Thiogranum longum (DSM 19610, NBRC 101260, gps52)

Name: Thiogranum longum (DSM 19610, NBRC 101260, gps52)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 130290

Type strain

Strain Designation gps52

Culture col. no. DSM 19610 NBRC 101260 gps52

NCBI tax ID(s) 1537524

Special Collections DSMZ

History DSMZ <- K. Mori, NBRC; NBRC 101260 <- K. Mori and S. Hanada, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan; gps52 {2003}

Links

Thiogranum longum gps52 is a microaerophile bacterium that was isolated from rock samples from a deep-sea hydrothermal field.

microaerophile genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 402744

NBRC 101260,DSM 19610

@ref 20215

Last LPSN update 2026-05-29 08:37:20

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Chromatiales

Family Ectothiorhodospiraceae

Genus Thiogranum

Species Thiogranum longum

Full scientific name Thiogranum longum Mori et al. 2015

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	92.226
125438	negative	99.494

Colony morphology

22132

Incubation period3-7 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
22132	THIOGRANUM MEDIUM (DSMZ Medium 1570)		Medium recipe at MediaDive	Name: THIOGRANUM MEDIUM (DSMZ Medium 1570) Composition: MgCl2 x 6 H2O 3.00197 g/l Na2S2O3 x 5 H2O 1.47638 g/l Na2CO3 0.984252 g/l (NH4)2SO4 0.649606 g/l KH2PO4 0.58563 g/l KCl 0.324803 g/l K2HPO4 0.103346 g/l MgSO4 x 7 H2O 0.0295276 g/l Nitrilotriacetic acid 0.0147638 g/l NaCl 0.00984252 g/l MnSO4 x H2O 0.00492126 g/l ZnSO4 x 7 H2O 0.00177165 g/l CoSO4 x 7 H2O 0.00177165 g/l FeSO4 x 7 H2O 0.000984252 g/l CaCl2 x 2 H2O 0.000984252 g/l NiCl2 x 6 H2O 0.000295276 g/l AlK(SO4)2 x 12 H2O 0.00019685 g/l Pyridoxine hydrochloride 9.84252e-05 g/l CuSO4 x 5 H2O 9.84252e-05 g/l Na2MoO4 x 2 H2O 9.84252e-05 g/l H3BO3 9.84252e-05 g/l (DL)-alpha-Lipoic acid 4.92126e-05 g/l p-Aminobenzoic acid 4.92126e-05 g/l Calcium D-(+)-pantothenate 4.92126e-05 g/l Nicotinic acid 4.92126e-05 g/l Riboflavin 4.92126e-05 g/l Thiamine HCl 4.92126e-05 g/l Folic acid 1.9685e-05 g/l Biotin 1.9685e-05 g/l Na2WO4 x 2 H2O 3.93701e-06 g/l Na2SeO3 x 5 H2O 2.95276e-06 g/l Vitamin B12 9.84252e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
22132	positive	growth	30

Physiology and metabolism

Oxygen tolerance

22132

Oxygen tolerancemicroaerophile

Spore formation

@ref	Spore formation	Confidence
125439		99.778

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	ppGpp biosynthesis	100	4 of 4
66794	denitrification	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	aspartate and asparagine metabolism	100	9 of 9
66794	methylglyoxal degradation	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	glycogen metabolism	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	cardiolipin biosynthesis	100	7 of 7
66794	ubiquinone biosynthesis	100	7 of 7
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	palmitate biosynthesis	95.45	21 of 22
66794	photosynthesis	92.86	13 of 14
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	threonine metabolism	80	8 of 10
66794	d-mannose degradation	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	serine metabolism	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	phenylalanine metabolism	76.92	10 of 13
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	flavin biosynthesis	73.33	11 of 15
66794	peptidoglycan biosynthesis	73.33	11 of 15
66794	pentose phosphate pathway	72.73	8 of 11
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	acetoin degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	CO2 fixation in Crenarchaeota	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	purine metabolism	65.96	62 of 94
66794	lipid metabolism	64.52	20 of 31
66794	glutathione metabolism	64.29	9 of 14
66794	glutamate and glutamine metabolism	64.29	18 of 28
66794	vitamin B6 metabolism	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	isoleucine metabolism	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	gluconeogenesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	leucine metabolism	61.54	8 of 13
66794	methionine metabolism	61.54	16 of 26
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	cellulose degradation	60	3 of 5
66794	alanine metabolism	58.62	17 of 29
66794	pyrimidine metabolism	57.78	26 of 45
66794	propanol degradation	57.14	4 of 7
66794	citric acid cycle	57.14	8 of 14
66794	cysteine metabolism	55.56	10 of 18
66794	degradation of hexoses	55.56	10 of 18
66794	arginine metabolism	54.17	13 of 24
66794	sulfopterin metabolism	50	2 of 4
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	tyrosine metabolism	50	7 of 14
66794	lysine metabolism	50	21 of 42
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	butanoate fermentation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	oxidative phosphorylation	48.35	44 of 91
66794	histidine metabolism	48.28	14 of 29
66794	sulfate reduction	46.15	6 of 13
66794	tryptophan metabolism	44.74	17 of 38
66794	nitrate assimilation	44.44	4 of 9
66794	D-cycloserine biosynthesis	40	2 of 5
66794	Entner Doudoroff pathway	40	4 of 10
66794	hydrogen production	40	2 of 5
66794	propionate fermentation	40	4 of 10
66794	starch degradation	40	4 of 10
66794	bacilysin biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	coenzyme M biosynthesis	40	4 of 10
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	cholesterol biosynthesis	36.36	4 of 11
66794	metabolism of disaccharids	36.36	4 of 11
66794	degradation of pentoses	35.71	10 of 28
66794	pantothenate biosynthesis	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	arachidonic acid metabolism	33.33	6 of 18
66794	L-lactaldehyde degradation	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	ascorbate metabolism	31.82	7 of 22
66794	degradation of sugar alcohols	31.25	5 of 16
66794	urea cycle	30.77	4 of 13
66794	polyamine pathway	30.43	7 of 23
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	carotenoid biosynthesis	27.27	6 of 22
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	toluene degradation	25	1 of 4
66794	vitamin B12 metabolism	20.59	7 of 34

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Geologic
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
22132	rock samples from a deep-sea hydrothermal field	off the eastern coast, Suiyo Seamount	Japan	JPN	Asia	28.6	140.633 28.6/140.633

Taxonmaps

69479

Global distribution of 16S sequence AB983478 (>99% sequence identity) for Thiogranum longum subclade from Microbeatlas

Aquatic Samples	1926
Soil Samples	79
Animal Samples	132
Plant Samples	3
Total Samples	2140

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
22132	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM433908v1 assembly for Thiogranum longum DSM 19610	scaffold	GCA_004339085	1537524.3	2770939547	1537524	71.61

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
22132	Thiogranum longum gene for 16S ribosomal RNA, partial sequence	AB983478	1508		1537524

GC content

@ref	GC-content (mol%)	Method
22132	53.8	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM433908v1 assembly for Thiogranum longum DSM 19610
NCBI: GCA_004339085

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	92.23	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	81.14	no
125439	motility	BacteriaNetⓘ	yes	72.89	no
125439	spore_formation	BacteriaNetⓘ	no	99.78	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Thiogranum longum DSM 19610
NCBI: GCA_004339085.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.49	no
125438	anaerobic	anaerobicⓘ	no	85.77	yes
125438	aerobic	aerobicⓘ	no	50.44	yes
125438	spore-forming	spore-formingⓘ	no	89.92	no
125438	thermophilic	thermophileⓘ	no	90.21	yes
125438	flagellated	motile2+ⓘ	yes	69.48	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Investigation of dirigent like domains from bacterial genomes.	Bardin M, Rousselot-Pailley P, Tron T, Robert V.	BMC Bioinformatics	10.1186/s12859-022-04832-6	2022
Phylogeny	Genomic Comparison, Phylogeny and Taxonomic Reevaluation of the Ectothiorhodospiraceae and Description of Halorhodospiraceae fam. nov. and Halochlorospira gen. nov.	Imhoff JF, Kyndt JA, Meyer TE.	Microorganisms	10.3390/microorganisms10020295	2022
Phylogeny	Thiogranum longum gen. nov., sp. nov., an obligately chemolithoautotrophic, sulfur-oxidizing bacterium of the family Ectothiorhodospiraceae isolated from a deep-sea hydrothermal field, and an emended description of the genus Thiohalomonas.	Mori K, Suzuki KI, Yamaguchi K, Urabe T, Hanada S	Int J Syst Evol Microbiol	10.1099/ijs.0.070599-0	2014

References

#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 )
#22132	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19610
#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 .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Content

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Thiogranum longum (DSM 19610, NBRC 101260, gps52)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004339085

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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