Name: Syntrophomonas palmitatica MPA
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 16688

Type strain:

Species: Syntrophomonas palmitatica

Strain Designation: MPA

Culture col. no.: DSM 18709, JCM 14374, NBRC 102128

Strain history: M. Hatamoto strain MPA.

NCBI tax ID(s): 1294023 (strain), 402877 (species)

SI-ID 309560

DSM 18709, JCM 14374, NBRC 102128

Special Collections

Section

When using BacDive for research please cite our paper

Syntrophomonas palmitatica MPA is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from granular sludge in a mesophilic upflow anaerobic sludge blanket reactor used to treat palm oil mill effluent.

Gram-negative
rod-shaped
anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Syntrophomonadaceae*
	Genus	*Syntrophomonas*
	Species	**Syntrophomonas palmitatica**
	Full Scientific Name (LPSN)	Syntrophomonas palmitatica Hatamoto et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32114]	Gram stain	negative

[Ref.: #32114]	Cell length	1.5-4.0 µm

[Ref.: #32114]	Cell width	0.4-0.6 µm

[Ref.: #32114]	Cell shape	rod-shaped

[Ref.: #32114]	Motility	no

[Ref.: #7670]

Incubation period

3-7 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7670]

Culture medium

PELOTOMACULUM MEDIUM (DSMZ Medium 960)

[Ref.: #7670]

Culture medium growth

[Ref.: #7670]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7670]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7670]	growth	37 °C
[Ref.: #32114]	growth	30-50 °C
[Ref.: #32114]	optimum	37 °C
[Ref.: #67770]	growth	37 °C

	pH	Kind of pH		pH
[Ref.: #32114]			optimum	7
[Ref.: #32114]			growth	6.5-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7670]	Oxygen tolerance	anaerobe
[Ref.: #32114]	Oxygen tolerance	aerobe
[Ref.: #125438]	Oxygen tolerance	anaerobe Confidence in %90.851

[Ref.: #32114]

Ability of spore formation

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

[Ref.: #7670]	Sample type/isolated from	granular sludge in a mesophilic upflow anaerobic sludge blanket reactor used to treat palm oil mill effluent
[Ref.: #7670]	Geographic location (country and/or sea, region)	Niigata, Nagaoka
[Ref.: #7670]	Country	Japan
[Ref.: #7670]	Country ISO 3 Code	JPN
[Ref.: #7670]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Granular sludge of an upflow anaerobic sludge blanket reactor treating palm oil mill effluent
* marker position based on {}

Isolation sources categories

#Engineered	#Bioreactor	-
#Engineered	#Waste	#Industrial wastewater
#Engineered	#Waste	#Activated sludge
#Condition	#Anoxic (anaerobic)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB274040 (>99% sequence identity) for Syntrophomonas palmitatica subclade from Microbeatlas

Aquatic Samples	231
Soil Samples	32
Animal Samples	56
Plant Samples	11
Total Samples	330

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

[Ref.: #7670]

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.: #7670]	Syntrophomonas palmitatica rrnA operon gene for 16S ribosomal RNA, partial sequence, strain: MPA	AB274039	1571	GenBank ENA	402877 tax ID
[Ref.: #7670]	Syntrophomonas palmitatica rrnB operon gene for 16S ribosomal RNA, partial sequence, strain: MPA	AB274040	1589	GenBank ENA	402877 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Syntrophomonas palmitatica JCM 14374	GCA_001311885	contig	GenBank ENA	1294023 tax ID
[Ref.: #66792]	Syntrophomonas palmitatica JCM 14374	1294023.3	wgs	PATRIC	1294023 tax ID	*
[Ref.: #66792]	Syntrophomonas palmitatica JCM 14374	2728369699	draft	JGI IMG/M	1294023 tax ID	*

[Ref.: #7670]	GC-content	45.0 mol%
[Ref.: #32114]	GC-content	45 mol%
[Ref.: #67770]	GC-content	45 mol%	high performance liquid chromatography (HPLC)

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Syntrophomonas palmitatica JCM 14374 PATRIC: 1294023.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	53.62	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	90.851	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	68.092	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	93.754	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	55.144	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	71.539	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Syntrophomonas palmitatica JCM 14374 NCBI: GCA_001311885
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	84.1
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	81.4
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	variable	87.9
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	anaerobe	88.6

Availability in culture collections External links

[Ref.: #7670]

Culture collection no.

DSM 18709, JCM 14374, NBRC 102128

[Ref.: #85707]

SI-ID 309560

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Syntrophomonas palmitatica sp. nov., an anaerobic, syntrophic, long-chain fatty-acid-oxidizing bacterium isolated from methanogenic sludge.	Hatamoto M, Imachi H, Fukayo S, Ohashi A, Harada H	Int J Syst Evol Microbiol	10.1099/ijs.0.64981-0	2007	*

References

#7670

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18709

#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 )

#32114

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28359 (see below)

#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) .

#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 .

#85707

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-ID309560.1 )

#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 .

#28359

IJSEM 2137 2007 ( DOI 10.1099/ijs.0.64981-0 , PubMed 17766887 )

* These data were automatically processed and therefore are not curated

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Syntrophomonas palmitatica JCM 14374

Syntrophomonas palmitatica JCM 14374

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