Acidithrix ferrooxidans (DSM 28176, JCM 19728, Py-F3)

Name: Acidithrix ferrooxidans (DSM 28176, JCM 19728, Py-F3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159490

Type strain

Strain Designation Py-F3

Culture col. no. DSM 28176 JCM 19728 Py-F3

NCBI tax ID(s) 1280514

Special Collections DSMZ JCM

History DSMZ <- R. Jones, Bangor Univ., Wales, U.K.; Py-F3 <- B. Johnson {2012} JCM <-- D. B. Johnson; Bangor Univ., UK; PY-F3.

Links

Acidithrix ferrooxidans Py-F3 is a bacterium that was isolated from acid streamers .

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 400979

JCM 19728,DSM 28176

@ref 20215

Last LPSN update 2026-05-29 08:44:12

Domain Bacteria

Phylum Actinomycetota

Class Acidimicrobiia

Order Acidimicrobiales

Family Acidimicrobiaceae

Genus Acidithrix

Species Acidithrix ferrooxidans

Full scientific name Acidithrix ferrooxidans Jones and Johnson 2022

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	95.317

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
66313	FERROUS SULFATE/YEAST EXTRACT MEDIUM (DSMZ Medium 1190)		Medium recipe at MediaDive	Name: FERROUS SULFATE/YEAST EXTRACT MEDIUM (DSMZ Medium 1190; with strain-specific modifications) Composition: FeSO4 x 7 H2O 5.56 g/l D-Glucose 1.0 g/l MgSO4 x 7 H2O 0.5 g/l (NH4)2SO4 0.45 g/l Yeast extract 0.2 g/l Na2SO4 x 10 H2O 0.15 g/l KCl 0.05 g/l KH2PO4 0.05 g/l Ca(NO3)2 x 4 H2O 0.014 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
66313	positive	growth	30
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	facultative anaerobe	91.595

Spore formation

@ref	Spore formation	Confidence
125439		99.951

Observation

67770

Observationquinones: MK-9(H₄)

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Other	#Mine
#Condition	#Acidic	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
66313	acid streamers (in acid mine drainage)	Anglesey	United Kingdom	GBR	Europe
67770	Acidic streamer draining an abandoned coper mine in north Wales

Taxonmaps

69479

Global distribution of 16S sequence KC208497 (>99% sequence identity) for Acidimicrobiaceae from Microbeatlas

Aquatic Samples	378
Soil Samples	226
Animal Samples	605
Plant Samples	34
Total Samples	1243

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM94929v1 assembly for Acidithrix ferrooxidans PY-F3	contig	GCA_000949295	1280514.8	2585428127	1280514	40.34
66792	Acidithrix ferrooxidans strain Py-F3	contig		1280514.4		1280514	39.23

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66313	Acidithrix ferrooxidans strain Py-F3 16S ribosomal RNA gene, partial sequence	KC208497	1192		1280514

GC content

@ref	GC-content (mol%)	Method
67770	57.4	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM94929v1 assembly for Acidithrix ferrooxidans PY-F3
NCBI: GCA_000949295

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	95.32	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	91.60	no
125439	motility	BacteriaNetⓘ	yes	67.81	no
125439	spore_formation	BacteriaNetⓘ	no	99.95	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Acidithrix ferrooxidans strain Py-F3
PATRIC: 1280514.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	76.71	no
125438	anaerobic	anaerobicⓘ	no	76.69	no
125438	spore-forming	spore-formingⓘ	no	67.93	no
125438	aerobic	aerobicⓘ	yes	73.64	no
125438	thermophilic	thermophileⓘ	no	84.13	yes
125438	flagellated	motile2+ⓘ	no	57.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome Sequence of the Acidophilic Ferrous Iron-Oxidizing Isolate Acidithrix ferrooxidans Strain Py-F3, the Proposed Type Strain of the Novel Actinobacterial Genus Acidithrix.	Eisen S, Poehlein A, Johnson DB, Daniel R, Schlomann M, Muhling M	Genome Announc	10.1128/genomeA.00382-15	2015
Phylogeny	Acidithrix ferrooxidans gen. nov., sp. nov.; a filamentous and obligately heterotrophic, acidophilic member of the Actinobacteria that catalyzes dissimilatory oxido-reduction of iron.	Jones RM, Johnson DB	Res Microbiol	10.1016/j.resmic.2015.01.003	2015

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 )
#66313	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28176
#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) .
#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 .
#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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Acidithrix ferrooxidans (DSM 28176, JCM 19728, Py-F3)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_000949295

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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