Sediminispirochaeta smaragdinae (DSM 11293, JCM 15392, SEBR 4228)

Cell morphology

Colony morphology

Multimedia

• @ref:	66793
  multimedia content:	EM_DSM_11293_1.jpg
  multimedia.multimedia content:	EM_DSM_11293_1.jpg
  caption:	electron microscopic image
  intellectual property rights:	© HZI/Manfred Rohde
  manual_annotation:	1

Culture medium

@ref	Name	Growth	Medium link	Composition
4283	SEDIMINISPIROCHAETA SMARAGDINAE MEDIUM (DSMZ Medium 819)		Medium recipe at MediaDive	Name: SEDIMINISPIROCHAETA SMARAGDINAE MEDIUM (DSMZ Medium 819) Composition: Yeast extract 5.0 g/l Na2CO3 1.0 g/l NH4Cl 1.0 g/l Na2S x 9 H2O 0.3 g/l KH2PO4 0.3 g/l K2HPO4 0.3 g/l L-Cysteine HCl x H2O 0.3 g/l MgCl2 x 6 H2O 0.2 g/l KCl 0.2 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l MnSO4 x H2O 0.005 g/l CoSO4 x 7 H2O 0.0018 g/l ZnSO4 x 7 H2O 0.0018 g/l FeSO4 x 7 H2O 0.001 g/l CaCl2 x 2 H2O 0.001 g/l Sodium resazurin 0.0005 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l H3BO3 0.0001 g/l Na2MoO4 x 2 H2O 0.0001 g/l CuSO4 x 5 H2O 0.0001 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Distilled water

Culture temp

Oxygen tolerance

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions	external links
66794	adipate degradation	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	ceramide biosynthesis	100	1 of 1
66794	cardiolipin biosynthesis	100	7 of 7
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ethanol fermentation	100	2 of 2
66794	cyanate degradation	100	3 of 3
66794	palmitate biosynthesis	90.91	20 of 22
66794	pentose phosphate pathway	90.91	10 of 11
66794	starch degradation	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	d-mannose degradation	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	pyrimidine metabolism	86.67	39 of 45
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	purine metabolism	81.91	77 of 94
66794	degradation of sugar alcohols	81.25	13 of 16
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	lipoate biosynthesis	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	Entner Doudoroff pathway	80	8 of 10
66794	myo-inositol biosynthesis	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	phenylalanine metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	vitamin B12 metabolism	76.47	26 of 34
66794	ketogluconate metabolism	75	6 of 8
66794	ppGpp biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	biotin biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	methionine metabolism	73.08	19 of 26
66794	vitamin B6 metabolism	72.73	8 of 11
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	citric acid cycle	71.43	10 of 14
66794	oxidative phosphorylation	69.23	63 of 91
66794	alanine metabolism	68.97	20 of 29
66794	flavin biosynthesis	66.67	10 of 15
66794	octane oxidation	66.67	2 of 3
66794	pantothenate biosynthesis	66.67	4 of 6
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
66794	UDP-GlcNAc biosynthesis	66.67	2 of 3
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	d-xylose degradation	63.64	7 of 11
66794	gluconeogenesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	urea cycle	61.54	8 of 13
66794	degradation of hexoses	61.11	11 of 18
66794	degradation of pentoses	60.71	17 of 28
66794	non-pathway related	60.53	23 of 38
66794	tryptophan metabolism	60.53	23 of 38
66794	methylglyoxal degradation	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	glycine betaine biosynthesis	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	creatinine degradation	60	3 of 5
66794	lysine metabolism	59.52	25 of 42
66794	propanol degradation	57.14	4 of 7
66794	cysteine metabolism	55.56	10 of 18
66794	histidine metabolism	55.17	16 of 29
66794	lipid metabolism	54.84	17 of 31
66794	ascorbate metabolism	54.55	12 of 22
66794	proline metabolism	54.55	6 of 11
66794	leucine metabolism	53.85	7 of 13
66794	quinate degradation	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	kanosamine biosynthesis II	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	butanoate fermentation	50	2 of 4
66794	CMP-KDO biosynthesis	50	2 of 4
66794	ribulose monophosphate pathway	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	tetrahydrofolate metabolism	50	7 of 14
66794	selenocysteine biosynthesis	50	3 of 6
66794	degradation of sugar acids	48	12 of 25
66794	sulfate reduction	46.15	6 of 13
66794	metabolism of disaccharids	45.45	5 of 11
66794	polyamine pathway	43.48	10 of 23
66794	heme metabolism	42.86	6 of 14
66794	tyrosine metabolism	42.86	6 of 14
66794	arachidonate biosynthesis	40	2 of 5
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	coenzyme M biosynthesis	30	3 of 10
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	phenol degradation	30	6 of 20
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	glutathione metabolism	28.57	4 of 14
66794	catecholamine biosynthesis	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	methanogenesis from CO2	25	3 of 12
66794	sulfopterin metabolism	25	1 of 4
66794	arachidonic acid metabolism	22.22	4 of 18
66794	chlorophyll metabolism	22.22	4 of 18
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation source categories

Isolation

Taxonmaps

69479

Global distribution of 16S sequence U80597 (>99% sequence identity) for Sediminispirochaeta smaragdinae from Microbeatlas

Aquatic Samples	93
Soil Samples	20
Animal Samples	15
Plant Samples
Total Samples	128

Risk assessment

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM14398v1 assembly for Sediminispirochaeta smaragdinae DSM 11293	complete	GCA_000143985	573413.23	648028052	573413	98.63
66792	Spirochaeta smaragdinae DSM 11293	complete		573413.5		573413	63.4

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Spirochaeta smaragdinae 16S ribosomal RNA gene, complete sequence	U80597	1533		573413

GC content

Predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Conserved Molecular Mechanism of TyrA Dehydrogenase Substrate Specificity Underlying Alternative Tyrosine Biosynthetic Pathways in Plants and Microbes.	Schenck CA, Men Y, Maeda HA.	Front Mol Biosci	10.3389/fmolb.2017.00073	2017
Metabolism	Phyloproteomic and functional analyses do not support a split in the genus Borrelia (phylum Spirochaetes).	Estrada-Pena A, Cabezas-Cruz A.	BMC Evol Biol	10.1186/s12862-019-1379-2	2019
Genetics	Complete genome sequence of Spirochaeta smaragdinae type strain (SEBR 4228).	Mavromatis K, Yasawong M, Chertkov O, Lapidus A, Lucas S, Nolan M, Del Rio TG, Tice H, Cheng JF, Pitluck S, Liolios K, Ivanova N, Tapia R, Han C, Bruce D, Goodwin L, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Rohde M, Brambilla E, Spring S, Goker M, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC	Stand Genomic Sci	10.4056/sigs.1143106	2010
Phylogeny	Spirochaeta sinaica sp. nov., a halophilic spirochaete isolated from a cyanobacterial mat.	Dubinina G, Grabovich M, Leshcheva N, Gronow S, Gavrish E, Akimov V	Int J Syst Evol Microbiol	10.1099/ijsem.0.000506	2015
Phylogeny	Spirochaeta dissipatitropha sp. nov., an alkaliphilic, obligately anaerobic bacterium, and emended description of the genus Spirochaeta Ehrenberg 1835.	Pikuta EV, Hoover RB, Bej AK, Marsic D, Whitman WB, Krader P	Int J Syst Evol Microbiol	10.1099/ijs.0.65862-0	2009
Phylogeny	Spirochaeta smaragdinae sp. nov., a new mesophilic strictly anaerobic spirochete from an oil field.	Magot M, Fardeau ML, Arnauld O, Lanau C, Ollivier B, Thomas P, Patel BK	FEMS Microbiol Lett	10.1111/j.1574-6968.1997.tb13876.x	1997