Name: Pelotomaculum schinkii HH
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 11835

Type strain:

Species: Pelotomaculum schinkii

Strain Designation: HH

Culture col. no.: DSM 15200, ATCC BAA-615

Strain history: <- F. A. M. de Bok, Wageningen University, Laboratory of Microbiology, Netherlands; HH <- H. J. M. Harmsen and F. A. M. de Bok {2002}

NCBI tax ID(s): 78350 (species)

SI-ID 401977

DSM 15200

Section

Pelotomaculum schinkii HH is an anaerobe, spore-forming, mesophilic bacterium that was isolated from freeze-dried granular sludge from a UASB reactor treating sugar beet waste in co-culture with Methanospirillum hungatei JF-1.

Gram-positive
rod-shaped
spore-forming
anaerobe
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	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Peptococcaceae*
	Genus	*Pelotomaculum*
	Species	**Pelotomaculum schinkii**
	Full Scientific Name (LPSN)	Pelotomaculum schinkii de Bok et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #30047]	Gram stain	positive

[Ref.: #30047]	Cell length	2.25 µm

[Ref.: #30047]	Cell width	1 µm

[Ref.: #30047]	Cell shape	rod-shaped

[Ref.: #30047]	Motility	no

[Ref.: #5753]

Incubation period

>14 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5753]

Culture medium

PELOTOMACULUM MEDIUM (DSMZ Medium 960)

[Ref.: #5753]

Culture medium growth

[Ref.: #5753]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5753]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #5753]	growth	37 °C
[Ref.: #30047]	growth	37 °C
[Ref.: #30047]	optimum	37 °C

[Ref.: #5753]	Temperature range	mesophilic
[Ref.: #30047]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30047]			optimum	7.2
[Ref.: #30047]			growth	7.2

Information on physiology and metabolism Physiology and metabolism

[Ref.: #5753]	Oxygen tolerance	anaerobe
[Ref.: #30047]	Oxygen tolerance	anaerobe

[Ref.: #30047]

Ability of spore formation

yes

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30047]		formate ChEBI	+	carbon source
[Ref.: #30047]		propionate ChEBI	+	carbon source

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	hydrogen production	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	glutamate and glutamine metabolism	89.29	25 of 28
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	selenocysteine biosynthesis	83.33	5 of 6
[Ref.: #66794]	vitamin B12 metabolism	82.35	28 of 34
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	factor 420 biosynthesis	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	purine metabolism	70.21	66 of 94
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	oxidative phosphorylation	59.34	54 of 91
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	tryptophan metabolism	50	19 of 38
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	lysine metabolism	40.48	17 of 42
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	Entner Doudoroff pathway	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	glutathione metabolism	35.71	5 of 14
[Ref.: #66794]	phenol degradation	35	7 of 20
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	vitamin B6 metabolism	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
[Ref.: #66794]	4-hydroxymandelate 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.: #5753]	Sample type/isolated from	freeze-dried granular sludge from a UASB reactor treating sugar beet waste in co-culture with Methanospirillum hungatei JF-1
[Ref.: #5753]	Host species	Methanospirillum hungatei
[Ref.: #5753]	Geographic location (country and/or sea, region)	Breda
[Ref.: #5753]	Country	Netherlands
[Ref.: #5753]	Country ISO 3 Code	NLD
[Ref.: #5753]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Biodegradation	#Anaerobic digestor
#Engineered	#Food production	#Sugary food
#Engineered	#Waste	#Solid plant waste
#Host	#Microbial	#Bacteria

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence X91170 (>99% sequence identity) for Pelotomaculum schinkii subclade from Microbeatlas

Aquatic Samples	6
Soil Samples	2
Animal Samples	18
Plant Samples
Total Samples	26

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

[Ref.: #5753]

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.: #5753]	Pelotomaculum schinkii 16S rRNA gene, type strain HHT	X91169	1361	ENA	78350 tax ID
[Ref.: #5753]	Pelotomaculum schinkii 16S rRNA gene, type strain HHT	X91170	1362	ENA	78350 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Pelotomaculum schinkii HH	GCA_004369205	contig	GenBank	78350 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pelotomaculum schinkii HH NCBI: GCA_004369205.1
[Ref.: #69480]	motile	yes	74.468	yes
[Ref.: #69480]	flagellated	no	91.909	yes
[Ref.: #69480]	gram-positive	no	92.942	no
[Ref.: #69480]	anaerobic	yes	99.998	yes
[Ref.: #69480]	aerobic	no	98.479	yes
[Ref.: #69480]	halophile	no	95.547	no
[Ref.: #69480]	spore-forming	yes	95.331	yes
[Ref.: #69480]	glucose-util	yes	65.564	no
[Ref.: #69480]	thermophile	no	74.245	no
[Ref.: #69480]	glucose-ferment	no	77.914	no

Availability in culture collections External links

[Ref.: #5753]

Culture collection no.

DSM 15200, ATCC BAA-615

[Ref.: #81053]

SI-ID 401977

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	The first true obligately syntrophic propionate-oxidizing bacterium, Pelotomaculum schinkii sp. nov., co-cultured with Methanospirillum hungatei, and emended description of the genus Pelotomaculum.	de Bok FAM, Harmsen HJM, Plugge CM, de Vries MC, Akkermans ADL, de Vos WM, Stams AJM	Int J Syst Evol Microbiol	10.1099/ijs.0.02880-0	2005	*

References

#5753

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15200

#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 )

#30047

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 #26408 (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) .

#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 )

#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) .

#81053

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-ID401977.1 )

#26408

IJSEM 1697 2005 ( DOI 10.1099/ijs.0.02880-0 , PubMed 16014504 )

* These data were automatically processed and therefore are not curated

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