Microterricola viridarii (DSM 21772, NBRC 102123, NRRL B-24538)

Name: Microterricola viridarii (DSM 21772, NBRC 102123, NRRL B-24538)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7499

Type strain

Strain Designation KV-677

Culture col. no. DSM 21772 NBRC 102123 NRRL B-24538 KV-677 JCM 15926

NCBI tax ID(s) 412690

Special Collections DSMZ JCM Literature strains

History <- NBRC <- S. Omura, Kitasato Univ., Tokyo <- A. Matsumoto, The Kitasato Inst., Tokyo, Japan NRRL B-24538 <-- S. ?mura KV-677.

Links

Microterricola viridarii KV-677 is an aerobe, Gram-positive, motile bacterium that was isolated from park soil.

Gram-positive motile rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 400982

NBRC 102123,JCM 15926,DSM 21772

@ref 20215

Last LPSN update 2026-02-09 11:19:29

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Microbacteriaceae

Genus Microterricola

Species Microterricola viridarii

Full scientific name Microterricola viridarii Matsumoto et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
32171	positive	0.9 µm	0.45 µm	rod-shaped
125438	positive					90.567

Pigmentation

32171

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15938	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)		Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
15938	positive	growth	28
32171	positive	growth	10-38
32171	positive	optimum	22.5
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
32171	positive	growth	06-11	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32171	aerobe
125439	obligate aerobe	94.5

Spore formation

@ref	Spore formation	Confidence
125439		92.7

Observation

67770

Observationquinones: MK-12 (69%), MK-11 (21%), MK-13 (10%)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32171	22599 ChEBI	arabinose	+	carbon source
32171	17754 ChEBI	glycerol	+	carbon source
32171	28087 ChEBI	glycogen	+	carbon source
32171	17306 ChEBI	maltose	+	carbon source
32171	33942 ChEBI	ribose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32171	acid phosphatase	+	3.1.3.2
32171	catalase	+	1.11.1.6

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	starch degradation	100	10 of 10
66794	vitamin K metabolism	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	acetate fermentation	100	4 of 4
66794	cardiolipin biosynthesis	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	cyanate degradation	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	coenzyme A metabolism	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	cellulose degradation	100	5 of 5
66794	teichoic acid biosynthesis	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	formaldehyde oxidation	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	pentose phosphate pathway	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	ketogluconate metabolism	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	photosynthesis	85.71	12 of 14
66794	pyrimidine metabolism	84.44	38 of 45
66794	NAD metabolism	83.33	15 of 18
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	3-chlorocatechol degradation	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	citric acid cycle	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	purine metabolism	77.66	73 of 94
66794	phenylalanine metabolism	76.92	10 of 13
66794	leucine metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	butanoate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	dTDPLrhamnose biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	tryptophan metabolism	73.68	28 of 38
66794	methionine metabolism	73.08	19 of 26
66794	metabolism of disaccharids	72.73	8 of 11
66794	proline metabolism	72.73	8 of 11
66794	d-xylose degradation	72.73	8 of 11
66794	alanine metabolism	72.41	21 of 29
66794	degradation of sugar acids	72	18 of 25
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	propionate fermentation	70	7 of 10
66794	4-hydroxyphenylacetate degradation	70	7 of 10
66794	phenol degradation	70	14 of 20
66794	isoprenoid biosynthesis	69.23	18 of 26
66794	degradation of sugar alcohols	68.75	11 of 16
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	degradation of hexoses	66.67	12 of 18
66794	d-mannose degradation	66.67	6 of 9
66794	enterobactin biosynthesis	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	histidine metabolism	65.52	19 of 29
66794	heme metabolism	64.29	9 of 14
66794	degradation of pentoses	64.29	18 of 28
66794	oxidative phosphorylation	61.54	56 of 91
66794	lipid metabolism	61.29	19 of 31
66794	factor 420 biosynthesis	60	3 of 5
66794	3-phenylpropionate degradation	60	9 of 15
66794	gallate degradation	60	3 of 5
66794	lysine metabolism	59.52	25 of 42
66794	ascorbate metabolism	59.09	13 of 22
66794	arginine metabolism	58.33	14 of 24
66794	non-pathway related	57.89	22 of 38
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	cysteine metabolism	55.56	10 of 18
66794	4-hydroxymandelate degradation	55.56	5 of 9
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	CMP-KDO biosynthesis	50	2 of 4
66794	carotenoid biosynthesis	50	11 of 22
66794	ribulose monophosphate pathway	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	glycine metabolism	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	quinate degradation	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	tyrosine metabolism	50	7 of 14
66794	cyclohexanol degradation	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	vitamin B6 metabolism	45.45	5 of 11
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	arachidonate biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	polyamine pathway	39.13	9 of 23
66794	vitamin B1 metabolism	38.46	5 of 13
66794	carnitine metabolism	37.5	3 of 8
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	cholesterol biosynthesis	36.36	4 of 11
66794	glutathione metabolism	35.71	5 of 14
66794	IAA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	arachidonic acid metabolism	33.33	6 of 18
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	urea cycle	30.77	4 of 13
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	bile acid biosynthesis, neutral pathway	29.41	5 of 17
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	sulfate reduction	23.08	3 of 13
66794	nitrate assimilation	22.22	2 of 9
66794	daunorubicin biosynthesis	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15938	park soil	Tokyo	Japan	JPN	Asia
67770	Soil	Arisugawa Park, Tokyo	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB282862 (>99% sequence identity) for Microterricola from Microbeatlas

Aquatic Samples	3680
Soil Samples	6929
Animal Samples	3725
Plant Samples	3868
Total Samples	18202

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15938	1	Risk group (German 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	IMG-taxon 2634166341 annotated assembly for Microterricola viridarii DSM 21772	chromosome	GCA_900104895	412690.4	2634166341	412690	89.23

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15938	Microterricola viridarii gene for 16S rRNA, partial sequence	AB282862	1442		412690

GC content

@ref	GC-content (mol%)	Method
15938	70
67770	70	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Microterricola viridarii DSM 21772
IMG: 2634166341

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	92.70	no
125439	motility	BacteriaNetⓘ	yes	60.50	no
125439	gram_stain	BacteriaNetⓘ	positive	78.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	94.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Microterricola viridarii strain DSM 21772
PATRIC: 412690.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.57	yes
125438	anaerobic	anaerobicⓘ	no	99.04	yes
125438	spore-forming	spore-formingⓘ	no	75.83	no
125438	aerobic	aerobicⓘ	yes	83.79	yes
125438	thermophilic	thermophileⓘ	no	96.50	no
125438	flagellated	motile2+ⓘ	no	78.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Reclassification of Phycicola gilvus (Lee et al. 2008) and Leifsonia pindariensis (Reddy et al. 2008) as Microterricola gilva comb. nov. and Microterricola pindariensis comb. nov. and emended description of the genus Microterricola.	Dhotre DP, Rajabal V, Sharma A, Kulkarni GJ, Prakash O, Vemuluri VR, Joseph N, Rahi P, Shouche YS	Int J Syst Evol Microbiol	10.1099/ijsem.0.002019	2017
Phylogeny	Amnibacterium kyonggiense gen. nov., sp. nov., a new member of the family Microbacteriaceae.	Kim SJ, Lee SS	Int J Syst Evol Microbiol	10.1099/ijs.0.018788-0	2010
Phylogeny	Microterricola viridarii gen. nov., sp. nov., a new member of the family Microbacteriaceae.	Matsumoto A, Yamada M, Omura S, Takahashi Y	Int J Syst Evol Microbiol	10.1099/ijs.0.65070-0	2008

References

#15938	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21772
#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 )
#28413	IJSEM 1019 2008 ( DOI 10.1099/ijs.0.65070-0 , PubMed 18398212 )
#32171	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 #28413
#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;
#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 .
#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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Microterricola viridarii (DSM 21772, NBRC 102123, NRRL B-24538)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900104895

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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