Alkalibacter saccharofermentans (DSM 14828, Uniqem U-218, VKM B-2308)

Name: Alkalibacter saccharofermentans (DSM 14828, Uniqem U-218, VKM B-2308)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5412

Type strain

Strain Designation Z-79820

Culture col. no. DSM 14828 Uniqem U-218 VKM B-2308 Z-79820

NCBI tax ID(s) 1120975 235931

Special Collections DSMZ

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

Links

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

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 138967

DSM 14828,VKM B-2308

@ref 20215

Last LPSN update 2026-02-09 11:18:57

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Eubacteriaceae

Genus Alkalibacter

Species Alkalibacter saccharofermentans

Full scientific name Alkalibacter saccharofermentans Garnova et al. 2005

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5565	ANAEROBRANCA GOTTSCHALKII MEDIUM (DSMZ Medium 895)		Medium recipe at MediaDive	Name: ANAEROBRANCA GOTTSCHALKII MEDIUM (DSMZ Medium 895; with strain-specific modifications) Composition: D-Glucose 4.93583 g/l Na2CO3 2.9615 g/l Tryptone 1.97433 g/l (NH4)2SO4 0.987167 g/l L-Cysteine HCl x H2O 0.493583 g/l K2HPO4 0.493583 g/l NH4Cl 0.394867 g/l Yeast extract 0.246792 g/l Na2S2O3 x 5 H2O 0.0987167 g/l MgSO4 x 7 H2O 0.029615 g/l Nitrilotriacetic acid 0.0148075 g/l NaCl 0.00987167 g/l MnSO4 x H2O 0.00493583 g/l ZnSO4 x 7 H2O 0.0017769 g/l CoSO4 x 7 H2O 0.0017769 g/l FeSO4 x 7 H2O 0.000987167 g/l CaCl2 x 2 H2O 0.000987167 g/l Sodium resazurin 0.000493583 g/l NiCl2 x 6 H2O 0.00029615 g/l AlK(SO4)2 x 12 H2O 0.000197433 g/l CuSO4 x 5 H2O 9.87167e-05 g/l H3BO3 9.87167e-05 g/l Pyridoxine hydrochloride 9.87167e-05 g/l Na2MoO4 x 2 H2O 9.87167e-05 g/l p-Aminobenzoic acid 4.93583e-05 g/l (DL)-alpha-Lipoic acid 4.93583e-05 g/l Calcium D-(+)-pantothenate 4.93583e-05 g/l Nicotinic acid 4.93583e-05 g/l Riboflavin 4.93583e-05 g/l Thiamine HCl 4.93583e-05 g/l Folic acid 1.97433e-05 g/l Biotin 1.97433e-05 g/l Na2WO4 x 2 H2O 3.94867e-06 g/l Na2SeO3 x 5 H2O 2.9615e-06 g/l Vitamin B12 9.87167e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
5565	positive	growth	35	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
5565	anaerobe
125439	anaerobe	99.5

Pathway annotation

Computationally determined by

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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	-
#Environmental	#Terrestrial	#Mud (Sludge)
#Environmental	#Microbial community	#Microbial mat
#Host	#Microbial	#Bacteria

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
5565	mixture of mud and surface cyanobacterial mat from a lagoon	southeastern Transbaikal region, Lake Nizhnee Beloe	Russia	RUS	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5565	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	IMG-taxon 2582581275 annotated assembly for Alkalibacter saccharofermentans DSM 14828	scaffold	GCA_900128885	1120975.4	2582581275	1120975	70.86

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5565	Alkalibacter saccharofermentans strain Z-79820 16S ribosomal RNA gene, partial sequence	AY312403	1465		235931

GC content

@ref	GC-content (mol%)	Method
5565	42.1	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Alkalibacter saccharofermentans DSM 14828
NCBI: GCA_900128885

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	62.20	no
125439	motility	BacteriaNetⓘ	yes	61.80	no
125439	gram_stain	BacteriaNetⓘ	variable	88.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Alkalibacter saccharofermentans DSM 14828 DSM 14828
NCBI: GCA_900128885.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	72.41	no
125438	anaerobic	anaerobicⓘ	yes	89.42	yes
125438	aerobic	aerobicⓘ	no	97.46	yes
125438	spore-forming	spore-formingⓘ	no	60.51	no
125438	thermophilic	thermophileⓘ	no	88.51	yes
125438	flagellated	motile2+ⓘ	no	77.05	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Exploring Protein Functions of Gut Bacteriome and Mycobiome in Thai Infants Associated with Atopic Dermatitis Through Metaproteomic and Host Interaction Analysis.	Chantanaskul T, Patumcharoenpol P, Roytrakul S, Kingkaw A, Vongsangnak W.	Int J Mol Sci	10.3390/ijms252413533	2024
Metabolism	Anoxic Biodegradation of Isosaccharinic Acids at Alkaline pH by Natural Microbial Communities.	Rout SP, Charles CJ, Doulgeris C, McCarthy AJ, Rooks DJ, Loughnane JP, Laws AP, Humphreys PN.	PLoS One	10.1371/journal.pone.0137682	2015
	Dose-Dependent Effects of Aloin on the Intestinal Bacterial Community Structure, Short Chain Fatty Acids Metabolism and Intestinal Epithelial Cell Permeability.	Gokulan K, Kolluru P, Cerniglia CE, Khare S.	Front Microbiol	10.3389/fmicb.2019.00474	2019
Phylogeny	Alkalibacter mobilis sp. nov., an anaerobic bacterium isolated from a coastal lake.	Khomyakova M, Merkel A, Novikov A, Klyukina A, Slobodkin A.	Int J Syst Evol Microbiol	10.1099/ijsem.0.005174	2021
Phylogeny	Rhabdanaerobium thermarum gen. nov., sp. nov., a novel anaerobic bacterium isolated from a hot spring.	Liu L, Jiao JY, Salam N, Zhou EM, Fang BZ, Xian WD, Li MM, Ding YP, Li WJ.	Int J Syst Evol Microbiol	10.1099/ijsem.0.002335	2017
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 .
#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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Alkalibacter saccharofermentans (DSM 14828, Uniqem U-218, VKM B-2308)

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

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900128885

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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