Clostridium nitritogenes (DSM 3985, ATCC 25547, VPI 0263)

Name: Clostridium nitritogenes (DSM 3985, ATCC 25547, VPI 0263)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5436

Type strain

Strain Designation TA 20A

Culture col. no. DSM 3985 ATCC 25547 VPI 0263 TA 20A JCM 6485

NCBI tax ID(s) 1561

Special Collections DSMZ JCM

History DSMZ <- ATCC <- L.V. Holdeman, VPI 0263 <- A. Prévot, TA 20A JCM <-- T. Mitsuoka <-- ATCC 25547 <-- L. V. Holdeman VPI 0263 <-- A. Prévot TA 20A.

Links

Clostridium nitritogenes TA 20A is an anaerobe bacterium that was isolated from antarctic soil.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 38590

ATCC 25547,DSM 3985,JCM 6485

@ref 20215

Last LPSN update 2026-05-29 08:26:10

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium nitritogenes

Full scientific name Clostridium nitritogenes (Prévot 1940) Bernard et al. 2018

Synonyms (1)

Eubacterium nitritogenes

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1543	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)		Medium recipe at MediaDive	Name: PYG MEDIUM (modified) (DSMZ Medium 104; with strain-specific modifications) Composition: Yeast extract 10.0 g/l Maltose 5.0 g/l Trypticase peptone 5.0 g/l Peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Vitamin K1 NaOH Tween 80 Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
1543	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
1543	anaerobe
125439	facultative anaerobe	97.639

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Condition	#Psychrophilic (<10°C)	-
#Climate	#Cold	#Polar

Isolation

@ref	Sample type
1543	antarctic soil
67770	Antarctic soil

Taxonmaps

69479

Global distribution of 16S sequence LC480784 (>99% sequence identity) for Clostridium baratii from Microbeatlas

Aquatic Samples	927
Soil Samples	585
Animal Samples	10123
Plant Samples	218
Total Samples	11853

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1543	2	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3952154v1 assembly for Clostridium nitritogenes JCM 6485	scaffold	GCA_039521545	83340	72.61

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Eubacterium nitritogenes gene for 16S rRNA, partial sequence	AB018185	1477		83340
67770	Clostridium nitritogenes JCM 6485 gene for 16S ribosomal RNA, partial sequence	LC480784	1475		83340

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM3952154v1 assembly for Clostridium nitritogenes JCM 6485
NCBI: GCA_039521545

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	97.64	no
125439	gram_stain	BacteriaNetⓘ	positive	72.74	no
125439	motility	BacteriaNetⓘ	yes	62.46	no
125439	spore_formation	BacteriaNetⓘ	yes	51.33	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Clostridium neonatale sp. nov. linked to necrotizing enterocolitis in neonates and a clarification of species assignable to the genus Clostridium (Prazmowski 1880) emend. Lawson and Rainey 2016.	Bernard K, Burdz T, Wiebe D, Alfa M, Bernier AM.	Int J Syst Evol Microbiol	10.1099/ijsem.0.002827	2018

References

#1543	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3985
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Clostridium nitritogenes (DSM 3985, ATCC 25547, VPI 0263)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_039521545

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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