Simkania negevensis (DSM 27360, ATCC VR-1471, Z)

Name: Simkania negevensis (DSM 27360, ATCC VR-1471, Z)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23253

Type strain

Strain Designation Z

Culture col. no. DSM 27360 ATCC VR-1471 Z

NCBI tax ID(s) 83561

Special Collections DSMZ

History DSMZ <- M. Horn, Univ. Vienna, Dept. Microbial Ecol., Austria; strain Z <- R. Michel <- S. Kahane, Ben-Gurion-Univ., Beer-Sheva, Israel

Links

Simkania negevensis Z is a bacterium that was isolated from detected as cell culture contaminant .

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 402989

ATCC VR-1471,DSM 27360

@ref 20215

Last LPSN update 2026-05-29 08:30:24

Domain Bacteria

Phylum Chlamydiota

Class Chlamydiia

Order Chlamydiales

Family Simkaniaceae

Genus Simkania

Species Simkania negevensis

Full scientific name Simkania negevensis Everett et al. 1999

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	94.12

Colony morphology

19036

Incubation period2-3 days

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
19036	ACANTHAMOEBA MEDIUM (DSMZ Medium 1500)		Medium recipe at MediaDive	Name: ACANTHAMOEBA MEDIUM (DSMZ Medium 1500) Composition: Trypticase soy broth 30.0 g/l Proteose peptone 20.0 g/l Glucose 18.0 g/l Yeast extract 2.0 g/l Sodium citrate dihydrate 1.0 g/l MgSO4 x 7 H2O 0.98 g/l Na2HPO4 x 7 H2O 0.355 g/l KH2PO4 0.34 g/l Fe(NH4)2(SO4)2 x 6 H2O 0.02 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
19036	positive	growth	25

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		99.847
125438		93.195

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Laboratory	#Contaminant
#Host Body-Site	#Urogenital tract	#Kidney

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent	Latitude	Longitude
19036	detected as cell culture contaminant (in Vero cells)	Israel	ISR	Asia	31.5	34.75 31.5/34.75

Taxonmaps

69479

Global distribution of 16S sequence NR_074932 (>99% sequence identity) for Simkania negevensis subclade from Microbeatlas

Aquatic Samples	3323
Soil Samples	281
Animal Samples	173
Plant Samples	45
Total Samples	3822

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19036	2	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	ASM23720v1 assembly for Simkania negevensis Z	complete	GCA_000237205	331113.3	650716085	331113	91.37

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19036	Simkania negevensis strain Z 16S ribosomal RNA, partial sequence	NR_074932	1546		83561

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM23720v1 assembly for Simkania negevensis Z
BV-BRC: 331113.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	89.27	no
125439	gram_stain	BacteriaNetⓘ	negative	94.12	no
125439	motility	BacteriaNetⓘ	no	73.00	no
125439	spore_formation	BacteriaNetⓘ	no	99.85	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Simkania negevensis Z Z
NCBI: GCA_000237205.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	87.87	no
125438	anaerobic	anaerobicⓘ	no	79.78	no
125438	aerobic	aerobicⓘ	no	53.33	no
125438	spore-forming	spore-formingⓘ	no	93.20	no
125438	thermophilic	thermophileⓘ	no	84.62	no
125438	flagellated	motile2+ⓘ	no	71.25	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Identification and characterization of a ubiquitin E3 RING ligase of the Chlamydia-like bacterium Simkania negevensis.	Horner EM, Lachmayer V, Hermanns T, Moldovan A, Hofmann K, Kozjak-Pavlovic V.	PLoS Pathog	10.1371/journal.ppat.1013626	2025
	A conserved Chlamydiota-specific Type III Secretion System effector linked to stress response.	Kozusnik T, Kebbi-Beghdadi C, Ardissone S, Adams SE, Greub G.	Microbiology (Reading)	10.1099/mic.0.001545	2025
	A new TaqMan real-time PCR assay to detect Parachlamydia acanthamoebae and to monitor its co-existence with SARS-COV-2 among COVID-19 patients.	Baccari O, Barkallah M, Elleuch J, Ben Ayed N, Chtourou A, Karray-Hakim H, Hammami A, Michaud P, Fendri I, Abdelkafi S.	Environ Sci Pollut Res Int	10.1007/s11356-022-23227-x	2023
	Simkania negevensis may produce long-lasting infections in human pneumocytes and endometrial cells.	Vouga M, Baud D, Greub G.	Pathog Dis	10.1093/femspd/ftw115	2017
Phylogeny	Serological cross-reactivity between different Chlamydia-like organisms.	Casson N, Entenza JM, Greub G.	J Clin Microbiol	10.1128/jcm.01867-06	2007
Genetics	Metagenomic analysis of soybean endosphere microbiome to reveal signatures of microbes for health and disease.	Chouhan U, Gamad U, Choudhari JK.	J Genet Eng Biotechnol	10.1186/s43141-023-00535-4	2023
Metabolism	Chlamydia infection depends on a functional MDM2-p53 axis.	Gonzalez E, Rother M, Kerr MC, Al-Zeer MA, Abu-Lubad M, Kessler M, Brinkmann V, Loewer A, Meyer TF.	Nat Commun	10.1038/ncomms6201	2014
Enzymology	New diagnostic real-time PCR for specific detection of Parachlamydia acanthamoebae DNA in clinical samples.	Casson N, Posfay-Barbe KM, Gervaix A, Greub G.	J Clin Microbiol	10.1128/jcm.02302-07	2008
Phylogeny	Protochlamydia naegleriophila as etiologic agent of pneumonia.	Casson N, Michel R, Muller KD, Aubert JD, Greub G.	Emerg Infect Dis	10.3201/eid1401.070980	2008
Enzymology	Development of a new chlamydiales-specific real-time PCR and its application to respiratory clinical samples.	Lienard J, Croxatto A, Aeby S, Jaton K, Posfay-Barbe K, Gervaix A, Greub G.	J Clin Microbiol	10.1128/jcm.00114-11	2011
	An NlpC/P60 protein catalyzes a key step in peptidoglycan recycling at the intersection of energy recovery, cell division and immune evasion in the intracellular pathogen Chlamydia trachomatis.	Reuter J, Otten C, Jacquier N, Lee J, Mengin-Lecreulx D, Lockener I, Kluj R, Mayer C, Corona F, Dannenberg J, Aeby S, Buhl H, Greub G, Vollmer W, Ouellette SP, Schneider T, Henrichfreise B.	PLoS Pathog	10.1371/journal.ppat.1011047	2023
	An unspliced group I intron in 23S rRNA links Chlamydiales, chloroplasts, and mitochondria.	Everett KD, Kahane S, Bush RM, Friedman MG.	J Bacteriol	10.1128/jb.181.16.4734-4740.1999	1999
	Undressing of Waddlia chondrophila to enrich its outer membrane proteins to develop a new species-specific ELISA.	Lienard J, Croxatto A, Gervaix A, Posfay-Barbe K, Baud D, Kebbi-Beghdadi C, Greub G.	New Microbes New Infect	10.1002/2052-2975.26	2014

References

#19036	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27360
#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) .
#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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About us

Simkania negevensis (DSM 27360, ATCC VR-1471, Z)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000237205

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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