Name: Syntrophothermus lipocalidus TGB-C1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 16695

Type strain:

Species: Syntrophothermus lipocalidus

Strain Designation: TGB-C1

Culture col. no.: DSM 12680

Strain history: <- Y. Sekiguchi, Nagaoka Univ. Technology, Japan; TGB-C1 <- Y. Sekiguchi {1998}

NCBI tax ID(s): 643648 (strain), 86170 (species)

SI-ID 49341

DSM 12680

Other strains from Syntrophothermus lipocalidus

S. lipocalidus TGB-C1/Delta H, DSM 12681

Section

Syntrophothermus lipocalidus TGB-C1 is an anaerobe, spore-forming, thermophilic bacterium that was isolated from anaerobic granular sludge, thermophilic UASB reactor.

motile
spore-forming
anaerobe
thermophilic
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	*Syntrophomonadaceae*
	Genus	*Syntrophothermus*
	Species	**Syntrophothermus lipocalidus**
	Full Scientific Name (LPSN)	Syntrophothermus lipocalidus Sekiguchi et al. 2000

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %91.15

[Ref.: #69480]	Motility	yes Confidence in %94.918

[Ref.: #4790]

Incubation period

3-7 days

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4790]

Culture medium

SYNTROPHOTHERMUS MEDIUM (DSMZ Medium 870)

[Ref.: #4790]

Culture medium growth

[Ref.: #4790]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4790]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4790]			growth	55 °C

[Ref.: #4790]	Temperature range	thermophilic
[Ref.: #69480]	Temperature range	thermophilic Confidence in %99.442

Information on physiology and metabolism Physiology and metabolism

[Ref.: #4790]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %100

[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %99.447

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	CO2 fixation in Crenarchaeota	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]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	vitamin B12 metabolism	76.47	26 of 34
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	purine metabolism	61.7	58 of 94
[Ref.: #66794]	phenylalanine metabolism	61.54	8 of 13
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	threonine metabolism	60	6 of 10
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	cardiolipin biosynthesis	57.14	4 of 7
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	serine metabolism	55.56	5 of 9
[Ref.: #66794]	alanine metabolism	55.17	16 of 29
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	50	3 of 6
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	citric acid cycle	50	7 of 14
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	degradation of hexoses	44.44	8 of 18
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	benzoyl-CoA degradation	42.86	3 of 7
[Ref.: #66794]	arginine metabolism	41.67	10 of 24
[Ref.: #66794]	oxidative phosphorylation	40.66	37 of 91
[Ref.: #66794]	phenylacetate degradation (aerobic)	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	non-pathway related	39.47	15 of 38
[Ref.: #66794]	leucine metabolism	38.46	5 of 13
[Ref.: #66794]	lysine metabolism	38.1	16 of 42
[Ref.: #66794]	C4 and CAM-carbon fixation	37.5	3 of 8
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	proline metabolism	36.36	4 of 11
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	L-lactaldehyde degradation	33.33	1 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	propionate fermentation	30	3 of 10
[Ref.: #66794]	glutathione metabolism	28.57	4 of 14
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	degradation of pentoses	25	7 of 28
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
		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.: #4790]	Sample type/isolated from	anaerobic granular sludge, thermophilic UASB reactor
[Ref.: #4790]	Country	Japan
[Ref.: #4790]	Country ISO 3 Code	JPN
[Ref.: #4790]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Biodegradation	#Anaerobic digestor
#Engineered	#Waste	#Activated sludge
#Condition	#Anoxic (anaerobic)	-
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JQ346743 (>99% sequence identity) for Syntrophothermus lipocalidus subclade from Microbeatlas

Aquatic Samples	326
Soil Samples	24
Animal Samples	88
Plant Samples	58
Total Samples	496

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

[Ref.: #4790]

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.: #4790]	Syntrophothermus lipocalidus gene for 16S rRNA	AB021305	1588	ENA	643648 tax ID
[Ref.: #20218]	Syntrophothermus lipocalidus DSM 12680 strain TGB-C1 16S ribosomal RNA gene, partial sequence	JQ346743	1500	ENA	643648 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Syntrophothermus lipocalidus DSM 12680	GCA_000092405	complete	GenBank	643648 tax ID	*
[Ref.: #66792]	Syntrophothermus lipocalidus DSM 12680	643648.3	complete	PATRIC	643648 tax ID	*
[Ref.: #66792]	Syntrophothermus lipocalidus DSM 12680	646564577	complete	JGI IMG/M	643648 tax ID	*

[Ref.: #4790]

GC-content

51.0 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: Syntrophothermus lipocalidus DSM 12680 DSM 12680 NCBI: GCA_000092405.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Syntrophothermus lipocalidus DSM 12680 DSM 12680 NCBI: GCA_000092405.1
[Ref.: #69480]	motile	yes	79.586	no
[Ref.: #69480]	flagellated	no	94.079	no
[Ref.: #69480]	gram-positive	no	90.793	no
[Ref.: #69480]	anaerobic	yes	99.998	yes
[Ref.: #69480]	aerobic	no	98.252	yes
[Ref.: #69480]	halophile	no	97.609	no
[Ref.: #69480]	spore-forming	yes	70.27	no
[Ref.: #69480]	thermophile	yes	99.536	no
[Ref.: #69480]	glucose-util	yes	68.233	no
[Ref.: #69480]	glucose-ferment	no	81.591	no

Availability in culture collections External links

[Ref.: #4790]

Culture collection no.

DSM 12680

[Ref.: #85714]

SI-ID 49341

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Comparative proteomic analysis of Methanothermobacter themautotrophicus DeltaH in pure culture and in co-culture with a butyrate-oxidizing bacterium.	Enoki M, Shinzato N, Sato H, Nakamura K, Kamagata Y	PLoS One	10.1371/journal.pone.0024309	2011	*
Metabolism	Differential expression of methanogenesis genes of Methanothermobacter thermoautotrophicus (formerly Methanobacterium thermoautotrophicum) in pure culture and in cocultures with fatty acid-oxidizing syntrophs.	Luo HW, Zhang H, Suzuki T, Hattori S, Kamagata Y	Appl Environ Microbiol	10.1128/AEM.68.3.1173-1179.2002	2002	*
Phylogeny	Syntrophothermus lipocalidus gen. nov., sp. nov., a novel thermophilic, syntrophic, fatty-acid-oxidizing anaerobe which utilizes isobutyrate.	Sekiguchi Y, Kamagata Y, Nakamura K, Ohashi A, Harada H	Int J Syst Evol Microbiol	10.1099/00207713-50-2-771	2000	*
Genetics	Comparative Genomics of Syntrophic Branched-Chain Fatty Acid Degrading Bacteria.	Narihiro T, Nobu MK, Tamaki H, Kamagata Y, Sekiguchi Y, Liu WT	Microbes Environ	10.1264/jsme2.ME16057	2016	*
Genetics	Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1).	Djao OD, Zhang X, Lucas S, Lapidus A, Del Rio TG, Nolan M, Tice H, Cheng JF, Han C, Tapia R, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Ovchinnikova G, Pati A, Brambilla E, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Sikorski J, Spring S, Goker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP	Stand Genomic Sci	10.4056/sigs.1233249	2010	*

References

#4790

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12680

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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) .

#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 )

#85714

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-ID49341.1 )

* 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 Syntrophothermus lipocalidus in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Syntrophothermus lipocalidus DSM 12680 DSM 12680

Syntrophothermus lipocalidus DSM 12680 DSM 12680

Change proposal

Change proposal