Name: Exiguobacterium sibiricum 255-15
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 18116

Type strain:

Species: Exiguobacterium sibiricum

Strain Designation: 255-15

Culture col. no.: CCUG 55495, DSM 17290, CIP 109462, JCM 13490

Strain history: CIP <- 2007, DSMZ <- D.F. Rodrigues, NASA, East Lansing, Michigan, USA <- T.Vishnivetskaya, Russian Acad. Sci., Moscow, Russia: strain 255-15

NCBI tax ID(s): 332410 (species)

SI-ID 297184

DSM 17290, JCM 13490, CIP 109462, CCUG 55495

Other strains from Exiguobacterium sibiricum

E. sibiricum CCUG 52046 B

Section

Exiguobacterium sibiricum 255-15 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from permafrost core.

Gram-positive
motile
rod-shaped
aerobe
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	*Bacillota*
	Class	*Bacilli*
	Order	*Caryophanales*
	Family	*Bacillaceae*
	Genus	*Exiguobacterium*
	Species	**Exiguobacterium sibiricum**
	Full Scientific Name (LPSN)	Exiguobacterium sibiricum Rodrigues et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #122598]	Gram stain	positive

[Ref.: #122598]	Cell shape	rod-shaped

[Ref.: #122598]	Motility	yes

[Ref.: #60613]

Incubation period

1 day

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6875]

Culture medium

TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)

[Ref.: #6875]

Culture medium growth

[Ref.: #6875]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6875]

Culture medium composition

expand / minimize

[Ref.: #37567]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #37567]

Culture medium growth

[Ref.: #37567]

Culture medium composition

expand / minimize

[Ref.: #122598]

Culture medium

CIP Medium 338

[Ref.: #122598]

Culture medium growth

[Ref.: #122598]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #122598]

Culture medium

CIP Medium 72

[Ref.: #122598]

Culture medium growth

[Ref.: #122598]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #6875]	growth	28 °C
[Ref.: #37567]	growth	30 °C
[Ref.: #60613]	growth	30 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #6875]	Temperature range	mesophilic
[Ref.: #37567]	Temperature range	mesophilic
[Ref.: #60613]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #60613]	Oxygen tolerance	aerobe
[Ref.: #122598]	Oxygen tolerance	facultative anaerobe

[Ref.: #67770]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68371]	cellobiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fructose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-galactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-glucose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-lyxose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-mannose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-ribose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-sorbitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-tagatose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	D-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	erythritol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	galactitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	gentiobiose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	gluconate ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycerol ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	glycogen ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	inulin ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-arabitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-fucose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-rhamnose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-sorbose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	L-xylose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	lactose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	maltose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	melezitose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	melibiose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-glucopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl alpha-D-mannoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	methyl beta-D-xylopyranoside ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	myo-inositol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	N-acetylglucosamine ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #122598]	nitrate ChEBI	-	reduction
[Ref.: #122598]	nitrite ChEBI	-	reduction
[Ref.: #68371]	Potassium 2-ketogluconate ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	Potassium 5-ketogluconate ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	raffinose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	ribitol ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	salicin ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	starch ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	sucrose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	trehalose ChEBI	+	builds acid from	* from API 50CH acid
[Ref.: #68371]	turanose ChEBI	-	builds acid from	* from API 50CH acid
[Ref.: #68371]	xylitol ChEBI	-	builds acid from	* from API 50CH acid
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #122598]		indole ChEBI	no

	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.: #122598]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[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.: #122598]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #122598]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 50CH acid:

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

	API ID	ControlQ	Acid from glycerolGLY	Acid from erythritolERY	Acid from D-arabinoseDARA	Acid from L-arabinoseLARA	Acid from D-riboseRIB	Acid from D-xyloseDXYL	Acid from L-xyloseLXYL	Acid from D-adonitolADO	Acid from methyl beta-D-xylopyranosideMDX	Acid from D-galactoseGAL	Acid from D-glucoseGLU	Acid from D-fructoseFRU	Acid from D-mannoseMNE	Acid from L-sorboseSBE	Acid from L-rhamnoseRHA	Acid from dulcitolDUL	Acid from inositolINO	Acid from D-mannitolMAN	Acid from D-sorbitolSOR	Acid from methyl alpha-D-mannopyranosideMDM	Acid from methyl alpha-D-glucopyranosideMDG	Acid from N-acetyl-glucosamineNAG	Acid from amygdalinAMY	Acid from arbutinARB	Acid from esculinESC	Acid from salicinSAL	Acid from cellobioseCEL	Acid from maltoseMAL	Acid from lactoseLAC	Acid from melibioseMEL	Acid from sucroseSAC	Acid from trehaloseTRE	Acid from inulinINU	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from starchAMD	Acid from glycogenGLYG	Acid from xylitolXLT	Acid from gentiobioseGEN	Acid from turanoseTUR	Acid from D-lyxoseLYX	Acid from D-tagatoseTAG	Acid from D-fucoseDFUC	Acid from L-fucoseLFUC	Acid from D-arabitolDARL	Acid from L-arabitolLARL	Acid from gluconateGNT	Acid from 2-Ketogluconate2KG	Acid from 5-Ketogluconate5KG
[Ref.: #122598]	11565	not determinedn.d.	+	-	-	-	+	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	+	+/-	+/-	+/-	+	-	+	-	-	+	+	-	-	-	+	+	-	+	-	-	-	-	-	-	-	+	-	+

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.: #122598]	11881	-	+	+	+	-	-	-	-	-	-	+	-	+	-	-	+	+	-	-	-

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

[Ref.: #6875]	Sample type/isolated from	permafrost core
[Ref.: #6875]	Geographic location (country and/or sea, region)	Kolyma Lowland
[Ref.: #6875]	Country	Russia
[Ref.: #6875]	Country ISO 3 Code	RUS
[Ref.: #6875]	Continent	Asia

[Ref.: #60613]	Sample type/isolated from	Permafrost core

[Ref.: #67770]	Sample type/isolated from	Siberian permafrost

[Ref.: #122598]	Sample type/isolated from	Permafrost core
[Ref.: #122598]	Geographic location (country and/or sea, region)	Siberia
[Ref.: #122598]	Country	Russian Federation
[Ref.: #122598]	Country ISO 3 Code	RUS
[Ref.: #122598]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Core sample
#Environmental	#Terrestrial	#Permafrost

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence NR_075006 (>99% sequence identity) for Exiguobacterium from Microbeatlas

Aquatic Samples	2950
Soil Samples	710
Animal Samples	3659
Plant Samples	946
Total Samples	8265

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

[Ref.: #6875]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #122598]	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.: #6875]	Exiguobacterium sibiricum 255-15 small subunit ribosomal RNA (rrn) gene, partial sequence	AY444839	688	ENA	262543 tax ID
[Ref.: #67770]	Exiguobacterium sibiricum strain 255-15 16S ribosomal RNA, partial sequence	NR_075006	1555	GenBank	332410 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Exiguobacterium sibiricum 255-15	GCA_000019905	complete	GenBank	262543 tax ID	*
[Ref.: #66792]	Exiguobacterium sibiricum 255-15	262543.36	plasmid	PATRIC	262543 tax ID	*
[Ref.: #66792]	Exiguobacterium sibiricum 255-15	262543.35	plasmid	PATRIC	262543 tax ID	*
[Ref.: #66792]	Exiguobacterium sibiricum 255-15	262543.8	complete	PATRIC	262543 tax ID	*
[Ref.: #66792]	Exiguobacterium sibiricum 255-15	641522626	complete	JGI IMG/M	262543 tax ID	*

[Ref.: #6875]

GC-content

47.7 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: Exiguobacterium sibiricum 255-15 255-15 NCBI: GCA_000019905.1
[Ref.: #69480]	motile	yes	90.742	no
[Ref.: #69480]	flagellated	yes	73.813	no
[Ref.: #69480]	gram-positive	yes	88.796	no
[Ref.: #69480]	anaerobic	no	98.438	no
[Ref.: #69480]	aerobic	yes	90.703	yes
[Ref.: #69480]	halophile	yes	74.525	no
[Ref.: #69480]	spore-forming	no	80.086	no
[Ref.: #69480]	thermophile	no	99.566	yes
[Ref.: #69480]	glucose-util	yes	90.015	no
[Ref.: #69480]	glucose-ferment	no	76.377	no

Availability in culture collections External links

[Ref.: #6875]

Culture collection no.

CCUG 55495, DSM 17290, CIP 109462, JCM 13490

[Ref.: #87104]

SI-ID 297184

Literature:

Only first 10 entries are displayed. Click here to see all.

	Title	Authors	Journal	DOI	Year
Metabolism	The Gram-negative bacterium Azotobacter chroococcum NCIMB 8003 employs a new glycoside hydrolase family 70 4,6-alpha-glucanotransferase enzyme (GtfD) to synthesize a reuteran like polymer from maltodextrins and starch.	Gangoiti J, van Leeuwen SS, Vafiadi C, Dijkhuizen L	Biochim Biophys Acta	10.1016/j.bbagen.2016.02.005	2016	*
Genetics	Complete genome sequence of the Thermophilic Bacterium Exiguobacterium sp. AT1b.	Vishnivetskaya TA, Lucas S, Copeland A, Lapidus A, Glavina del Rio T, Dalin E, Tice H, Bruce DC, Goodwin LA, Pitluck S, Saunders E, Brettin T, Detter C, Han C, Larimer F, Land ML, Hauser LJ, Kyrpides NC, Ovchinnikova G, Kathariou S, Ramaley RF, Rodrigues DF, Hendrix C, Richardson P, Tiedje JM	J Bacteriol	10.1128/JB.00303-11	2011	*
Metabolism	Metabolic activity of Siberian permafrost isolates, Psychrobacter arcticus and Exiguobacterium sibiricum, at low water activities.	Ponder MA, Thomashow MF, Tiedje JM	Extremophiles	10.1007/s00792-008-0151-0	2008	*
Phylogeny	Exiguobacterium flavidum sp. nov., isolated from the Red Maple Lake.	Meng X, Chang YQ, Zhou LY, Du ZJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.004048	2020	*
Enzymology	The Exiguobacterium sibiricum 255-15 GtfC Enzyme Represents a Novel Glycoside Hydrolase 70 Subfamily of 4,6-alpha-Glucanotransferase Enzymes.	Gangoiti J, Pijning T, Dijkhuizen L	Appl Environ Microbiol	10.1128/AEM.03420-15	2015	*
Genetics	Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15.	Han GW, Elsliger MA, Yeates TO, Xu Q, Murzin AG, Krishna SS, Jaroszewski L, Abdubek P, Astakhova T, Axelrod HL, Carlton D, Chen C, Chiu HJ, Clayton T, Das D, Deller MC, Duan L, Ernst D, Feuerhelm J, Grant JC, Grzechnik A, Jin KK, Johnson HA, Klock HE, Knuth MW, Kozbial P, Kumar A, Lam WW, Marciano D, McMullan D, Miller MD, Morse AT, Nigoghossian E, Okach L, Reyes R, Rife CL, Sefcovic N, Tien HJ, Trame CB, van den Bedem H, Weekes D, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/S1744309110025534	2010	*
Metabolism	Architecture of thermal adaptation in an Exiguobacterium sibiricum strain isolated from 3 million year old permafrost: a genome and transcriptome approach.	Rodrigues DF, Ivanova N, He Z, Huebner M, Zhou J, Tiedje JM	BMC Genomics	10.1186/1471-2164-9-547	2008	*
Phylogeny	Exiguobacterium soli sp. nov., a psychrophilic bacterium from the McMurdo Dry Valleys, Antarctica.	Chaturvedi P, Prabahar V, Manorama R, Pindi PK, Bhadra B, Begum Z, Shivaji S	Int J Syst Evol Microbiol	10.1099/ijs.0.2008/000067-0	2008	*
Cultivation	Effect of low temperature and culture media on the growth and freeze-thawing tolerance of Exiguobacterium strains.	Vishnivetskaya TA, Siletzky R, Jefferies N, Tiedje JM, Kathariou S	Cryobiology	10.1016/j.cryobiol.2007.01.008	2007	*
Genetics	Proteomic analysis of cold adaptation in a Siberian permafrost bacterium--Exiguobacterium sibiricum 255-15 by two-dimensional liquid separation coupled with mass spectrometry.	Qiu Y, Kathariou S, Lubman DM	Proteomics	10.1002/pmic.200600071	2006	*
Phylogeny	Characterization of Exiguobacterium isolates from the Siberian permafrost. Description of Exiguobacterium sibiricum sp. nov.	Rodrigues DF, Goris J, Vishnivetskaya T, Gilichinsky D, Thomashow MF, Tiedje JM	Extremophiles	10.1007/s00792-005-0497-5	2006	*
	Xerotolerance: A New Property in Exiguobacterium Genus.	Lopez MC, Galan B, Carmona M, Navarro Llorens JM, Pereto J, Porcar M, Getino L, Olivera ER, Luengo JM, Castro L, Garcia JL	Microorganisms	10.3390/microorganisms9122455	2021	*

References

#6875

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17290

#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 )

#37567 ; Curators of the CIP;
#60613 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55495

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68371

Automatically annotated from API 50CH acid .

#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) .

#87104

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-ID297184.1 )

#122598 Collection of Institut Pasteur ; Curators of the CIP; CIP 109462
* These data were automatically processed and therefore are not curated

Change proposal

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Exiguobacterium sibiricum 255-15 255-15

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Change proposal