Name: Alkalibacter saccharofermentans Z-79820
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5412

Type strain:

Species: Alkalibacter saccharofermentans

Strain Designation: Z-79820

Culture col. no.: DSM 14828, Uniqem U-218, VKM B-2308

Strain history: <- T. N. Zhilina, Russian Academy of Sciences, Inst. of Microbiology, Moscow, Russia; Z-79820 <- T. N. Zhilina {1998}

NCBI tax ID(s): 1120975 (strain), 235931 (species)

SI-ID 138967

DSM 14828, VKM B-2308

Special Collections

DSMZ

Section

Alkalibacter saccharofermentans Z-79820 is an anaerobe, spore-forming bacterium that was isolated from mixture of mud and surface cyanobacterial mat from a lagoon.

spore-forming
anaerobe
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	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Eubacteriaceae*
	Genus	*Alkalibacter*
	Species	**Alkalibacter saccharofermentans**
	Full Scientific Name (LPSN)	Alkalibacter saccharofermentans Garnova et al. 2005

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5565]

Culture medium

ANAEROBRANCA GOTTSCHALKII MEDIUM (DSMZ Medium 895)

[Ref.: #5565]

Culture medium growth

[Ref.: #5565]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5565]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #5565]			growth	35 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #5565]

Oxygen tolerance

anaerobe

[Ref.: #69481]

Ability of spore formation

yes Confidence in %96

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	degradation of sugar alcohols	93.75	15 of 16
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	purine metabolism	64.89	61 of 94
[Ref.: #66794]	degradation of sugar acids	64	16 of 25
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	lysine metabolism	52.38	22 of 42
[Ref.: #66794]	oxidative phosphorylation	51.65	47 of 91
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	biotin biosynthesis	50	2 of 4
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	tryptophan metabolism	50	19 of 38
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	polyamine pathway	43.48	10 of 23
[Ref.: #66794]	citric acid cycle	42.86	6 of 14
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	lipid metabolism	41.94	13 of 31
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	degradation of pentoses	35.71	10 of 28
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	propionate fermentation	30	3 of 10
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	vitamin B12 metabolism	29.41	10 of 34
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
		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.: #5565]	Sample type/isolated from	mixture of mud and surface cyanobacterial mat from a lagoon
[Ref.: #5565]	Geographic location (country and/or sea, region)	southeastern Transbaikal region, Lake Nizhnee Beloe
[Ref.: #5565]	Country	Russia
[Ref.: #5565]	Country ISO 3 Code	RUS
[Ref.: #5565]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	-
#Environmental	#Terrestrial	#Mud (Sludge)
#Environmental	#Microbial community	#Microbial mat
#Host	#Microbial	#Bacteria

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY312403 (>99% sequence identity) for Alkalibacter saccharofermentans subclade from Microbeatlas

Aquatic Samples	26
Soil Samples	5
Animal Samples	60
Plant Samples
Total Samples	91

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

[Ref.: #5565]

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.: #5565]	Alkalibacter saccharofermentans strain Z-79820 16S ribosomal RNA gene, partial sequence	AY312403	1465	GenBank ENA	235931 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Alkalibacter saccharofermentans DSM 14828	GCA_900128885	scaffold	GenBank ENA	1120975 tax ID	*
[Ref.: #66792]	Alkalibacter saccharofermentans DSM 14828	1120975.4	wgs	PATRIC	1120975 tax ID	*
[Ref.: #66792]	Alkalibacter saccharofermentans DSM 14828	2582581275	draft	JGI IMG/M	1120975 tax ID	*

[Ref.: #5565]

GC-content

42.1 mol%

thermal denaturation, midpoint method (Tm)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Alkalibacter saccharofermentans DSM 14828 DSM 14828 NCBI: GCA_900128885.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	yes	96	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Alkalibacter saccharofermentans DSM 14828 DSM 14828 NCBI: GCA_900128885.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	yes	72.41	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	89.419	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	97.461	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	60.51	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	88.512	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	77.045	no

Availability in culture collections External links

[Ref.: #5565]

Culture collection no.

DSM 14828, Uniqem U-218, VKM B-2308

[Ref.: #74901]

SI-ID 138967

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Anaerobic, alkaliphilic, saccharolytic bacterium Alkalibacter saccharofermentans gen. nov., sp. nov. from a soda lake in the Transbaikal region of Russia.	Garnova ES, Zhilina TN, Tourova TP, Kostrikina NA, Zavarzin GA	Extremophiles	10.1007/s00792-004-0390-7	2004	*
Phylogeny	Alkalibacter rhizosphaerae sp. nov., a CO-utilizing bacterium isolated from tidal flat sediment, and emended description of the genus Alkalibacter.	Namirimu T, Yu J, Yang JA, Yang SH, Kim YJ, Kwon KK	Int J Syst Evol Microbiol	10.1099/ijsem.0.005495	2022	*

References

#5565

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14828

#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 )

#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 )

#74901

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-ID138967.1 )

* These data were automatically processed and therefore are not curated

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Alkalibacter saccharofermentans DSM 14828 DSM 14828

Alkalibacter saccharofermentans DSM 14828 DSM 14828

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