Name: Holophaga foetida TMBS4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17671

Type strain:

Species: Holophaga foetida

Strain Designation: TMBS4

Culture col. no.: DSM 6591

Strain history: <- F. Bak, TMBS4

NCBI tax ID(s): 903818 (strain), 35839 (species)

SI-ID 48241

DSM 6591

Section

Holophaga foetida TMBS4 is an anaerobe, mesophilic bacterium that was isolated from freshwater mud.

anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Acidobacteriota*
	Class	*Holophagae*
	Order	*Holophagales*
	Family	*Holophagaceae*
	Genus	*Holophaga*
	Species	**Holophaga foetida**
	Full Scientific Name (LPSN)	Holophaga foetida Liesack et al. 1995

Information on morphological and physiological properties Morphology

[Ref.: #2741]

Incubation period

3-7 days

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #2741]

Culture medium

TMBS4 MEDIUM (DSMZ Medium 559)

[Ref.: #2741]

Culture medium growth

[Ref.: #2741]

Culture medium link

Medium recipe at MediaDive

[Ref.: #2741]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #2741]			growth	30 °C

[Ref.: #2741]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #2741]

Oxygen tolerance

anaerobe

[Ref.: #2741]

Name of produced compound

dimethylsulfide

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #2741]	Sample type/isolated from	freshwater mud
[Ref.: #2741]	Geographic location (country and/or sea, region)	Konstanz
[Ref.: #2741]	Country	Germany
[Ref.: #2741]	Country ISO 3 Code	DEU
[Ref.: #2741]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Terrestrial	#Mud (Sludge)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence X77215 (>99% sequence identity) for Holophaga foetida subclade from Microbeatlas

Aquatic Samples	1401
Soil Samples	686
Animal Samples	380
Plant Samples	109
Total Samples	2576

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #2741]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #2741]	H.foetida strain TMBS4-T (DSM 6591-T) 16S rRNA gene	X77215	1501	ENA	903818 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Holophaga foetida DSM 6591	GCA_000242615	contig	GenBank	903818 tax ID	*
[Ref.: #66792]	Holophaga foetida DSM 6591	903818.3	wgs	PATRIC	903818 tax ID	*
[Ref.: #66792]	Holophaga foetida TMBS4, DSM 6591	2509601028	draft	JGI IMG/M	903818 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Holophaga foetida DSM 6591 DSM 6591 NCBI: GCA_000242615.3
[Ref.: #69480]	motile	yes	84.504	no
[Ref.: #69480]	flagellated	no	67.77	no
[Ref.: #69480]	gram-positive	no	98.325	no
[Ref.: #69480]	anaerobic	yes	98.142	yes
[Ref.: #69480]	aerobic	no	95.275	yes
[Ref.: #69480]	halophile	no	96.805	no
[Ref.: #69480]	spore-forming	no	80.009	no
[Ref.: #69480]	thermophile	no	95.454	no
[Ref.: #69480]	glucose-util	yes	51.819	no
[Ref.: #69480]	glucose-ferment	no	78.014	no

Availability in culture collections External links

[Ref.: #2741]

Culture collection no.

DSM 6591

[Ref.: #86662]

SI-ID 48241

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4(T)).	Anderson I, Held B, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Brambilla EM, Rohde M, Spring S, Goker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NC	Stand Genomic Sci	10.4056/sigs.2746047	2012	*
Phylogeny	Acanthopleuribacter pedis gen. nov., sp. nov., a marine bacterium isolated from a chiton, and description of Acanthopleuribacteraceae fam. nov., Acanthopleuribacterales ord. nov., Holophagaceae fam. nov., Holophagales ord. nov. and Holophagae classis nov. in the phylum 'Acidobacteria'.	Fukunaga Y, Kurahashi M, Yanagi K, Yokota A, Harayama S	Int J Syst Evol Microbiol	10.1099/ijs.0.65589-0	2008	*
Metabolism	O-demethylation by the homoacetogenic anaerobe Holophaga foetida studied by a new photometric methylation assay using electrochemically produced cob(I)alamin.	Kreft JU, Schink B	Eur J Biochem	10.1111/j.1432-1033.1994.00945.x	1994	*
Phylogeny	Holophaga foetida gen. nov., sp. nov., a new, homoacetogenic bacterium degrading methoxylated aromatic compounds.	Liesack W, Bak F, Kreft JU, Stackebrandt E	Arch Microbiol	10.1007/BF00264378	1994	*

References

#2741

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 6591

#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) .

#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 )

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#86662

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID48241.1 )

* These data were automatically processed and therefore are not curated

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Holophaga foetida DSM 6591 DSM 6591

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