Methanoregula formicica (DSM 22288, NBRC 105244, SMSP)

Name: Methanoregula formicica (DSM 22288, NBRC 105244, SMSP)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17857

Type strain

Strain Designation SMSP

Culture col. no. DSM 22288 NBRC 105244 SMSP

NCBI tax ID(s) 882104

Special Collections DSMZ Literature strains

History <- H. Imachi, Japan Agency for Marine-Earth Sci. and Technol. (JAMSTEC), Extremobiosphere Res. Center, Yokosuka, Japan; SMSP <- Y. Yashiro; {2008}

Links

Methanoregula formicica SMSP is an anaerobe, rod-shaped archaeon that was isolated from methanogenic granular sludge.

rod-shaped anaerobe genome sequence 16S sequence Archaea

Name and taxonomic classification

SI-ID 405601

NBRC 105244,DSM 22288

@ref 20215

Last LPSN update 2026-02-09 11:22:19

Domain Archaea

Phylum Methanobacteriota

Class "Methanomicrobia"

Order Methanomicrobiales

Family Methanoregulaceae

Genus Methanoregula

Species Methanoregula formicica

Full scientific name Methanoregula formicica Yashiro et al. 2011

Morphology

Cell morphology

@ref	Cell length	Cell width	Cell shape	Motility	Gram stain	Confidence
29522	4 µm	0.5 µm	rod-shaped
125439					negative	97

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16134	PELOTOMACULUM MEDIUM (DSMZ Medium 960)		Medium recipe at MediaDive	Name: PELOTOMACULUM MEDIUM (DSMZ Medium 960; with strain-specific modifications) Composition: Na-formate 2.71457 g/l Na2CO3 1.49701 g/l NH4Cl 0.538922 g/l Na2S x 9 H2O 0.299401 g/l L-Cysteine HCl x H2O 0.299401 g/l MgCl2 x 6 H2O 0.199601 g/l KH2PO4 0.139721 g/l Yeast extract 0.0998004 g/l Na acetate 0.0998004 g/l 2-Mercaptoethanesulfonic acid 0.0798403 g/l Nitrilotriacetic acid 0.0127745 g/l FeCl2 x 4 H2O 0.000998004 g/l NaCl 0.000998004 g/l Sodium resazurin 0.000499002 g/l ZnCl2 9.98004e-05 g/l Pyridoxine hydrochloride 9.98004e-05 g/l MnCl2 x 4 H2O 9.98004e-05 g/l CaCl2 x 2 H2O 9.98004e-05 g/l NiCl2 x 6 H2O 9.98004e-05 g/l Calcium D-(+)-pantothenate 4.99002e-05 g/l Nicotinic acid 4.99002e-05 g/l Riboflavin 4.99002e-05 g/l p-Aminobenzoic acid 4.99002e-05 g/l (DL)-alpha-Lipoic acid 4.99002e-05 g/l Thiamine HCl 4.99002e-05 g/l Na2WO4 x 2 H2O 3.99202e-05 g/l CoCl2 x 6 H2O 2.99401e-05 g/l Na2MoO4 x 2 H2O 2.99401e-05 g/l Na2SeO3 x 5 H2O 2.99401e-05 g/l CuCl2 1.99601e-05 g/l Folic acid 1.99601e-05 g/l Biotin 1.99601e-05 g/l H3BO3 9.98004e-06 g/l Vitamin B12 9.98004e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
16134	positive	growth	30
29522	positive	growth	10-40
29522	positive	optimum	31.5

Culture pH

@ref	Ability	Type	PH
29522	positive	optimum	7.4
29522	positive	growth	7.0-7.6

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
16134	anaerobe
29522	anaerobe
125439	anaerobe	98.3

Spore formation

@ref	Spore formation	Confidence
125439		94

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29522	NaCl	positive	growth	0-1 %

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Activated sludge
#Condition	#Anoxic (anaerobic)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
16134	methanogenic granular sludge	Ehime, Saijo	Japan	JPN	Asia

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16134	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	ASM32748v1 assembly for Methanoregula formicica SMSP	complete	GCA_000327485	593750.7	2508501105	593750	99.51

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16134	Methanoregula formicicum SMSP gene for 16S rRNA, partial sequence	AB479390	1397		593750

GC content

@ref	GC-content (mol%)	Method
16134	56.2	high performance liquid chromatography (HPLC)
29522	56.2

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Methanoregula formicica SMSP, DSM 22288
IMG: 2508501105

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	94.00	no
125439	motility	BacteriaNetⓘ	no	63.70	no
125439	gram_stain	BacteriaNetⓘ	negative	97.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	98.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Methanoregula formicica SMSP SMSP
NCBI: GCA_000327485.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	69.57	no
125438	anaerobic	anaerobicⓘ	yes	87.33	no
125438	aerobic	aerobicⓘ	no	90.06	no
125438	spore-forming	spore-formingⓘ	no	85.09	no
125438	thermophilic	thermophileⓘ	no	78.39	no
125438	flagellated	motile2+ⓘ	no	88.53	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	Structural conservation of chemotaxis machinery across Archaea and Bacteria.	Briegel A, Ortega DR, Huang AN, Oikonomou CM, Gunsalus RP, Jensen GJ.	Environ Microbiol Rep	10.1111/1758-2229.12265	2015
Phylogeny	Methanoregula formicica sp. nov., a methane-producing archaeon isolated from methanogenic sludge.	Yashiro Y, Sakai S, Ehara M, Miyazaki M, Yamaguchi T, Imachi H	Int J Syst Evol Microbiol	10.1099/ijs.0.014811-0	2009

References

#16134	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 22288
#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 )
#25919	IJSEM 53 2011 ( DOI 10.1099/ijs.0.014811-0 , PubMed 19667393 )
#29522	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 #25919
#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) .
#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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Methanoregula formicica (DSM 22288, NBRC 105244, SMSP)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000327485

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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