Desulfatirhabdium butyrativorans (DSM 18734, JCM 14470, HB1)

Name: Desulfatirhabdium butyrativorans (DSM 18734, JCM 14470, HB1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3996

Type strain

Strain Designation HB1

Culture col. no. DSM 18734 JCM 14470 HB1

NCBI tax ID(s) 1121394 340467

Special Collections DSMZ JCM Literature strains

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Desulfatirhabdium butyrativorans HB1 is an anaerobe, mesophilic, Gram-negative prokaryote that was isolated from upflow anaerobic sludge blanket reactor.

Gram-negative rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 323960

DSM 18734,JCM 14470

@ref 20215

Last LPSN update 2025-12-16 09:47:42

Domain Pseudomonadati

Phylum Thermodesulfobacteriota

Class Desulfobacteria

Order Desulfobacterales

Family Desulfatirhabdiaceae

Genus Desulfatirhabdium

Species Desulfatirhabdium butyrativorans

Full scientific name Desulfatirhabdium butyrativorans Balk et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
32373	negative	3.05 µm	1.15 µm	rod-shaped
125438	negative
125439	negative

Colony morphology

7679

Incubation period>14 days

Pigmentation

32373

Productionyes

Multimedia

@ref:	66793
multimedia content:	EM_DSM_18734_1.jpg
multimedia.multimedia content:	EM_DSM_18734_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_18734_2.jpg
multimedia.multimedia content:	EM_DSM_18734_2.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_18734_3.jpg
multimedia.multimedia content:	EM_DSM_18734_3.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_18734_4.jpg
multimedia.multimedia content:	EM_DSM_18734_4.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7679	DESULFATIRHABDIUM MEDIUM (DSMZ Medium 1086)		Medium recipe at MediaDive	Name: DESULFATIRHABDIUM MEDIUM (DSMZ Medium 1086) Composition: Na2SO4 2.79163 g/l Crotonic acid 1.71486 g/l Na2CO3 1.49551 g/l Na2HPO4 x 2 H2O 0.528415 g/l Na2S x 9 H2O 0.498504 g/l Na-benzoate 0.428714 g/l KH2PO4 0.408774 g/l NH4Cl 0.299103 g/l NaCl 0.299103 g/l CaCl2 x 2 H2O 0.109671 g/l MgCl2 x 6 H2O 0.0997009 g/l Yeast extract 0.0199402 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l Pyridoxine hydrochloride 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l p-Aminobenzoic acid 4.98504e-05 g/l Calcium D-(+)-pantothenate 4.98504e-05 g/l Nicotinic acid 4.98504e-05 g/l (DL)-alpha-Lipoic acid 4.98504e-05 g/l Riboflavin 4.98504e-05 g/l Thiamine HCl 4.98504e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l Biotin 1.99402e-05 g/l Folic acid 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Vitamin B12 9.97009e-07 g/l NaOH Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7679	positive	growth	28	mesophilic
32373	positive	growth	15-37
32373	positive	optimum	29	mesophilic
67770	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH
32373	positive	optimum	7
32373	positive	growth	6.5-8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
7679	anaerobe
32373	anaerobe

Spore formation

@ref	Spore formation
32373
125439

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32373	62064 ChEBI	2,3-butanediol	+	carbon source
32373	17879 ChEBI	4-hydroxybenzoate	+	carbon source
32373	30089 ChEBI	acetate	+	carbon source
32373	16236 ChEBI	ethanol	+	carbon source
32373	15740 ChEBI	formate	+	carbon source
32373	17272 ChEBI	propionate	+	carbon source
32373	15361 ChEBI	pyruvate	+	carbon source
32373	30031 ChEBI	succinate	+	carbon source

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Biodegradation	#Anaerobic digestor
#Condition	#Anoxic (anaerobic)	-

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
7679	upflow anaerobic sludge blanket (UASB) reactor	Netherlands	NLD	Europe
67770	Upflow anaerobic sludge blanket (UASB) reactor treating paper-mill wastewater	Netherlands	NLD	Europe

Taxonmaps

69479

Global distribution of 16S sequence DQ146482 (>99% sequence identity) for Desulfatirhabdium butyrativorans subclade from Microbeatlas

Aquatic Samples	1057
Soil Samples	132
Animal Samples	19
Plant Samples	9
Total Samples	1217

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7679	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
67770	ASM42992v1 assembly for Desulfatirhabdium butyrativorans DSM 18734	scaffold	GCA_000429925	1121394.3	2524023145	1121394	60.75

Genome browser: GCA_000429925

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7679	Desulfatirhabdium butyrativorans strain HB1 16S ribosomal RNA gene, partial sequence	DQ146482	1535		340467

GC content

@ref	GC-content (mol%)	Method
7679	55.1	high performance liquid chromatography (HPLC)
32373	55.1

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Desulfatirhabdium butyrativorans DSM 18734
NCBI: GCA_000429925

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	67.50	no
125439	gram_stain	BacteriaNetⓘ	negative	94.90	no
125439	motility	BacteriaNetⓘ	no	55.30	no
125439	spore_formation	BacteriaNetⓘ	no	94.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Desulfatirhabdium butyrativorans DSM 18734
PATRIC: 1121394.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.63	yes
125438	anaerobic	anaerobicⓘ	yes	81.84	yes
125438	spore-forming	spore-formingⓘ	no	84.00	yes
125438	aerobic	aerobicⓘ	no	86.85	no
125438	thermophilic	thermophileⓘ	no	76.42	no
125438	flagellated	motile2+ⓘ	yes	71.47	no

Literature

Title	Authors	Journal	DOI	Year
Dissimilatory sulfate reduction in an anaerobic biofilm reactor for tofu processing wastewater treatment: Bacterial community and their functional genes.	Zhou L, Dong N, Fu M, Yue X, Jian Y, Li H, Russenberger M, Zhuang WQ.	Sci Total Environ	10.1016/j.scitotenv.2023.164579	2023
Potential of indigenous bacteria driven U(VI) reduction under relevant deep geological repository (DGR) conditions.	Jeong D, Baik MH, Jung EC, Ko MS, Um W, Ryu JH.	Environ Pollut	10.1016/j.envpol.2023.121674	2023
In Situ Metabolic Rates of Alkane-Degrading Sulphate-Reducing Bacteria in Hydrocarbon Seep Sediments Revealed by Combining CARD-FISH, NanoSIMS, and Mathematical Modelling.	Kleindienst S, Polerecky L, Amann R, Musat F, Knittel K.	Environ Microbiol	10.1111/1462-2920.70151	2025
Core Sulphate-Reducing Microorganisms in Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of Methanogens.	Rezadehbashi M, Baldwin SA.	Microorganisms	10.3390/microorganisms6010016	2018
A deep-sea sulfate-reducing bacterium generates zero-valent sulfur via metabolizing thiosulfate.	Liu R, Shan Y, Xi S, Zhang X, Sun C.	mLife	10.1002/mlf2.12038	2022
Hydraulic retention time and pH affect the performance and microbial communities of passive bioreactors for treatment of acid mine drainage.	Aoyagi T, Hamai T, Hori T, Sato Y, Kobayashi M, Sato Y, Inaba T, Ogata A, Habe H, Sakata T.	AMB Express	10.1186/s13568-017-0440-z	2017
Metagenomics revealing molecular profiling of community structure and metabolic pathways in natural hot springs of the Sikkim Himalaya.	Sharma N, Kumar J, Abedin MM, Sahoo D, Pandey A, Rai AK, Singh SP.	BMC Microbiol	10.1186/s12866-020-01923-3	2020
Identity of major sulfur-cycle prokaryotes in freshwater lake ecosystems revealed by a comprehensive phylogenetic study of the dissimilatory adenylylsulfate reductase.	Watanabe T, Kojima H, Fukui M.	Sci Rep	10.1038/srep36262	2016
Complete Genome Sequence and Comparative Genomics of a Novel Myxobacterium Myxococcus hansupus.	Sharma G, Narwani T, Subramanian S.	PLoS One	10.1371/journal.pone.0148593	2016
Microbial communities and chemosynthesis in yellowstone lake sublacustrine hydrothermal vent waters.	Yang T, Lyons S, Aguilar C, Cuhel R, Teske A.	Front Microbiol	10.3389/fmicb.2011.00130	2011
Physiological and comparative proteomic characterization of Desulfolithobacter dissulfuricans gen. nov., sp. nov., a novel mesophilic, sulfur-disproportionating chemolithoautotroph from a deep-sea hydrothermal vent.	Hashimoto Y, Shimamura S, Tame A, Sawayama S, Miyazaki J, Takai K, Nakagawa S.	Front Microbiol	10.3389/fmicb.2022.1042116	2022
Desulfatirhabdium butyrativorans gen. nov., sp. nov., a butyrate-oxidizing, sulfate-reducing bacterium isolated from an anaerobic bioreactor.	Balk M, Altinbas M, Rijpstra WI, Sinninghe Damste JS, Stams AJ	Int J Syst Evol Microbiol	10.1099/ijs.0.65396-0	2008

References

#7679	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18734
#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 )
#32373	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 #28601 (see below)
#66793	Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )
#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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Desulfatirhabdium butyrativorans (DSM 18734, JCM 14470, HB1)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000429925

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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