Name: Vicinamibacter silvestris Ac_5_C6
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132582

Type strain:

Species: Vicinamibacter silvestris

Strain Designation: Ac_5_C6

Culture col. no.: DSM 29464, LMG 29035

Strain history: <- K. J. Huber, Leibniz-Institut DSMZ GmbH, Braunschweig, Germany; Ac_5_C6 <- A. Geppert

NCBI tax ID(s): 1612172 (species)

SI-ID 406125

DSM 29464

Section

Vicinamibacter silvestris Ac_5_C6 is an aerobe, chemoorganoheterotroph, Gram-negative bacterium that forms circular colonies and was isolated from sandy subtropical savannah soil from a riparian woodland.

colony-forming
Gram-negative
rod-shaped
aerobe
chemoorganoheterotroph
16S sequence
Bacteria

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Acidobacteriota*
	Class	*Vicinamibacteria*
	Order	*Vicinamibacterales*
	Family	*Vicinamibacteraceae*
	Genus	*Vicinamibacter*
	Species	**Vicinamibacter silvestris**
	Full Scientific Name (LPSN)	Vicinamibacter silvestris Huber et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43580]	Gram stain	negative

[Ref.: #43580]	Cell length	1.3-2 µm

[Ref.: #43580]	Cell width	0.6-0.7 µm

[Ref.: #43580]	Cell shape	rod-shaped

[Ref.: #43580]	Motility	no

[Ref.: #43580]	Colony size	1-2 mm
[Ref.: #43580]	Colony color	Yellow
[Ref.: #43580]	Colony shape	circular
[Ref.: #43580]	Cultivation medium used	Agar plates

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43580]

Culture medium

Agar plates

[Ref.: #43580]

Culture medium growth

[Ref.: #24371]

Culture medium

SSE/HD1:10 (DSMZ Medium 1426)

[Ref.: #24371]

Culture medium growth

[Ref.: #24371]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24371]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24371]	growth	28 °C
[Ref.: #43580]	growth	12-40 °C
[Ref.: #43580]	optimum	25.5-31.1 °C

[Ref.: #24371]	Temperature range	mesophilic
[Ref.: #43580]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #43580]			optimum	6.5-8.1
[Ref.: #43580]			growth	4.7-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43580]

Oxygen tolerance

aerobe

[Ref.: #43580]

Nutrition type

chemoorganoheterotroph

[Ref.: #43580]

Ability of spore formation

[Ref.: #43580]

Halophily / tolerance level

non-halophilic

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43580]		NaCl		growth	0-1	%(w/v)
[Ref.: #43580]		NaCl		optimum	0	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43580]	1,2-butandiol ChEBI	-	growth
[Ref.: #43580]	1,2-propandiol ChEBI	-	growth
[Ref.: #43580]	2,3-butanediol ChEBI	-	growth
[Ref.: #43580]	2-hydroxybutyrate ChEBI	-	growth
[Ref.: #43580]	2-oxogluconate	-	growth
[Ref.: #43580]	2-oxoglutarate ChEBI	+/-	growth
[Ref.: #43580]	2-oxopentanoate ChEBI	-	growth
[Ref.: #43580]	4-hydroxybutyrate ChEBI	-	growth
[Ref.: #43580]	4-nitrophenyl beta-D-galactopyranoside ChEBI	-	assimilation
[Ref.: #43580]	4-oxopentanoate ChEBI	-	growth
[Ref.: #43580]	acetate ChEBI	-	growth
[Ref.: #43580]	acetoin ChEBI	+/-	growth
[Ref.: #43580]	adipate ChEBI	-	growth
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #43580]	alanine ChEBI	+/-	growth
[Ref.: #43580]	arabinitol ChEBI	-	growth
[Ref.: #43580]	arabinose ChEBI	+	growth
[Ref.: #43580]	arginine ChEBI	-	growth
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #43580]	ascorbate ChEBI	+/-	growth
[Ref.: #43580]	asparagine ChEBI	+/-	growth
[Ref.: #43580]	aspartate ChEBI	+/-	growth
[Ref.: #43580]	benzoate ChEBI	-	growth
[Ref.: #43580]	beta-hydroxybutyrate ChEBI	-	growth
[Ref.: #43580]	butanol ChEBI	-	growth
[Ref.: #43580]	butyrate ChEBI	-	growth
[Ref.: #43580]	casamino acids	+	growth
[Ref.: #43580]	casein hydrolysate	+	growth
[Ref.: #43580]	cellobiose ChEBI	+	growth
[Ref.: #43580]	citrate ChEBI	+/-	growth
[Ref.: #43580]	crotonate ChEBI	-	growth
[Ref.: #43580]	cysteine ChEBI	-	growth
[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.: #43580]	decanoate ChEBI	-	growth
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #43580]	erythrose ChEBI	-	growth
[Ref.: #43580]	erythrulose ChEBI	-	growth
[Ref.: #43580]	esculin ChEBI	+	hydrolysis
[Ref.: #43580]	ethanol ChEBI	-	growth
[Ref.: #43580]	ethylene glycol ChEBI	-	growth
[Ref.: #43580]	fermented rumen extract	+	growth
[Ref.: #43580]	formate ChEBI	-	growth
[Ref.: #43580]	fructose ChEBI	+	growth
[Ref.: #43580]	fucose ChEBI	+/-	growth
[Ref.: #43580]	fumarate ChEBI	+	growth
[Ref.: #43580]	galactitol ChEBI	-	growth
[Ref.: #43580]	galactose ChEBI	+	growth
[Ref.: #43580]	gelatin ChEBI	+	hydrolysis
[Ref.: #43580]	gluconate ChEBI	+	growth
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #43580]	glucosamine ChEBI	-	growth
[Ref.: #43580]	glucose ChEBI	-	fermentation
[Ref.: #43580]	glucose ChEBI	+	growth
[Ref.: #43580]	glucuronate ChEBI	-	growth
[Ref.: #43580]	glutamine ChEBI	-	growth
[Ref.: #43580]	glycine ChEBI	-	growth
[Ref.: #43580]	glycolate ChEBI	-	growth
[Ref.: #43580]	glyoxylate ChEBI	-	growth
[Ref.: #43580]	heptanoate ChEBI	+/-	growth
[Ref.: #43580]	histidine ChEBI	-	growth
[Ref.: #43580]	hydroxyproline ChEBI	+	growth
[Ref.: #43580]	isobutyrate ChEBI	-	growth
[Ref.: #43580]	isocitrate ChEBI	-	growth
[Ref.: #43580]	isoleucine ChEBI	-	growth
[Ref.: #43580]	isovalerate ChEBI	+/-	growth
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #43580]	L-glutamate ChEBI	+	growth
[Ref.: #43580]	lactate ChEBI	-	growth
[Ref.: #43580]	lactose ChEBI	+	growth
[Ref.: #43580]	laminarin ChEBI	+/-	growth
[Ref.: #43580]	leucine ChEBI	-	growth
[Ref.: #43580]	lysine ChEBI	-	growth
[Ref.: #43580]	lyxose ChEBI	+	growth
[Ref.: #43580]	malate ChEBI	-	growth
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #43580]	maleic acid ChEBI	+/-	growth
[Ref.: #43580]	maltose ChEBI	+	growth
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #43580]	mannitol ChEBI	-	growth
[Ref.: #43580]	mannose ChEBI	+/-	growth
[Ref.: #43580]	melezitose ChEBI	+	growth
[Ref.: #43580]	methanol ChEBI	-	growth
[Ref.: #43580]	methionine ChEBI	-	growth
[Ref.: #43580]	myo-inositol ChEBI	-	growth
[Ref.: #43580]	N-acetylgalactosamine ChEBI	+	growth
[Ref.: #43580]	N-acetylglucosamine ChEBI	+	growth
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #43580]	nicotinate ChEBI	-	growth
[Ref.: #43580]	nitrate ChEBI	-	reduction
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #43580]	octanoate ChEBI	-	growth
[Ref.: #43580]	ornithine ChEBI	-	growth
[Ref.: #43580]	oxaloacetate ChEBI	-	growth
[Ref.: #43580]	peptone	+	growth
[Ref.: #43580]	phenylalanine ChEBI	-	growth
[Ref.: #43580]	proline ChEBI	+/-	growth
[Ref.: #43580]	propanol ChEBI	-	growth
[Ref.: #43580]	propionate ChEBI	-	growth
[Ref.: #43580]	protocatechuate ChEBI	+/-	growth
[Ref.: #43580]	pyruvate ChEBI	+/-	growth
[Ref.: #43580]	raffinose ChEBI	+	growth
[Ref.: #43580]	rhamnose ChEBI	+	growth
[Ref.: #43580]	ribitol ChEBI	-	growth
[Ref.: #43580]	serine ChEBI	-	growth
[Ref.: #43580]	shikimate ChEBI	+/-	growth
[Ref.: #43580]	sodium malonate ChEBI	-	growth
[Ref.: #43580]	sorbitol ChEBI	-	growth
[Ref.: #43580]	sorbose ChEBI	-	growth
[Ref.: #43580]	succinate ChEBI	-	growth
[Ref.: #43580]	sucrose ChEBI	+	growth
[Ref.: #43580]	tartrate ChEBI	-	growth
[Ref.: #43580]	threonine ChEBI	-	growth
[Ref.: #43580]	trehalose ChEBI	+	growth
[Ref.: #43580]	trimethoxybenzoate	+/-	growth
[Ref.: #43580]	tryptophan ChEBI	-	growth
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #43580]	tween 80 ChEBI	-	growth
[Ref.: #43580]	tyrosine ChEBI	-	growth
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #43580]	valine ChEBI	-	growth
[Ref.: #43580]	xylitol ChEBI	-	growth
[Ref.: #43580]	xylose ChEBI	+	growth
[Ref.: #43580]	yeast extract	+	growth
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #43580]	ampicillin ChEBI				yes	100	µg/mL
[Ref.: #43580]	carbenicillin ChEBI				yes	100	µg/mL
[Ref.: #43580]	chloramphenicol ChEBI				yes	34	µg/mL
[Ref.: #43580]	erythromycin ChEBI				yes	25	µg/mL
[Ref.: #43580]	gentamicin ChEBI				yes	16	µg/mL
[Ref.: #43580]	kanamycin ChEBI				yes	50	µg/mL
[Ref.: #43580]	spectinomycin ChEBI	yes	25	µg/mL
[Ref.: #43580]	streptomycin ChEBI	yes	25	µg/mL
[Ref.: #43580]	tetracycline ChEBI				yes	12.5	µg/mL

	Metabolite production	Metabolite	Production
[Ref.: #43580]		indole ChEBI	no
[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.: #43580]	acid phosphatase	+	3.1.3.2
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #43580]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #43580]	alpha-chymotrypsin	+	3.4.21.1
[Ref.: #68382]	alpha-chymotrypsin	+	3.4.21.1	* from API zym
[Ref.: #43580]	alpha-fucosidase	-	3.2.1.51
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #43580]	alpha-galactosidase	-	3.2.1.22
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #43580]	alpha-glucosidase	-	3.2.1.20
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #43580]	alpha-mannosidase	-	3.2.1.24
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #43580]	arginine dihydrolase	-	3.5.3.6
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #43580]	beta-galactosidase	-	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #43580]	beta-glucosidase	-	3.2.1.21
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #43580]	beta-glucuronidase	-	3.2.1.31
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #43580]	cystine arylamidase	+/-	3.4.11.3
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #43580]	esterase (C 4)	+
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #43580]	esterase Lipase (C 8)	+/-
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #43580]	leucine arylamidase	+	3.4.11.1
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #43580]	lipase (C 14)	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #43580]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #43580]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #43580]	trypsin	+	3.4.21.4
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #43580]	urease	-	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #43580]	valine arylamidase	+
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #24371]	24185	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	+
[Ref.: #24371]	25387	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	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.: #24371]	14352	-	+	-	-	-	+	+	-	+	+	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #24371]	Sample type/isolated from	sandy subtropical savannah soil from a riparian woodland
[Ref.: #24371]	Geographic location (country and/or sea, region)	south of the Okavango river near the village of Mashare (17° 53' 35.52'' S 20° 14' 57.52'' E; 1061 m above sea level)
[Ref.: #24371]	Country	Namibia
[Ref.: #24371]	Country ISO 3 Code	NAM
[Ref.: #24371]	Continent	Africa
[Ref.: #24371]	Geographic location	-17.8932°/20.2493°

[Ref.: #43580]	Sample type/isolated from	a riparian woodland soil collected from south of the Okavango river, 1061 m abover sea level
[Ref.: #43580]	Geographic location (country and/or sea, region)	Village od Mashare
[Ref.: #43580]	Country	Namibia
[Ref.: #43580]	Country ISO 3 Code	NAM
[Ref.: #43580]	Continent	Africa
[Ref.: #43580]	Geographic location	-17.8930°/20.2490°
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Sandy
#Climate	#Temperate	#Subtropical
#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

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

[Ref.: #24371]

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.: #24371]	Vicinamibacter silvestris strain Ac_5_C6 16S ribosomal RNA gene, partial sequence	KP761690	1515	ENA	1612172 tax ID

[Ref.: #43580]	GC-content	65.9 mol%	high performance liquid chromatography (HPLC)
[Ref.: #24371]	GC-content	65.9 mol%

Availability in culture collections External links

[Ref.: #24371]

Culture collection no.

DSM 29464, LMG 29035

[Ref.: #90899]

SI-ID 406125

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	The first representative of the globally widespread subdivision 6 Acidobacteria,Vicinamibacter silvestris gen. nov., sp. nov., isolated from subtropical savannah soil.	Huber KJ, Geppert AM, Wanner G, Fosel BU, Wust PK, Overmann J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001131	2016	*
Phylogeny	Luteitalea pratensis gen. nov., sp. nov. a new member of subdivision 6 Acidobacteria isolated from temperate grassland soil.	Vieira S, Luckner M, Wanner G, Overmann J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001827	2017	*

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 )

#24371

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29464

#43580

Katharina J. Huber, Alicia M. Geppert, Gerhard Wanner, Bärbel U. Fösel, Pia K. Wüst, Jörg Overmann: The first representative of the globally widespread subdivision 6 Acidobacteria, Vicinamibacter silvestris gen. nov., sp. nov., isolated from subtropical savannah soil. IJSEM 66: 2971 - 2979 2016 ( DOI 10.1099/ijsem.0.001131 , PubMed 27150379 )

#68369

Automatically annotated from API 20NE .

#68382

Automatically annotated from API zym .

#90899

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-ID406125.1 )

* These data were automatically processed and therefore are not curated

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