Name: Thiogranum longum gps52
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 130290

Type strain:

Species: Thiogranum longum

Strain Designation: gps52

Culture col. no.: DSM 19610, NBRC 101260

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

NCBI tax ID(s): 1537524 (species)

SI-ID 402744

DSM 19610

Special Collections

DSMZ

Section

When using BacDive for research please cite our paper

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

mesophilic
microaerophile
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Chromatiales*
	Family	*Ectothiorhodospiraceae*
	Genus	*Thiogranum*
	Species	**Thiogranum longum**
	Full Scientific Name (LPSN)	Thiogranum longum Mori et al. 2015

Information on morphological and physiological properties Morphology

[Ref.: #125439]	Gram stain	negative Confidence in %97.1
[Ref.: #125438]	Gram stain	negative Confidence in %99.494

[Ref.: #22132]

Incubation period

3-7 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #22132]

Culture medium

THIOGRANUM MEDIUM (DSMZ Medium 1570)

[Ref.: #22132]

Culture medium growth

[Ref.: #22132]

Culture medium link

Medium recipe at MediaDive

[Ref.: #22132]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #22132]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #22132]

Oxygen tolerance

microaerophile

[Ref.: #125439]

Ability of spore formation

no Confidence in %99.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	peptidoglycan biosynthesis	73.33	11 of 15
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	purine metabolism	65.96	62 of 94
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	alanine metabolism	58.62	17 of 29
[Ref.: #66794]	pyrimidine metabolism	57.78	26 of 45
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	oxidative phosphorylation	48.35	44 of 91
[Ref.: #66794]	histidine metabolism	48.28	14 of 29
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	tryptophan metabolism	44.74	17 of 38
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	Entner Doudoroff pathway	40	4 of 10
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	starch degradation	40	4 of 10
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	degradation of pentoses	35.71	10 of 28
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	L-lactaldehyde degradation	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	degradation of sugar alcohols	31.25	5 of 16
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	carotenoid biosynthesis	27.27	6 of 22
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	vitamin B12 metabolism	20.59	7 of 34
		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.: #22132]	Sample type/isolated from	rock samples from a deep-sea hydrothermal field
[Ref.: #22132]	Geographic location (country and/or sea, region)	off the eastern coast, Suiyo Seamount
[Ref.: #22132]	Country	Japan
[Ref.: #22132]	Country ISO 3 Code	JPN
[Ref.: #22132]	Continent	Asia
[Ref.: #22132]	Geographic location	28.6000°/140.6330°
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #22132]

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.: #22132]	Thiogranum longum gene for 16S ribosomal RNA, partial sequence	AB983478	1508	GenBank ENA	1537524 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Thiogranum longum DSM 19610	GCA_004339085	scaffold	GenBank ENA	1537524 tax ID	*
[Ref.: #66792]	Thiogranum longum strain DSM 19610	1537524.3	wgs	PATRIC	1537524 tax ID	*
[Ref.: #66792]	Thiogranum longum DSM 19610	2770939547	draft	JGI IMG/M	1537524 tax ID	*

[Ref.: #22132]

GC-content

53.8 mol%

high performance liquid chromatography (HPLC)

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

	Model	Trait	Prediction	Confidence in %	In training data
	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.: #125438]	gram-positive	gram-positiveⓘ	no	99.494	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	85.766	yes
[Ref.: #125438]	aerobic	aerobicⓘ	no	50.442	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	89.922	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	90.206	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	69.476	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Thiogranum longum DSM 19610 NCBI: GCA_004339085
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	99.1
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	79.5
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	97.1
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	aerobe	81.6

Availability in culture collections External links

[Ref.: #22132]

Culture collection no.

DSM 19610, NBRC 101260

[Ref.: #88825]

SI-ID 402744

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 .

#88825

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-ID402744.1 )

#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 .

* These data were automatically processed and therefore are not curated

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Thiogranum longum DSM 19610

Thiogranum longum DSM 19610

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