Massilia agri (KEMB 9005-446, KACC 19000, JCM 31661)

Name: Massilia agri (KEMB 9005-446, KACC 19000, JCM 31661)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140986

Type strain

Strain Designation K-3-1

Culture col. no. KEMB 9005-446 KACC 19000 JCM 31661 K-3-1

NCBI tax ID(s) 1886785

Special Collections JCM Literature strains

Links

Massilia agri K-3-1 is an aerobe, Gram-negative, motile prokaryote that forms circular colonies and was isolated from reclaimed grassland soil of Belbari, Morang, Nepal.

Gram-negative motile rod-shaped colony-forming aerobe genome sequence 16S sequence

Name and taxonomic classification

SI-ID 286401

JCM 31661

@ref 20215

Last LPSN update 2025-12-16 10:03:44

Domain Pseudomonadati

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Oxalobacteraceae

Genus Massilia

Species Massilia agri

Full scientific name Massilia agri Chaudhary and Kim 2017

Synonyms (1)

Telluria agri

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Flagellum arrangement
43874	negative	1.2-1.4 µm	0.3-0.7 µm	rod-shaped		polar
125438	negative

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43874	1-2 mm	light yellow	circular	5 days	R2A agar

Culture and growth conditions

Culture medium

@ref	Name	Growth
43874	Nutrient agar (NA)
43874	Reasoner's 2A agar (R2A)
43874	Tryptic soy agar
43874	Brain-Heart infusion agar
43874	LB (Luria-Bertani) MEDIUM
43874	MacConkey agar
43874	Marine agar (MA)
43874	Veal infusion agar

Culture temp

@ref	Growth	Type	Temperature (°C)
43874	positive	growth	4-45
43874	positive	optimum	20-40
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH
43874	positive	optimum	6.5-8.5
43874	positive	growth	5.0-10.0

Physiology and metabolism

Oxygen tolerance

43874

Oxygen toleranceaerobe

Spore formation

43874

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43874	NaCl	positive	optimum	0 %(w/v)
43874	NaCl	positive	growth	0-2 %(w/v)

Observation

43874

Observationquinone Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43874	16808 ChEBI	2-dehydro-D-gluconate	+	carbon source
43874	16193 ChEBI	3-hydroxybenzoate	+	carbon source
43874	37054 ChEBI	3-hydroxybutyrate	+	carbon source
43874	17879 ChEBI	4-hydroxybenzoate	+	carbon source
43874	355715 ChEBI	4-nitrophenyl beta-D-galactopyranoside	-	builds acid from
43874	58143 ChEBI	5-dehydro-D-gluconate	+	carbon source
43874	17128 ChEBI	adipate	-	assimilation
43874	85146 ChEBI	carboxymethylcellulose	+	hydrolysis
43874		casein	+	hydrolysis
43874	17029 ChEBI	chitin	-	hydrolysis
43874	17634 ChEBI	D-glucose	+	assimilation
43874	17634 ChEBI	D-glucose	+	carbon source
43874	16899 ChEBI	D-mannitol	-	assimilation
43874	16899 ChEBI	D-mannitol	+	carbon source
43874	16024 ChEBI	D-mannose	+	assimilation
43874	16988 ChEBI	D-ribose	+	carbon source
43874	17924 ChEBI	D-sorbitol	+	carbon source
43874	27689 ChEBI	decanoate	-	assimilation
43874	27689 ChEBI	decanoate	+	carbon source
43874	16991 ChEBI	dna	+	hydrolysis
43874	4853 ChEBI	esculin	+	hydrolysis
43874		esculin ferric citrate	+	builds acid from
43874	5291 ChEBI	gelatin	+	builds acid from
43874	5291 ChEBI	gelatin	+	hydrolysis
43874	17234 ChEBI	glucose	-	fermentation
43874	28087 ChEBI	glycogen	+	carbon source
43874	17240 ChEBI	itaconate	+	carbon source
43874	16977 ChEBI	L-alanine	+	carbon source
43874	30849 ChEBI	L-arabinose	+	assimilation
43874	30849 ChEBI	L-arabinose	+	carbon source
43874	16467 ChEBI	L-arginine	-	builds acid from
43874	18287 ChEBI	L-fucose	+	carbon source
43874	15971 ChEBI	L-histidine	+	carbon source
43874	17203 ChEBI	L-proline	+/-	carbon source
43874	62345 ChEBI	L-rhamnose	+	carbon source
43874	17115 ChEBI	L-serine	+/-	carbon source
43874	16828 ChEBI	L-tryptophan	-	builds acid from
43874	24996 ChEBI	lactate	+	carbon source
43874	25115 ChEBI	malate	+	assimilation
43874	17306 ChEBI	maltose	+	assimilation
43874	17306 ChEBI	maltose	+	carbon source
43874	28053 ChEBI	melibiose	+	carbon source
43874	17268 ChEBI	myo-inositol	+	carbon source
43874	506227 ChEBI	N-acetylglucosamine	+	assimilation
43874	506227 ChEBI	N-acetylglucosamine	+	carbon source
43874	17632 ChEBI	nitrate	+	reduction
43874	18401 ChEBI	phenylacetate	+	assimilation
43874	32032 ChEBI	potassium gluconate	-	assimilation
43874	17272 ChEBI	propionate	+	carbon source
43874	17814 ChEBI	salicin	+	carbon source
43874	32954 ChEBI	sodium acetate	+/-	carbon source
43874	53258 ChEBI	sodium citrate	-	assimilation
43874	53258 ChEBI	sodium citrate	+	carbon source
43874	62983 ChEBI	sodium malonate	+	carbon source
43874	28017 ChEBI	starch	+	hydrolysis
43874	9300 ChEBI	suberic acid	+	carbon source
43874	17992 ChEBI	sucrose	+	carbon source
43874	53423 ChEBI	tween 40	+/-	hydrolysis
43874	53426 ChEBI	tween 80	-	hydrolysis
43874	18186 ChEBI	tyrosine	+	hydrolysis
43874	16199 ChEBI	urea	-	builds acid from
43874	31011 ChEBI	valerate	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite
43874	15688 ChEBI	acetoin
43874	16136 ChEBI	hydrogen sulfide
43874	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test
43874	15688 ChEBI	acetoin	-
43874	17234 ChEBI	glucose

Enzymes

@ref	Value	Activity	Ec
43874	acid phosphatase	+	3.1.3.2
43874	alkaline phosphatase	+	3.1.3.1
43874	alpha-chymotrypsin	+	3.4.21.1
43874	alpha-fucosidase	-	3.2.1.51
43874	alpha-galactosidase	-	3.2.1.22
43874	alpha-glucosidase	+/-	3.2.1.20
43874	alpha-mannosidase	-	3.2.1.24
43874	beta-galactosidase	-	3.2.1.23
43874	beta-glucosidase	-	3.2.1.21
43874	beta-glucuronidase	-	3.2.1.31
43874	catalase	+	1.11.1.6
43874	cystine arylamidase	+	3.4.11.3
43874	cytochrome oxidase	-	1.9.3.1
43874	esterase (C 4)	+
43874	esterase Lipase (C 8)	+
43874	leucine arylamidase	+	3.4.11.1
43874	lipase (C 14)	+/-
43874	N-acetyl-beta-glucosaminidase	-	3.2.1.52
43874	naphthol-AS-BI-phosphohydrolase	+
43874	trypsin	+/-	3.4.21.4
43874	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

43874

Fatty acid	Percentage
C16:1ω7c / C16:1ω6c	36.4
C16:0	27
C12:0	14.2
C10:0 3OH	9.4
C18:1ω7c / C18:1ω6c	5.9
C17:0 cyclo	1.7
C14:0	1.5
C10:0	1.2
C12:0 2OH	0.7
C16:0 3OH	0.5
C18:0	0.3

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Grassland
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
43874	reclaimed grassland soil of Belbari, Morang, Nepal	Belbari, Morang	Nepal	NPL	Asia
67770	Reclaimed grassland soils of Belbari	Morang	Nepal	NPL	Asia

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2475325v1 assembly for Massilia agri JCM 31661	contig	GCA_024753255	1886785.3	8047662315	1886785	63.24

Genome browser: GCA_024753255

16S sequences

@ref	Description	Accession	Database
43874	Massilia agri strain K-3-1 16S ribosomal RNA gene, partial sequence	KX672812

GC content

@ref	GC-content (mol%)	Method
43874	66.8	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Massilia agri JCM 31661
NCBI: GCA_024753255.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	yes
125438	anaerobic	anaerobicⓘ	no	97.97	yes
125438	aerobic	aerobicⓘ	yes	89.86	yes
125438	spore-forming	spore-formingⓘ	no	84.74	no
125438	thermophilic	thermophileⓘ	no	97.75	yes
125438	flagellated	motile2+ⓘ	yes	86.01	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Massilia arenosa sp. nov., isolated from the soil of a cultivated maize field.	Raths R, Peta V, Bucking H	Int J Syst Evol Microbiol	10.1099/ijsem.0.004266	2020
Phylogeny	Massilia agri sp. nov., isolated from reclaimed grassland soil.	Chaudhary DK, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002002	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 )
#43874	Dhiraj Kumar Chaudhary, Jaisoo Kim: Massilia agri sp. nov., isolated from reclaimed grassland soil. IJSEM 67: 2696 - 2703 2017 ( DOI 10.1099/ijsem.0.002002 , PubMed 28809142 )
#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;
#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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Massilia agri (KEMB 9005-446, KACC 19000, JCM 31661)

Name and taxonomic classification