Name: Rhodobaca bogoriensis DSM 18756
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13827

Type strain:

Species: Rhodobaca bogoriensis

Culture col. no.: DSM 18756, ATCC 700920, LBB 1

Strain history: <- M. T. Madigan, Dept. Microbiology, Southern Illinois Univ., Carbondale, USA; LBB1

NCBI tax ID(s): 1188254 (strain), 119542 (species)

SI-ID 45448

ATCC 700920, DSM 18756

Section

Rhodobaca bogoriensis DSM 18756 is a mesophilic, Gram-negative bacterium that was isolated from marine sediment .

Gram-negative
mesophilic
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	*Rhodobacterales*
	Family	*Paracoccaceae*
	Genus	*Rhodobaca*
	Species	**Rhodobaca bogoriensis**
	Full Scientific Name (LPSN)	Rhodobaca bogoriensis Milford et al. 2001

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.984

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7604]

Culture medium

RV5 MEDIUM (DSMZ Medium 1147)

[Ref.: #7604]

Culture medium growth

[Ref.: #7604]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7604]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #7604]			growth	35 °C

[Ref.: #7604]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.989

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

[Ref.: #7604]	Sample type/isolated from	marine sediment (Lake Bogoria)
[Ref.: #7604]	Geographic location (country and/or sea, region)	Kenya, African Rift Valley
[Ref.: #7604]	Country	Kenya
[Ref.: #7604]	Country ISO 3 Code	KEN
[Ref.: #7604]	Continent	Africa
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AF248638 (>99% sequence identity) for Rhodobaca from Microbeatlas

Aquatic Samples	120
Soil Samples	20
Animal Samples	24
Plant Samples	3
Total Samples	167

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #7604]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #7604]	Rhodobaca bogoriensis 16S ribosomal RNA gene, partial sequence	AF248638	1457	ENA	1188254 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhodobaca bogoriensis DSM 18756	GCA_004366635	scaffold	GenBank	1188254 tax ID	*
[Ref.: #66792]	Rhodobaca bogoriensis DSM 18756 LBB1	GCA_014197665	scaffold	GenBank	1188254 tax ID	*
[Ref.: #66792]	Rhodobaca bogoriensis DSM 18756	1188254.3	wgs	PATRIC	1188254 tax ID	*
[Ref.: #66792]	Rhodobaca bogoriensis DSM 18756 strain LBB1	1188254.4	wgs	PATRIC	1188254 tax ID	*
[Ref.: #66792]	Rhodobaca bogoriensis DSM 18756	2795385466	draft	JGI IMG/M	1188254 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Rhodobaca bogoriensis DSM 18756 DSM 18756 NCBI: GCA_004366635.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhodobaca bogoriensis DSM 18756 DSM 18756 NCBI: GCA_004366635.1
[Ref.: #69480]	motile	no	57.575	no
[Ref.: #69480]	flagellated	no	77.071	no
[Ref.: #69480]	gram-positive	no	98.389	no
[Ref.: #69480]	anaerobic	no	92.246	no
[Ref.: #69480]	aerobic	yes	76.173	no
[Ref.: #69480]	halophile	yes	66.621	no
[Ref.: #69480]	spore-forming	no	94.823	no
[Ref.: #69480]	glucose-util	yes	80.689	no
[Ref.: #69480]	thermophile	no	95.86	yes
[Ref.: #69480]	glucose-ferment	no	91.547	no

Availability in culture collections External links

[Ref.: #7604]

Culture collection no.

DSM 18756, ATCC 700920, LBB 1

[Ref.: #83003]

SI-ID 45448

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhabdonatronobacter sediminivivens gen. nov., sp. nov. isolated from the sediment of Hutong Qagan Soda Lake.	Zhou H, Yang M, Xue Q, Kumar S, Zhang S, Zhou J, Zhao D, Xiang H	Arch Microbiol	10.1007/s00203-022-02758-4	2022	*
Phylogeny	Alkalilacustris brevis gen. nov., sp. nov., isolated from a soda lake.	Zhang R, Ju Z, Han S, Hou X, Yu Y, Zhang X, Ye Y, Sun C, Zhang G, Wu M	Int J Syst Evol Microbiol	10.1099/ijsem.0.003373	2019	*
Phylogeny	Rhodobaca bogoriensis gen. nov. and sp. nov., an alkaliphilic purple nonsulfur bacterium from African Rift Valley soda lakes.	Milford AD, Achenbach LA, Jung DO, Madigan MT	Arch Microbiol	10.1007/s002030000166	2000	*
	Structure of the dimeric RC-LH1-PufX complex from Rhodobaca bogoriensis investigated by electron microscopy.	Semchonok DA, Chauvin JP, Frese RN, Jungas C, Boekema EJ	Philos Trans R Soc Lond B Biol Sci	10.1098/rstb.2012.0063	2012	*
	Accumulation of unusual carotenoids in the spheroidene pathway, demethylspheroidene and demethylspheroidenone, in an alkaliphilic purple nonsulfur bacterium Rhodobaca bogoriensis.	Takaichi S, Jung DO, Madigan MT	Photosynth Res	10.1023/A:1010666406176	2001	*

References

#7604

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18756

#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 )

#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 .

#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 )

#83003

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID45448.1 )

* 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 Rhodobaca bogoriensis in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Rhodobaca bogoriensis DSM 18756 DSM 18756

Rhodobaca bogoriensis DSM 18756 DSM 18756

Change proposal

Change proposal