Acetitomaculum ruminis (DSM 5522, ATCC 43876, 12185)

Name: Acetitomaculum ruminis (DSM 5522, ATCC 43876, 12185)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6338

Type strain

Strain Designation 12185, 139 B

Culture col. no. DSM 5522 ATCC 43876 12185 139 B

NCBI tax ID(s) 1120918 2382

Special Collections DSMZ

Links

Acetitomaculum ruminis 12185 is an anaerobe, mesophilic prokaryote that was isolated from rumen, bovine.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 46854

ATCC 43876,DSM 5522,KCTC 5005

@ref 20215

Last LPSN update 2025-12-16 09:48:18

Domain Bacillati

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Lachnospiraceae

Genus Acetitomaculum

Species Acetitomaculum ruminis

Full scientific name Acetitomaculum ruminis Greening and Leedle 1995

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
2090	METHANOBACTERIUM MEDIUM (DSMZ Medium 119)		Medium recipe at MediaDive	Name: METHANOBACTERIUM MEDIUM (DSMZ Medium 119) Composition: NaHCO3 3.98804 g/l Na-formate 1.99402 g/l Na-acetate 0.997009 g/l Na2S x 9 H2O 0.498504 g/l L-Cysteine HCl x H2O 0.498504 g/l KH2PO4 0.498504 g/l NH4Cl 0.398804 g/l NaCl 0.398804 g/l MgSO4 x 7 H2O 0.398804 g/l Yeast extract 0.199402 g/l CaCl2 x 2 H2O 0.0498504 g/l HCl 0.00249252 g/l FeSO4 x 7 H2O 0.00199402 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498504 g/l CoCl2 x 6 H2O 0.000189432 g/l MnCl2 x 4 H2O 9.97009e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l H3BO3 5.98205e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Isobutyric acid DL-2-Methylbutyric acid Valeric acid Isovaleric acid H2SO4 Sludge Distilled water
2090	ACETITOMACULUM MEDIUM (DSMZ Medium 540)		Medium recipe at MediaDive	Name: ACETITOMACULUM MEDIUM (DSMZ Medium 540) Composition: D-Glucose 4.92611 g/l NaHCO3 3.94089 g/l Yeast extract 1.47783 g/l MgCl2 x 6 H2O 1.18227 g/l KCl 0.492611 g/l NH4Cl 0.295566 g/l Na2S x 9 H2O 0.295566 g/l L-Cysteine HCl x H2O 0.295566 g/l KH2PO4 0.197044 g/l Na2SO4 0.0985222 g/l MgSO4 x 7 H2O 0.0295567 g/l Nitrilotriacetic acid 0.0147783 g/l NaCl 0.00985222 g/l MnSO4 x H2O 0.00492611 g/l ZnSO4 x 7 H2O 0.0017734 g/l CoSO4 x 7 H2O 0.0017734 g/l FeSO4 x 7 H2O 0.000985222 g/l CaCl2 x 2 H2O 0.000985222 g/l NiCl2 x 6 H2O 0.000985222 g/l Sodium resazurin 0.000492611 g/l AlK(SO4)2 x 12 H2O 0.000197044 g/l CuSO4 x 5 H2O 9.85222e-05 g/l H3BO3 9.85222e-05 g/l Na2MoO4 x 2 H2O 9.85222e-05 g/l Na2WO4 x 2 H2O 9.85222e-05 g/l Pyridoxine hydrochloride 9.85222e-05 g/l Niacinamide 4.92611e-05 g/l Myo-inositol 4.92611e-05 g/l Ascorbic acid 4.92611e-05 g/l (DL)-alpha-Lipoic acid 4.92611e-05 g/l p-Aminobenzoic acid 4.92611e-05 g/l Choline chloride 4.92611e-05 g/l Calcium D-(+)-pantothenate 4.92611e-05 g/l Nicotinic acid 4.92611e-05 g/l Riboflavin 4.92611e-05 g/l Thiamine HCl 4.92611e-05 g/l Folic acid 1.97044e-05 g/l Biotin 1.97044e-05 g/l Na2SeO3 x 5 H2O 2.95566e-06 g/l Vitamin B12 9.85222e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
2090	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
2090	anaerobe
125439	anaerobe	99.7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68368	27613 ChEBI	amygdalin	-	fermentation	from API 20E
68368	28053 ChEBI	melibiose	+	fermentation	from API 20E
68368	17992 ChEBI	sucrose	-	fermentation	from API 20E

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	coenzyme A metabolism	100	4 of 4
66794	teichoic acid biosynthesis	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	palmitate biosynthesis	90.91	20 of 22
66794	starch degradation	90	9 of 10
66794	threonine metabolism	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	flavin biosynthesis	80	12 of 15
66794	peptidoglycan biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	NAD metabolism	77.78	14 of 18
66794	valine metabolism	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	acetate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	heme metabolism	71.43	10 of 14
66794	vitamin B12 metabolism	70.59	24 of 34
66794	serine metabolism	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	histidine metabolism	65.52	19 of 29
66794	glutamate and glutamine metabolism	64.29	18 of 28
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	isoleucine metabolism	62.5	5 of 8
66794	alanine metabolism	62.07	18 of 29
66794	purine metabolism	60.64	57 of 94
66794	glycogen metabolism	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	glycolysis	58.82	10 of 17
66794	pyrimidine metabolism	57.78	26 of 45
66794	propanol degradation	57.14	4 of 7
66794	oxidative phosphorylation	56.04	51 of 91
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	vitamin B1 metabolism	53.85	7 of 13
66794	methionine metabolism	53.85	14 of 26
66794	glutathione metabolism	50	7 of 14
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	adipate degradation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	cysteine metabolism	50	9 of 18
66794	toluene degradation	50	2 of 4
66794	butanoate fermentation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	tryptophan metabolism	47.37	18 of 38
66794	leucine metabolism	46.15	6 of 13
66794	urea cycle	46.15	6 of 13
66794	sulfate reduction	46.15	6 of 13
66794	proline metabolism	45.45	5 of 11
66794	non-pathway related	44.74	17 of 38
66794	nitrate assimilation	44.44	4 of 9
66794	d-mannose degradation	44.44	4 of 9
66794	citric acid cycle	42.86	6 of 14
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	arginine metabolism	41.67	10 of 24
66794	lysine metabolism	40.48	17 of 42
66794	lipoate biosynthesis	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	lipid metabolism	38.71	12 of 31
66794	isoprenoid biosynthesis	38.46	10 of 26
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	ketogluconate metabolism	37.5	3 of 8
66794	pentose phosphate pathway	36.36	4 of 11
66794	metabolism of disaccharids	36.36	4 of 11
66794	IAA biosynthesis	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	enterobactin biosynthesis	33.33	1 of 3
66794	lipid A biosynthesis	33.33	3 of 9
66794	ascorbate metabolism	31.82	7 of 22
66794	degradation of sugar alcohols	31.25	5 of 16
66794	coenzyme M biosynthesis	30	3 of 10
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	degradation of pentoses	28.57	8 of 28
66794	tyrosine metabolism	28.57	4 of 14
66794	degradation of hexoses	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	CMP-KDO biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	allantoin degradation	22.22	2 of 9
66794	4-hydroxymandelate degradation	22.22	2 of 9

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
2090	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Bovinae (Cow, Cattle)
#Host Body-Site	#Organ	#Rumen

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
2090	rumen, bovine	USA	USA	North America

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2090	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
66792	IMG-taxon 2651870361 annotated assembly for Acetitomaculum ruminis DSM 5522	scaffold	GCA_900112085	1120918.3	2651870361	1120918	64.69

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
2090	Acetitomaculum ruminis strain 139B 16S ribosomal RNA gene, partial sequence	M59083	1478		2382

GC content

2090

GC-content (mol%)34.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Acetitomaculum ruminis DSM 5522
NCBI: GCA_900112085

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	63.00	no
125439	motility	BacteriaNetⓘ	yes	65.90	no
125439	gram_stain	BacteriaNetⓘ	variable	73.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.70	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Acetitomaculum ruminis DSM 5522 DSM 5522
NCBI: GCA_900112085.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	66.20	no
125438	anaerobic	anaerobicⓘ	yes	87.48	yes
125438	aerobic	aerobicⓘ	no	88.20	yes
125438	spore-forming	spore-formingⓘ	no	53.08	no
125438	thermophilic	thermophileⓘ	no	82.48	no
125438	flagellated	motile2+ⓘ	yes	70.83	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Dietary selection of metabolically distinct microorganisms drives hydrogen metabolism in ruminants.	Li QS, Wang R, Ma ZY, Zhang XM, Jiao JZ, Zhang ZG, Ungerfeld EM, Yi KL, Zhang BZ, Long L, Long Y, Tao Y, Huang T, Greening C, Tan ZL, Wang M.	ISME J	10.1038/s41396-022-01294-9	2022
	Energy conservation under extreme energy limitation: the role of cytochromes and quinones in acetogenic bacteria.	Rosenbaum FP, Muller V.	Extremophiles	10.1007/s00792-021-01241-0	2021
	In silico Screening Unveil the Great Potential of Ruminal Bacteria Synthesizing Lasso Peptides.	Sabino YNV, de Araujo KC, de Assis FGDV, Moreira SM, Lopes TDS, Mendes TAO, Huws SA, Mantovani HC.	Front Microbiol	10.3389/fmicb.2020.576738	2020
	Phylogenetic diversity of core rumen microbiota as described by cryo-ET.	Wimmer BH, Morais S, Zalk R, Mizrahi I, Medalia O.	Microlife	10.1093/femsml/uqad010	2023
	Genetic Evidence Reveals the Indispensable Role of the rseC Gene for Autotrophy and the Importance of a Functional Electron Balance for Nitrate Reduction in Clostridium ljungdahlii.	Klask CM, Jager B, Casini I, Angenent LT, Molitor B.	Front Microbiol	10.3389/fmicb.2022.887578	2022
Metabolism	The Sporomusa type Nfn is a novel type of electron-bifurcating transhydrogenase that links the redox pools in acetogenic bacteria.	Kremp F, Roth J, Muller V.	Sci Rep	10.1038/s41598-020-71038-2	2020
Phylogeny	Functional gene analysis suggests different acetogen populations in the bovine rumen and tammar wallaby forestomach.	Gagen EJ, Denman SE, Padmanabha J, Zadbuke S, Al Jassim R, Morrison M, McSweeney CS.	Appl Environ Microbiol	10.1128/aem.01679-10	2010
Phylogeny	Presence of novel, potentially homoacetogenic bacteria in the rumen as determined by analysis of formyltetrahydrofolate synthetase sequences from ruminants.	Henderson G, Naylor GE, Leahy SC, Janssen PH.	Appl Environ Microbiol	10.1128/aem.02580-09	2010
Metabolism	Using gas mixtures of CO, CO₂ and H₂ as microbial substrates: the do's and don'ts of successful technology transfer from laboratory to production scale.	Takors R, Kopf M, Mampel J, Bluemke W, Blombach B, Eikmanns B, Bengelsdorf FR, Weuster-Botz D, Durre P.	Microb Biotechnol	10.1111/1751-7915.13270	2018
Metabolism	Enrichment and isolation of Acetitomaculum ruminis, gen. nov., sp. nov.: acetogenic bacteria from the bovine rumen.	Greening RC, Leedle JA	Arch Microbiol	10.1007/BF00416597	1989

References

#2090	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5522
#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) .
#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 )
#68368	Automatically annotated from API 20E .
#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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Acetitomaculum ruminis (DSM 5522, ATCC 43876, 12185)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Pathway annotation

API 20E

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900112085

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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