Micromonospora siamensis (DSM 45097, CIP 109112, JCM 12769)

Name: Micromonospora siamensis (DSM 45097, CIP 109112, JCM 12769)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7998

Type strain

Strain Designation TT2-4

Culture col. no. DSM 45097 CIP 109112 JCM 12769 NBRC 101914 PCU 266 3 more

NCBI tax ID(s) 299152

Special Collections DSMZ JCM CIP

History DSMZ <- JCM <- C. Thawai; TT2-4 JCM <-- C. Thawai TT2-4. CIP <- 2006, JCM <- 2004, C. Thawai: strain TT2-4

Links

Micromonospora siamensis TT2-4 is an obligate aerobe, Gram-positive, rod-shaped bacterium that was isolated from soil sample from peat swamp forest.

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

Name and taxonomic classification

SI-ID 289864

JCM 12769,TISTR 1554,CIP 109112,NBRC 101914,DSM 45097

@ref 20215

Last LPSN update 2026-05-29 08:26:46

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micromonosporales

Family Micromonosporaceae

Genus Micromonospora

Species Micromonospora siamensis

Full scientific name Micromonospora siamensis Thawai et al. 2006

BacDive ID	Other strains from **Micromonospora siamensis** (1)	Type strain
161261	M. siamensis JCM 12768

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
122595	positive	rod-shaped
125438			90
125438	positive		91.358
125439			96.329
125439	positive		99.869

Colony morphology

122595

Hemolysis ability0

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
12339	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
12339	N-Z-AMINE-MEDIUM (DSMZ Medium 554)	Medium recipe at MediaDive	Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water
122595	CIP Medium 277	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
12339	positive	growth	28
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
122595	obligate aerobe
125439	obligate aerobe	99.563

Spore formation

@ref	Spore formation	Confidence
125439		94.71
125438		92.592

Observation

67770

Observationquinones: MK-10(H₄), MK-10(H₆)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
122595	17632 ChEBI	nitrate	-	reduction
122595	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
122595	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
122595	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
68382	beta-galactosidase	+	3.2.1.23	from API zym
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
122595	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
122595	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
122595	ornithine decarboxylase	-	4.1.1.17
122595	oxidase	-
68382	trypsin	+	3.4.21.4	from API zym
122595	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	cardiolipin biosynthesis	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	pentose phosphate pathway	100	11 of 11
66794	adipate degradation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	starch degradation	100	10 of 10
66794	threonine metabolism	100	10 of 10
66794	ethanol fermentation	100	2 of 2
66794	acetate fermentation	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	octane oxidation	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	ribulose monophosphate pathway	100	2 of 2
66794	leucine metabolism	92.31	12 of 13
66794	phenylalanine metabolism	92.31	12 of 13
66794	propionate fermentation	90	9 of 10
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	peptidoglycan biosynthesis	86.67	13 of 15
66794	glutathione metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	selenocysteine biosynthesis	83.33	5 of 6
66794	NAD metabolism	83.33	15 of 18
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	tryptophan metabolism	81.58	31 of 38
66794	flavin biosynthesis	80	12 of 15
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	d-mannose degradation	77.78	7 of 9
66794	purine metabolism	77.66	73 of 94
66794	glycolysis	76.47	13 of 17
66794	histidine metabolism	75.86	22 of 29
66794	biotin biosynthesis	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	arginine metabolism	75	18 of 24
66794	glycogen biosynthesis	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	proline metabolism	72.73	8 of 11
66794	metabolism of disaccharids	72.73	8 of 11
66794	carotenoid biosynthesis	72.73	16 of 22
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	lipid metabolism	70.97	22 of 31
66794	Entner Doudoroff pathway	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	methionine metabolism	69.23	18 of 26
66794	urea cycle	69.23	9 of 13
66794	alanine metabolism	68.97	20 of 29
66794	pyrimidine metabolism	68.89	31 of 45
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	oxidative phosphorylation	65.93	60 of 91
66794	non-pathway related	65.79	25 of 38
66794	phenol degradation	65	13 of 20
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	tyrosine metabolism	64.29	9 of 14
66794	citric acid cycle	64.29	9 of 14
66794	d-xylose degradation	63.64	7 of 11
66794	degradation of sugar alcohols	62.5	10 of 16
66794	ketogluconate metabolism	62.5	5 of 8
66794	lysine metabolism	61.9	26 of 42
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	phosphatidylethanolamine bioynthesis	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	glycine betaine biosynthesis	60	3 of 5
66794	arachidonate biosynthesis	60	3 of 5
66794	3-phenylpropionate degradation	60	9 of 15
66794	lipoate biosynthesis	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	propanol degradation	57.14	4 of 7
66794	androgen and estrogen metabolism	56.25	9 of 16
66794	ascorbate metabolism	50	11 of 22
66794	glycine metabolism	50	5 of 10
66794	cyclohexanol degradation	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	coenzyme M biosynthesis	50	5 of 10
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	quinate degradation	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	degradation of pentoses	50	14 of 28
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	vitamin B12 metabolism	47.06	16 of 34
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	sulfate reduction	46.15	6 of 13
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	nitrate assimilation	44.44	4 of 9
66794	lipid A biosynthesis	44.44	4 of 9
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	vitamin K metabolism	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	arachidonic acid metabolism	38.89	7 of 18
66794	chlorophyll metabolism	38.89	7 of 18
66794	degradation of hexoses	38.89	7 of 18
66794	carnitine metabolism	37.5	3 of 8
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	cholesterol biosynthesis	36.36	4 of 11
66794	degradation of sugar acids	36	9 of 25
66794	enterobactin biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	polyamine pathway	30.43	7 of 23
66794	mevalonate metabolism	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	vitamin E metabolism	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	allantoin degradation	22.22	2 of 9
66794	daunorubicin biosynthesis	22.22	2 of 9

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
122595	-	+	+	+	-	+	-	-	+	-	+	+	+	+	-	+	+	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Forest
#Environmental	#Terrestrial	#Soil
#Environmental	#Terrestrial	#Wetland (Swamp)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
12339	soil sample from peat swamp forest	Pataloong Province	Thailand	THA	Asia
67770	Soil from peat swamp forest	Pattaloong Province	Thailand	THA	Asia
122595	Environment, Thai peat swamp forest	Pattaloong	Thailand	THA	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
12339	1	Risk group (German classification) According to TRBA 466
122595	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	IMG-taxon 2634166273 annotated assembly for Micromonospora siamensis DSM 45097	chromosome	GCA_900090305	299152.5	2634166273	299152	86.23
124043	ASM4243196v1 assembly for Micromonospora siamensis PCU 266	scaffold	GCA_042431965			299152	57.85

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
12339	Micromonospora siamensis gene for 16S rRNA, partial sequence	AB193565	1444	299152
124043	Micromonospora siamensis strain PCU 266 16S ribosomal RNA gene, partial sequence.	MT760021	1331	299152
124043	Micromonospora siamensis strain PCU 266 16S ribosomal RNA gene, partial sequence.	MT758138	1334	299152

GC content

@ref	GC-content (mol%)	Method
67770	73	high performance liquid chromatography (HPLC)
67770	73.2	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: IMG-taxon 2634166273 annotated assembly for Micromonospora siamensis DSM 45097
NCBI: GCA_900090305

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.56	no
125439	gram_stain	BacteriaNetⓘ	positive	99.87	no
125439	motility	BacteriaNetⓘ	no	96.33	no
125439	spore_formation	BacteriaNetⓘ	yes	94.71	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Micromonospora siamensis strain DSM 45097
PATRIC: 299152.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.36	no
125438	anaerobic	anaerobicⓘ	no	90.85	yes
125438	spore-forming	spore-formingⓘ	yes	92.59	no
125438	aerobic	aerobicⓘ	yes	85.53	yes
125438	thermophilic	thermophileⓘ	no	94.50	no
125438	flagellated	motile2+ⓘ	no	90.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Transcriptome	Discovery of novel carbohydrate-active enzymes through the rational exploration of the protein sequences space.	Helbert W, Poulet L, Drouillard S, Mathieu S, Loiodice M, Couturier M, Lombard V, Terrapon N, Turchetto J, Vincentelli R, Henrissat B.	Proc Natl Acad Sci U S A	10.1073/pnas.1815791116	2019
Phylogeny	Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential.	Carro L, Nouioui I, Sangal V, Meier-Kolthoff JP, Trujillo ME, Montero-Calasanz MDC, Sahin N, Smith DL, Kim KE, Peluso P, Deshpande S, Woyke T, Shapiro N, Kyrpides NC, Klenk HP, Goker M, Goodfellow M.	Sci Rep	10.1038/s41598-017-17392-0	2018
Phylogeny	Micromonospora azadirachtae sp. nov., isolated from roots of Azadirachta indica A. Juss. var. siamensis Valeton.	Kuncharoen N, Kudo T, Ohkuma M, Tanasupawat S	Antonie Van Leeuwenhoek	10.1007/s10482-018-1152-3	2018
Phylogeny	Micromonospora haikouensis sp. nov., isolated from mangrove soil.	Xie QY, Qu Z, Lin HP, Li L, Hong K	Antonie Van Leeuwenhoek	10.1007/s10482-011-9682-y	2012
Phylogeny	Micromonospora siamensis sp. nov., isolated from Thai peat swamp forest.	Thawai C, Tanasupawat S, Itoh T, Suwanborirux K, Kudo T	J Gen Appl Microbiol	10.2323/jgam.51.229	2005

References

#12339	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45097
#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 )
#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;
#68382	Automatically annotated from API zym .
#122595	Collection of Institut Pasteur ; Curators of the CIP; CIP 109112
#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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Micromonospora siamensis (DSM 45097, CIP 109112, JCM 12769)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900090305

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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