Archive BacDiveID:10.13145/bacdive16695.20230509.8.1

Strain identifier

BacDive ID: 16695

Type strain:

Species: Syntrophothermus lipocalidus

Strain Designation: TGB-C1

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

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

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

General

@ref: 4790

BacDive-ID: 16695

DSM-Number: 12680

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, thermophilic, motile

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

NCBI tax id

NCBI tax id	Matching level
86170	species
643648	strain

strain history

@ref: 4790
history: <- Y. Sekiguchi, Nagaoka Univ. Technology, Japan; TGB-C1 <- Y. Sekiguchi {1998}

doi: 10.13145/bacdive16695.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Clostridia
order: Eubacteriales
family: Syntrophomonadaceae
genus: Syntrophothermus
species: Syntrophothermus lipocalidus
full scientific name: Syntrophothermus lipocalidus Sekiguchi et al. 2000

@ref: 4790

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Syntrophomonadaceae

genus: Syntrophothermus

species: Syntrophothermus lipocalidus

full scientific name: Syntrophothermus lipocalidus Sekiguchi et al. 2000

strain designation: TGB-C1

type strain: yes

Morphology

cell morphology

@ref	motility	confidence	gram stain
69480	yes	94.918
69480		91.15	positive

colony morphology

@ref: 4790
incubation period: 3-7 days

multimedia

@ref: 66793
multimedia content: EM_DSM_12680_1.jpg
caption: electron microscopic image
intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@ref: 4790
name: SYNTROPHOTHERMUS MEDIUM (DSMZ Medium 870)
growth: yes
link: https://mediadive.dsmz.de/medium/870
composition: Name: SYNTROPHOTHERMUS MEDIUM (DSMZ Medium 870) Composition: Na2CO3 0.988142 g/l Crotonic acid 0.849802 g/l NH4Cl 0.533597 g/l L-Cysteine HCl x H2O 0.296443 g/l Na2S x 9 H2O 0.296443 g/l MgCl2 x 6 H2O 0.197628 g/l KH2PO4 0.13834 g/l MgSO4 x 7 H2O 0.00296443 g/l Nitrilotriacetic acid 0.00148221 g/l NaCl 0.000988142 g/l MnSO4 x H2O 0.000494071 g/l Sodium resazurin 0.000494071 g/l CoSO4 x 7 H2O 0.000177866 g/l ZnSO4 x 7 H2O 0.000177866 g/l FeSO4 x 7 H2O 9.88142e-05 g/l Pyridoxine hydrochloride 9.88142e-05 g/l CaCl2 x 2 H2O 9.88142e-05 g/l p-Aminobenzoic acid 4.94071e-05 g/l Calcium D-(+)-pantothenate 4.94071e-05 g/l Nicotinic acid 4.94071e-05 g/l (DL)-alpha-Lipoic acid 4.94071e-05 g/l Thiamine HCl 4.94071e-05 g/l Riboflavin 4.94071e-05 g/l NiCl2 x 6 H2O 2.96443e-05 g/l AlK(SO4)2 x 12 H2O 1.97628e-05 g/l Biotin 1.97628e-05 g/l Folic acid 1.97628e-05 g/l CuSO4 x 5 H2O 9.88142e-06 g/l H3BO3 9.88142e-06 g/l Na2MoO4 x 2 H2O 9.88142e-06 g/l Vitamin B12 9.88142e-07 g/l Na2WO4 x 2 H2O 3.95257e-07 g/l Na2SeO3 x 5 H2O 2.96443e-07 g/l NaOH Distilled water

culture temp

@ref	growth	type	temperature	range	confidence
4790	positive	growth	55	thermophilic
69480				thermophilic	99.442

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
4790	anaerobe
69480	anaerobe	100

spore formation

@ref	spore formation	confidence
69481	yes	100
69480	yes	99.447

Isolation, sampling and environmental information

isolation

@ref: 4790
sample type: anaerobic granular sludge, thermophilic UASB reactor
country: Japan
origin.country: JPN
continent: Asia

isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Biodegradation	#Anaerobic digestor
#Engineered	#Waste	#Activated sludge
#Condition	#Anoxic (anaerobic)
#Condition	#Thermophilic (>45°C)

taxonmaps

@ref: 69479
File name: preview.99_5510.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_526;96_2665;97_3270;98_4114;99_5510&stattab=map
Last taxonomy: Syntrophothermus lipocalidus subclade
16S sequence: JQ346743
Sequence Identity:
Total samples: 496
soil counts: 24
aquatic counts: 326
animal counts: 88
plant counts: 58

Safety information

risk assessment

@ref: 4790
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Syntrophothermus lipocalidus DSM 12680 strain TGB-C1 16S ribosomal RNA gene, partial sequence	JQ346743	1500	ena	643648
4790	Syntrophothermus lipocalidus gene for 16S rRNA	AB021305	1588	ena	643648

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Syntrophothermus lipocalidus DSM 12680	GCA_000092405	complete	ncbi	643648
66792	Syntrophothermus lipocalidus DSM 12680	643648.3	complete	patric	643648
66792	Syntrophothermus lipocalidus DSM 12680	646564577	complete	img	643648

GC content

@ref: 4790
GC-content: 51.0
method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	100	no
motile	yes	79.586	no
flagellated	no	94.079	no
gram-positive	no	90.793	no
anaerobic	yes	99.998	yes
aerobic	no	98.252	yes
halophile	no	97.609	no
spore-forming	yes	70.27	no
thermophile	yes	99.536	no
glucose-util	yes	68.233	no
glucose-ferment	no	81.591	no

External links

@ref: 4790

culture collection no.: DSM 12680

straininfo link

@ref: 85714
straininfo: 49341

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	10758888	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	Bacterial Typing Techniques, Butyrates/metabolism, Culture Media, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/metabolism, Gram-Negative Anaerobic Bacteria/*classification/metabolism/physiology/ultrastructure, Isobutyrates, Methanobacterium/growth & development, Molecular Sequence Data, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/microbiology, Temperature, Waste Disposal, Fluid	Metabolism
Metabolism	11872465	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	Acetates/metabolism, Archaeal Proteins/genetics/metabolism, Carbon Dioxide/metabolism, Culture Media, Euryarchaeota/growth & development/metabolism, Gene Expression Regulation, Archaeal, Hydrogen/metabolism, Methane/metabolism, Methanobacteriaceae/enzymology/genetics/growth & development, Oxidation-Reduction, Transcription, Genetic	Cultivation
Genetics	21304731	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
Metabolism	21904627	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	Bacteria/metabolism, Bacterial Proteins/metabolism, Butyrates/metabolism, Coculture Techniques, Methanobacteriaceae/metabolism, Proteomics/methods
Genetics	27431485	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	Biotransformation, Butyrates/metabolism, Clostridiales/genetics/metabolism, Genome, Bacterial, Genomics, Isobutyrates/metabolism, Metabolic Networks and Pathways	Metabolism

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
4790	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12680)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-12680
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
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
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)
66793	Mukherjee et al.		10.1038/nbt.3886	GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life	35: 676-683 2017	28604660
66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates	Nucleic Acids Res. 49: D498-D508 2020	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.		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)
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
85714	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID49341.1	StrainInfo: A central database for resolving microbial strain identifiers