Acidaminococcus fermentans (CCUG 9996, CIP 106432, DSM 20731)

Name: Acidaminococcus fermentans (CCUG 9996, CIP 106432, DSM 20731)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 98

Type strain

Strain Designation VR4

Culture col. no. CCUG 9996 CIP 106432 DSM 20731 ATCC 25085 VR4

NCBI tax ID(s) 591001 905

Special Collections DSMZ CCUG CIP Pig DSMZ

History <- ATCC <- M. Rogosa, VR4 <- R. Fuller CIP <- 2000, CCUG <- 1985, ATCC <- M. Rogosa: strain VR4 <- R. Fuller

Links

Acidaminococcus fermentans VR4 is an anaerobe, Gram-negative, coccus-shaped human pathogen that was isolated from pig gut.

Gram-negative coccus-shaped anaerobe human pathogen genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 44705

ATCC 25085,CCUG 9996,DSM 20731,CIP 106432

@ref 20215

Last LPSN update 2026-02-09 11:17:47

Domain Bacteria

Phylum Bacillota

Class Negativicutes

Order Acidaminococcales

Family Acidaminococcaceae

Genus Acidaminococcus

Species Acidaminococcus fermentans

Full scientific name Acidaminococcus fermentans Rogosa 1969 (Approved Lists 1980)

BacDive ID	Other strains from **Acidaminococcus fermentans** (1)	Type strain
158826	A. fermentans WCA-389-WT-5B, DSM 105754

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
119306	negative	coccus-shaped

Colony morphology

Multimedia

@ref:	66793
multimedia content:	EM_DSM_20731_1.jpg
multimedia.multimedia content:	EM_DSM_20731_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
42016	MEDIUM 348 - for Acidaminococcus		Distilled water make up to (1000.000 ml);Agar (20.000 g);Glucose (5.000g);Yeast extract (5.000 g);Potassium di-hydrogen phosphate (2.000 g);Tween 80 (0.500 ml);Tryptone (5.000 g);Sodium glutamate (4.000 g);Casamino acids (10.000 g);Cysteine hydrochloride
9041	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
9041	ACIDAMINOCOCCUS FERMENTANS MEDIUM (DSMZ Medium 414)	Medium recipe at MediaDive	Name: ACIDAMINOCOCCUS FERMENTANS MEDIUM (DSMZ Medium 414) Composition: Casamino acids 10.0 g/l Yeast extract 5.0 g/l Trypticase peptone 5.0 g/l Glucose 5.0 g/l Na glutamate 4.0 g/l KH2PO4 2.0 g/l Arginine 1.0 g/l Glycine 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l DL-Tryptophan 0.1 g/l Tween 80 Distilled water
9041	CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)	Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
119306	CIP Medium 348	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
9041	positive	growth	37
42016	positive	growth	37
45249	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
9041	anaerobe
45249	anaerobe
125438	anaerobe	95.566
125439	anaerobe	100

Murein

@ref	Murein short key	Type
9041	A31	A1gamma m-Dpm-direct

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
119306	17057 ChEBI	cellobiose	-	degradation
119306	17108 ChEBI	D-arabinose	-	degradation
119306	15824 ChEBI	D-fructose	-	degradation
119306	17634 ChEBI	D-glucose	-	degradation
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
119306	65327 ChEBI	D-xylose	-	degradation
119306	4853 ChEBI	esculin	-	hydrolysis
119306	606565 ChEBI	hippurate	-	hydrolysis
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
119306	17716 ChEBI	lactose	-	degradation
119306	17306 ChEBI	maltose	-	degradation
119306	17632 ChEBI	nitrate	-	reduction
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
119306	16301 ChEBI	nitrite	-	reduction
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
119306	17814 ChEBI	salicin	-	degradation
119306	17992 ChEBI	sucrose	-	degradation
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Antibiotic resistance

@ref	ChEBI	Metabolite	Is sensitive	Is resistant
119306	86455	optochin

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68380	alanine arylamidase	-	3.4.11.2	from API rID32A
119306	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68380	alkaline phosphatase	-	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68380	alpha-galactosidase	-	3.2.1.22	from API rID32A
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68380	alpha-glucosidase	-	3.2.1.20	from API rID32A
68382	alpha-mannosidase	-	3.2.1.24	from API zym
119306	amylase	-
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
119306	beta-galactosidase	-	3.2.1.23
68380	beta-galactosidase	-	3.2.1.23	from API rID32A
68382	beta-galactosidase	-	3.2.1.23	from API zym
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68382	beta-glucosidase	-	3.2.1.21	from API zym
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
119306	caseinase	-	3.4.21.50
119306	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
119306	DNase	-
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
119306	gamma-glutamyltransferase	+	2.3.2.2
119306	gelatinase	-
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	+		from API rID32A
68380	histidine arylamidase	+		from API rID32A
68380	L-arginine arylamidase	+		from API rID32A
119306	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
68380	leucine arylamidase	+	3.4.11.1	from API rID32A
119306	lipase	-
68382	lipase (C 14)	-		from API zym
119306	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
119306	ornithine decarboxylase	-	4.1.1.17
119306	oxidase	-
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
119306	protease	-
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68382	trypsin	-	3.4.21.4	from API zym
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
119306	tween esterase	-
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	sulfopterin metabolism	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	formaldehyde oxidation	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	methylglyoxal degradation	100	5 of 5
66794	threonine metabolism	90	9 of 10
66794	serine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	flavin biosynthesis	86.67	13 of 15
66794	palmitate biosynthesis	86.36	19 of 22
66794	propanol degradation	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	peptidoglycan biosynthesis	80	12 of 15
66794	gallate degradation	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	phenylalanine metabolism	76.92	10 of 13
66794	pyrimidine metabolism	75.56	34 of 45
66794	biotin biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	purine metabolism	72.34	68 of 94
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	starch degradation	70	7 of 10
66794	propionate fermentation	70	7 of 10
66794	leucine metabolism	69.23	9 of 13
66794	histidine metabolism	68.97	20 of 29
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	aspartate and asparagine metabolism	66.67	6 of 9
66794	glycolysis	64.71	11 of 17
66794	alanine metabolism	62.07	18 of 29
66794	oxidative phosphorylation	60.44	55 of 91
66794	factor 420 biosynthesis	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	methionine metabolism	57.69	15 of 26
66794	heme metabolism	57.14	8 of 14
66794	polyamine pathway	56.52	13 of 23
66794	d-mannose degradation	55.56	5 of 9
66794	lysine metabolism	54.76	23 of 42
66794	pentose phosphate pathway	54.55	6 of 11
66794	arginine metabolism	54.17	13 of 24
66794	urea cycle	53.85	7 of 13
66794	tryptophan metabolism	52.63	20 of 38
66794	lipid metabolism	51.61	16 of 31
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	phenylmercury acetate degradation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	cysteine metabolism	50	9 of 18
66794	glutathione metabolism	50	7 of 14
66794	isoprenoid biosynthesis	46.15	12 of 26
66794	proline metabolism	45.45	5 of 11
66794	molybdenum cofactor biosynthesis	44.44	4 of 9
66794	degradation of sugar acids	44	11 of 25
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	tyrosine metabolism	42.86	6 of 14
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	glycine metabolism	40	4 of 10
66794	Entner Doudoroff pathway	40	4 of 10
66794	non-pathway related	39.47	15 of 38
66794	sulfate reduction	38.46	5 of 13
66794	vitamin B6 metabolism	36.36	4 of 11
66794	d-xylose degradation	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 hexoses	33.33	6 of 18
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	degradation of pentoses	32.14	9 of 28
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	ascorbate metabolism	27.27	6 of 22
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	degradation of sugar alcohols	25	4 of 16
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	allantoin degradation	22.22	2 of 9
66794	nitrate assimilation	22.22	2 of 9

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
119306	-	-	-	-	-	+	-	-	-	-	+	-	-	-	-	-	-	-	-	-

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
9041	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	-	-	-	+	+	-	-
9041	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	+	-	+	-	-	-	+	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Suidae (Pig,Swine)
#Host Body-Site	#Gastrointestinal tract	-

Isolation

@ref	Sample type
9041	pig gut
45249	Pig gut
119306	Animal, Pig, gut

Taxonmaps

69479

Global distribution of 16S sequence X78017 (>99% sequence identity) for Acidaminococcus fermentans subclade from Microbeatlas

Aquatic Samples	1130
Soil Samples	391
Animal Samples	25473
Plant Samples	323
Total Samples	27317

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Pathogenicity animal	Biosafety level	Biosafety level comment
9041			2	Risk group (German classification) According to TRBA 466
119306			1	Risk group (French 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	ASM2530v1 assembly for Acidaminococcus fermentans DSM 20731	complete	GCA_000025305	591001.3	646311901	591001	98.66
66792	ASM2073564v1 assembly for Acidaminococcus fermentans DSM 20731 FDAARGOS_1571	complete	GCA_020735645	591001.17	8111069107	591001	97.8
66792	Acidaminococcus fermentans DSM 20731 strain FDAARGOS_1571	complete		591001.18		591001	96.13

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	A.fermentans 16S rRNA	X65935	1488		591001
20218	A.fermentans (DSM 20731) 16S rRNA gene	X78017	1516		591001

GC content

9041

GC-content (mol%)56.6

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Acidaminococcus fermentans DSM 20731
NCBI: GCA_000025305

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	63.20	no
125439	motility	BacteriaNetⓘ	no	57.30	no
125439	gram_stain	BacteriaNetⓘ	positive	76.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	100.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Acidaminococcus fermentans DSM 20731 DSM 20731
NCBI: GCA_000025305.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	86.21	no
125438	anaerobic	anaerobicⓘ	yes	95.57	no
125438	aerobic	aerobicⓘ	no	95.29	no
125438	spore-forming	spore-formingⓘ	no	74.20	no
125438	thermophilic	thermophileⓘ	no	93.07	yes
125438	flagellated	motile2+ⓘ	no	86.73	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Complete genome sequence of Acidaminococcus fermentans type strain (VR4).	Chang YJ, Pukall R, Saunders E, Lapidus A, Copeland A, Nolan M, Glavina Del Rio T, Lucas S, Chen F, Tice H, Cheng JF, Han C, Detter JC, Bruce D, Goodwin L, Pitluck S, Mikhailova N, Liolios K, Pati A, Ivanova N, Mavromatis K, Chen A, Palaniappan K, Land M, Hauser L, Jeffries CD, Brettin T, Rohde M, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP.	Stand Genomic Sci	10.4056/sigs.1002553	2010
	Cardiometabolic disease risk in gorillas is associated with altered gut microbial metabolism.	Davison S, Mascellani Bergo A, Ward Z, Sackett A, Strykova A, Jaimes JD, Travis D, Clayton JB, Murphy HW, Danforth MD, Smith BK, Blekhman R, Fuh T, Niatou Singa FS, Havlik J, Petrzelkova K, Gomez A.	NPJ Biofilms Microbiomes	10.1038/s41522-025-00664-3	2025
	Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization.	Jin X, Yu FB, Yan J, Weakley AM, Dubinkina V, Meng X, Pollard KS.	Nat Commun	10.1038/s41467-023-39121-0	2023
Genetics	Bacteria may have multiple replication origins.	Gao F.	Front Microbiol	10.3389/fmicb.2015.00324	2015
	Role of the gut microbiome in three major psychiatric disorders.	Borkent J, Ioannou M, Laman JD, Haarman BCM, Sommer IEC, Sommer IEC.	Psychol Med	10.1017/s0033291722000897	2022
Metabolism	Arabinoxylan and Pectin Metabolism in Crohn's Disease Microbiota: An In Silico Study.	Sabater C, Calvete-Torre I, Ruiz L, Margolles A.	Int J Mol Sci	10.3390/ijms23137093	2022
Genetics	De novo assembly and comparative genome analysis for polyhydroxyalkanoates-producing Bacillus sp. BNPI-92 strain.	Ebu SM, Ray L, Panda AN, Gouda SK.	J Genet Eng Biotechnol	10.1186/s43141-023-00578-7	2023
Genetics	Methane-yielding microbial communities processing lactate-rich substrates: a piece of the anaerobic digestion puzzle.	Detman A, Mielecki D, Plesniak L, Bucha M, Janiga M, Matyasik I, Chojnacka A, Jedrysek MO, Blaszczyk MK, Sikora A.	Biotechnol Biofuels	10.1186/s13068-018-1106-z	2018
	CMG-biotools, a free workbench for basic comparative microbial genomics.	Vesth T, Lagesen K, Acar O, Ussery D.	PLoS One	10.1371/journal.pone.0060120	2013
Metabolism	Molecular and Low-Resolution Structural Characterization of the Na⁺-Translocating Glutaconyl-CoA Decarboxylase From Clostridium symbiosum.	Vitt S, Prinz S, Hellwig N, Morgner N, Ermler U, Buckel W.	Front Microbiol	10.3389/fmicb.2020.00480	2020
Metabolism	Studies on the mechanism of electron bifurcation catalyzed by electron transferring flavoprotein (Etf) and butyryl-CoA dehydrogenase (Bcd) of Acidaminococcus fermentans.	Chowdhury NP, Mowafy AM, Demmer JK, Upadhyay V, Koelzer S, Jayamani E, Kahnt J, Hornung M, Demmer U, Ermler U, Buckel W.	J Biol Chem	10.1074/jbc.m113.521013	2014
Metabolism	Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome.	Wang M, Osborn LJ, Jain S, Meng X, Weakley A, Yan J, Massey WJ, Varadharajan V, Horak A, Banerjee R, Allende DS, Chan ER, Hajjar AM, Wang Z, Dimas A, Zhao A, Nagashima K, Cheng AG, Higginbottom S, Hazen SL, Brown JM, Fischbach MA.	Cell	10.1016/j.cell.2023.05.037	2023
Metabolism	Reduction of Flavodoxin by Electron Bifurcation and Sodium Ion-dependent Reoxidation by NAD+ Catalyzed by Ferredoxin-NAD+ Reductase (Rnf).	Chowdhury NP, Klomann K, Seubert A, Buckel W.	J Biol Chem	10.1074/jbc.m116.726299	2016
	Veillonella, Firmicutes: Microbes disguised as Gram negatives.	Vesth T, Ozen A, Andersen SC, Kaas RS, Lukjancenko O, Bohlin J, Nookaew I, Wassenaar TM, Ussery DW.	Stand Genomic Sci	10.4056/sigs.2981345	2013
	Auxiliary tRNAs: large-scale analysis of tRNA genes reveals patterns of tRNA repertoire dynamics.	Wald N, Margalit H.	Nucleic Acids Res	10.1093/nar/gku245	2014
	Design, construction, and in vivo augmentation of a complex gut microbiome.	Cheng AG, Ho PY, Aranda-Diaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, Deutschbauer A, Neff N, Sonnenburg JL, Huang KC, Fischbach MA.	Cell	10.1016/j.cell.2022.08.003	2022
Metabolism	Clostridium sticklandii, a specialist in amino acid degradation:revisiting its metabolism through its genome sequence.	Fonknechten N, Chaussonnerie S, Tricot S, Lajus A, Andreesen JR, Perchat N, Pelletier E, Gouyvenoux M, Barbe V, Salanoubat M, Le Paslier D, Weissenbach J, Cohen GN, Kreimeyer A.	BMC Genomics	10.1186/1471-2164-11-555	2010
Phylogeny	Across bacterial phyla, distantly-related genomes with similar genomic GC content have similar patterns of amino acid usage.	Lightfield J, Fram NR, Ely B.	PLoS One	10.1371/journal.pone.0017677	2011
	Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms.	Nasir A, Naeem A, Khan MJ, Nicora HD, Caetano-Anolles G.	Genes (Basel)	10.3390/genes2040869	2011
Metabolism	Quantification of the flavonoid-degrading bacterium Eubacterium ramulus in human fecal samples with a species-specific oligonucleotide hybridization probe.	Simmering R, Kleessen B, Blaut M.	Appl Environ Microbiol	10.1128/aem.65.8.3705-3709.1999	1999
Metabolism	An rRNA approach for assessing the role of obligate amino acid-fermenting bacteria in ruminal amino acid deamination.	Krause DO, Russell JB.	Appl Environ Microbiol	10.1128/aem.62.3.815-821.1996	1996
Enzymology	Superoxide dismutase in anaerobes: survey.	Gregory EM, Moore WE, Holdeman LV.	Appl Environ Microbiol	10.1128/aem.35.5.988-991.1978	1978
Phylogeny	Acidaminococcus gen. n., Acidaminococcus fermentans sp. n., anaerobic gram-negative diplococci using amino acids as the sole energy source for growth.	Rogosa M.	J Bacteriol	10.1128/jb.98.2.756-766.1969	1969
Metabolism	Two pathways of glutamate fermentation by anaerobic bacteria.	Buckel W, Barker HA.	J Bacteriol	10.1128/jb.117.3.1248-1260.1974	1974
	Compilation of small ribosomal subunit RNA structures.	Neefs JM, Van de Peer Y, De Rijk P, Chapelle S, De Wachter R.	Nucleic Acids Res	10.1093/nar/21.13.3025	1993
Metabolism	Fermentation of trans-aconitate via citrate, oxaloacetate, and pyruvate by Acidaminococcus fermentans.	Hartel U, Buckel W	Arch Microbiol	10.1007/s002030050393	1996
	'Acidaminococcus timonensis' sp. nov. and 'Acidaminococcus massiliensis' sp. nov. isolated from human gut.	Ricaboni D, Mailhe M, Benezech A, Cadoret F, Fournier PE, Raoult D.	New Microbes New Infect	10.1016/j.nmni.2016.11.010	2017

References

#9041	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20731
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#42016	; Curators of the CIP;
#45249	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 9996
#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 )
#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 )
#68380	Automatically annotated from API rID32A .
#68382	Automatically annotated from API zym .
#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 .
#119306	Collection of Institut Pasteur ; Curators of the CIP; CIP 106432
#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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Acidaminococcus fermentans (CCUG 9996, CIP 106432, DSM 20731)

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