Name: Rhizorhabdus histidinilytica UM2
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14262

Type strain:

Species: Rhizorhabdus histidinilytica

Strain Designation: UM2

Culture col. no.: DSM 24951, CCM 7545, MTCC 9473

Strain history: <- CCM <- R. Lal, Department of Zoology, Univ. of Delhi; UM2

NCBI tax ID(s): 439228 (species)

Section

Rhizorhabdus histidinilytica UM2 is an aerobe, Gram-negative, motile bacterium that was isolated from contaminated soil from hexachlorocyclohexane dump site.

Gram-negative
motile
rod-shaped
aerobe
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	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Rhizorhabdus*
	Species	**Rhizorhabdus histidinilytica**
	Full Scientific Name (LPSN)	Rhizorhabdus histidinilytica (Nigam et al. 2010) Hördt et al. 2020

Synonym

Sphingomonas histidinilytica

Information on morphological and physiological properties Morphology

[Ref.: #29228]	Gram stain	negative

[Ref.: #29228]	Cell length	1.4 µm

[Ref.: #29228]	Cell width	0.4 µm

[Ref.: #29228]	Cell shape	rod-shaped

[Ref.: #29228]	Motility	yes

[Ref.: #29228]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #29228]			growth	04-40 °C
[Ref.: #29228]			optimum	28 °C

[Ref.: #29228]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #29228]			optimum	7.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29228]

Oxygen tolerance

aerobe

[Ref.: #29228]

Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29228]		NaCl		optimum	1.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29228]	arabinose ChEBI	+	carbon source
[Ref.: #29228]	D-tryptophan ChEBI	+	carbon source
[Ref.: #29228]	histidine ChEBI	+	carbon source
[Ref.: #29228]	mannose ChEBI	+	carbon source
[Ref.: #29228]	melibiose ChEBI	+	carbon source
[Ref.: #29228]	nitrate ChEBI	+	reduction
[Ref.: #29228]	ornithine ChEBI	+	carbon source
[Ref.: #29228]	proline ChEBI	+	carbon source
[Ref.: #29228]	serine ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29228]		catalase	+	1.11.1.6

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

[Ref.: #17806]	Sample type/isolated from	contaminated soil from hexachlorocyclohexane dump site
[Ref.: #17806]	Geographic location (country and/or sea, region)	Uttar Pradesh, Lucknow, Ummari village
[Ref.: #17806]	Country	India
[Ref.: #17806]	Country ISO 3 Code	IND
[Ref.: #17806]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	-
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EF530202 (>99% sequence identity) for Sphingomonas from Microbeatlas

Aquatic Samples	171
Soil Samples	335
Animal Samples	94
Plant Samples	56
Total Samples	656

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

[Ref.: #17806]

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.: #17806]	Sphingomonas histidinilytica strain UM2 16S ribosomal RNA gene, partial sequence	EF530202	1394	ENA	439228 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rhizorhabdus histidinilytica UM2	GCA_900167915	contig	GenBank	439228 tax ID	*

[Ref.: #29228]

GC-content

66.9 mol%

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rhizorhabdus histidinilytica UM2 NCBI: GCA_900167915.1
[Ref.: #69480]	motile	yes	84.62	yes
[Ref.: #69480]	flagellated	no	89.746	no
[Ref.: #69480]	gram-positive	no	96.035	no
[Ref.: #69480]	anaerobic	no	99.061	yes
[Ref.: #69480]	aerobic	yes	94.996	yes
[Ref.: #69480]	halophile	no	95.806	yes
[Ref.: #69480]	spore-forming	no	95.223	yes
[Ref.: #69480]	thermophile	no	97.79	yes
[Ref.: #69480]	glucose-util	yes	78.133	no
[Ref.: #69480]	glucose-ferment	no	92.514	no

Availability in culture collections External links

[Ref.: #17806]

Culture collection no.

DSM 24951, CCM 7545, MTCC 9473

References

#17806

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24951

#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 )

#29228

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 #25649 (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) .

#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) .

#25649

IJSEM 1038 2010 ( DOI 10.1099/ijs.0.008995-0 , PubMed 19666786 )

* These data were automatically processed and therefore are not curated

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