Name: Pontibacter roseus SRC-1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 3829

Type strain:

Species: Pontibacter roseus

Strain Designation: SRC-1

Culture col. no.: DSM 17521, CCTCC AB 207222, CIP 109903, MTCC 7260

Strain history: CIP <- 2008, DSMZ <- MTCC <- K. Suresh, Chandigarh, India: strain SRC-1

NCBI tax ID(s): 1122967 (strain), 336989 (species)

SI-ID 297177

DSM 17521, CIP 109903

Section

Pontibacter roseus SRC-1 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from muddy water from an occasional drainage system.

Gram-negative
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	*Bacteroidota*
	Class	*Cytophagia*
	Order	*Cytophagales*
	Family	*Hymenobacteraceae*
	Genus	*Pontibacter*
	Species	**Pontibacter roseus**
	Full Scientific Name (LPSN)	Pontibacter roseus (Suresh et al. 2006) Wang et al. 2010

Synonym

Effluviibacter roseus

Information on morphological and physiological properties Morphology

[Ref.: #31733]	Gram stain	negative
[Ref.: #122264]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.995

[Ref.: #31733]	Cell length	01-03 µm

[Ref.: #31733]	Cell width	0.3-0.5 µm

[Ref.: #31733]	Cell shape	rod-shaped
[Ref.: #122264]	Cell shape	rod-shaped

[Ref.: #31733]	Motility	no
[Ref.: #122264]	Motility	no

[Ref.: #31733]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #33336]

Culture medium

MEDIUM 328- for nutrient agar

[Ref.: #33336]

Culture medium growth

[Ref.: #33336]

Culture medium composition

expand / minimize

[Ref.: #122264]

Culture medium

CIP Medium 328

[Ref.: #122264]

Culture medium growth

[Ref.: #122264]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #31733]	growth	04-37 °C
[Ref.: #31733]	optimum	30-37 °C
[Ref.: #33336]	growth	30 °C

[Ref.: #31733]	Temperature range	mesophilic
[Ref.: #33336]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31733]			optimum	08-10
[Ref.: #31733]			growth	06-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31733]	Oxygen tolerance	aerobe
[Ref.: #122264]	Oxygen tolerance	obligate aerobe

[Ref.: #31733]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.918

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31733]		NaCl		growth	0-8	%
[Ref.: #31733]		NaCl		optimum	0-8	%

[Ref.: #31733]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31733]	fructose ChEBI	+	carbon source
[Ref.: #31733]	galactose ChEBI	+	carbon source
[Ref.: #31733]	glucose ChEBI	+	carbon source
[Ref.: #31733]	lactose ChEBI	+	carbon source
[Ref.: #122264]	nitrate ChEBI	-	reduction
[Ref.: #122264]	nitrite ChEBI	-	reduction
[Ref.: #31733]	raffinose ChEBI	+	carbon source
[Ref.: #31733]	sucrose ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #31733]	catalase	+	1.11.1.6
[Ref.: #122264]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #31733]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #122264]	oxidase	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #122264]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #122264]	12208	-	+	-	-	-	+	+	+	+	-	-	+	-	-	-	-	-	-	-	-

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

[Ref.: #7040]	Sample type/isolated from	muddy water from an occasional drainage system
[Ref.: #7040]	Geographic location (country and/or sea, region)	Chandigarh
[Ref.: #7040]	Country	India
[Ref.: #7040]	Country ISO 3 Code	IND
[Ref.: #7040]	Continent	Asia

[Ref.: #122264]	Sample type/isolated from	Environment, Muddy water, drainage system
[Ref.: #122264]	Geographic location (country and/or sea, region)	Chandigarh
[Ref.: #122264]	Country	India
[Ref.: #122264]	Country ISO 3 Code	IND
[Ref.: #122264]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	-
#Environmental	#Terrestrial	#Mud (Sludge)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AM049256 (>99% sequence identity) for Pontibacter roseus subclade from Microbeatlas

Aquatic Samples	52
Soil Samples	261
Animal Samples	53
Plant Samples	24
Total Samples	390

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

[Ref.: #7040]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122264]	Biosafety level	1	Risk group (French classification)

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.: #7040]	Effluviibacter roseus partial 16S rRNA gene, type strain SRC-1T	AM049256	1401	ENA	336989 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pontibacter roseus DSM 17521	GCA_000373265	scaffold	GenBank	1122967 tax ID	*
[Ref.: #66792]	Pontibacter roseus DSM 17521	1122967.3	wgs	PATRIC	1122967 tax ID	*
[Ref.: #66792]	Pontibacter roseus DSM 17521	2515154084	draft	JGI IMG/M	1122967 tax ID	*

[Ref.: #7040]

GC-content

59.5 mol%

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: Pontibacter roseus DSM 17521 DSM 17521 NCBI: GCA_000373265.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pontibacter roseus DSM 17521 DSM 17521 NCBI: GCA_000373265.1
[Ref.: #69480]	motile	no	89.119	no
[Ref.: #69480]	flagellated	no	96.314	yes
[Ref.: #69480]	gram-positive	no	98.091	yes
[Ref.: #69480]	anaerobic	no	99.11	no
[Ref.: #69480]	aerobic	yes	90.214	yes
[Ref.: #69480]	halophile	no	78.545	no
[Ref.: #69480]	spore-forming	no	93.928	no
[Ref.: #69480]	thermophile	no	96.314	yes
[Ref.: #69480]	glucose-util	yes	90.465	no
[Ref.: #69480]	glucose-ferment	no	83.721	no

Availability in culture collections External links

[Ref.: #7040]

Culture collection no.

DSM 17521, CCTCC AB 207222, CIP 109903, MTCC 7260

[Ref.: #73340]

SI-ID 297177

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	High quality draft genome sequence and analysis of Pontibacter roseus type strain SRC-1(T) (DSM 17521(T)) isolated from muddy waters of a drainage system in Chandigarh, India.	Mukherjee S, Lapidus A, Shapiro N, Cheng JF, Han J, Reddy T, Huntemann M, Ivanova N, Mikhailova N, Chen A, Palaniappan K, Spring S, Goker M, Markowitz V, Woyke T, Tindall BJ, Klenk HP, Kyrpides NC, Pati A	Stand Genomic Sci	10.1186/1944-3277-10-8	2015	*
Phylogeny	Pontibacter humi sp. nov., isolated from mountain soil.	Srinivasan S, Lee JJ, Lee SS, Kim MK	Curr Microbiol	10.1007/s00284-014-0580-1	2014	*
Phylogeny	Pontibacter xinjiangensis sp. nov., in the phylum 'Bacteroidetes', and reclassification of [Effluviibacter] roseus as Pontibacter roseus comb. nov.	Wang Y, Zhang K, Cai F, Zhang L, Tang Y, Dai J, Fang C	Int J Syst Evol Microbiol	10.1099/ijs.0.011395-0	2009	*
Phylogeny	Effluviibacter roseus gen. nov., sp. nov., isolated from muddy water, belonging to the family "Flexibacteraceae".	Suresh K, Mayilraj S, Chakrabarti T	Int J Syst Evol Microbiol	10.1099/ijs.0.64144-0	2006	*

References

#7040

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17521

#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 )

#31733

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 #28009 (see below)

#33336 ; Curators of the CIP;

#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) .

#68382

Automatically annotated from API zym .

#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 )

#73340

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-ID297177.1 )

#122264 Collection of Institut Pasteur ; Curators of the CIP; CIP 109903

#28009

IJSEM 1703 2006 ( DOI 10.1099/ijs.0.64144-0 , PubMed 16825654 )

* These data were automatically processed and therefore are not curated

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Pontibacter roseus DSM 17521 DSM 17521

Pontibacter roseus DSM 17521 DSM 17521

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