Name: Rivihabitans pingtungensis Npb-03
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 130470

Type strain:

Species: Rivihabitans pingtungensis

Strain Designation: Npb-03

Culture col. no.: DSM 29661, BCRC 80376, KCTC 23712, LMG 26668

Strain history: <- KCTC <- S.-Y. Sheu et al., Dept. of Marine Biotechnology, Kaohsiung, Taiwan

NCBI tax ID(s): 1054498 (species)

SI-ID 398761

DSM 29661

Section

Rivihabitans pingtungensis Npb-03 is a mesophilic, motile bacterium that was isolated from freshwater sample.

motile
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	*Betaproteobacteria*
	Order	*Neisseriales*
	Family	*Neisseriaceae*
	Genus	*Rivihabitans*
	Species	**Rivihabitans pingtungensis**
	Full Scientific Name (LPSN)	Rivihabitans pingtungensis (Sheu et al. 2014) Deshmukh and Oren 2023

Synonym

Rivicola pingtungensis

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.993

[Ref.: #69480]	Motility	yes Confidence in %96.757

Multimedia content

[Ref.: #22105]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #22105]

Culture medium

REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)

[Ref.: #22105]

Culture medium growth

[Ref.: #22105]

Culture medium link

Medium recipe at MediaDive

[Ref.: #22105]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #22105]			growth	28 °C

[Ref.: #22105]

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 %99.971

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #22105]	23414	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	-	-	+

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

[Ref.: #22105]	Sample type/isolated from	freshwater sample
[Ref.: #22105]	Geographic location (country and/or sea, region)	Pingtung County, Beishi River
[Ref.: #22105]	Country	Taiwan
[Ref.: #22105]	Country ISO 3 Code	TWN
[Ref.: #22105]	Continent	Asia
[Ref.: #22105]	Geographic location	22.3703°/120.5920°
* marker position based on {}

Isolation sources categories

#Environmental

#Aquatic

#Freshwater

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JN104394 (>99% sequence identity) for Rivicola pingtungensis subclade from Microbeatlas

Aquatic Samples	3856
Soil Samples	51
Animal Samples	325
Plant Samples	56
Total Samples	4288

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

[Ref.: #22105]

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.: #22105]	Rivicola pingtungensis strain Npb-03 16S ribosomal RNA gene, partial sequence	JN104394	1424	ENA	1054498 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Rivihabitans pingtungensis DSM 29661	GCA_003201855	scaffold	GenBank	1054498 tax ID	*
[Ref.: #66792]	Rivicola pingtungensis strain DSM 29661	1054498.3	wgs	PATRIC	1054498 tax ID	*
[Ref.: #66792]	Rivicola pingtungensis DSM 29661	2770939562	draft	JGI IMG/M	1054498 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: Rivicola pingtungensis DSM 29661 NCBI: GCA_003201855.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rivicola pingtungensis DSM 29661 NCBI: GCA_003201855.1
[Ref.: #69480]	flagellated	yes	83.179	no
[Ref.: #69480]	gram-positive	no	98.926	no
[Ref.: #69480]	anaerobic	no	95.59	no
[Ref.: #69480]	halophile	no	92.899	no
[Ref.: #69480]	spore-forming	no	94.617	no
[Ref.: #69480]	thermophile	no	98.452	yes
[Ref.: #69480]	glucose-util	no	51.742	no
[Ref.: #69480]	aerobic	yes	59.439	no
[Ref.: #69480]	motile	yes	93.203	no
[Ref.: #69480]	glucose-ferment	no	91.122	no

Availability in culture collections External links

[Ref.: #22105]

Culture collection no.

DSM 29661, BCRC 80376, KCTC 23712, LMG 26668

[Ref.: #88999]

SI-ID 398761

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rivicola pingtungensis gen. nov., sp. nov., a new member of the family Neisseriaceae isolated from a freshwater river.	Sheu SY, Chen JC, Young CC, Chen WM	Int J Syst Evol Microbiol	10.1099/ijs.0.055285-0	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 )

#22105

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29661

#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) .

#68369

Automatically annotated from API 20NE .

#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 )

#88999

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-ID398761.1 )

* 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 Rivicola pingtungensis in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Rivicola pingtungensis DSM 29661

Rivicola pingtungensis DSM 29661

Change proposal

Change proposal