Gemmobacter lanyuensis (BCRC 80378, LMG 26667, KCTC 23714)

Name: Gemmobacter lanyuensis (BCRC 80378, LMG 26667, KCTC 23714)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 134036

Type strain

Strain Designation Orc-4

Culture col. no. BCRC 80378 LMG 26667 KCTC 23714 Orc-4

NCBI tax ID(s) 1054497

Special Collections KCTC Literature strains

Links

Gemmobacter lanyuensis Orc-4 is a facultative anaerobe, Gram-negative, rod-shaped bacterium that was isolated from freshwater .

Gram-negative rod-shaped facultative anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 272184

LMG 26667,KCTC 23714

@ref 20215

Last LPSN update 2026-02-09 11:32:05

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Rhodobacterales

Family Paracoccaceae

Genus Gemmobacter

Species Gemmobacter lanyuensis

Full scientific name Gemmobacter lanyuensis Sheu et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31111	negative	2 µm	0.45 µm	rod-shaped
125438	negative				98.5
125439	negative				93.2

Pigmentation

31111

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
31111	positive	growth	15-40
31111	positive	optimum	27.5

Culture pH

@ref	Ability	Type	PH	PH range
31111	positive	optimum	7
31111	positive	growth	6.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31111	facultative anaerobe
125439	obligate aerobe	93.2

Spore formation

31111

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31111	NaCl	positive	growth	0-1 %
31111	NaCl	positive	optimum	0.25 %

Observation

31111

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31111	4853 ChEBI	esculin	+	hydrolysis
31111	17754 ChEBI	glycerol	+	carbon source
31111	24996 ChEBI	lactate	+	carbon source
31111	29864 ChEBI	mannitol	+	carbon source
31111	37684 ChEBI	mannose	+	carbon source
31111	51850 ChEBI	methyl pyruvate	+	carbon source
31111	17632 ChEBI	nitrate	+	reduction

Enzymes

@ref	Value	Activity	Ec
31111	acid phosphatase	+	3.1.3.2
31111	alkaline phosphatase	+	3.1.3.1
31111	catalase	+	1.11.1.6
31111	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)
#Environmental	#Aquatic	#Pond (small)
#Environmental	#Aquatic	#River (Creek)

Isolation

31111

Sample typefreshwater (river, lake, pond)

Taxonmaps

69479

Global distribution of 16S sequence JN104393 (>99% sequence identity) for Gemmobacter lanyuensis from Microbeatlas

Aquatic Samples	159
Soil Samples	1
Animal Samples	21
Plant Samples
Total Samples	181

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM4266084v1 assembly for Gemmobacter lanyuensis KCTC 23714	contig	GCA_042660845			1054497	76.19
66792	ASM1465235v1 assembly for Gemmobacter lanyuensis KCTC 23714	scaffold	GCA_014652355	1054497.3	2995380663	1054497	67.73
124043	ASM4268134v1 assembly for Gemmobacter lanyuensis KCTC 23714	contig	GCA_042681345			1054497

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
31111	Gemmobacter lanyuensis strain Orc-4 16S ribosomal RNA gene, partial sequence	JN104393	1404		1054497

GC content

31111

GC-content (mol%)63.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Gemmobacter lanyuensis KCTC 23714
NCBI: GCA_014652355

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.20	no
125439	gram_stain	BacteriaNetⓘ	negative	93.20	no
125439	motility	BacteriaNetⓘ	yes	53.40	no
125439	spore_formation	BacteriaNetⓘ	no	89.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Gemmobacter lanyuensis KCTC 23714
NCBI: GCA_014652355.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	yes
125438	anaerobic	anaerobicⓘ	no	87.99	no
125438	aerobic	aerobicⓘ	yes	67.90	yes
125438	spore-forming	spore-formingⓘ	no	87.19	no
125438	thermophilic	thermophileⓘ	no	96.60	yes
125438	flagellated	motile2+ⓘ	yes	70.61	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 lanyuensis sp. nov., isolated from a freshwater spring.	Sheu SY, Shiau YW, Wei YT, Chen WM	Int J Syst Evol Microbiol	10.1099/ijs.0.052399-0	2013

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 )
#27440	IJSEM 4039 2013 ( DOI 10.1099/ijs.0.052399-0 , PubMed 23728371 )
#31111	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 #27440
#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) .
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Gemmobacter lanyuensis (BCRC 80378, LMG 26667, KCTC 23714)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_042660845

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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