Gemmobacter lutimaris (KCTC 62715, JCM 32828, YJ-T1-11)

Name: Gemmobacter lutimaris (KCTC 62715, JCM 32828, YJ-T1-11)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 164373

Type strain

Strain Designation YJ-T1-11

Culture col. no. KCTC 62715 JCM 32828 YJ-T1-11

NCBI tax ID(s) 2306023

Special Collections JCM KCTC Literature strains

History B. S. Kim; Korea Univ., South Korea; YJ-T1-11.

Links

Gemmobacter lutimaris YJ-T1-11 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from Tidal sediment.

Gram-negative rod-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 288096

KCTC 62715,JCM 32828

@ref 20215

Last LPSN update 2026-02-09 11:39:50

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Paracoccaceae

Genus Gemmobacter

Species Gemmobacter lutimaris

Full scientific name Gemmobacter lutimaris Yoo et al. 2019

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
67928	negative	2.9-3.1 µm	0.6-0.8 µm	rod-shaped
125439	negative					93.6

Colony morphology

@ref	Colony size	Colony color	Incubation period	Medium used
67928	1.5 mm	cream-coloured	3 days	Marine agar (MA)

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
67770	positive	growth	30	mesophilic
67928	positive	growth	4-45
67928	positive	optimum	30-37	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
67928	positive	optimum	9.0-12.0
67928	positive	growth	5.0-12.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67928	aerobe
125439	aerobe	90.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
67928	NaCl	positive	growth	0.0-7.0 %(w/v)
67928	NaCl	positive	optimum	1.0-3.0 %(w/v)

Observation

@ref	Observation
67770	quinones: Q-10
67928	The major respiratory quinone is Q-10
67928	The polar lipids consist of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and three unidentified lipids

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
67928	16810 ChEBI	2-oxoglutarate	+	carbon source
67928	18101 ChEBI	4-hydroxyphenylacetic acid	+	carbon source
67928	13705 ChEBI	acetoacetate	+	carbon source
67928	17925 ChEBI	alpha-D-glucose	+	carbon source
67928	64552 ChEBI	alpha-hydroxybutyrate	+	carbon source
67928	8295 ChEBI	beta-hydroxybutyrate	+	carbon source
67928	73706 ChEBI	bromosuccinate	+	carbon source
67928	85146 ChEBI	carboxymethylcellulose	-	hydrolysis
67928		casein	-	hydrolysis
67928	17057 ChEBI	cellobiose	+	carbon source
67928	16947 ChEBI	citrate	+	carbon source
67928	16947 ChEBI	citrate	+	assimilation
67928		crab shell chitin	-	hydrolysis
67928	17108 ChEBI	D-arabinose	+	assimilation
67928	18333 ChEBI	D-arabitol	+	carbon source
67928	15824 ChEBI	D-fructose	+	carbon source
67928	78697 ChEBI	D-fructose 6-phosphate	+	carbon source
67928	28847 ChEBI	D-fucose	+	carbon source
67928	12936 ChEBI	D-galactose	+	carbon source
67928	17634 ChEBI	D-glucose	+	assimilation
67928	14314 ChEBI	D-glucose 6-phosphate	+	carbon source
67928	15588 ChEBI	D-malate	+	carbon source
67928	16899 ChEBI	D-mannitol	+	carbon source
67928	16899 ChEBI	D-mannitol	+	assimilation
67928	16024 ChEBI	D-mannose	+	carbon source
67928	16024 ChEBI	D-mannose	+	assimilation
67928	17924 ChEBI	D-sorbitol	+	carbon source
67928	16991 ChEBI	dna	-	hydrolysis
67928		esculin ferric citrate	+	degradation
67928	16865 ChEBI	gamma-aminobutyric acid	+	carbon source
67928	17754 ChEBI	glycerol	+	carbon source
67928	70744 ChEBI	glycyl-L-proline	+	carbon source
67928	17368 ChEBI	hypoxanthine	+	hydrolysis
67928	16977 ChEBI	L-alanine	+	carbon source
67928	16467 ChEBI	L-arginine	+	carbon source
67928	29991 ChEBI	L-aspartate	+	carbon source
67928	18287 ChEBI	L-fucose	+	carbon source
67928		L-glutamate-gamma-3-carboxy-4-nitroanilide	+	carbon source
67928	15971 ChEBI	L-histidine	+	carbon source
67928		L-lactate	+	carbon source
67928	15589 ChEBI	L-malate	+	carbon source
67928	17115 ChEBI	L-serine	+	carbon source
67928	6472 ChEBI	lincomycin	+	carbon source
67928	48607 ChEBI	lithium chloride	+	carbon source
67928	25115 ChEBI	malate	+	assimilation
67928	17306 ChEBI	maltose	+	carbon source
67928	17306 ChEBI	maltose	+	assimilation
67928	51850 ChEBI	methyl pyruvate	+	carbon source
67928	17268 ChEBI	myo-inositol	+	carbon source
67928	28800 ChEBI	N-acetylgalactosamine	+	carbon source
67928	59640 ChEBI	N-acetylglucosamine	+	assimilation
67928	100147 ChEBI	nalidixic acid	+	carbon source
67928	18401 ChEBI	phenylacetate	+	carbon source
67928	18401 ChEBI	phenylacetate	+	assimilation
67928	75248 ChEBI	potassium tellurite	+	carbon source
67928	29673 ChEBI	rifamycin sv	+	carbon source
67928	62965 ChEBI	sodium formate	+	carbon source
67928	132106 ChEBI	sodium propionate	+	carbon source
67928	9215 ChEBI	spectinomycin	+	carbon source
67928	28017 ChEBI	starch	+	hydrolysis
67928	17992 ChEBI	sucrose	+	carbon source
67928	75193 ChEBI	tetrazolium violet	+	carbon source
67928	27082 ChEBI	trehalose	+	carbon source
67928	32528 ChEBI	turanose	+	carbon source
67928	53423 ChEBI	tween 40	+	carbon source
67928	18186 ChEBI	tyrosine	-	hydrolysis
67928	15318 ChEBI	xanthine	-	hydrolysis

Enzymes

@ref	Value	Activity	Ec
67928	acid phosphatase	+	3.1.3.2
67928	alkaline phosphatase	+	3.1.3.1
67928	alpha-glucosidase	+	3.2.1.20
67928	beta-galactosidase	+	3.2.1.23
67928	catalase	+	1.11.1.6
67928	cytochrome oxidase	+	1.9.3.1
67928	esterase (C 4)	+
67928	esterase Lipase (C 8)	+/-
67928	leucine arylamidase	+	3.4.11.1
67928	naphthol-AS-BI-phosphohydrolase	+/-

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
67770	Tidal sediment		Yeongjong-do	Republic of Korea	KOR	Asia
67928	tidal marine sediment	2017-04	Yeongjong-do	Republic of Korea	KOR	Asia	37.4333	126.383 37.4333/126.383

Taxonmaps

69479

Global distribution of 16S sequence MH778538 (>99% sequence identity) for Gemmobacter from Microbeatlas

Aquatic Samples	1176
Soil Samples	123
Animal Samples	835
Plant Samples	38
Total Samples	2172

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67928	ASM357071v1 assembly for Gemmobacter lutimaris YJ-T1-11	scaffold	GCA_003570715	2306023.3	2835163134	2306023	63.21

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67928	Gemmobacter lutimaris strain YJ-T1-11 16S ribosomal RNA gene, partial sequence	MH778538	1374		2306023

GC content

@ref	GC-content (mol%)	Method
67928	65.6	high performance liquid chromatography (HPLC)
67770	64.4	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Gemmobacter lutimaris YJ-T1-11
NCBI: GCA_003570715

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	89.40	no
125439	motility	BacteriaNetⓘ	yes	64.30	no
125439	gram_stain	BacteriaNetⓘ	negative	93.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	90.70	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Gemmobacter serpentinus sp. nov., isolated from conserved forages.	Lim K, Kannan AD, Shobnam N, Mahmood M, Lee J, Im J	Int J Syst Evol Microbiol	10.1099/ijsem.0.004276	2020
Phylogeny	Gemmobacter lutimaris sp. nov., a marine bacterium isolated from a tidal flat.	Yoo Y, Lee DW, Lee H, Kwon BO, Khim JS, Yim UH, Park H, Park B, Choi IG, Kim BS, Jeon SW, Kim GH, Kim JJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003375	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;
#67928	Yeonjae Yoo, Dong Wan Lee, Hanbyul Lee, Bong-Oh Kwon, Jong Seong Khim, Un Hyuk Yim, Hongjae Park, Byeonghyeok Park, In-Geol Choi, Beom Seok Kim, Seong Woo Jeon, Gyu-Hyeok Kim, Jae-Jin Kim: Gemmobacter lutimaris sp. nov., a marine bacterium isolated from a tidal flat. IJSEM 69: 1676 - 1681 2019 ( DOI 10.1099/ijsem.0.003375 )
#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 .
#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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Gemmobacter lutimaris (KCTC 62715, JCM 32828, YJ-T1-11)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_003570715

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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