR	Asia
68077	67-cm-long freshwater sediment core collected at a water depth of 17 m	Daechung Reservoir, Daejeon	Republic of Korea	KOR	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
68077	ASM883126v1 assembly for Lacisediminimonas profundi CHu64-6-4	scaffold	GCA_008831265	2603856.3	2886751880	2603856	74.65

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
68077	Lacisediminimonas profundi 16S ribosomal RNA gene, partial sequence	MF770246	1473		2603856

GC content

@ref	GC-content (mol%)	Method
67770	62.1	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Lacisediminimonas profundi CHu64-6-4
NCBI: GCA_008831265

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.20	no
125439	motility	BacteriaNetⓘ	yes	74.20	no
125439	gram_stain	BacteriaNetⓘ	negative	98.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.40	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Lacisediminimonas profundi gen. nov., sp. nov., a member of the family Oxalobacteraceae isolated from freshwater sediment.	Wu X, Jin CZ, Jin FJ, Li T, Sung YJ, Oh HM, Lee HG, Jin L	Antonie Van Leeuwenhoek	10.1007/s10482-019-01334-z	2019

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;
#68077	Xuewen Wu, Chun-Zhi Jin, Feng-Jie Jin, Taihua Li, Yun Ju Sung, Hee-Mock Oh, Hyung-Gwan Lee, Long Jin: Lacisediminimonas profundi gen. nov., sp. nov., a member of the family Oxalobacteraceae isolated from freshwater sediment. Antonie Van Leeuwenhoek 113: 253 - 264 2020 ( DOI 10.1007/s10482-019-01334-z )
#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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Lacisediminimonas profundi (KCTC 62287, JCM 32676, CHu64-6-4)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_008831265

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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