Name: Rhodomicrobium udaipurense JA643
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133915

Type strain:

Species: Rhodomicrobium udaipurense

Strain Designation: JA643

Culture col. no.: KCTC 15219, NBRC 109057

Strain history: <- Ch Sasikala, JNT Univ. India

NCBI tax ID(s): 1202716 (species)

Special Collections

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Hyphomicrobiaceae*
	Genus	*Rhodomicrobium*
	Species	**Rhodomicrobium udaipurense**
	Full Scientific Name (LPSN)	Rhodomicrobium udaipurense Ramana et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30868]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.328

[Ref.: #30868]	Cell length	3.25 µm

[Ref.: #30868]	Cell width	1.3 µm

[Ref.: #30868]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	ovoid-shaped

[Ref.: #30868]	Motility	yes
[Ref.: #67771]	Motility	yes

[Ref.: #30868]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #30868]	growth	10-40 °C
[Ref.: #30868]	optimum	30 °C
[Ref.: #67771]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #30868]			optimum	7
[Ref.: #30868]			growth	5.5-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30868]	Oxygen tolerance	facultative anaerobe
[Ref.: #67771]	Oxygen tolerance	anaerobe

[Ref.: #30868]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30868]		NaCl		growth	0-0.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30868]	acetate ChEBI	+	carbon source
[Ref.: #30868]	aspartate ChEBI	+	carbon source
[Ref.: #30868]	butanol ChEBI	+	carbon source
[Ref.: #30868]	formate ChEBI	+	carbon source
[Ref.: #30868]	glutamate ChEBI	+	carbon source
[Ref.: #30868]	lactate ChEBI	+	carbon source
[Ref.: #30868]	malate ChEBI	+	carbon source
[Ref.: #30868]	malonate ChEBI	+	carbon source
[Ref.: #30868]	propionate ChEBI	+	carbon source
[Ref.: #30868]	pyruvate ChEBI	+	carbon source
[Ref.: #30868]	succinate ChEBI	+	carbon source
[Ref.: #30868]	valerate ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #30868]	Sample type/isolated from	freshwater (river, lake, pond)

[Ref.: #67771]	Sample type/isolated from	From freshwater sample collected from a stream at Udaipur
[Ref.: #67771]	Geographic location (country and/or sea, region)	Himachal Pradesh, the western Himalayas, altitude of 8970 feet(2734 m) above sea level)
[Ref.: #67771]	Country	India
[Ref.: #67771]	Country ISO 3 Code	IND
[Ref.: #67771]	Continent	Asia
[Ref.: #67771]	Geographic location	32.7252°/76.6654°
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #30868]	Rhodomicrobium udaipurense JA643 partial 16S rRNA gene, type strain JA643T	FN995218	1343	GenBank ENA	858455 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhodomicrobium udaipurense JA643	GCA_000636015	contig	GenBank ENA	858455 tax ID	*
[Ref.: #66792]	Rhodomicrobium udaipurense JA643	GCA_016461795	contig	GenBank ENA	1202716 tax ID	*
[Ref.: #66792]	Rhodomicrobium udaipurense JA643	858455.3	wgs	PATRIC	858455 tax ID	*
[Ref.: #66792]	Rhodomicrobium udaipurense JA643	2576861659	draft	JGI IMG/M	858455 tax ID	*

[Ref.: #30868]	GC-content	64.2 mol%
[Ref.: #67771]	GC-content	64.2 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Rhodomicrobium udaipurense JA643 NCBI: GCA_016461795.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodomicrobium udaipurense JA643 PATRIC: 858455.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	99.328	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	52.22	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	52.391	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	72.062	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	91.141	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	66.115	no

Availability in culture collections External links

[Ref.: #30868]

Culture collection no.

KCTC 15219, NBRC 109057

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	*
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	*
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	*

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 )

#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 (see below)

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#27198

IJSEM 2684 2013 ( DOI 10.1099/ijs.0.046409-0 , PubMed 23291882 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Rhodomicrobium udaipurense in external resources:
SILVA
BRENDA
PANGAEA
GBIF