Ramlibacter alkalitolerans (KACC 19305, JCM 32081, CJ661)

Name: Ramlibacter alkalitolerans (KACC 19305, JCM 32081, CJ661)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 141112

Type strain

Strain Designation CJ661

Culture col. no. KACC 19305 JCM 32081 CJ661

NCBI tax ID(s) 2039631

Special Collections JCM Literature strains

History C.-J. Cha; Chung-Ang Univ., South Korea; CJ661.

Links

Ramlibacter alkalitolerans CJ661 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from ginseng soil.

Gram-negative rod-shaped colony-forming aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 391007

JCM 32081

@ref 20215

Last LPSN update 2026-02-09 11:33:49

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Comamonadaceae

Genus Ramlibacter

Species Ramlibacter alkalitolerans

Full scientific name Ramlibacter alkalitolerans Lee and Cha 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
44020	negative	2 µm	1 µm	rod-shaped
125438	negative				97.47
125439	negative				99.3

Colony morphology

@ref	Colony color	Colony shape	Medium used
44020	white, become red-brown with aging	circular	R2A agar

Culture and growth conditions

Culture medium

@ref	Name	Growth
44020	Reasoners 2A agar

Culture temp

@ref	Growth	Type	Temperature (°C)
44020	positive	growth	25-37
44020	positive	optimum	30
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
44020	positive	optimum	7
44020	positive	growth	5.0-10.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
44020	aerobe
125439	obligate aerobe	99.6

Spore formation

@ref	Spore formation	Confidence
125439		98.1

Halophily

@ref	Salt	Growth	Tested relation	Concentration
44020	NaCl	positive	growth	0 %

Observation

@ref	Observation
44020	orange fluorescence typical for the Nile red complex with PHA appears
44020	the isoprenoid quinone is Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
44020	18101 ChEBI	4-hydroxyphenylacetic acid	+	carbon source
44020	17128 ChEBI	adipate	-	assimilation
44020	17925 ChEBI	alpha-D-glucose	+	carbon source
44020	17665 ChEBI	alpha-D-glucose 6-phosphate	+	carbon source
44020	27613 ChEBI	amygdalin	-	builds acid from
44020	18305 ChEBI	arbutin	-	builds acid from
44020	8295 ChEBI	beta-hydroxybutyrate	+	carbon source
44020		casein	+	hydrolysis
44020	17057 ChEBI	cellobiose	-	builds acid from
44020	17057 ChEBI	cellobiose	+	carbon source
44020	62968 ChEBI	cellulose	-	hydrolysis
44020	16383 ChEBI	cis-aconitate	+	carbon source
44020	16947 ChEBI	citrate	+	carbon source
44020	15570 ChEBI	D-alanine	+	carbon source
44020	17108 ChEBI	D-arabinose	-	builds acid from
44020	17108 ChEBI	D-arabinose	+	carbon source
44020	18333 ChEBI	D-arabitol	-	builds acid from
44020	15824 ChEBI	D-fructose	+	builds acid from
44020	15824 ChEBI	D-fructose	+	carbon source
44020	28847 ChEBI	D-fucose	-	builds acid from
44020	15895 ChEBI	D-galactonic acid lactone	+	carbon source
44020	12936 ChEBI	D-galactose	+	builds acid from
44020	18024 ChEBI	D-galacturonic acid	+	carbon source
44020	8391 ChEBI	D-gluconate	+	carbon source
44020	17634 ChEBI	D-glucose	+	assimilation
44020	17634 ChEBI	D-glucose	+	builds acid from
44020	15748 ChEBI	D-glucuronate	+	carbon source
44020	62318 ChEBI	D-lyxose	-	builds acid from
44020	16899 ChEBI	D-mannitol	-	builds acid from
44020	16899 ChEBI	D-mannitol	+	assimilation
44020	16899 ChEBI	D-mannitol	+	carbon source
44020	16024 ChEBI	D-mannose	+	assimilation
44020	16024 ChEBI	D-mannose	+	builds acid from
44020	16024 ChEBI	D-mannose	+	carbon source
44020	27605 ChEBI	D-psicose	+	carbon source
44020	16988 ChEBI	D-ribose	+	builds acid from
44020	33801 ChEBI	D-saccharate	+	carbon source
44020	17924 ChEBI	D-sorbitol	-	builds acid from
44020	17924 ChEBI	D-sorbitol	+	carbon source
44020	16443 ChEBI	D-tagatose	-	builds acid from
44020	65327 ChEBI	D-xylose	+	builds acid from
44020	27689 ChEBI	decanoate	-	assimilation
44020	23652 ChEBI	dextrin	+	carbon source
44020	17113 ChEBI	erythritol	-	builds acid from
44020	4853 ChEBI	esculin	+	hydrolysis
44020		esculin ferric citrate	+	builds acid from
44020	16813 ChEBI	galactitol	-	builds acid from
44020	5291 ChEBI	gelatin	+	hydrolysis
44020	28066 ChEBI	gentiobiose	-	builds acid from
44020	28066 ChEBI	gentiobiose	+	carbon source
44020	29042 ChEBI	glucose 1-phosphate	+	carbon source
44020	17754 ChEBI	glycerol	-	builds acid from
44020	17754 ChEBI	glycerol	+	carbon source
44020	28087 ChEBI	glycogen	-	builds acid from
44020	28087 ChEBI	glycogen	+	carbon source
44020	17596 ChEBI	inosine	+	carbon source
44020	15443 ChEBI	inulin	-	builds acid from
44020		L-alanine 4-nitroanilide	+	carbon source
44020	73786 ChEBI	L-alanylglycine	+	carbon source
44020	30849 ChEBI	L-arabinose	+	assimilation
44020	30849 ChEBI	L-arabinose	+	builds acid from
44020	30849 ChEBI	L-arabinose	+	carbon source
44020	18403 ChEBI	L-arabitol	-	builds acid from
44020	17196 ChEBI	L-asparagine	+	carbon source
44020	29991 ChEBI	L-aspartate	+	carbon source
44020	18287 ChEBI	L-fucose	-	builds acid from
44020	18287 ChEBI	L-fucose	+	carbon source
44020	29985 ChEBI	L-glutamate	+	carbon source
44020	62345 ChEBI	L-rhamnose	+	builds acid from
44020	62345 ChEBI	L-rhamnose	+	carbon source
44020	17266 ChEBI	L-sorbose	-	builds acid from
44020	65328 ChEBI	L-xylose	-	builds acid from
44020	24996 ChEBI	lactate	+	carbon source
44020	17716 ChEBI	lactose	-	builds acid from
44020	17716 ChEBI	lactose	+	carbon source
44020	6359 ChEBI	lactulose	+	carbon source
44020	25115 ChEBI	malate	+	assimilation
44020	17306 ChEBI	maltose	-	builds acid from
44020	17306 ChEBI	maltose	+	assimilation
44020	17306 ChEBI	maltose	+	carbon source
44020	6731 ChEBI	melezitose	-	builds acid from
44020	28053 ChEBI	melibiose	-	builds acid from
44020	320061 ChEBI	methyl alpha-D-glucopyranoside	+	carbon source
44020	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
44020	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
44020	51850 ChEBI	methyl pyruvate	+	carbon source
44020	17268 ChEBI	myo-inositol	-	builds acid from
44020	506227 ChEBI	N-acetylglucosamine	+	assimilation
44020	506227 ChEBI	N-acetylglucosamine	+	builds acid from
44020	506227 ChEBI	N-acetylglucosamine	+	carbon source
44020	17632 ChEBI	nitrate	+	reduction
44020	18401 ChEBI	phenylacetate	+	assimilation
44020		potassium 2-dehydro-D-gluconate	-	builds acid from
44020		potassium 5-dehydro-D-gluconate	+	builds acid from
44020	32032 ChEBI	potassium gluconate	-	builds acid from
44020	32032 ChEBI	potassium gluconate	+	assimilation
44020	17272 ChEBI	propionate	+	carbon source
44020	16634 ChEBI	raffinose	-	builds acid from
44020	15963 ChEBI	ribitol	+	builds acid from
44020	15963 ChEBI	ribitol	+	carbon source
44020	17814 ChEBI	salicin	-	builds acid from
44020	17822 ChEBI	serine	+	carbon source
44020	53258 ChEBI	sodium citrate	+	assimilation
44020	28017 ChEBI	starch	-	builds acid from
44020	28017 ChEBI	starch	-	hydrolysis
44020	143136 ChEBI	succinamate	+	carbon source
44020	17992 ChEBI	sucrose	-	builds acid from
44020	17992 ChEBI	sucrose	+	carbon source
44020	63528 ChEBI	thymidine 5'-monophosphate	+	carbon source
44020	27082 ChEBI	trehalose	-	builds acid from
44020	32528 ChEBI	turanose	-	builds acid from
44020	32528 ChEBI	turanose	+	carbon source
44020	53423 ChEBI	tween 40	+	carbon source
44020	53426 ChEBI	tween 80	+	carbon source
44020	27248 ChEBI	urocanic acid	+	carbon source
44020	17151 ChEBI	xylitol	-	builds acid from

Metabolite production

@ref	Chebi-ID	Metabolite	Production
44020	16301 ChEBI	nitrite

Enzymes

@ref	Value	Activity	Ec
44020	acid phosphatase	-	3.1.3.2
44020	alkaline phosphatase	-	3.1.3.1
44020	alpha-chymotrypsin	-	3.4.21.1
44020	alpha-galactosidase	+	3.2.1.22
44020	alpha-glucosidase	-	3.2.1.20
44020	alpha-mannosidase	-	3.2.1.24
44020	arginine dihydrolase	-	3.5.3.6
44020	beta-D-fucosidase	-	3.2.1.38
44020	beta-galactosidase	-	3.2.1.23
44020	beta-glucosidase	-	3.2.1.21
44020	beta-glucuronidase	-	3.2.1.31
44020	esterase (C 4)	+
44020	esterase Lipase (C 8)	+
44020	lipase (C 14)	+
44020	N-acetyl-beta-glucosaminidase	-	3.2.1.52
44020	naphthol-AS-BI-phosphohydrolase	+
44020	trypsin	-	3.4.21.4
44020	urease	-	3.5.1.5
44020	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

44020

Fatty acid	Percentage
C16:1ω6c and/or C16:1ω7c	44.4
C16:0	32.1
C18:1ω7c and/or C18:1ω6c	7.3
C10:0 3OH	4.4
C14:0	4.4
C12:0	3.1
C14:1ω5c	1.1
C17:0 cyclo	1
C17:1 iso ω5c	0.9
C15:0 anteiso	0.7

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture duration	Enrichment culture temperature	Isolation procedure
44020	ginseng soil	Anseong	Republic of Korea	KOR	Asia	37.9993	127 37.9993/127	3 days	30	R2A agar (BD) and preserved with glycerol suspension (30 %, v/v)
67770	Soil of ginseng in Anseong		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence KF740333 (>99% sequence identity) for Ramlibacter from Microbeatlas

Aquatic Samples	13
Soil Samples	143
Animal Samples	8
Plant Samples	63
Total Samples	227

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1672276v1 assembly for Ramlibacter alkalitolerans KACC 19305	contig	GCA_016722765	2039631.3	2995427879	2039631	71.6

16S sequences

@ref	Description	Accession	Database
44020	Ramlibacter alkalitolerans strain CJ661 16S ribosomal RNA gene, partial sequence	KF740333

GC content

@ref	GC-content (mol%)	Method
44020	65.4	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Ramlibacter alkalitolerans KACC 19305
NCBI: GCA_016722765

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.10	no
125439	motility	BacteriaNetⓘ	yes	78.10	no
125439	gram_stain	BacteriaNetⓘ	negative	99.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Ramlibacter alkalitolerans strain KACC 19305
PATRIC: 2039631.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.47	yes
125438	anaerobic	anaerobicⓘ	no	94.84	yes
125438	spore-forming	spore-formingⓘ	no	88.71	no
125438	aerobic	aerobicⓘ	yes	83.47	no
125438	thermophilic	thermophileⓘ	no	93.42	yes
125438	flagellated	motile2+ⓘ	yes	80.40	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Ramlibacter alkalitolerans sp. nov., alkali-tolerant bacterium isolated from soil of ginseng.	Lee DH, Cha CJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.002342	2017
Phylogeny	Genome mining revealed polyhydroxybutyrate biosynthesis by Ramlibacter agri sp. nov., isolated from agriculture soil in Korea.	Dahal RH, Kim J, Chaudhary DK, Le TTN, Kim DU, Jang H, Kim J	Antonie Van Leeuwenhoek	10.1007/s10482-022-01721-z	2022

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 )
#44020	Do-Hoon Lee, Chang-Jun Cha: Ramlibacter alkalitolerans sp. nov., alkali-tolerant bacterium isolated from soil of ginseng. IJSEM 67: 4619 - 4623 2017 ( DOI 10.1099/ijsem.0.002342 , PubMed 28920850 )
#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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#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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Ramlibacter alkalitolerans (KACC 19305, JCM 32081, CJ661)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_016722765

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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