Sedimentibacter saalensis (DSM 13558, ATCC BAA-283, ZF2)

Name: Sedimentibacter saalensis (DSM 13558, ATCC BAA-283, ZF2)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 18008

Type strain

Strain Designation ZF2

Culture col. no. DSM 13558 ATCC BAA-283 ZF2

NCBI tax ID(s) 1123246 130788

Special Collections DSMZ

Links

Sedimentibacter saalensis ZF2 is an anaerobe, mesophilic prokaryote that was isolated from Freshwater sediment.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 100948

ATCC BAA-283,DSM 13558

@ref 20215

Last LPSN update 2025-12-16 09:51:14

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Tissierellales

Family Sedimentibacteraceae

Genus Sedimentibacter

Species Sedimentibacter saalensis

Full scientific name Sedimentibacter saalensis Breitenstein et al. 2002

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5086	SEDIMENTIBACTER SAALENSIS MEDIUM (DSMZ Medium 943)		Medium recipe at MediaDive	Name: SEDIMENTIBACTER SAALENSIS MEDIUM (DSMZ Medium 943) Composition: NaHCO3 3.8 g/l Yeast extract 3.0 g/l L-Arginine x HCl 2.11 g/l Glycine 0.75 g/l (NH4)HCO3 0.45 g/l Na2S x 9 H2O 0.15 g/l MgSO4 x 6 H2O 0.13 g/l CaCl2 x 2 H2O 0.12 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l Sodium resazurin 0.0005 g/l NaOH 0.0005 g/l Pyridoxine hydrochloride 0.0003 g/l Nicotinic acid 0.0002 g/l Thiamine-HCl x 2 H2O 0.0002 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l Vitamin B12 0.0001 g/l Calcium pantothenate 0.0001 g/l p-Aminobenzoic acid 8e-05 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l D-(+)-biotin 2e-05 g/l H3BO3 6e-06 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Sodium Potassium phosphate buffer Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
5086	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

5086

Oxygen toleranceanaerobe

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	formaldehyde oxidation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	adipate degradation	100	2 of 2
66794	aspartate and asparagine metabolism	100	9 of 9
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ribulose monophosphate pathway	100	2 of 2
66794	lipoate biosynthesis	100	5 of 5
66794	isoleucine metabolism	100	8 of 8
66794	L-lactaldehyde degradation	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	vitamin B1 metabolism	92.31	12 of 13
66794	urea cycle	92.31	12 of 13
66794	pyrimidine metabolism	91.11	41 of 45
66794	propionate fermentation	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	flavin biosynthesis	86.67	13 of 15
66794	alanine metabolism	86.21	25 of 29
66794	citric acid cycle	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	purine metabolism	85.11	80 of 94
66794	selenocysteine biosynthesis	83.33	5 of 6
66794	vitamin B12 metabolism	82.35	28 of 34
66794	pentose phosphate pathway	81.82	9 of 11
66794	cellulose degradation	80	4 of 5
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	starch degradation	80	8 of 10
66794	photosynthesis	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	acetate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	gluconeogenesis	75	6 of 8
66794	biotin biosynthesis	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	histidine metabolism	72.41	21 of 29
66794	NAD metabolism	72.22	13 of 18
66794	propanol degradation	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	Entner Doudoroff pathway	70	7 of 10
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	methane metabolism	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	lysine metabolism	64.29	27 of 42
66794	proline metabolism	63.64	7 of 11
66794	vitamin B6 metabolism	63.64	7 of 11
66794	arginine metabolism	62.5	15 of 24
66794	ketogluconate metabolism	62.5	5 of 8
66794	methionine metabolism	61.54	16 of 26
66794	leucine metabolism	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	glycine betaine biosynthesis	60	3 of 5
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	factor 420 biosynthesis	60	3 of 5
66794	oxidative phosphorylation	58.24	53 of 91
66794	degradation of sugar acids	56	14 of 25
66794	non-pathway related	52.63	20 of 38
66794	coenzyme A metabolism	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	toluene degradation	50	2 of 4
66794	isoprenoid biosynthesis	46.15	12 of 26
66794	lipid metabolism	45.16	14 of 31
66794	tryptophan metabolism	44.74	17 of 38
66794	nitrate assimilation	44.44	4 of 9
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	polyamine pathway	43.48	10 of 23
66794	tyrosine metabolism	42.86	6 of 14
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	tetrahydrofolate metabolism	42.86	6 of 14
66794	glutathione metabolism	42.86	6 of 14
66794	phenol degradation	40	8 of 20
66794	arachidonate biosynthesis	40	2 of 5
66794	gallate degradation	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	3-phenylpropionate degradation	40	6 of 15
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	ascorbate metabolism	36.36	8 of 22
66794	degradation of pentoses	35.71	10 of 28
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	methanogenesis from CO2	33.33	4 of 12
66794	lipid A biosynthesis	33.33	3 of 9
66794	enterobactin biosynthesis	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	pantothenate biosynthesis	33.33	2 of 6
66794	allantoin degradation	33.33	3 of 9
66794	degradation of sugar alcohols	31.25	5 of 16
66794	sulfate reduction	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	metabolism of disaccharids	27.27	3 of 11
66794	cyclohexanol degradation	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	carnitine metabolism	25	2 of 8
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Environmental	#Aquatic	#Freshwater

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
5086	Freshwater sediment	Sachsen-Anhalt, River Saale, near Halle	Germany	DEU	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5086	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM783017v1 assembly for Sedimentibacter saalensis DSM 13558	scaffold	GCA_007830175	130788.3	2596583544	130788	68.58

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5086	Sedimentibacter saalensis ZF2 16S rRNA gene	AJ404680	1434		130788

GC content

@ref	GC-content (mol%)	Method
5086	34	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: Sedimentibacter saalensis DSM 13558
NCBI: GCA_007830175

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	60.20	no
125439	motility	BacteriaNetⓘ	no	60.10	no
125439	gram_stain	BacteriaNetⓘ	variable	66.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	74.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Sedimentibacter saalensis DSM 13558
NCBI: GCA_007830175.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	56.27	no
125438	anaerobic	anaerobicⓘ	yes	84.61	no
125438	aerobic	aerobicⓘ	no	94.16	yes
125438	spore-forming	spore-formingⓘ	yes	63.29	no
125438	thermophilic	thermophileⓘ	no	95.28	yes
125438	flagellated	motile2+ⓘ	yes	74.36	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Algal exudates promote conjugation in marine Roseobacters.	Duchin Rapp Y, Lipsman V, Yuda L, Kublanov IV, Matsliyah D, Segev E.	mBio	10.1128/mbio.01062-24	2024
Genetics	Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential.	Isokpehi RD, Kim Y, Krejci SE, Trivedi VD.	Microorganisms	10.3390/microorganisms12040791	2024
Phylogeny	Proposal for the new genus Allokutzneria gen. nov. within the suborder Pseudonocardineae and transfer of Kibdelosporangium albatum Tomita et al. 1993 as Allokutzneria albata comb. nov.	Labeda DP, Kroppenstedt RM.	Int J Syst Evol Microbiol	10.1099/ijs.0.65474-0	2008
	Fatal affairs - conjugational transfer of a dinoflagellate-killing plasmid between marine Rhodobacterales.	Tomasch J, Ringel V, Wang H, Freese HM, Bartling P, Brinkmann H, Vollmers J, Jarek M, Wagner-Dobler I, Petersen J.	Microb Genom	10.1099/mgen.0.000787	2022
Metabolism	Methane monooxygenases: central enzymes in methanotrophy with promising biotechnological applications.	Khider MLK, Brautaset T, Irla M.	World J Microbiol Biotechnol	10.1007/s11274-021-03038-x	2021
Metabolism	Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria.	Rochman FF, Kwon M, Khadka R, Tamas I, Lopez-Jauregui AA, Sheremet A, V Smirnova A, Malmstrom RR, Yoon S, Woyke T, Dunfield PF, Verbeke TJ.	ISME J	10.1038/s41396-019-0561-2	2020
Genetics	Marinobacter arenosus sp. nov., a halotolerant bacterium isolated from a tidal flat.	Lee Y, Weerawongwiwat V, Kim JH, Suh MK, Kim HS, Lee JS, Yoon JH, Sukhoom A, Kim W.	Arch Microbiol	10.1007/s00203-021-02696-7	2022
Phylogeny	Reclassification of Clostridium hydroxybenzoicum as Sedimentibacter hydroxybenzoicus gen. nov., comb. nov., and description of Sedimentibacter saalensis sp. nov..	Breitenstein A, Wiegel J, Haertig C, Weiss N, Andreesen JR, Lechner U	Int J Syst Evol Microbiol	10.1099/00207713-52-3-801	2002

References

#5086	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13558
#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 )
#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 )
#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 )

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Sedimentibacter saalensis (DSM 13558, ATCC BAA-283, ZF2)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_007830175

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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