Name: Zymobacter palmae T 109
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 6008

Type strain:

Species: Zymobacter palmae

Strain Designation: T 109

Culture col. no.: DSM 10491, ATCC 51623, IAM 14233, JCM 21091, NBRC 102412

Strain history: IAM 14233 <-- T. Okamoto T109.

NCBI tax ID(s): 1123510 (strain), 33074 (species)

SI-ID 45304

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

Other strains from Zymobacter palmae

Z. palmae JCM 21092, IAM 14234
Z. palmae JCM 21093, IAM 14235
Z. palmae JCM 21094, IAM 14236

Section

Zymobacter palmae T 109 is a mesophilic, Gram-negative bacterium that produces alcohol and was isolated from palm sap.

alcohol production
Gram-negative
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	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Oceanospirillales*
	Family	*Halomonadaceae*
	Genus	*Zymobacter*
	Species	**Zymobacter palmae**
	Full Scientific Name (LPSN)	Zymobacter palmae Okamoto et al. 1995

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.981

Information on culture and growth conditions Culture and growth conditions

[Ref.: #3938]

Culture medium

MY MEDIUM (DSMZ Medium 753)

[Ref.: #3938]

Culture medium growth

[Ref.: #3938]

Culture medium link

Medium recipe at MediaDive

[Ref.: #3938]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #3938]			growth	26 °C
[Ref.: #67770]			growth	30 °C

[Ref.: #3938]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

[Ref.: #3938]

Name of produced compound

ethanol

[Ref.: #67770]

Observation

quinones: Q-9

	Metabolite production	Metabolite	Production
[Ref.: #67770]		ethanol ChEBI	yes

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

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

[Ref.: #3938]	Sample type/isolated from	palm sap
[Ref.: #3938]	Geographic location (country and/or sea, region)	Okinawa Prefecture
[Ref.: #3938]	Country	Japan
[Ref.: #3938]	Country ISO 3 Code	JPN
[Ref.: #3938]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Palm sap
[Ref.: #67770]	Geographic location (country and/or sea, region)	Okinawa
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Tree
#Host Body Product	#Plant	#Plant sap (Flux)

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #3938]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #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	ENA	33074 tax ID	*
[Ref.: #20218]	Zymobacter palmae gene for 16S rRNA, partial sequence, strain: NBRC 102412	AB681768	1465	ENA	33074 tax ID	*
[Ref.: #20218]	Zymobacter palmae gene for 16S rRNA, partial sequence	D14555	1503	ENA	33074 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Zymobacter palmae DSM 10491	GCA_000620025	scaffold	GenBank	1123510 tax ID
[Ref.: #66792]	Zymobacter palmae IAM14233	GCA_003610015	complete	GenBank	33074 tax ID	*
[Ref.: #66792]	Zymobacter palmae DSM 10491	1123510.3	wgs	PATRIC	1123510 tax ID	*
[Ref.: #66792]	Zymobacter palmae strain IAM14233	33074.3	wgs	PATRIC	33074 tax ID	*
[Ref.: #66792]	Zymobacter palmae DSM 10491	2556921094	draft	JGI IMG/M	1123510 tax ID	*
[Ref.: #66792]	Zymobacter palmae IAM14233	2832896515	complete	JGI IMG/M	33074 tax ID	*

[Ref.: #67770]

GC-content

56.2 mol%

high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Zymobacter palmae IAM14233 NCBI: GCA_003610015.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Zymobacter palmae IAM14233 NCBI: GCA_003610015.1
[Ref.: #69480]	motile	yes	81.672	no
[Ref.: #69480]	flagellated	no	61.606	no
[Ref.: #69480]	gram-positive	no	98.225	no
[Ref.: #69480]	anaerobic	no	84.477	no
[Ref.: #69480]	aerobic	no	61.66	no
[Ref.: #69480]	halophile	no	69.285	no
[Ref.: #69480]	spore-forming	no	95.455	no
[Ref.: #69480]	glucose-util	yes	76.101	no
[Ref.: #69480]	thermophile	no	97.954	yes
[Ref.: #69480]	glucose-ferment	no	57.047	no

Availability in culture collections External links

[Ref.: #3938]

Culture collection no.

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

[Ref.: #75495]

SI-ID 45304

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#75495

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID45304.1 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Zymobacter palmae in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Zymobacter palmae IAM14233

Zymobacter palmae IAM14233

Change proposal

Change proposal