Name: Micromonospora zingiberis NBRC 113144
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 159791

Type strain:

Species: Micromonospora zingiberis

Culture col. no.: NBRC 113144, TBRC 7644, PLAI 1-1, JCM 32592

Strain history: C. Thawai; King Mongkut's Inst. of Technol. Ladkrabang, Thailand; PLAI 1-1.

Section

Micromonospora zingiberis NBRC 113144 is a spore-forming, mesophilic, Gram-positive bacterium that has a pale yellow pigmentation and was isolated from from the root of Zingiber montanum.

Gram-positive
pigmented
spore-forming
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micromonosporales*
	Family	*Micromonosporaceae*
	Genus	*Micromonospora*
	Species	**Micromonospora zingiberis**
	Full Scientific Name (LPSN)	Micromonospora zingiberis (Thawai et al. 2018) Kuncharoen et al. 2019

Synonym

Jishengella zingiberis

Information on morphological and physiological properties Morphology

[Ref.: #66715]	Gram stain	positive

[Ref.: #66715]	Colony color	strong orange-dark brownish with age
[Ref.: #66715]	Cultivation medium used	ISP 2

[Ref.: #66715]	Pigment production	yes
[Ref.: #66715]	Pigmentation color	pale yellow
[Ref.: #66715]	Pigment name	soluble pigment

[Ref.: #66715]	Multicellular complex forming ability	no
[Ref.: #66715]	Multicellular complex name	aerial mycelia

Information on culture and growth conditions Culture and growth conditions

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Culture medium

Czapek's sucrose agar

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Culture medium growth

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Culture medium

ISP 2

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Culture medium growth

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Culture medium

ISP 3

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Culture medium growth

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Culture medium

ISP 4

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Culture medium growth

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Culture medium

ISP 6

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Culture medium growth

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Culture medium

Nutrient agar (NA)

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

glucose-asparagine agar

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Culture medium growth

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Culture medium composition

expand / minimize

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Culture medium

ISP 5

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Culture medium growth

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Culture medium

ISP 7

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Culture medium growth

	Kind of temperature		Temperature
[Ref.: #66715]		optimum	30 °C
[Ref.: #66715]	no	growth	45 °C
[Ref.: #66715]		growth	12-40 °C
[Ref.: #67770]		growth	28 °C

[Ref.: #66715]	Temperature range	mesophilic
[Ref.: #66715]	Temperature range	thermophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #66715]			growth	4-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #66715]	Spore description	forms a single spore borne on the substrate mycelium. The spore surface is spiny.
[Ref.: #66715]	Type of spore	spore
[Ref.: #66715]	Ability of spore formation	yes

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #66715]		NaCl		growth	4	%(w/v)

[Ref.: #66715]	Observation	cell-wall peptidoglycan contains meso-diaminopimelic acid and 3-hydroxydiaminopimelic acid
[Ref.: #66715]	Observation	acyl type of the cell-wall muramic acid is glycolyl
[Ref.: #66715]	Observation	The predominant menaquinone is MK-9(H 4), while MK-9(H 2), MK-9(H 6), MK-10(H 4), MK-9(H 8) and MK-10(H 6) are present as minor components
[Ref.: #66715]	Observation	polar lipid profile contains diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylserine, two unidentified phospholipids and one unidentified lipid.
[Ref.: #67770]	Observation	quinones: MK-9(H₄), MK-9(H₂), MK-9(H₆), MK-10(H₄), MK-9(H₈), MK-10(H₆)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #66715]	2-aminobutyrate ChEBI	-	nitrogen source
[Ref.: #66715]	adenine ChEBI	-	hydrolysis
[Ref.: #66715]	beta-D-xylose ChEBI	+	builds acid from
[Ref.: #66715]	cellobiose ChEBI	+	builds acid from
[Ref.: #66715]	crystalline cellulose	-	hydrolysis
[Ref.: #66715]	D-fructose ChEBI	+	builds acid from
[Ref.: #66715]	D-galactose ChEBI	-	builds acid from
[Ref.: #66715]	D-glucose ChEBI	+	builds acid from
[Ref.: #66715]	D-mannitol ChEBI	+	builds acid from
[Ref.: #66715]	D-ribose ChEBI	+	builds acid from
[Ref.: #66715]	dextran ChEBI	-	builds acid from
[Ref.: #66715]	glycerol ChEBI	-	builds acid from
[Ref.: #66715]	hydroxyproline ChEBI	-	nitrogen source
[Ref.: #66715]	hypoxanthine ChEBI	-	hydrolysis
[Ref.: #66715]	L-arginine ChEBI	+	nitrogen source
[Ref.: #66715]	L-asparagine ChEBI	+	nitrogen source
[Ref.: #66715]	L-cysteine ChEBI	+	nitrogen source
[Ref.: #66715]	L-histidine ChEBI	+	nitrogen source
[Ref.: #66715]	L-methionine ChEBI	+	nitrogen source
[Ref.: #66715]	L-phenylalanine ChEBI	+	nitrogen source
[Ref.: #66715]	L-proline ChEBI	+	nitrogen source
[Ref.: #66715]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #66715]	L-serine ChEBI	+	nitrogen source
[Ref.: #66715]	L-threonine ChEBI	-	nitrogen source
[Ref.: #66715]	L-valine ChEBI	-	nitrogen source
[Ref.: #66715]	lactose ChEBI	-	builds acid from
[Ref.: #66715]	melezitose ChEBI	-	builds acid from
[Ref.: #66715]	nitrate ChEBI	-	reduction
[Ref.: #66715]	ribitol ChEBI	-	builds acid from
[Ref.: #66715]	starch ChEBI	+	hydrolysis
[Ref.: #66715]	sucrose ChEBI	+	builds acid from
[Ref.: #66715]	trehalose ChEBI	+	builds acid from
[Ref.: #66715]	tyrosine ChEBI	-	hydrolysis
[Ref.: #66715]	xanthine ChEBI	-	hydrolysis
[Ref.: #66715]	xylitol ChEBI	+	builds acid from
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #66715]	catalase	+	1.11.1.6
[Ref.: #66715]	cytochrome oxidase	-	1.9.3.1
[Ref.: #66715]	gelatinase	+
[Ref.: #66715]	urease	-	3.5.1.5

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #66715]

Fatty acid	Percentage
C15:0 iso	38
C17:1 w8c	10.3

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #66715]	Sample type/isolated from	from the root of Zingiber montanum
[Ref.: #66715]	Host species	Zingiber montanum
[Ref.: #66715]	Country	Thailand
[Ref.: #66715]	Country ISO 3 Code	THA
[Ref.: #66715]	Continent	Asia
[Ref.: #66715]	Enrichment culture	humic acid-vitamin (HV) agar
[Ref.: #66715]	Enrichment culture composition	supplemented with 25 mg/l nalidixic acid and 50 mg/l nystatin
[Ref.: #66715]	Enrichment culture duration	30 days
[Ref.: #66715]	Enrichment culture temperature	30 ̊C
[Ref.: #66715]	Isolation/enrichment procedure	sample was gently washed in tap water and cut into small pieces. After cutting, the samples were surface-sterilized with 95 % ethanol for 10 min and subsequently with 1 % sodium hypochlorite for 10 min, and immediately washed in sterile distilled water five times. Finally, the surface-sterilized samples were ground with 0.5 ml sterile distilled water

[Ref.: #67770]	Sample type/isolated from	Root of Zingiber montanum
[Ref.: #67770]	Host species	Zingiber montanum
[Ref.: #67770]	Country	Thailand
[Ref.: #67770]	Country ISO 3 Code	THA
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

What are isolation sources categories?

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #66715]	Micromonospora zingiberis PLAI1-1 gene for 16S ribosomal RNA, partial sequence	LC333555	1411	ENA	2053011 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Micromonospora zingiberis PLAI 1-1	GCA_004331455	contig	GenBank	2053011 tax ID

[Ref.: #66715]	GC-content	70.6 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	71.2 mol%	genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Micromonospora zingiberis PLAI 1-1 NCBI: GCA_004331455.1
[Ref.: #69480]	flagellated	no	97.367	no
[Ref.: #69480]	gram-positive	yes	89.459	yes
[Ref.: #69480]	anaerobic	no	99.366	no
[Ref.: #69480]	aerobic	yes	92.074	no
[Ref.: #69480]	halophile	no	92.584	no
[Ref.: #69480]	spore-forming	yes	92.933	yes
[Ref.: #69480]	glucose-util	yes	87.204	no
[Ref.: #69480]	thermophile	no	97.798	no
[Ref.: #69480]	motile	no	92.987	no
[Ref.: #69480]	glucose-ferment	no	92.266	no

Availability in culture collections External links

[Ref.: #66715]

Culture collection no.

NBRC 113144, TBRC 7644, PLAI 1-1, JCM 32592

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Micromonospora radicis sp. nov., isolated from roots of Azadirachta indica var. siamensis Valenton, and reclassification of Jishengella zingiberis as Micromonospora zingiberis comb. nov.	Kuncharoen N, Kudo T, Yuki M, Okuma M, Pittayakhajonwut P, Tanasupawat S	Int J Syst Evol Microbiol	10.1099/ijsem.0.003574	2019	*

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 )

#66715

Chitti Thawai, Ya-Wen He, Sarin Tadtong: Jishengella zingiberis sp. nov., isolated from root tissue of Zingiber montanum. IJSEM 68: 3345 - 3350 2018 ( DOI 10.1099/ijsem.0.002998 , PubMed 30168792 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

* These data were automatically processed and therefore are not curated

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Micromonospora zingiberis PLAI 1-1

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