Buttiauxella agrestis (DSM 4586, ATCC 33320, CIP 80.31)

Name: Buttiauxella agrestis (DSM 4586, ATCC 33320, CIP 80.31)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 4311

Type strain

Strain Designation Gavini-F-44, F44

Culture col. no. DSM 4586 ATCC 33320 CIP 80.31 Gavini-F-44 CCUG 11756 8 more

NCBI tax ID(s) 1006004 82977

Special Collections DSMZ CCUG JCM CIP

History DSMZ <- CIP <- H. Leclerc, CUETM; 77.167 JCM <-- Y. Kosako 536 <-- R. Sakazaki 536 <-- F. Gavini F44. CIP <- 1980, H. Leclerc, Villeneuve d'Ascq, France: strain CUETM 77-167 <- F. Gavini, INSERM, Lille, France: strain F44

Links

Buttiauxella agrestis Gavini-F-44 is a bacterium that was isolated from soil.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 265473

LMG 7861,ATCC 33320,CCRC 12221,CCUG 11756,DSM 4586,JCM 1090,NCTC 12119,CIP 80.31,BCRC 12221,CNCTC 6263

@ref 20215

Last LPSN update 2026-05-29 08:25:54

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Enterobacteriaceae

Genus Buttiauxella

Species Buttiauxella agrestis

Full scientific name Buttiauxella agrestis Ferragut et al. 1982

BacDive ID	Other strains from **Buttiauxella agrestis** (6)	Type strain
130885	B. agrestis S3/3-162, DSM 9388
4312	B. agrestis S3/6-333, DSM 9389
143712	B. agrestis CCUG 21133, ATCC 33993
143713	B. agrestis CCUG 21134, ATCC 33995
143714	B. agrestis CCUG 21135
143715	B. agrestis CCUG 21136

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	94.006
125438	negative	99.75

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
1781	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
1781	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
38575	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
116163	CIP Medium 3	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
1781	positive	growth	30
38575	positive	growth	30
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	95.353

Spore formation

@ref	Spore formation	Confidence
125439		98.458

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68368	27613 ChEBI	amygdalin	+	fermentation	from API 20E
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
68368	16947 ChEBI	citrate	+	assimilation	from API 20E
68368	17634 ChEBI	D-glucose	+	fermentation	from API 20E
68368	16899 ChEBI	D-mannitol	+	fermentation	from API 20E
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
68368	30849 ChEBI	L-arabinose	+	fermentation	from API 20E
68368	62345 ChEBI	L-rhamnose	+	fermentation	from API 20E
68368	25094 ChEBI	lysine	-	degradation	from API 20E
68368	28053 ChEBI	melibiose	+	fermentation	from API 20E
68368	17268 ChEBI	myo-inositol	-	fermentation	from API 20E
68368	18257 ChEBI	ornithine	+	degradation	from API 20E
68368	30911 ChEBI	sorbitol	-	fermentation	from API 20E
68368	17992 ChEBI	sucrose	-	fermentation	from API 20E
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	-		from API 20E
68368	35581 ChEBI	indole		-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68368	cytochrome oxidase	-	1.9.3.1	from API 20E
68368	gelatinase	-		from API 20E
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68368	ornithine decarboxylase	+	4.1.1.17	from API 20E
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
68368	urease	-	3.5.1.5	from API 20E

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	quinate degradation	100	2 of 2
66794	ethanol fermentation	100	2 of 2
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	adipate degradation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	sulfoquinovose degradation	100	3 of 3
66794	kanosamine biosynthesis II	100	2 of 2
66794	aminopropanol phosphate biosynthesis	100	2 of 2
66794	d-mannose degradation	100	9 of 9
66794	enterobactin biosynthesis	100	3 of 3
66794	lipoate biosynthesis	100	5 of 5
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	starch degradation	100	10 of 10
66794	palmitate biosynthesis	100	22 of 22
66794	biotin biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	acetate fermentation	100	4 of 4
66794	threonine metabolism	100	10 of 10
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	ubiquinone biosynthesis	100	7 of 7
66794	sulfopterin metabolism	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	gluconeogenesis	100	8 of 8
66794	suberin monomers biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	taurine degradation	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	cellulose degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	tetrahydrofolate metabolism	100	14 of 14
66794	formaldehyde oxidation	100	3 of 3
66794	vitamin K metabolism	100	5 of 5
66794	NAD metabolism	94.44	17 of 18
66794	photosynthesis	92.86	13 of 14
66794	heme metabolism	92.86	13 of 14
66794	vitamin B6 metabolism	90.91	10 of 11
66794	pentose phosphate pathway	90.91	10 of 11
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	purine metabolism	87.23	82 of 94
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	glutathione metabolism	85.71	12 of 14
66794	citric acid cycle	85.71	12 of 14
66794	vitamin B12 metabolism	85.29	29 of 34
66794	vitamin B1 metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	metabolism of disaccharids	81.82	9 of 11
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	pyrimidine metabolism	77.78	35 of 45
66794	allantoin degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	4-hydroxymandelate degradation	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	CMP-KDO biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	degradation of pentoses	75	21 of 28
66794	glycogen biosynthesis	75	3 of 4
66794	ketogluconate metabolism	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	proline metabolism	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	degradation of sugar acids	72	18 of 25
66794	oxidative phosphorylation	71.43	65 of 91
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	lipid metabolism	70.97	22 of 31
66794	alanine metabolism	68.97	20 of 29
66794	degradation of sugar alcohols	68.75	11 of 16
66794	non-pathway related	68.42	26 of 38
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	cysteine metabolism	66.67	12 of 18
66794	octane oxidation	66.67	2 of 3
66794	degradation of hexoses	66.67	12 of 18
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	cyanate degradation	66.67	2 of 3
66794	arginine metabolism	66.67	16 of 24
66794	acetoin degradation	66.67	2 of 3
66794	methionine metabolism	65.38	17 of 26
66794	tyrosine metabolism	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	urea cycle	61.54	8 of 13
66794	lysine metabolism	59.52	25 of 42
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	tryptophan metabolism	57.89	22 of 38
66794	propanol degradation	57.14	4 of 7
66794	glycine metabolism	50	5 of 10
66794	ribulose monophosphate pathway	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	coenzyme M biosynthesis	50	5 of 10
66794	butanoate fermentation	50	2 of 4
66794	pantothenate biosynthesis	50	3 of 6
66794	propionate fermentation	50	5 of 10
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	ascorbate metabolism	45.45	10 of 22
66794	nitrate assimilation	44.44	4 of 9
66794	phenol degradation	40	8 of 20
66794	3-chlorocatechol degradation	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	arachidonic acid metabolism	38.89	7 of 18
66794	sulfate reduction	38.46	5 of 13
66794	methane metabolism	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	polyamine pathway	26.09	6 of 23
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	androgen and estrogen metabolism	25	4 of 16
66794	alginate biosynthesis	25	1 of 4

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
1781	+	-	-	+	+	-	-	-	-	-	-	+	+	-	-	+	-	+	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type
1781	soil
67770	Surface water
116163	Environment, Soil

Taxonmaps

69479

Global distribution of 16S sequence AJ293685 (>99% sequence identity) for Buttiauxella from Microbeatlas

Aquatic Samples	1274
Soil Samples	778
Animal Samples	4089
Plant Samples	1017
Total Samples	7158

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1781	1	Risk group (German classification) According to TRBA 466
116163	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
66792	50592_F01 assembly for Buttiauxella agrestis NCTC12119	contig	GCA_900446255	82977.5	2808606796	82977	78.15
67770	GBAG_DRAFTv1 assembly for Buttiauxella agrestis ATCC 33320	contig	GCA_000735355	1006004.4	2588253793	1006004	60.2
124043	ASM2416944v1 assembly for Buttiauxella agrestis ATCC 33320 DSM 4586	contig	GCA_024169445	1006004.12	2917518688	1006004	53.62

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Buttiauxella agrestis 16S rRNA gene, strain CDC 1176-81T (ATCC 33320T)	AJ293685	1450		1006004
20218	Buttiauxella agrestis 16S rRNA gene (strain DSM 4586)	AJ233400	1504		1006004

GC content

@ref	GC-content (mol%)	Method
67770	47.9	thermal denaturation, midpoint method (Tm)
67770	49	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: 50592_F01 assembly for Buttiauxella agrestis NCTC12119
NCBI: GCA_900446255

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.35	no
125439	gram_stain	BacteriaNetⓘ	negative	94.01	no
125439	motility	BacteriaNetⓘ	yes	50.46	no
125439	spore_formation	BacteriaNetⓘ	no	98.46	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Buttiauxella agrestis ATCC 33320
PATRIC: 1006004.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.75	no
125438	anaerobic	anaerobicⓘ	no	96.06	no
125438	spore-forming	spore-formingⓘ	no	86.20	no
125438	aerobic	aerobicⓘ	no	64.15	no
125438	thermophilic	thermophileⓘ	no	98.50	yes
125438	flagellated	motile2+ⓘ	yes	76.73	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Interaction of Bacterial Membrane Vesicles with Specific Species and Their Potential for Delivery to Target Cells.	Tashiro Y, Hasegawa Y, Shintani M, Takaki K, Ohkuma M, Kimbara K, Futamata H.	Front Microbiol	10.3389/fmicb.2017.00571	2017
Phylogeny	Application of whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry for rapid identification and clustering analysis of pantoea species.	Rezzonico F, Vogel G, Duffy B, Tonolla M.	Appl Environ Microbiol	10.1128/aem.03112-09	2010
Enzymology	Multiplex detection of nine food-borne pathogens by mPCR and capillary electrophoresis after using a universal pre-enrichment medium.	Villamizar-Rodriguez G, Fernandez J, Marin L, Muniz J, Gonzalez I, Lombo F.	Front Microbiol	10.3389/fmicb.2015.01194	2015
	Comparative Analysis of Mesophilic YqfB-Type Amidohydrolases.	Statkeviciute R, Sadauskas M, Rainyte J, Kavaliauskaite K, Meskys R.	Biomolecules	10.3390/biom12101492	2022
	Occurrence of disinfectant-resistant bacteria in a fresh-cut vegetables processing facility and their role in protecting Salmonella enteritidis.	Xu JG, Meng J, Bao WJ, Kang JM, Chen JY, Han BZ.	RSC Adv	10.1039/d0ra09325d	2021
Enzymology	Molecular method for detection of total coliforms in drinking water samples.	Maheux AF, Boudreau DK, Bisson MA, Dion-Dupont V, Bouchard S, Nkuranga M, Bergeron MG, Rodriguez MJ.	Appl Environ Microbiol	10.1128/aem.00546-14	2014
Enzymology	Description and evaluation of the semiautomated 4-hour ATB 32E method for identification of members of the family Enterobacteriaceae.	Freney J, Herve C, Desmonceaux M, Allard F, Boeufgras JM, Monget D, Fleurette J.	J Clin Microbiol	10.1128/jcm.29.1.138-141.1991	1991
	Bacterial extracellular vesicles: biotechnological perspective for enhanced productivity.	Munoz-Echeverri LM, Benavides-Lopez S, Geiger O, Trujillo-Roldan MA, Valdez-Cruz NA.	World J Microbiol Biotechnol	10.1007/s11274-024-03963-7	2024
Phylogeny	Single-cell analyses revealed transfer ranges of IncP-1, IncP-7, and IncP-9 plasmids in a soil bacterial community.	Shintani M, Matsui K, Inoue J, Hosoyama A, Ohji S, Yamazoe A, Nojiri H, Kimbara K, Ohkuma M.	Appl Environ Microbiol	10.1128/aem.02571-13	2014
Genetics	Complete Genome Sequence of Buttiauxella agrestis DSM 9389.	Nakamichi N, Moriuchi R, Dohra H, Futamata H, Tashiro Y	Microbiol Resour Announc	10.1128/MRA.00301-21	2021
Metabolism	Multilamellar and Multivesicular Outer Membrane Vesicles Produced by a Buttiauxella agrestis tolB Mutant.	Takaki K, Tahara YO, Nakamichi N, Hasegawa Y, Shintani M, Ohkuma M, Miyata M, Futamata H, Tashiro Y	Appl Environ Microbiol	10.1128/AEM.01131-20	2020
Genetics	Scandinavium goeteborgense gen. nov., sp. nov., a New Member of the Family Enterobacteriaceae Isolated From a Wound Infection, Carries a Novel Quinolone Resistance Gene Variant.	Marathe NP, Salva-Serra F, Karlsson R, Larsson DGJ, Moore ERB, Svensson-Stadler L, Jakobsson HE.	Front Microbiol	10.3389/fmicb.2019.02511	2019

References

#1781	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 4586
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#38575	; 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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68368	Automatically annotated from API 20E .
#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 .
#116163	Collection of Institut Pasteur ; Curators of the CIP; CIP 80.31
#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 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#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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Buttiauxella agrestis (DSM 4586, ATCC 33320, CIP 80.31)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API 20E

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900446255

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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