Name: Sediminispirochaeta smaragdinae DSM 11293
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14329

Type strain:

Species: Sediminispirochaeta smaragdinae

Culture col. no.: DSM 11293, JCM 15392, SEBR 4228

Strain history: DSM 11293 <-- M.-L. Fardeau SEBR 4228.

NCBI tax ID(s): 573413 (strain), 55206 (species)

SI-ID 49067

DSM 11293, JCM 15392

Section

Sediminispirochaeta smaragdinae DSM 11293 is an anaerobe, mesophilic, motile bacterium that was isolated from oil field production waters.

motile
anaerobe
mesophilic
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	*Spirochaetota*
	Class	*Spirochaetia*
	Order	*Spirochaetales*
	Family	*Spirochaetaceae*
	Genus	*Sediminispirochaeta*
	Species	**Sediminispirochaeta smaragdinae**
	Full Scientific Name (LPSN)	Sediminispirochaeta smaragdinae (Magot et al. 1998) Shivani et al. 2016

Synonym

Spirochaeta smaragdinae

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.989

[Ref.: #69480]	Motility	yes Confidence in %97.802

[Ref.: #4283]

Incubation period

2-3 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.: #4283]

Culture medium

SEDIMINISPIROCHAETA SMARAGDINAE MEDIUM (DSMZ Medium 819)

[Ref.: #4283]

Culture medium growth

[Ref.: #4283]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4283]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #4283]			growth	35 °C
[Ref.: #67770]			growth	37 °C

[Ref.: #4283]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #4283]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.999

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.646

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	90.91	20 of 22
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	pyrimidine metabolism	86.67	39 of 45
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	purine metabolism	81.91	77 of 94
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	myo-inositol biosynthesis	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	78.57	22 of 28
[Ref.: #66794]	CO2 fixation in Crenarchaeota	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]	glycolysis	76.47	13 of 17
[Ref.: #66794]	vitamin B12 metabolism	76.47	26 of 34
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	oxidative phosphorylation	69.23	63 of 91
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	pantothenate biosynthesis	66.67	4 of 6
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	UDP-GlcNAc biosynthesis	66.67	2 of 3
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	creatinine degradation	60	3 of 5
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	lipid metabolism	54.84	17 of 31
[Ref.: #66794]	ascorbate metabolism	54.55	12 of 22
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	50	7 of 14
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	degradation of sugar acids	48	12 of 25
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	heme metabolism	42.86	6 of 14
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	phenol degradation	30	6 of 20
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	glutathione metabolism	28.57	4 of 14
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	sulfopterin metabolism	25	1 of 4
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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.: #4283]	Sample type/isolated from	oil field production waters
[Ref.: #4283]	Geographic location (country and/or sea, region)	Emeraude oil fields
[Ref.: #4283]	Country	Republic of the Congo
[Ref.: #4283]	Country ISO 3 Code	COG
[Ref.: #4283]	Continent	Africa

[Ref.: #67770]	Sample type/isolated from	Oil field of Congo
[Ref.: #67770]	Country	Congo
[Ref.: #67770]	Continent	Africa
* marker position based on {}

Isolation sources categories

#Engineered

#Industrial

#Oil reservoir

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #4283]

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.: #20218]	Spirochaeta smaragdinae 16S ribosomal RNA gene, complete sequence	U80597	1533	ENA	573413 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sediminispirochaeta smaragdinae DSM 11293	GCA_000143985	complete	GenBank	573413 tax ID	*
[Ref.: #66792]	Spirochaeta smaragdinae DSM 11293	573413.5	complete	PATRIC	573413 tax ID	*
[Ref.: #66792]	Sediminispirochaeta smaragdinae DSM 11293	648028052	complete	JGI IMG/M	573413 tax ID	*

[Ref.: #4283]	GC-content	49.0 mol%	sequence analysis
[Ref.: #67770]	GC-content	50 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: Sediminispirochaeta smaragdinae DSM 11293 DSM 11293 NCBI: GCA_000143985.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sediminispirochaeta smaragdinae DSM 11293 DSM 11293 NCBI: GCA_000143985.1
[Ref.: #69480]	motile	yes	88.689	no
[Ref.: #69480]	flagellated	no	76.102	no
[Ref.: #69480]	gram-positive	no	93.998	no
[Ref.: #69480]	anaerobic	yes	98.363	no
[Ref.: #69480]	aerobic	no	98.061	yes
[Ref.: #69480]	halophile	no	77.711	no
[Ref.: #69480]	spore-forming	no	89.138	no
[Ref.: #69480]	thermophile	no	94.091	yes
[Ref.: #69480]	glucose-util	yes	87.155	no
[Ref.: #69480]	glucose-ferment	yes	68.417	no

Availability in culture collections External links

[Ref.: #4283]

Culture collection no.

DSM 11293, JCM 15392, SEBR 4228

[Ref.: #83477]

SI-ID 49067

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	*
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 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	*

References

#4283

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 11293

#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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 )

#83477

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-ID49067.1 )

* 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 Sediminispirochaeta smaragdinae in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Sediminispirochaeta smaragdinae DSM 11293 DSM 11293

Sediminispirochaeta smaragdinae DSM 11293 DSM 11293

Change proposal

Change proposal