Name: Romboutsia lituseburensis A25K
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 2614

Type strain:

Species: Romboutsia lituseburensis

Strain Designation: A25K

Culture col. no.: DSM 797, ATCC 25759, BCRC 14536, CCUG 18920, JCM 1404, NCIMB 10637, VTT E-021853, VPI 2751

Strain history: ATCC 25759 <-- L. DS. Smith VPI 2751.

NCBI tax ID(s): 1121325 (strain), 1537 (species)

SI-ID 38658

ATCC 25759, CCUG 18920, DSM 797, NCIB 10637, JCM 1404, CCRC 14536, NCIMB 10637, BCRC 14536, VTT E-021853

Special Collections

Section

When using BacDive for research please cite our paper

Romboutsia lituseburensis A25K is an anaerobe, spore-forming, mesophilic bacterium that was isolated from mud.

spore-forming
anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Peptostreptococcaceae*
	Genus	*Romboutsia*
	Species	**Romboutsia lituseburensis**
	Full Scientific Name (LPSN)	Romboutsia lituseburensis (Laplanche and Saissac 1948) Gerritsen et al. 2014

	Synonym	Clostridium lituseburense
	Synonym	"Inflabilis* lituseburense"*

Information on morphological and physiological properties Morphology

[Ref.: #46926]

Incubation period

1 day

Information on culture and growth conditions Culture and growth conditions

[Ref.: #453]

Culture medium

PY + X MEDIUM (DSMZ Medium 104b)

[Ref.: #453]

Culture medium growth

[Ref.: #453]

Culture medium link

Medium recipe at MediaDive

[Ref.: #453]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #453]	growth	37 °C
[Ref.: #46926]	growth	37 °C
[Ref.: #67770]	growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #453]	Oxygen tolerance	anaerobe
[Ref.: #46926]	Oxygen tolerance	anaerobe
[Ref.: #125439]	Oxygen tolerance	facultative anaerobe Confidence in %96.2

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	vitamin B12 metabolism	88.24	30 of 34
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	methionine metabolism	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	oxidative phosphorylation	58.24	53 of 91
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	pentose phosphate pathway	54.55	6 of 11
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	lipid metabolism	51.61	16 of 31
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	acetate fermentation	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	isoleucine metabolism	50	4 of 8
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	histidine metabolism	44.83	13 of 29
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	degradation of sugar acids	44	11 of 25
[Ref.: #66794]	citric acid cycle	42.86	6 of 14
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	proline metabolism	36.36	4 of 11
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	valine metabolism	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	leucine metabolism	23.08	3 of 13
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	glutathione metabolism	21.43	3 of 14
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #453]	Sample type/isolated from	mud

[Ref.: #46926]	Sample type/isolated from	Mud

[Ref.: #67770]	Sample type/isolated from	Mud
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Mud (Sludge)

What are isolation sources categories?

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

[Ref.: #453]

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.: #67770]	Romboutsia lituseburensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 1404	LC007106	1464	GenBank ENA	1537 tax ID
[Ref.: #453]	[Clostridium] lituseburense strain ATCC 25759 16S ribosomal RNA gene, partial sequence	M59107	1510	GenBank ENA	1121325 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Romboutsia lituseburensis DSM 797	GCA_900103615	scaffold	GenBank ENA	1121325 tax ID
[Ref.: #66792]	Romboutsia lituseburensis A25K	GCA_900002825	scaffold	GenBank ENA	1537 tax ID	*
[Ref.: #66792]	Romboutsia lituseburensis DSM 797	1121325.3	wgs	PATRIC	1121325 tax ID	*
[Ref.: #66792]	Romboutsia lituseburensis strain A25K	1537.3	wgs	PATRIC	1537 tax ID	*
[Ref.: #66792]	Romboutsia lituseburensis DSM 797	2634166902	draft	JGI IMG/M	1121325 tax ID	*

[Ref.: #453]	GC-content	27.0 mol%
[Ref.: #67770]	GC-content	27 mol%	thermal denaturation, midpoint method (Tm)

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Romboutsia lituseburensis DSM 797 PATRIC: 1121325.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	71.618	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	84.308	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	73.16	no
[Ref.: #125438]	aerobic	aerobicⓘ	no	97.108	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	93.955	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	76.687	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Romboutsia lituseburensis A25K NCBI: GCA_900002825
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	facultative anaerobe	96.2
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	84.8
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	74.5
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	yes	65

Availability in culture collections External links

[Ref.: #453]

Culture collection no.

DSM 797, ATCC 25759, BCRC 14536, CCUG 18920, JCM 1404, NCIMB 10637, VTT E-021853, VPI 2751

[Ref.: #72145]

SI-ID 38658

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Romboutsia hominis sp. nov., the first human gut-derived representative of the genus Romboutsia, isolated from ileostoma effluent.	Gerritsen J, Umanets A, Staneva I, Hornung B, Ritari J, Paulin L, Rijkers GT, de Vos WM, Smidt H	Int J Syst Evol Microbiol	10.1099/ijsem.0.003012	2018	*
Metabolism	[Anaerobic bacteria involved in the degradation of aromatic sulfonates to methane].	Shcherbakova VA, Laurinavichyus KS, Chuvil'skaya NA, Ryzhmanova YV, Akimenko VK	Prikl Biokhim Mikrobiol	10.7868/s0555109915020191	2015	*
Phylogeny	Romboutsia sedimentorum sp. nov., isolated from an alkaline-saline lake sediment and emended description of the genus Romboutsia.	Wang Y, Song J, Zhai Y, Zhang C, Gerritsen J, Wang H, Chen X, Li Y, Zhao B, Zhao B, Ruan Z	Int J Syst Evol Microbiol	10.1099/ijs.0.000079	2015	*
Phylogeny	Characterization of a potentially novel 'blown pack' spoilage bacterium isolated from bovine hide.	Moschonas G, Bolton DJ	J Appl Microbiol	10.1111/jam.12077	2012	*
Phylogeny	[Identification and metabolism characterization of a Clostridium lituseburense strain isolated from high-altitude soil].	Liu Q, Liu H, Deng Y, Hu G, Zhang H	Wei Sheng Wu Xue Bao		2010	*

References

#453	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 797

#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 )

#46926 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 18920

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#72145

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-ID38658.1 )

#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 .

* These data were automatically processed and therefore are not curated

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Romboutsia lituseburensis DSM 797

Romboutsia lituseburensis A25K

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