Streptomyces palmae (CMU-AB204, JCM 31289, TBRC 1999)

Name: Streptomyces palmae (CMU-AB204, JCM 31289, TBRC 1999)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133134

Type strain

Strain Designation CMU-AB204

Culture col. no. CMU-AB204 JCM 31289 TBRC 1999 DSM 111123

NCBI tax ID(s) 1701085

Special Collections DSMZ JCM Literature strains

Links

Streptomyces palmae CMU-AB204 is an aerobe, spore-forming, mesophilic prokaryote that was isolated from rhizosphere soil of an oil palm .

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

Name and taxonomic classification

SI-ID 399669

TBRC 1999,JCM 31289,DSM 111123

@ref 20215

Last LPSN update 2025-12-16 10:01:41

Domain Bacillati

Phylum Actinomycetota

Class Actinomycetes

Order Kitasatosporales

Family Streptomycetaceae

Genus Streptomyces

Species Streptomyces palmae

Full scientific name Streptomyces palmae Sujarit et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Confidence
24896	positive
125438	positive	92.305
125439	positive	99.9
125439		94.3

Multimedia

@ref:	66469
multimedia content:	DSM_111123.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_111123.jpg
caption:	Medium 252 28°C
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
24896	Yeast extract-malt extract agar (ISP2)
24896	Inorganic salts-starch agar (ISP4)
66469	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
66469	STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)	Medium recipe at MediaDive	Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water
66469	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
24896	positive	optimum	30.0-35.0	mesophilic
24896	negative	growth	10
24896	positive	growth	45	thermophilic
66469	positive	growth	28	mesophilic
67770	positive	growth	28	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
24896	positive	optimum	6.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
24896	aerobe
125439	obligate aerobe	97.9

Spore formation

@ref	Spore description	Type of spore	Spore formation	Confidence
24896	oval-shaped, spiny to hairy surfaced,0.7-1.0x1.0-1.3 µm	spore
125439				93.3

Halophily

@ref	Salt	Growth	Tested relation	Concentration
24896	NaCl	positive	growth	3 %(w/v)
24896	NaCl		growth	7 %(w/v)

Observation

67770

Observationquinones: MK-9(H₄), MK-9(H₆), MK-9(H₂), MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
24896	15824 ChEBI	D-fructose	+	carbon source
24896	17634 ChEBI	D-glucose	+	carbon source
24896	16899 ChEBI	D-mannitol	-	carbon source
24896	65327 ChEBI	D-xylose	-	carbon source
24896	30849 ChEBI	L-arabinose	-	carbon source
24896	17268 ChEBI	myo-inositol	+	carbon source
24896	16634 ChEBI	raffinose	+	carbon source
24896	26546 ChEBI	rhamnose	-	carbon source
24896	17992 ChEBI	sucrose	-	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
24896	89634 ChEBI	melanin

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	factor 420 biosynthesis	100	5 of 5
66794	butanoate fermentation	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	valine metabolism	100	9 of 9
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	myo-inositol biosynthesis	100	10 of 10
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	pentose phosphate pathway	100	11 of 11
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	cyanate degradation	100	3 of 3
66794	ribulose monophosphate pathway	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	hydrogen production	100	5 of 5
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	cardiolipin biosynthesis	100	7 of 7
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	aerobactin biosynthesis	100	1 of 1
66794	taurine degradation	100	1 of 1
66794	acetate fermentation	100	4 of 4
66794	cellulose degradation	100	5 of 5
66794	methylglyoxal degradation	100	5 of 5
66794	ceramide biosynthesis	100	1 of 1
66794	glutamate and glutamine metabolism	92.86	26 of 28
66794	phenylalanine metabolism	92.31	12 of 13
66794	proline metabolism	90.91	10 of 11
66794	starch degradation	90	9 of 10
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	gluconeogenesis	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	heme metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	citric acid cycle	85.71	12 of 14
66794	vitamin B12 metabolism	85.29	29 of 34
66794	leucine metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	arginine metabolism	83.33	20 of 24
66794	NAD metabolism	83.33	15 of 18
66794	alanine metabolism	82.76	24 of 29
66794	glycolysis	82.35	14 of 17
66794	metabolism of disaccharids	81.82	9 of 11
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	glycine betaine biosynthesis	80	4 of 5
66794	flavin biosynthesis	80	12 of 15
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	purine metabolism	78.72	74 of 94
66794	d-mannose degradation	77.78	7 of 9
66794	4-hydroxymandelate degradation	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	lipid metabolism	74.19	23 of 31
66794	pyrimidine metabolism	73.33	33 of 45
66794	isoprenoid biosynthesis	73.08	19 of 26
66794	histidine metabolism	72.41	21 of 29
66794	propanol degradation	71.43	5 of 7
66794	tryptophan metabolism	71.05	27 of 38
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	lysine metabolism	69.05	29 of 42
66794	oxidative phosphorylation	68.13	62 of 91
66794	enterobactin biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	cysteine metabolism	66.67	12 of 18
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	tyrosine metabolism	64.29	9 of 14
66794	glutathione metabolism	64.29	9 of 14
66794	non-pathway related	63.16	24 of 38
66794	degradation of sugar alcohols	62.5	10 of 16
66794	ketogluconate metabolism	62.5	5 of 8
66794	sulfate reduction	61.54	8 of 13
66794	urea cycle	61.54	8 of 13
66794	3-chlorocatechol degradation	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	arachidonate biosynthesis	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	degradation of pentoses	57.14	16 of 28
66794	daunorubicin biosynthesis	55.56	5 of 9
66794	phenylpropanoid biosynthesis	53.85	7 of 13
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	coenzyme M biosynthesis	50	5 of 10
66794	androgen and estrogen metabolism	50	8 of 16
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	cyclohexanol degradation	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	glycine metabolism	50	5 of 10
66794	toluene degradation	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	vitamin E metabolism	50	2 of 4
66794	degradation of hexoses	50	9 of 18
66794	quinate degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	carotenoid biosynthesis	45.45	10 of 22
66794	vitamin B6 metabolism	45.45	5 of 11
66794	cholesterol biosynthesis	45.45	5 of 11
66794	ascorbate metabolism	45.45	10 of 22
66794	phenol degradation	45	9 of 20
66794	nitrate assimilation	44.44	4 of 9
66794	lipid A biosynthesis	44.44	4 of 9
66794	polyamine pathway	43.48	10 of 23
66794	aclacinomycin biosynthesis	42.86	3 of 7
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	gallate degradation	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	carnitine metabolism	37.5	3 of 8
66794	d-xylose degradation	36.36	4 of 11
66794	sphingosine metabolism	33.33	2 of 6
66794	chlorophyll metabolism	33.33	6 of 18
66794	methanogenesis from CO2	33.33	4 of 12
66794	degradation of sugar acids	32	8 of 25
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	mevalonate metabolism	28.57	2 of 7
66794	arachidonic acid metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	alginate biosynthesis	25	1 of 4
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	lactate fermentation	25	1 of 4

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature
24896	rhizosphere soil of an oil palm (Elaeis guineensis Jacq.)	Chiang Mai University, Chiang Mai Province	Thailand	THA	Asia	starch casein agar (SCA)	supplemented with nalidixic acid (25 µg ml-1) and cycloheximide (50 µg ml-1)	14 days	30
66469	Rhizosphere of oil palm (Elaeis guineensis Jacq.)	Chiang Mai Univ, Chiang Mai, Thailand	Thailand	THA	Asia
67770	Oil palm rhizosphere soil in Chiang Mai Univ.	Chiang Mai	Thailand	THA	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
66469	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM4243407v1 assembly for Streptomyces palmae TBRC 1999	scaffold	GCA_042434075			1701085	59.61
67770	ASM468480v1 assembly for Streptomyces palmae JCM 31289	contig	GCA_004684805	1701085.3	2866937661	1701085

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24896	Streptomyces palmae gene for 16S ribosomal RNA, partial sequence	LC073309	1451		1701085

GC content

@ref	GC-content (mol%)	Method
66469	70.9	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: Streptomyces palmae JCM 31289
NCBI: GCA_004684805

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	93.30	no
125439	motility	BacteriaNetⓘ	no	94.30	no
125439	gram_stain	BacteriaNetⓘ	positive	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Streptomyces palmae strain JCM 31289
PATRIC: 1701085.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.31	yes
125438	anaerobic	anaerobicⓘ	no	90.55	yes
125438	spore-forming	spore-formingⓘ	yes	89.93	no
125438	aerobic	aerobicⓘ	yes	87.42	yes
125438	thermophilic	thermophileⓘ	no	95.00	no
125438	flagellated	motile2+ⓘ	no	89.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Bacterial-fungal interactions under agricultural settings: from physical to chemical interactions.	Zhou Y, Wang H, Xu S, Liu K, Qi H, Wang M, Chen X, Berg G, Ma Z, Cernava T, Chen Y.	Stress Biol	10.1007/s44154-022-00046-1	2022
Phylogeny	New Antimicrobial Phenyl Alkenoic Acids Isolated from an Oil Palm Rhizosphere-Associated Actinomycete, Streptomyces palmae CMU-AB204(T).	Sujarit K, Mori M, Dobashi K, Shiomi K, Pathom-Aree W, Lumyong S	Microorganisms	10.3390/microorganisms8030350	2020
	Streptomyces chengmaiensis sp. nov., isolated from the stem of a mangrove plant in Hainan.	Lin Y, Chu X, Xie Y, Xie X, Huang X, Zhou S.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006101	2023
	Streptomyces humicola sp. nov., a novel actinobacterium isolated from peat swamp forest soil in Thailand.	Klaysubun C, Srisuk N, Duangmal K.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005665	2022
Phylogeny	Streptomyces alkaliterrae sp. nov., isolated from an alkaline soil, and emended descriptions of Streptomyces alkaliphilus, Streptomyces calidiresistens and Streptomyces durbertensis.	Swiecimska M, Golinska P, Nouioui I, Wypij M, Rai M, Sangal V, Goodfellow M.	Syst Appl Microbiol	10.1016/j.syapm.2020.126153	2020
Phylogeny	Streptomyces benahoarensis sp. nov. Isolated From a Lava Tube of La Palma, Canary Islands, Spain.	Gonzalez-Pimentel JL, Hermosin B, Saiz-Jimenez C, Jurado V	Front Microbiol	10.3389/fmicb.2022.907816	2022
Phylogeny	Streptomyces lichenis sp. nov., isolated from lichen.	Saeng-In P, Phongsopitanun W, Savarajara A, Tanasupawat S	Int J Syst Evol Microbiol	10.1099/ijsem.0.003052	2018
Phylogeny	Streptomyces durbertensis sp. nov., isolated from saline-alkali soil.	Yu Y, Fu Y, Guo X, Yan R, Wang H, Zhao J, Wang X, Zhang J, Xiang W	Int J Syst Evol Microbiol	10.1099/ijsem.0.003047	2018
Phylogeny	Streptomyces palmae sp. nov., isolated from oil palm (Elaeis guineensis) rhizosphere soil.	Sujarit K, Kudo T, Ohkuma M, Pathom-Aree W, Lumyong S	Int J Syst Evol Microbiol	10.1099/ijsem.0.001298	2016

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 )
#24896	K. K. Sujarit, Takuji,Ohkuma, Moriya,Pathom-Aree, Wasu,Lumyong, Saisamorn: Streptomyces palmae sp. nov., isolated from oil palm (Elaeis guineensis) rhizosphere soil. IJSEM 66: 3983 - 3988 2016 ( DOI 10.1099/ijsem.0.001298 , PubMed 27405543 )
#66469	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 111123
#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;
#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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Streptomyces palmae (CMU-AB204, JCM 31289, TBRC 1999)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_042434075

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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