Nonomuraea phyllanthi (TISTR 2497, NBRC 112774, JCM 33073)

Name: Nonomuraea phyllanthi (TISTR 2497, NBRC 112774, JCM 33073)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 164452

Type strain

Strain Designation PA1-10

Culture col. no. TISTR 2497 NBRC 112774 JCM 33073 PA1-10 DSM 118955

NCBI tax ID(s) 2219224

Special Collections JCM Literature strains

Links

Nonomuraea phyllanthi PA1-10 is an aerobe, spore-forming, mesophilic prokaryote that was isolated from Stem of Phyllanthus amarus from a botanical garden of the Faculty of Pharmaceutical Sciences.

spore-forming Gram-positive filament-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 285466

DSM 118955,NBRC 112774,JCM 33073

@ref 20215

Last LPSN update 2025-12-16 10:09:28

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Streptosporangiales

Family Streptosporangiaceae

Genus Nonomuraea

Species Nonomuraea phyllanthi

Full scientific name Nonomuraea phyllanthi Klykleung et al. 2020

Synonyms (1)

Nonomuraea nitratireducens

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
68254	positive	filament-shaped
125439	positive			99.6

Multicellular morphology

@ref	Forms multicellular complex	Complex color	Medium name
68254		forms abundant white aerial mycelia and yellow to brown vegetative mycelia	ISP2, ISP3, ISP4, ISP5, ISP6, ISP7, nutrient agar

Multimedia

@ref:	125888
multimedia content:	DSM_118955.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_118955.jpg
caption:	M.65, 28°C
intellectual property rights:	Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
125888	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 20.0 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
125888	ISP2 MEDIUM (DSMZ Medium 987)	Medium recipe at MediaDive	Name: ISP2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water
125888	ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)	Medium recipe at MediaDive	Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
125888	ISP 6 MEDIUM (DSMZ Medium 1269)	Medium recipe at MediaDive	Name: ISP 6 MEDIUM (DSMZ Medium 1269) Composition: Agar 20.0 g/l Peptone 15.0 g/l Proteose peptone 5.0 g/l Yeast extract 1.0 g/l Dipotassium Phosphate 1.0 g/l Ferric ammonium citrate 0.5 g/l Sodium Thiosulfate 0.08 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
67770	positive	growth	28	mesophilic
68254	positive	growth	15-40
68254	positive	optimum	25-37	mesophilic
125888	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
68254	positive	optimum	7
68254	positive	growth	5-9	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
68254	aerobe
125439	obligate aerobe	98.1

Spore formation

68254

Spore formationyes

Halophily

@ref	Salt	Growth	Tested relation	Concentration
68254	NaCl	positive	growth	0-4 %(w/v)

Observation

@ref	Observation
67770	quinones: MK-9(H₂), MK-9(H₄), MK-9(H₆)
68254	formes the spiral short chains of the rugose spores and pseudosporangia on aerial mycelium

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68254	17057 ChEBI	cellobiose	-	assimilation
68254	62968 ChEBI	cellulose	-	assimilation
68254	17634 ChEBI	D-glucose	+	assimilation
68254	16899 ChEBI	D-mannitol	-	assimilation
68254	16024 ChEBI	D-mannose	+	assimilation
68254	28757 ChEBI	fructose	-	assimilation
68254	5291 ChEBI	gelatin	-	hydrolysis
68254	17754 ChEBI	glycerol	-	assimilation
68254	30849 ChEBI	L-arabinose	-	assimilation
68254	62345 ChEBI	L-rhamnose	-	assimilation
68254	28053 ChEBI	melibiose	+	assimilation
68254	17268 ChEBI	myo-inositol	+	assimilation
68254	17632 ChEBI	nitrate	+	reduction
68254	16634 ChEBI	raffinose	+	assimilation
68254		skimmed milk	-	assimilation
68254	28017 ChEBI	starch	-	hydrolysis
68254	17992 ChEBI	sucrose	+	assimilation
68254	18222 ChEBI	xylose	-	assimilation

Enzymes

@ref	Value	Activity	Ec
68254	acid phosphatase	+/-	3.1.3.2
68254	alkaline phosphatase	+	3.1.3.1
68254	alpha-chymotrypsin	+	3.4.21.1
68254	alpha-fucosidase	-	3.2.1.51
68254	alpha-galactosidase	+/-	3.2.1.22
68254	alpha-glucosidase	+	3.2.1.20
68254	alpha-mannosidase	+/-	3.2.1.24
68254	beta-galactosidase	+	3.2.1.23
68254	beta-glucosidase	+/-	3.2.1.21
68254	beta-glucuronidase	-	3.2.1.31
68254	cystine arylamidase	+/-	3.4.11.3
68254	esterase (C 4)	+/-
68254	esterase Lipase (C 8)	+/-
68254	leucine arylamidase	+	3.4.11.1
68254	lipase (C 14)	-
68254	N-acetyl-beta-glucosaminidase	+	3.2.1.52
68254	naphthol-AS-BI-phosphohydrolase	+
68254	trypsin	+/-	3.4.21.4
68254	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

68254

Fatty acid	Percentage
C16:0 iso	32.2
C17:0 10-methyl	11.2
C16:0	8.3
C15:0 iso	6.9
C17:0	5.6
C17:1 w8c	5.4
C17:0 anteiso	5
C16:0 10-methyl	4.4
C16:1 w7c/C16:1 w6c	3.1
C17:0 iso	2.5
C16:1 iso H	2.2
C15:0 anteiso	2.1
C18:0	1.9
C18:1 w9c	1.8
C18:0 10-methyl	1.4
C18:0 iso	1.4
C14:0	1.2
C15:0 2OH	0.7
C14:0 iso	0.7
C16:0 2OH	0.6
C17:1 anteiso w9c	0.5

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture duration	Enrichment culture temperature	Host species
67770	Stem of Phyllanthus amarus from a botanical garden of the Faculty of Pharmaceutical Sciences	Chulalongkorn University, Bangkok	Thailand	THA	Asia				Phyllanthus amarus
68254	stem of Phyllanthus amarus	botanical garden of the Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok	Thailand	THA	Asia	starch casein nitrate medium	3-4 weeks	30
125888	Stem of Phyllanthus amarus	botanical garden of the Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok	Thailand	THA	Asia

Taxonmaps

69479

Global distribution of 16S sequence LC387602 (>99% sequence identity) for Nonomuraea from Microbeatlas

Aquatic Samples
Soil Samples	72
Animal Samples	4
Plant Samples	15
Total Samples	91

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM633498v2 assembly for Nonomuraea phyllanthi PA1-10	contig	GCA_006334985	2219224.4	2895442618	2219224	57.3

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
68254	Nonomuraea phyllanthi PA1-10 gene for 16S ribosomal RNA, partial sequence	LC387602	1459		2219224

GC content

@ref	GC-content (mol%)	Method
68254	72	high performance liquid chromatography (HPLC)
67770	71.2	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Nonomuraea phyllanthi PA1-10
NCBI: GCA_006334985

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	79.20	no
125439	motility	BacteriaNetⓘ	no	88.20	no
125439	gram_stain	BacteriaNetⓘ	positive	99.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.10	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nonomuraea nitratireducens Qu et al. 2020 is a later heterotypic synonym of Nonomuraea phyllanthi Klykleung et al. 2020.	Wu Y, Peng M, Gao Y, Pei J, Zhang Y, Li S, Fang J, Wei Y	Int J Syst Evol Microbiol	10.1099/ijsem.0.005013	2021
Phylogeny	Nonomuraea phyllanthi sp. nov., an endophytic actinomycete isolated from the leaf of Phyllanthus amarus.	Klykleung N, Yuki M, Kudo T, Ohkuma M, Phongsopitanun W, Pittayakhajonwut P, Tanasupawat S	Arch Microbiol	10.1007/s00203-019-01717-w	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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68254	Nattaporn Klykleung, Masahiro Yuki, Takuji Kudo, Moriya Ohkuma, Wongsakorn Phongsopitanun, Pattama Pittayakhajonwut and Somboon Tanasupawat: Nonomuraea phyllanthi sp. nov., an endophytic actinomycete isolated from the leaf of Phyllanthus amarus. Arch Microbiol 202: 55 - 61 2020 ( DOI 10.1007/s00203-019-01717-w )
#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 .
#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 .
#125888	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 118955
#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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Nonomuraea phyllanthi (TISTR 2497, NBRC 112774, JCM 33073)

Name and taxonomic classification