Zavarzinella formosa (DSM 19928, VKM B-2478, A10)

Name: Zavarzinella formosa (DSM 19928, VKM B-2478, A10)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11946

Type strain

Strain Designation A10

Culture col. no. DSM 19928 VKM B-2478 A10

NCBI tax ID(s) 1123508 360055

Special Collections DSMZ Literature strains

History <- S. N. Dedysh, Winogradsky Inst. Microbiol., RAS, Moscow, Russia; A10 <- I. S. Kulichevskaya

Links

Zavarzinella formosa A10 is an aerobe, ovoid-shaped bacterium that was isolated from Sphagnum peat bog Bakchar .

ovoid-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 360725

DSM 19928,VKM B-2478

@ref 20215

Last LPSN update 2026-02-09 11:20:42

Domain Bacteria

Phylum Planctomycetota

Class Planctomycetia

Order Gemmatales

Family Gemmataceae

Genus Zavarzinella

Species Zavarzinella formosa

Full scientific name Zavarzinella formosa Kulichevskaya et al. 2009

Morphology

Cell morphology

@ref	Cell length	Cell width	Cell shape	Gram stain	Confidence
28947	2.85 µm	2.25 µm	ovoid-shaped
125438				negative	92.87
125439				negative	93.9

Pigmentation

28947

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8394	ZAVARZINELLA FORMOSA MEDIUM (DSMZ Medium 1196)		Medium recipe at MediaDive	Name: ZAVARZINELLA FORMOSA MEDIUM (DSMZ Medium 1196) Composition: Agar 15.0 g/l N-Acetylglucosamine 1.0 g/l Glucose 0.5 g/l KH2PO4 0.1 g/l MgSO4 x 7 H2O 0.1 g/l Peptone 0.1 g/l Yeast extract 0.1 g/l Casamino acids 0.1 g/l CaCl2 x 6 H2O 0.05 g/l NaCl 0.01 g/l ZnSO4 x 7 H2O 0.001095 g/l FeSO4 x 7 H2O 0.0005 g/l Na-EDTA 0.00025 g/l MnSO4 x H2O 0.000154 g/l CuSO4 x 5 H2O 3.92e-05 g/l Co(NO3)2 x 6 H2O 2.48e-05 g/l Na2B4O7 x 10 H2O 1.77e-05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
8394	positive	growth	20
28947	positive	growth	10-30
28947	positive	optimum	22.5

Culture pH

@ref	Ability	Type	PH	PH range
28947	positive	optimum	5.75
28947	positive	growth	3.8-7.2	acidophile

Physiology and metabolism

Oxygen tolerance

28947

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		96.1

Halophily

@ref	Salt	Growth	Tested relation	Concentration
28947	NaCl	positive	growth	<0.6 %

Observation

28947

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
28947	17057 ChEBI	cellobiose	+	carbon source
28947	4853 ChEBI	esculin	+	hydrolysis
28947	28260 ChEBI	galactose	+	carbon source
28947	17234 ChEBI	glucose	+	carbon source
28947	17716 ChEBI	lactose	+	carbon source
28947	17306 ChEBI	maltose	+	carbon source
28947	506227 ChEBI	N-acetylglucosamine	+	carbon source
28947	15361 ChEBI	pyruvate	+	carbon source
28947	16634 ChEBI	raffinose	+	carbon source
28947	26546 ChEBI	rhamnose	+	carbon source
28947	33942 ChEBI	ribose	+	carbon source
28947	17814 ChEBI	salicin	+	carbon source
28947	17992 ChEBI	sucrose	+	carbon source
28947	27082 ChEBI	trehalose	+	carbon source
28947	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
28947	acid phosphatase	+	3.1.3.2
28947	alkaline phosphatase	+	3.1.3.1
28947	catalase	+	1.11.1.6
28947	cytochrome oxidase	+	1.9.3.1
28947	gelatinase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Peat moss

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
8394	Sphagnum peat bog Bakchar (at a depth of 10-20 cm)	Sphagnum	West Siberia	Russia	RUS	Asia

Taxonmaps

69479

Global distribution of 16S sequence AM162406 (>99% sequence identity) for Zavarzinella formosa subclade from Microbeatlas

Aquatic Samples	76
Soil Samples	62
Animal Samples	12
Plant Samples
Total Samples	150

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8394	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score	IMG accession
66792	TH-08apr19-96 assembly for Zavarzinella formosa DSM 19928	contig	GCA_945906165	1123508.8	1123508	20.2
66792	ASM25570v1 assembly for Zavarzinella formosa DSM 19928	scaffold	GCA_000255705	1123508.10	1123508		2548877000
66792	Zavarzinella formosa DSM 19928	contig		1123508.3	1123508

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
8394	Zavarzinella formosa partial 16S rRNA gene, type strain A10T	AM162406	1426		360055

GC content

@ref	GC-content (mol%)	Method
8394	62.3
28947	62.5
8394	59	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Zavarzinella formosa DSM 19928
NCBI: GCA_000255705

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	88.20	no
125439	gram_stain	BacteriaNetⓘ	negative	93.90	no
125439	motility	BacteriaNetⓘ	yes	59.70	no
125439	spore_formation	BacteriaNetⓘ	no	96.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Zavarzinella formosa DSM 19928 DSM 19928
NCBI: GCA_000255705.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	92.87	no
125438	anaerobic	anaerobicⓘ	no	89.04	yes
125438	aerobic	aerobicⓘ	yes	79.59	yes
125438	spore-forming	spore-formingⓘ	no	76.14	no
125438	thermophilic	thermophileⓘ	no	94.70	no
125438	flagellated	motile2+ⓘ	no	60.04	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Evolution of DNA packaging in gene transfer agents.	Esterman ES, Wolf YI, Kogay R, Koonin EV, Zhaxybayeva O.	Virus Evol	10.1093/ve/veab015	2021
Metabolism	Evolutionary gradient of predicted nuclear localization signals (NLS)-bearing proteins in genomes of family Planctomycetaceae.	Guo M, Yang R, Huang C, Liao Q, Fan G, Sun C, Lee SM.	BMC Microbiol	10.1186/s12866-017-0981-y	2017
Phylogeny	Genomic evolution of 11 type strains within family Planctomycetaceae.	Guo M, Zhou Q, Zhou Y, Yang L, Liu T, Yang J, Chen Y, Su L, Xu J, Chen J, Liu F, Chen J, Dai W, Ni P, Fang C, Yang R.	PLoS One	10.1371/journal.pone.0086752	2014
Genetics	Genome sequences of three species in the family Planctomycetaceae.	Guo M, Han X, Jin T, Zhou L, Yang J, Li Z, Chen J, Geng B, Zou Y, Wan D, Li D, Dai W, Wang H, Chen Y, Ni P, Fang C, Yang R	J Bacteriol	10.1128/JB.00639-12	2012
Phylogeny	Zavarzinella formosa gen. nov., sp. nov., a novel stalked, Gemmata-like planctomycete from a Siberian peat bog.	Kulichevskaya IS, Baulina OI, Bodelier PL, Rijpstra WI, Damste JS, Dedysh SN	Int J Syst Evol Microbiol	10.1099/ijs.0.002378-0	2009

References

#8394	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19928
#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 )
#25386	IJSEM 357 2009 ( DOI 10.1099/ijs.0.002378-0 , PubMed 19196778 )
#28947	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25386
#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) .
#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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Zavarzinella formosa (DSM 19928, VKM B-2478, A10)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_945906165

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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