Zymobacter palmae (DSM 10491, ATCC 51623, IAM 14233)

Name: Zymobacter palmae (DSM 10491, ATCC 51623, IAM 14233)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6008

Type strain

Strain Designation T 109

Culture col. no. DSM 10491 ATCC 51623 IAM 14233 T 109 NBRC 102412 1 more

NCBI tax ID(s) 1123510 33074

Special Collections DSMZ JCM

History <- ATCC <- IAM <- T. Okamoto, T 109 IAM 14233 <-- T. Okamoto T109.

Links

Zymobacter palmae T 109 is a mesophilic prokaryote that produces alcohol and was isolated from palm sap.

alcohol production mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 45304

ATCC 51623,IAM 14233,DSM 10491,NBRC 102412,JCM 21091

@ref 20215

Last LPSN update 2026-02-09 11:19:06

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Oceanospirillales

Family Halomonadaceae

Genus Zymobacter

Species Zymobacter palmae

Full scientific name Zymobacter palmae Okamoto et al. 1995

BacDive ID	Other strains from **Zymobacter palmae** (3)	Type strain
163085	Z. palmae JCM 21092, IAM 14234
163086	Z. palmae JCM 21093, IAM 14235
163087	Z. palmae JCM 21094, IAM 14236

Morphology

Cell morphology

@ref	Confidence	Gram stain
125439	92.1
125439	99.6	negative
125438	95	negative

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
3938	MY MEDIUM (DSMZ Medium 753)		Medium recipe at MediaDive	Name: MY MEDIUM (DSMZ Medium 753) Composition: Maltose 20.0 g/l Yeast extract 10.0 g/l NaCl 5.0 g/l KH2PO4 2.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
3938	positive	growth	26	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		98.7
125438		90.691

Compound production

3938

Compoundethanol

Observation

67770

Observationquinones: Q-9

Metabolite production

@ref	Chebi-ID	Metabolite	Production
67770	16236 ChEBI	ethanol

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	coenzyme A metabolism	100	4 of 4
66794	biotin biosynthesis	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	acetoin degradation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	ubiquinone biosynthesis	100	7 of 7
66794	aerobactin biosynthesis	100	1 of 1
66794	ethanol fermentation	100	2 of 2
66794	enterobactin biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	tetrahydrofolate metabolism	100	14 of 14
66794	palmitate biosynthesis	95.45	21 of 22
66794	glutathione metabolism	92.86	13 of 14
66794	Entner Doudoroff pathway	90	9 of 10
66794	lipid A biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	ketogluconate metabolism	87.5	7 of 8
66794	heme metabolism	85.71	12 of 14
66794	vitamin B1 metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	proline metabolism	81.82	9 of 11
66794	peptidoglycan biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	chorismate metabolism	77.78	7 of 9
66794	pyrimidine metabolism	75.56	34 of 45
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	gluconeogenesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	purine metabolism	68.09	64 of 94
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	vitamin B12 metabolism	67.65	23 of 34
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	formaldehyde oxidation	66.67	2 of 3
66794	NAD metabolism	66.67	12 of 18
66794	octane oxidation	66.67	2 of 3
66794	alanine metabolism	65.52	19 of 29
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	methionine metabolism	61.54	16 of 26
66794	lipid metabolism	61.29	19 of 31
66794	cysteine metabolism	61.11	11 of 18
66794	cellulose degradation	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	coenzyme M biosynthesis	60	6 of 10
66794	lipoate biosynthesis	60	3 of 5
66794	citric acid cycle	57.14	8 of 14
66794	propanol degradation	57.14	4 of 7
66794	lysine metabolism	57.14	24 of 42
66794	photosynthesis	57.14	8 of 14
66794	oxidative phosphorylation	56.04	51 of 91
66794	d-mannose degradation	55.56	5 of 9
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	pentose phosphate pathway	54.55	6 of 11
66794	vitamin B6 metabolism	54.55	6 of 11
66794	leucine metabolism	53.85	7 of 13
66794	tryptophan metabolism	50	19 of 38
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	suberin monomers biosynthesis	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	glycogen biosynthesis	50	2 of 4
66794	butanoate fermentation	50	2 of 4
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	adipate degradation	50	1 of 2
66794	arginine metabolism	50	12 of 24
66794	isoprenoid biosynthesis	50	13 of 26
66794	tyrosine metabolism	50	7 of 14
66794	non-pathway related	50	19 of 38
66794	degradation of sugar alcohols	50	8 of 16
66794	glycine metabolism	50	5 of 10
66794	glycolysis	47.06	8 of 17
66794	sulfate reduction	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	histidine metabolism	41.38	12 of 29
66794	bacilysin biosynthesis	40	2 of 5
66794	propionate fermentation	40	4 of 10
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	methylglyoxal degradation	40	2 of 5
66794	polyamine pathway	39.13	9 of 23
66794	arachidonic acid metabolism	38.89	7 of 18
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	degradation of pentoses	35.71	10 of 28
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	cyanate degradation	33.33	1 of 3
66794	L-lactaldehyde degradation	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
66794	ascorbate metabolism	31.82	7 of 22
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	degradation of hexoses	27.78	5 of 18
66794	d-xylose degradation	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	degradation of sugar acids	24	6 of 25
66794	allantoin degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Tree
#Host Body Product	#Plant	#Plant sap (Flux)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
3938	palm sap	Okinawa Prefecture	Japan	JPN	Asia
67770	Palm sap	Okinawa	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AF211871 (>99% sequence identity) for Zymobacter palmae subclade from Microbeatlas

Aquatic Samples	397
Soil Samples	295
Animal Samples	3369
Plant Samples	175
Total Samples	4236

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
3938	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
66792	ASM361001v1 assembly for Zymobacter palmae IAM14233	complete	GCA_003610015	33074.3	2832896515	33074	93.02
67770	ASM62002v1 assembly for Zymobacter palmae DSM 10491	scaffold	GCA_000620025	1123510.3	2556921094	1123510	59.32

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Zymobacter palmae 16S ribosomal RNA gene, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequence	AF211871	4673	33074
20218	Zymobacter palmae gene for 16S rRNA, partial sequence, strain: NBRC 102412	AB681768	1465	33074
20218	Zymobacter palmae gene for 16S rRNA, partial sequence	D14555	1503	33074

GC content

@ref	GC-content (mol%)	Method
67770	56.2	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: Zymobacter palmae IAM14233
NCBI: GCA_003610015

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	85.80	no
125439	gram_stain	BacteriaNetⓘ	negative	99.60	no
125439	motility	BacteriaNetⓘ	yes	92.10	no
125439	spore_formation	BacteriaNetⓘ	no	98.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Zymobacter palmae IAM14233
NCBI: GCA_003610015.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.00	no
125438	anaerobic	anaerobicⓘ	no	81.32	no
125438	aerobic	aerobicⓘ	no	58.61	no
125438	spore-forming	spore-formingⓘ	no	90.69	no
125438	thermophilic	thermophileⓘ	no	93.78	no
125438	flagellated	motile2+ⓘ	yes	55.41	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Zymobacter palmae Pyruvate Decarboxylase is Less Effective Than That of Zymomonas mobilis for Ethanol Production in Metabolically Engineered Synechocystis sp. PCC6803.	Quinn L, Armshaw P, Soulimane T, Sheehan C, Ryan MP, Pembroke JT.	Microorganisms	10.3390/microorganisms7110494	2019
Metabolism	Effect of metabolosome encapsulation peptides on enzyme activity, coaggregation, incorporation, and bacterial microcompartment formation.	Juodeikis R, Lee MJ, Mayer M, Mantell J, Brown IR, Verkade P, Woolfson DN, Prentice MB, Frank S, Warren MJ.	Microbiologyopen	10.1002/mbo3.1010	2020
Metabolism	Genetic engineering of Zymobacter palmae for production of ethanol from xylose.	Yanase H, Sato D, Yamamoto K, Matsuda S, Yamamoto S, Okamoto K.	Appl Environ Microbiol	10.1128/aem.02302-06	2007
Enzymology	Cloning and characterization of the Zymobacter palmae pyruvate decarboxylase gene (pdc) and comparison to bacterial homologues.	Raj KC, Talarico LA, Ingram LO, Maupin-Furlow JA.	Appl Environ Microbiol	10.1128/aem.68.6.2869-2876.2002	2002
Phylogeny	Leuconostoc miyukkimchii sp. nov., isolated from brown algae (Undaria pinnatifida) kimchi.	Lee SH, Park MS, Jung JY, Jeon CO.	Int J Syst Evol Microbiol	10.1099/ijs.0.032367-0	2012
Phylogeny	Pseudoclavibacter chungangensis sp. nov., isolated from activated sludge.	Cho SL, Jung MY, Park MH, Chang YH, Yoon JH, Myung SC, Kim W.	Int J Syst Evol Microbiol	10.1099/ijs.0.015552-0	2010
Phylogeny	Pseudoclavibacter soli sp. nov., a {beta}-glucosidase-producing bacterium.	Kim MK, Jung HY.	Int J Syst Evol Microbiol	10.1099/ijs.0.65627-0	2009
Phylogeny	Halotalea alkalilenta gen. nov., sp. nov., a novel osmotolerant and alkalitolerant bacterium from alkaline olive mill wastes, and emended description of the family Halomonadaceae Franzmann et al. 1989, emend. Dobson and Franzmann 1996.	Ntougias S, Zervakis GI, Fasseas C	Int J Syst Evol Microbiol	10.1099/ijs.0.65078-0	2007
Phylogeny	Halomonas marisflavae sp. nov., a halophilic bacterium isolated from the Yellow Sea in Korea.	Yoon JH, Choi SH, Lee KC, Kho YH, Kang KH, Park YH	Int J Syst Evol Microbiol	10.1099/00207713-51-3-1171	2001
Phylogeny	Zymobacter palmae gen. nov., sp. nov., a new ethanol-fermenting peritrichous bacterium isolated from palm sap.	Okamoto T, Taguchi H, Nakamura K, Ikenaga H, Kuraishi H, Yamasato K	Arch Microbiol	10.1007/BF00252218	1993

References

#3938	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 10491
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#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;
#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 .
#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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Zymobacter palmae (DSM 10491, ATCC 51623, IAM 14233)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Compound production

Observation

Metabolite production

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003610015

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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