Micromonospora chaiyaphumensis (DSM 45246, JCM 12873, KCTC 19332)

Name: Micromonospora chaiyaphumensis (DSM 45246, JCM 12873, KCTC 19332)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 8012

Type strain

Strain Designation MC5-1

Culture col. no. DSM 45246 JCM 12873 KCTC 19332 PCU 267 TISTR 1564 4 more

NCBI tax ID(s) 307119

Special Collections DSMZ JCM KCTC Literature strains

History DSMZ <- JCM/RIKEN; JCM 12873 <- S. Tanasupawat; MC5-1 JCM <-- S. Tanasupawat; Chulalongkorn Univ., Thailand; MC5-1.

Links

Micromonospora chaiyaphumensis MC5-1 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from soil.

spore-forming Gram-positive aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 343809

DSM 45246,JCM 12873,KCTC 19332,TISTR 1564

@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 chaiyaphumensis

Full scientific name Micromonospora chaiyaphumensis Jongrungruangchok et al. 2008

BacDive ID	Other strains from **Micromonospora chaiyaphumensis** (2)	Type strain
161277	M. chaiyaphumensis JCM 12874
161278	M. chaiyaphumensis JCM 12875

Morphology

Cell morphology

@ref	Gram stain	Confidence
32506	positive
125439	positive	99.265
125438	positive	90.772

Pigmentation

32506

Productionyes

Multimedia

@ref:	15930
multimedia content:	DSM_45246.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_45246.jpg
caption:	Medium 65 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
15930	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
15930	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
15930	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

Culture temp

@ref	Growth	Type	Temperature (°C)
15930	positive	growth	28
32506	positive	growth	25-45
32506	positive	optimum	27.5
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
32506	positive	growth	04-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32506	aerobe
125438	aerobe	90.223
125439	obligate aerobe	99.686

Spore formation

@ref	Spore formation	Confidence
32506
125438		91.365

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32506	NaCl	positive	growth	<3 %

Observation

67770

Observationquinones: MK-10(H₈), MK-10(H₆), MK-9(H₈), MK-9(H₆)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32506	22599 ChEBI	arabinose	+	carbon source
32506	28757 ChEBI	fructose	+	carbon source
32506	28260 ChEBI	galactose	+	carbon source
32506	17234 ChEBI	glucose	+	carbon source
32506	17716 ChEBI	lactose	+	carbon source
32506	28053 ChEBI	melibiose	+	carbon source
32506	16634 ChEBI	raffinose	+	carbon source
32506	17814 ChEBI	salicin	+	carbon source
32506	18222 ChEBI	xylose	+	carbon source

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
15930	soil		Thailand	THA	Asia
67770	Mountain soil	Chaiyaphume Province	Thailand	THA	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15930	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
67770	IMG-taxon 2622736432 annotated assembly for Micromonospora chaiyaphumensis DSM 45246	scaffold	GCA_900091435	307119.5	2622736432	307119	71.18
124043	ASM4243198v1 assembly for Micromonospora chaiyaphumensis PCU 267	scaffold	GCA_042431985			307119	63.76

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
15930	Micromonospora chaiyaphumensis gene for 16S rRNA, partial sequence, strain: MC5-1	AB196710	1436	307119
124043	Micromonospora chaiyaphumensis strain PCU 267 16S ribosomal RNA gene, partial sequence.	MT760022	1267	307119
124043	Micromonospora chaiyaphumensis strain PCU 267 16S ribosomal RNA gene, partial sequence.	MT758139	1267	307119

GC content

@ref	GC-content (mol%)	Method
15930	72.8
67770	72.8	high performance liquid chromatography (HPLC)
67770	73.52	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 2622736432 annotated assembly for Micromonospora chaiyaphumensis DSM 45246
BV-BRC: 307119.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.69	no
125439	gram_stain	BacteriaNetⓘ	positive	99.27	no
125439	motility	BacteriaNetⓘ	no	89.80	no
125439	spore_formation	BacteriaNetⓘ	yes	67.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Micromonospora chaiyaphumensis strain DSM 45246
PATRIC: 307119.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.77	yes
125438	anaerobic	anaerobicⓘ	no	97.32	yes
125438	spore-forming	spore-formingⓘ	yes	91.37	yes
125438	aerobic	aerobicⓘ	yes	90.22	yes
125438	thermophilic	thermophileⓘ	no	95.00	yes
125438	flagellated	motile2+ⓘ	no	88.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Phocoenamicins B and C, New Antibacterial Spirotetronates Isolated from a Marine Micromonospora sp.	Perez-Bonilla M, Oves-Costales D, de la Cruz M, Kokkini M, Martin J, Vicente F, Genilloud O, Reyes F.	Mar Drugs	10.3390/md16030095	2018
Enzymology	Alkaline proteases from a newly isolated Micromonospora chaiyaphumensis S103: Characterization and application as a detergent additive and for chitin extraction from shrimp shell waste.	Mhamdi S, Ktari N, Hajji S, Nasri M, Sellami Kamoun A.	Int J Biol Macromol	10.1016/j.ijbiomac.2016.10.036	2017
	Testing the Luedemann hypothesis: the discovery of novel antimicrobials from slow-growing microbes from nutrient-limited environments.	Lin B, Woo S, Philbrick A, Bacsa J, Laskey E, Mehra N, Gondil VS, Mei JA, Jones G, Pavelka MS, Dziejman M, Shutter DA, Melander C, Perritt AM, Jakober R, Shen Y, Chang W-C, Quave CL, Dunman PM, Luedemann G.	mSphere	10.1128/msphere.00367-25	2025
Biotechnology	Characterization of high-yield Bacillus subtilis cysteine protease for diverse industrial applications.	Keshapaga UR, Jathoth K, Singh SS, Gogada R, Burgula S.	Braz J Microbiol	10.1007/s42770-023-00992-6	2023
Enzymology	A New Micromonospora Strain with Antibiotic Activity Isolated from the Microbiome of a Mid-Atlantic Deep-Sea Sponge.	Back CR, Stennett HL, Williams SE, Wang L, Ojeda Gomez J, Abdulle OM, Duffy T, Neal C, Mantell J, Jepson MA, Hendry KR, Powell D, Stach JEM, Essex-Lopresti AE, Willis CL, Curnow P, Race PR.	Mar Drugs	10.3390/md19020105	2021
	Phylogenetic diversity of actinomycetes cultured from coastal multipond solar saltern in Tuticorin, India.	Jose PA, Jebakumar SR.	Aquat Biosyst	10.1186/2046-9063-8-23	2012
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
Metabolism	Structural basis for ion selectivity in TMEM175 K⁺ channels.	Brunner JD, Jakob RP, Schulze T, Neldner Y, Moroni A, Thiel G, Maier T, Schenck S.	Elife	10.7554/elife.53683	2020
Phylogeny	Micromonospora fluminis sp. nov., isolated from mountain river sediment.	Camacho Pozo MI, Wieme AD, Rodriguez Perez S, Llaurado Maury G, Peeters C, Snauwaert C, Lescaylle Veranes Y, Pena Zamora L, Schumann P, Vandamme PA	Int J Syst Evol Microbiol	10.1099/ijsem.0.004554	2020
Phylogeny	Micromonospora fluostatini sp. nov., isolated from marine sediment.	Phongsopitanun W, Kudo T, Mori M, Shiomi K, Pittayakhajonwut P, Suwanborirux K, Tanasupawat S	Int J Syst Evol Microbiol	10.1099/ijsem.0.000589	2015
Phylogeny	Micromonospora equina sp. nov., isolated from soil from a racecourse.	Everest GJ, Meyers PR	Int J Syst Evol Microbiol	10.1099/ijs.0.042929-0	2012
Phylogeny	Micromonospora yangpuensis sp. nov., isolated from a sponge.	Zhang L, Xi L, Ruan J, Huang Y	Int J Syst Evol Microbiol	10.1099/ijs.0.029439-0	2011
Phylogeny	Micromonospora chaiyaphumensis sp. nov., isolated from Thai soils.	Jongrungruangchok S, Tanasupawat S, Kudo T	Int J Syst Evol Microbiol	10.1099/ijs.0.65594-0	2008

References

#15930	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45246
#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 )
#28726	IJSEM 924 2008 ( DOI 10.1099/ijs.0.65594-0 , PubMed 18398196 )
#32506	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 #28726
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 chaiyaphumensis (DSM 45246, JCM 12873, KCTC 19332)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900091435

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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