Archive BacDiveID:10.13145/bacdive16688.20230509.8.1

Strain identifier

BacDive ID: 16688

Type strain:

Species: Syntrophomonas palmitatica

Strain Designation: MPA

Strain history: M. Hatamoto strain MPA.

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

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 7670

BacDive-ID: 16688

DSM-Number: 18709

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

description: 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.

NCBI tax id

NCBI tax id	Matching level
1294023	strain
402877	species

strain history

@ref	history
7670	<- M. Hatamoto, Nagaoka Univ. Technology, Japan; MPA <- M. Hatamoto {2005}
67770	M. Hatamoto strain MPA.

doi: 10.13145/bacdive16688.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Clostridia
order: Eubacteriales
family: Syntrophomonadaceae
genus: Syntrophomonas
species: Syntrophomonas palmitatica
full scientific name: Syntrophomonas palmitatica Hatamoto et al. 2007

@ref: 7670

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Syntrophomonadaceae

genus: Syntrophomonas

species: Syntrophomonas palmitatica

full scientific name: Syntrophomonas palmitatica Hatamoto et al. 2007

strain designation: MPA

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
32114	negative	1.5-4.0 µm	0.4-0.6 µm	rod-shaped	no
69480	positive					99.562

colony morphology

@ref: 7670
incubation period: 3-7 days

Culture and growth conditions

culture medium

@ref: 7670
name: PELOTOMACULUM MEDIUM (DSMZ Medium 960)
growth: yes
link: https://mediadive.dsmz.de/medium/960
composition: Name: PELOTOMACULUM MEDIUM (DSMZ Medium 960; with strain-specific modifications) Composition: Na2CO3 1.49701 g/l Na-crotonate 0.858283 g/l NH4Cl 0.538922 g/l Yeast extract 0.499002 g/l Na2S x 9 H2O 0.299401 g/l L-Cysteine HCl x H2O 0.299401 g/l MgCl2 x 6 H2O 0.199601 g/l KH2PO4 0.139721 g/l Nitrilotriacetic acid 0.0127745 g/l NaCl 0.000998004 g/l FeCl2 x 4 H2O 0.000998004 g/l Sodium resazurin 0.000499002 g/l CaCl2 x 2 H2O 9.98004e-05 g/l NiCl2 x 6 H2O 9.98004e-05 g/l MnCl2 x 4 H2O 9.98004e-05 g/l Pyridoxine hydrochloride 9.98004e-05 g/l ZnCl2 9.98004e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l Na2WO4 x 2 H2O 3.99202e-05 g/l CoCl2 x 6 H2O 2.99401e-05 g/l Na2MoO4 x 2 H2O 2.99401e-05 g/l Na2SeO3 x 5 H2O 2.99401e-05 g/l CuCl2 1.99601e-05 g/l Biotin 1.99601e-05 g/l Folic acid 1.99601e-05 g/l H3BO3 9.98004e-06 g/l Vitamin B12 9.98004e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
7670	positive	growth	37	mesophilic
32114	positive	growth	30-50
32114	positive	optimum	37	mesophilic
67770	positive	growth	37	mesophilic

culture pH

@ref	ability	type	pH
32114	positive	growth	6.5-8.0
32114	positive	optimum	7

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
7670	anaerobe
32114	aerobe
69480	anaerobe	99.647

spore formation

@ref: 32114
spore formation: no

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
7670	granular sludge in a mesophilic upflow anaerobic sludge blanket reactor used to treat palm oil mill effluent	Niigata, Nagaoka	Japan	JPN	Asia
67770	Granular sludge of an upflow anaerobic sludge blanket reactor treating palm oil mill effluent

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Bioreactor
#Engineered	#Waste	#Industrial wastewater
#Engineered	#Waste	#Activated sludge
#Condition	#Anoxic (anaerobic)

taxonmaps

@ref: 69479
File name: preview.99_7075.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_397;96_3319;97_4070;98_5201;99_7075&stattab=map
Last taxonomy: Syntrophomonas palmitatica subclade
16S sequence: AB274040
Sequence Identity:
Total samples: 330
soil counts: 32
aquatic counts: 231
animal counts: 56
plant counts: 11

Safety information

risk assessment

@ref: 7670
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
7670	Syntrophomonas palmitatica rrnA operon gene for 16S ribosomal RNA, partial sequence, strain: MPA	AB274039	1571	ena	402877
7670	Syntrophomonas palmitatica rrnB operon gene for 16S ribosomal RNA, partial sequence, strain: MPA	AB274040	1589	ena	402877

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Syntrophomonas palmitatica JCM 14374	1294023.3	wgs	patric	1294023
66792	Syntrophomonas palmitatica JCM 14374	2728369699	draft	img	1294023
67770	Syntrophomonas palmitatica JCM 14374	GCA_001311885	contig	ncbi	1294023

GC content

@ref	GC-content	method
7670	45.0
32114	45
67770	45	high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	85	no
motile	yes	74.061	yes
gram-positive	no	93.193	yes
anaerobic	yes	99.327	no
aerobic	no	97.584	no
halophile	no	89.973	no
spore-forming	yes	68.313	yes
thermophile	yes	95.564	no
glucose-util	yes	64.668	no
flagellated	no	90.653	yes
glucose-ferment	no	81.751	no

External links

@ref: 7670

culture collection no.: DSM 18709, JCM 14374, NBRC 102128

straininfo link

@ref: 85707
straininfo: 309560

literature

topic: Phylogeny
Pubmed-ID: 17766887
title: Syntrophomonas palmitatica sp. nov., an anaerobic, syntrophic, long-chain fatty-acid-oxidizing bacterium isolated from methanogenic sludge.
authors: Hatamoto M, Imachi H, Fukayo S, Ohashi A, Harada H
journal: Int J Syst Evol Microbiol
DOI: 10.1099/ijs.0.64981-0
year: 2007
mesh: Bacteria, Anaerobic/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Bioreactors/microbiology, Coculture Techniques, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/*metabolism, Genes, rRNA, Gram-Negative Bacteria/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Industrial Waste, Japan, Methanospirillum/physiology, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sewage/*microbiology, Temperature
topic2: Enzymology

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
7670	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18709)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-18709
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
32114	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	28359	28776041
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
85707	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID309560.1	StrainInfo: A central database for resolving microbial strain identifiers