Rhodomicrobium udaipurense (KCTC 15219, NBRC 109057, JA643)

Name: Rhodomicrobium udaipurense (KCTC 15219, NBRC 109057, JA643)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133915

Type strain

Strain Designation JA643

Culture col. no. KCTC 15219 NBRC 109057 JA643

NCBI tax ID(s) 1202716

Special Collections KCTC Literature strains

History <- Ch Sasikala, JNT Univ. India

Links

Rhodomicrobium udaipurense JA643 is a facultative anaerobe, spore-forming, Gram-negative prokaryote that was isolated from freshwater .

spore-forming Gram-negative motile rod-shaped facultative anaerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 287571

KCTC 15219,NBRC 109057

@ref 20215

Last LPSN update 2025-12-16 10:01:55

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Hyphomicrobiaceae

Genus Rhodomicrobium

Species Rhodomicrobium udaipurense

Full scientific name Rhodomicrobium udaipurense Ramana et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30868	negative	3.25 µm	1.3 µm	rod-shaped
67771				rod-shaped
67771				ovoid-shaped
67771	negative
125438	negative				99.328
125439	negative				99.3

Pigmentation

30868

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
30868	positive	growth	10-40
30868	positive	optimum	30	mesophilic
67771	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
30868	positive	optimum	7
30868	positive	growth	5.5-8.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30868	facultative anaerobe
67771	anaerobe
125439	obligate aerobe	98.8

Spore formation

@ref	Spore formation	Confidence
30868
125439		96.8

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30868	NaCl	positive	growth	0-0.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30868	30089 ChEBI	acetate	+	carbon source
30868	35391 ChEBI	aspartate	+	carbon source
30868	28885 ChEBI	butanol	+	carbon source
30868	15740 ChEBI	formate	+	carbon source
30868	29987 ChEBI	glutamate	+	carbon source
30868	24996 ChEBI	lactate	+	carbon source
30868	25115 ChEBI	malate	+	carbon source
30868	15792 ChEBI	malonate	+	carbon source
30868	17272 ChEBI	propionate	+	carbon source
30868	15361 ChEBI	pyruvate	+	carbon source
30868	30031 ChEBI	succinate	+	carbon source
30868	31011 ChEBI	valerate	+	carbon source

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

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
30868	freshwater (river, lake, pond)
67771	From freshwater sample collected from a stream at Udaipur	Himachal Pradesh, the western Himalayas, altitude of 8970 feet(2734 m) above sea level)	India	IND	Asia	32.7252	76.6654 32.7252/76.6654

Taxonmaps

69479

Global distribution of 16S sequence FN995218 (>99% sequence identity) for Rhodomicrobium from Microbeatlas

Aquatic Samples	1719
Soil Samples	2659
Animal Samples	222
Plant Samples	235
Total Samples	4835

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1646179v1 assembly for Rhodomicrobium udaipurense JA643	contig	GCA_016461795	1202716.4	8118723390	1202716	60.57
66792	ASM63601v1 assembly for Rhodomicrobium udaipurense JA643	contig	GCA_000636015	858455.3	2576861659	858455	24.76

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
30868	Rhodomicrobium udaipurense JA643 partial 16S rRNA gene, type strain JA643T	FN995218	1343		858455

GC content

@ref	GC-content (mol%)	Method
30868	64.2
67771	64.2	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: Rhodomicrobium udaipurense JA643
NCBI: GCA_000636015

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.80	no
125439	motility	BacteriaNetⓘ	no	57.00	no
125439	gram_stain	BacteriaNetⓘ	negative	99.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhodomicrobium udaipurense JA643
PATRIC: 858455.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.33	yes
125438	anaerobic	anaerobicⓘ	no	52.22	no
125438	aerobic	aerobicⓘ	yes	52.39	no
125438	spore-forming	spore-formingⓘ	no	72.06	yes
125438	thermophilic	thermophileⓘ	no	91.14	yes
125438	flagellated	motile2+ⓘ	yes	66.12	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Revised Draft Genome Sequences of Rhodomicrobium vannielii ATCC 17100 and Rhodomicrobium udaipurense JA643.	Conners EM, Davenport EJ, Bose A	Microbiol Resour Announc	10.1128/MRA.00022-21	2021
Genetics	Draft genome sequence of Rhodomicrobium udaipurense JA643T with special reference to hopanoid biosynthesis.	Tushar L, Sasikala Ch, Ramana ChV	DNA Res	10.1093/dnares/dsu026	2014
Phylogeny	Rhodomicrobium lacus sp. nov., an alkalitolerent bacterium isolated from Umiam lake, Shillong, India.	G S, Kumar D, Uppada J, Ch S, Ch V R	Int J Syst Evol Microbiol	10.1099/ijsem.0.003813	2020
Phylogeny	Rhodomicrobium udaipurense sp. nov., a psychrotolerant, phototrophic alphaproteobacterium isolated from a freshwater stream.	Ramana VV, Raj PS, Tushar L, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijs.0.046409-0	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 )
#27198	IJSEM 2684 2013 ( DOI 10.1099/ijs.0.046409-0 , PubMed 23291882 )
#30868	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 #27198
#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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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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Rhodomicrobium udaipurense (KCTC 15219, NBRC 109057, JA643)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_016461795

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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