Paenibacillus timonensis (DSM 16943, CCUG 48216, CIP 108005)

Name: Paenibacillus timonensis (DSM 16943, CCUG 48216, CIP 108005)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11580

Type strain

Strain Designation 2301032

Culture col. no. DSM 16943 CCUG 48216 CIP 108005 KCTC 3995 2301032

NCBI tax ID(s) 225915

Special Collections DSMZ CCUG KCTC CIP Literature strains

History <- CIP 2003, V. Roux CHU de la Timone, Marseille, France: strain 2301032 CIP <- 2003, V. Roux, Timone Hosp., Marseille, France: strain 2301032

Links

Paenibacillus timonensis 2301032 is a facultative anaerobe, spore-forming, mesophilic prokaryote that was isolated from blood culture.

spore-forming Gram-positive motile rod-shaped facultative anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 132797

CCUG 48216,CIP 108005,DSM 16943,KCTC 3995

@ref 20215

Last LPSN update 2026-02-09 11:20:35

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Paenibacillaceae

Genus Paenibacillus

Species Paenibacillus timonensis

Full scientific name Paenibacillus timonensis Roux and Raoult 2004

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
30113	positive	2 µm	0.5 µm	rod-shaped
123549	positive			rod-shaped

Colony morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6660	CASO AGAR (MERCK 105458) (DSMZ Medium 220)	Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220; with strain-specific modifications) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l MnSO4 Distilled water
33870	MEDIUM 6 - Columbia agar with 10 % horse blood		Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
123549	CIP Medium 6	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6660	positive	growth	30	mesophilic
30113	positive	growth	30-50
33870	positive	growth	37	mesophilic
58044	positive	growth	30	mesophilic
123549	positive	growth	22-45
123549	negative	growth	10
123549	negative	growth	55

Culture pH

@ref	Ability	Type	PH
123549		growth	6

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
30113	facultative anaerobe
58044	aerobe
123549	facultative anaerobe

Spore formation

@ref	Spore formation	Confidence
30113
125438		92.843

Halophily

@ref	Salt	Growth	Tested relation	Concentration
123549	NaCl	positive	growth	0-2 %
123549	NaCl		growth	4 %
123549	NaCl		growth	6 %
123549	NaCl		growth	8 %
123549	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	+	builds acid from	from API 50CH acid
30113	22599 ChEBI	arabinose	+	carbon source
30113	17057 ChEBI	cellobiose	+	carbon source
68371	17057 ChEBI	cellobiose	+	builds acid from	from API 50CH acid
123549	16947 ChEBI	citrate	-	carbon source
68371	17108 ChEBI	D-arabinose	+	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	+	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	+	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	+	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	-	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	+	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	+	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
123549	4853 ChEBI	esculin	+	hydrolysis
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
30113	28757 ChEBI	fructose	+	carbon source
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
30113	28260 ChEBI	galactose	+	carbon source
68371	28066 ChEBI	gentiobiose	+	builds acid from	from API 50CH acid
30113	24265 ChEBI	gluconate	+	carbon source
68371	24265 ChEBI	gluconate	+	builds acid from	from API 50CH acid
30113	17234 ChEBI	glucose	+	carbon source
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
30113	28087 ChEBI	glycogen	+	carbon source
68371	28087 ChEBI	glycogen	+	builds acid from	from API 50CH acid
123549	606565 ChEBI	hippurate	+	hydrolysis
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
30113	17716 ChEBI	lactose	+	carbon source
68371	17716 ChEBI	lactose	+	builds acid from	from API 50CH acid
30113	17306 ChEBI	maltose	+	carbon source
68371	17306 ChEBI	maltose	+	builds acid from	from API 50CH acid
30113	37684 ChEBI	mannose	+	carbon source
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
30113	28053 ChEBI	melibiose	+	carbon source
68371	28053 ChEBI	melibiose	+	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	+	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	+	builds acid from	from API 50CH acid
30113	37657 ChEBI	methyl D-glucoside	+	carbon source
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
30113	506227 ChEBI	N-acetylglucosamine	+	carbon source
68371	59640 ChEBI	N-acetylglucosamine	+	builds acid from	from API 50CH acid
30113	17632 ChEBI	nitrate	+	reduction
123549	17632 ChEBI	nitrate	+	reduction
123549	17632 ChEBI	nitrate	+	respiration
123549	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		Potassium 5-ketogluconate	+	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	+	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
30113	17814 ChEBI	salicin	+	carbon source
68371	17814 ChEBI	salicin	+	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	+	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
30113	27082 ChEBI	trehalose	+	carbon source
68371	27082 ChEBI	trehalose	+	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid
30113	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
123549	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
123549	15688 ChEBI	acetoin	-
123549	17234 ChEBI	glucose		+

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
123549	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	+	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	+	3.2.1.24	from API zym
123549	amylase	+
68382	beta-galactosidase	+	3.2.1.23	from API zym
123549	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
123549	caseinase	-	3.4.21.50
30113	catalase	+	1.11.1.6
123549	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
123549	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
123549	gamma-glutamyltransferase	+	2.3.2.2
123549	gelatinase	-
123549	lecithinase	-
68382	leucine arylamidase	-	3.4.11.1	from API zym
123549	lipase	-
68382	lipase (C 14)	-		from API zym
123549	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
123549	ornithine decarboxylase	-	4.1.1.17
123549	oxidase	-
68382	trypsin	-	3.4.21.4	from API zym
123549	tryptophan deaminase	-
123549	tween esterase	+
123549	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
123549	-	-	+	+	-	-	-	-	-	-	-	+	+	+	-	+	+	-	+	-

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
123549	not determinedn.d.	-	-	+	+/-	+	-	-	-	+	+	+	+	+	-	-	-	-	-	-	+/-	+	+	+	+/-	+	+	+	+	+	+	-	+	-	-	+	+	+	-	+	+/-	-	-	-	+/-	-	-	+	-	+

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
123549	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Patient	#Blood culture
#Host Body Product	#Fluids	#Blood

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
6660	blood culture		Hospital de la Timone	France	FRA	Europe
58044	Human blood,75-yr-old woman,haemodialysis	2002	Marseille	France	FRA	Europe
123549	Human, Blood		Marseille	France	FRA	Europe	2002

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
6660	yes, in single cases	1	Risk group (German classification) According to TRBA 466
123549		1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM4267864v1 assembly for Paenibacillus timonensis CCUG 48216	scaffold	GCA_042678645			225915	48.57
66792	ASM2242714v1 assembly for Paenibacillus timonensis DSM 16943	contig	GCA_022427145	225915.5	8111039160	225915	43.47

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6660	Paenibacillus sp. 'Smarlab BioMol-2301032' clone 1 16S ribosomal RNA gene, partial sequence	AY323610	1475		1205673

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paenibacillus timonensis DSM 16943
NCBI: GCA_022427145.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	65.53	no
125438	anaerobic	anaerobicⓘ	no	92.25	yes
125438	aerobic	aerobicⓘ	no	57.80	no
125438	spore-forming	spore-formingⓘ	yes	92.84	yes
125438	thermophilic	thermophileⓘ	no	92.57	no
125438	flagellated	motile2+ⓘ	yes	84.03	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Paenibacillus rhizolycopersici sp. nov., an oligotrophic bacterium isolated from a tomato plant in China.	Thin KK, He SW, Ma R, Wang X, Han JG, Zhang XX.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005698	2023
Genetics	Paenibacillus phocaensis sp. nov., isolated from the gut microbiota of a healthy infant.	Tidjani Alou M, Rathored J, Nguyen TT, Andrieu C, Couderc C, Brah S, Diallo BA, Fournier PE, Raoult D, Dubourg G.	New Microbes New Infect	10.1016/j.nmni.2016.12.001	2017
Phylogeny	Paenibacillus cathormii sp. nov., isolated from tree bark.	Sitdhipol J, Paek J, Sin Y, Park IS, Thamacharoensuk T, Wannissorn B, Tanasupawat S, Chang YH	Int J Syst Evol Microbiol	10.1099/ijsem.0.000854	2015
Phylogeny	Paenibacillus faecis sp. nov., isolated from human faeces.	Clermont D, Gomard M, Hamon S, Bonne I, Fernandez JC, Wheeler R, Malosse C, Chamot-Rooke J, Gribaldo S, Boneca IG, Bizet C	Int J Syst Evol Microbiol	10.1099/ijsem.0.000622	2015
Phylogeny	Paenibacillus phoenicis sp. nov., isolated from the Phoenix Lander assembly facility and a subsurface molybdenum mine.	Benardini JN, Vaishampayan PA, Schwendner P, Swanner E, Fukui Y, Osman S, Satomi M, Venkateswaran K	Int J Syst Evol Microbiol	10.1099/ijs.0.021428-0	2010
Phylogeny	Paenibacillus fonticola sp. nov., isolated from a warm spring.	Chou JH, Chou YJ, Lin KY, Sheu SY, Sheu DS, Arun AB, Young CC, Chen WM	Int J Syst Evol Microbiol	10.1099/ijs.0.64872-0	2007
Phylogeny	Paenibacillus massiliensis sp. nov., Paenibacillus sanguinis sp. nov. and Paenibacillus timonensis sp. nov., isolated from blood cultures.	Roux V, Raoult D	Int J Syst Evol Microbiol	10.1099/ijs.0.02954-0	2004
Phylogeny	Paenibacillus mellifer sp. nov., isolated from gut of the honey bee Apis mellifera.	Cho ES, Hwang CY, Kwon HW, Seo MJ	Arch Microbiol	10.1007/s00203-022-03178-0	2022

References

#6660	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16943
#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 )
#26468	IJSEM 1049 2004 ( DOI 10.1099/ijs.0.02954-0 , PubMed 15280268 )
#30113	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 #26468
#33870	; Curators of the CIP;
#58044	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 48216
#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) .
#68371	Automatically annotated from API 50CH acid .
#68382	Automatically annotated from API zym .
#123549	Collection of Institut Pasteur ; Curators of the CIP; CIP 108005
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Paenibacillus timonensis (DSM 16943, CCUG 48216, CIP 108005)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 50CHac

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_042678645

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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