Rhodoferax lithotrophicus (DSM 113266, JCM 34246, MIZ03)

Name: Rhodoferax lithotrophicus (DSM 113266, JCM 34246, MIZ03)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 169459

Type strain

Strain Designation MIZ03

Culture col. no. DSM 113266 JCM 34246 MIZ03

NCBI tax ID(s) 2798804

Special Collections JCM DSMZ

History DSMZ <- S. Kato, JCM; JCM 34246 {2021}

Links

Rhodoferax lithotrophicus MIZ03 is a bacterium that was isolated from iron-rich floc in freshwater wetland.

genome sequence Bacteria

Name and taxonomic classification

SI-ID 401815

JCM 34246,DSM 113266

@ref 20215

Last LPSN update 2026-05-29 08:46:37

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Comamonadaceae

Genus Rhodoferax

Species Rhodoferax lithotrophicus

Full scientific name Rhodoferax lithotrophicus Kato et al. 2024

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	95.616
125438	negative	98

Multimedia

@ref:	68741
multimedia content:	DSM_113266.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_113266.jpg
caption:	DSM 113266; scale bar represents 10 µm
intellectual property rights:	Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
68741	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
68741	positive	growth	20

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		99.78

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
68741	iron-rich floc in freshwater wetland	Mizube Park, Tsukuba, Ibaraki, Japan	Japan	JPN	Asia	36.0781	140.09 36.0781/140.09

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
66792	Rhodoferax sp. MIZ03	complete		2798804.6	2798804	99.1
66792	Rhodoferax sp. MIZ03	complete		2798804.5	2798804	99.1
66792	Rhodoferax sp. MIZ03	complete		2798804.4	2798804	99.1
66792	ASM1997361v1 assembly for Rhodoferax lithotrophicus MIZ03	complete	GCA_019973615	2798804.3	2798804	98.34

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhodoferax sp. MIZ03
BV-BRC: 2798804.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.78	no
125439	motility	BacteriaNetⓘ	yes	76.46	no
125439	gram_stain	BacteriaNetⓘ	negative	95.62	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	83.88	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhodoferax sp. MIZ03 MIZ03
NCBI: GCA_019973615.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.00	no
125438	anaerobic	anaerobicⓘ	no	87.81	no
125438	aerobic	aerobicⓘ	yes	71.90	no
125438	spore-forming	spore-formingⓘ	no	85.36	no
125438	thermophilic	thermophileⓘ	no	95.95	yes
125438	flagellated	motile2+ⓘ	yes	84.26	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	A Single Bacterium Capable of Oxidation and Reduction of Iron at Circumneutral pH.	Kato S, Ohkuma M	Microbiol Spectr	10.1128/Spectrum.00161-21	2021

References

#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) .
#68741	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 113266
#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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Rhodoferax lithotrophicus (DSM 113266, JCM 34246, MIZ03)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Isolation, sampling and environmental information

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_019973615

Genome-based predictions

Predictions

Literature

Literature

References

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