Archive BacDiveID:10.13145/bacdive5412.20251217.10

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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

Links

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For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 5565

BacDive-ID: 5412

DSM-Number: 14828

keywords: genome sequence, 16S sequence, anaerobe, mesophilic

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

NCBI tax id

NCBI tax id	Matching level
235931	species
1120975	strain

strain history

@ref: 5565
history: <- T. N. Zhilina, Russian Academy of Sciences, Inst. of Microbiology, Moscow, Russia; Z-79820 <- T. N. Zhilina {1998}

doi: 10.13145/bacdive5412.20251217.10

Name and taxonomic classification

LPSN

@ref: 20215
description: kingdom/bacillati
keyword: phylum/bacillota
phylum: Bacillota
class: Clostridia
order: Eubacteriales
family: Eubacteriaceae
genus: Alkalibacter
species: Alkalibacter saccharofermentans
full scientific name: Alkalibacter saccharofermentans Garnova et al. 2005

@ref: 5565

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Eubacteriaceae

genus: Alkalibacter

species: Alkalibacter saccharofermentans

full scientific name: Alkalibacter saccharofermentans Garnova et al. 2005

strain designation: Z-79820

type strain: yes

Culture and growth conditions

culture medium

@ref: 5565
name: ANAEROBRANCA GOTTSCHALKII MEDIUM (DSMZ Medium 895)
growth: yes
link: https://mediadive.dsmz.de/medium/895
composition: 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: 5565
growth: positive
type: growth
temperature: 35

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
5565	anaerobe
125439	anaerobe	99.5

Isolation, sampling and environmental information

isolation

@ref: 5565
sample type: mixture of mud and surface cyanobacterial mat from a lagoon
geographic location: southeastern Transbaikal region, Lake Nizhnee Beloe
country: Russia
origin.country: RUS
continent: Asia

isolation source categories

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

taxonmaps

@ref: 69479
File name: preview.99_65306.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_2123;96_9228;97_11096;98_13634;99_65306&stattab=map
Last taxonomy: Alkalibacter saccharofermentans subclade
16S sequence: AY312403
Sequence Identity:
Total samples: 91
soil counts: 5
aquatic counts: 26
animal counts: 60

Interaction and safety

risk assessment

@ref: 5565
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

@ref: 66792
description: IMG-taxon 2582581275 annotated assembly for Alkalibacter saccharofermentans DSM 14828
assembly level: scaffold
INSDC accession: GCA_900128885
BV-BRC accession: 1120975.4
IMG accession: 2582581275
NCBI tax ID: 1120975
score: 70.86

16S sequences

@ref: 5565
description: Alkalibacter saccharofermentans strain Z-79820 16S ribosomal RNA gene, partial sequence
accession: AY312403
length: 1465
database: nuccore
NCBI tax ID: 235931

GC content

@ref: 5565
GC-content: 42.1
method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@ref	model	trait	description	prediction	confidence	training_data
125438	gram-positive	gram-positive	Positive reaction to Gram-staining	yes	72.41	no
125438	anaerobic	anaerobic	Ability to grow under anoxygenic conditions (including facultative anaerobes)	yes	89.419	yes
125438	aerobic	aerobic	Ability to grow under oxygenic conditions (including facultative aerobes)	no	97.461	yes
125438	spore-forming	spore-forming	Ability to form endo- or exospores	no	60.51	no
125438	thermophile	thermophilic	Ability to grow at temperatures above or equal to 45°C	no	88.512	yes
125438	motile2+	flagellated	Ability to perform flagellated movement	no	77.045	no
125439	BacteriaNet	spore_formation	Ability to form endo- or exospores	yes	62.2
125439	BacteriaNet	motility	Ability to perform movement	yes	61.8
125439	BacteriaNet	gram_stain	Reaction to gram-staining	variable	88.9
125439	BacteriaNet	oxygen_tolerance	Oxygenic conditions needed for growth	anaerobe	99.5

Literature

@ref: 5565

culture collection no.: DSM 14828, Uniqem U-218, VKM B-2308

straininfo link

@ref: 126262
straininfo: 138967

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	15127306	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	Bacteria, Anaerobic/classification/isolation & purification, Enterobacteriaceae/classification/genetics/isolation & purification/ultrastructure, Fresh Water/*microbiology, Geography, Hydrogen-Ion Concentration, Phylogeny, Russia	Enzymology
Metabolism	26367005	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	metabolism, Radioactive Waste, methods
Phylogeny	28945534	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	Tengchong, Hot spring, polyphasic taxonomy, microbiology, Phylogeny, classification
	30972034	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	Antimicrobial activity, aloin, Short Chain Fatty Acids, Epithelial Cell Barrier Function, Commensal Bacterial Community
Phylogeny	34913865	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	Alkaliphile, Acetogen, Methoxylated Aromatic Compounds, Eubacteriaceae, Fatty Acids, Phylogeny, Lakes, classification
Phylogeny	36001361	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	Bacteria/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA	Transcriptome
	39769296	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	Atopic Dermatitis, Microbiome, Metaproteomics, Human Gut, Mycobiome, Dermatitis, Atopic, Proteomics, Gastrointestinal Microbiome, Mycobiome

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
5565	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14828)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-14828
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates	Nucleic Acids Res. 49: D498-D508 2020	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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann		10.1101/2024.08.12.607695	Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy		https://github.com/GenomeNet/deepG	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		10.1093/database/baaf059	StrainInfo—the central database for linked microbial strain identifiers

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Archive

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

Culture and growth conditions

culture medium

culture temp

Physiology and metabolism

oxygen tolerance

Isolation, sampling and environmental information

isolation

isolation source categories

taxonmaps

Interaction and safety

risk assessment

Sequence information

Genome sequences

16S sequences

GC content

Genome-based predictions

predictions

Literature

straininfo link

literature

Reference

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