Rikenella microfusus (DSM 15922, ATCC 29728, JCM 2053)

Cell morphology

Colony morphology

Multimedia

• @ref:	66793
  multimedia content:	EM_DSM_15922_1.jpg
  multimedia.multimedia content:	EM_DSM_15922_1.jpg
  caption:	electron microscopic image
  intellectual property rights:	© HZI/Manfred Rohde
  manual_annotation:	1

Culture medium

@ref	Name	Growth	Medium link	Composition
6185	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
6185	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
6185	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)		Medium recipe at MediaDive	Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water

Culture temp

Oxygen tolerance

Spore formation

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions	external links
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	coenzyme A metabolism	100	4 of 4
66794	gluconeogenesis	100	8 of 8
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	glycogen metabolism	100	5 of 5
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	95.45	21 of 22
66794	starch degradation	90	9 of 10
66794	lipid A biosynthesis	88.89	8 of 9
66794	propanol degradation	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	Entner Doudoroff pathway	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	threonine metabolism	80	8 of 10
66794	glycine betaine biosynthesis	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	chorismate metabolism	77.78	7 of 9
66794	pyrimidine metabolism	75.56	34 of 45
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	NAD metabolism	72.22	13 of 18
66794	purine metabolism	71.28	67 of 94
66794	phenylalanine metabolism	69.23	9 of 13
66794	acetoin degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	valine metabolism	66.67	6 of 9
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	glycolysis	64.71	11 of 17
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	isoleucine metabolism	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	glutamate and glutamine metabolism	60.71	17 of 28
66794	propionate fermentation	60	6 of 10
66794	coenzyme M biosynthesis	60	6 of 10
66794	hydrogen production	60	3 of 5
66794	citric acid cycle	57.14	8 of 14
66794	serine metabolism	55.56	5 of 9
66794	histidine metabolism	55.17	16 of 29
66794	vitamin B6 metabolism	54.55	6 of 11
66794	pentose phosphate pathway	54.55	6 of 11
66794	d-xylose degradation	54.55	6 of 11
66794	proline metabolism	54.55	6 of 11
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	ethanol fermentation	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	1,4-dihydroxy-6-naphthoate biosynthesis	50	3 of 6
66794	adipate degradation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	ketogluconate metabolism	50	4 of 8
66794	toluene degradation	50	2 of 4
66794	butanoate fermentation	50	2 of 4
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	non-pathway related	50	19 of 38
66794	pantothenate biosynthesis	50	3 of 6
66794	alanine metabolism	48.28	14 of 29
66794	lysine metabolism	45.24	19 of 42
66794	lipid metabolism	45.16	14 of 31
66794	tryptophan metabolism	44.74	17 of 38
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	cysteine metabolism	44.44	8 of 18
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	methionine metabolism	42.31	11 of 26
66794	methylglyoxal degradation	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	arginine metabolism	37.5	9 of 24
66794	metabolism of disaccharids	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	oxidative phosphorylation	35.16	32 of 91
66794	formaldehyde oxidation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	UDP-GlcNAc biosynthesis	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	cyanate degradation	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	degradation of sugar acids	32	8 of 25
66794	ascorbate metabolism	31.82	7 of 22
66794	sulfate reduction	30.77	4 of 13
66794	urea cycle	30.77	4 of 13
66794	leucine metabolism	30.77	4 of 13
66794	myo-inositol biosynthesis	30	3 of 10
66794	glutathione metabolism	28.57	4 of 14
66794	degradation of hexoses	27.78	5 of 18
66794	polyamine pathway	26.09	6 of 23
66794	alginate biosynthesis	25	1 of 4
66794	degradation of pentoses	25	7 of 28
66794	degradation of sugar alcohols	25	4 of 16
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation source categories

Isolation

Taxonmaps

69479

Global distribution of 16S sequence AB971798 (>99% sequence identity) for Rikenella microfusus subclade from Microbeatlas

Aquatic Samples	710
Soil Samples	269
Animal Samples	10054
Plant Samples	76
Total Samples	11109

Risk assessment

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM42736v1 assembly for Rikenella microfusus DSM 15922	scaffold	GCA_000427365	880526.4	2509601020	880526	78.31
67770	52683_E03 assembly for Rikenella microfusus NCTC11190	contig	GCA_900455755	28139.3	2832823480	28139	76.83

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6185	Rikenella microfusus ATCC 29728 16S ribosomal RNA gene, complete sequence	L16498	1472		28139
67770	Rikenella microfusus gene for 16S ribosomal RNA, partial sequence, strain: JCM 2053	AB971798	1490		880526

GC content

Predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
	Enriched Aptamer Libraries in Fluorescence-Based Assays for Rikenella microfusus-Specific Gut Microbiome Analyses.	Zhang Y, Xing H, Bolotnikov G, Kramer M, Gotzmann N, Knippschild U, Kissmann AK, Rosenau F.	Microorganisms	10.3390/microorganisms11092266	2023
	Specific gFET-Based Aptasensors for Monitoring of Microbiome Quality: Quantification of the Enteric Health-Relevant Bacterium Roseburia Intestinalis.	Zhang Y, Xing H, Li R, Andersson J, Bozdogan A, Strassl R, Draphoen B, Linden M, Henkel M, Knippschild U, Hasler R, Kleber C, Knoll W, Kissmann AK, Rosenau F.	Adv Healthc Mater	10.1002/adhm.202403827	2025
	Lactobacillus acidophilus potentiates oncolytic virotherapy through modulating gut microbiota homeostasis in hepatocellular carcinoma.	Zhang J, Yang J, Luo J, Wu W, Luo H, Wei W, Lyu H, Wang Y, Yi H, Zhang Y, Fan Z, Lyu H, Kanakaveti VP, Qin B, Yuan P, Yang R, Zhang H, Zuo T, Felsher DW, Lee MH, Li K.	Nat Commun	10.1038/s41467-025-58407-z	2025
	A Polyclonal Selex Aptamer Library Directly Allows Specific Labelling of the Human Gut Bacterium Blautia producta without Isolating Individual Aptamers.	Xing H, Zhang Y, Kramer M, Kissmann AK, Henkel M, Weil T, Knippschild U, Rosenau F.	Molecules	10.3390/molecules27175693	2022
	Polyclonal Aptamers for Specific Fluorescence Labeling and Quantification of the Health Relevant Human Gut Bacterium Parabacteroides distasonis.	Xing H, Kissmann AK, Raber HF, Kramer M, Amann V, Kohn K, Weil T, Rosenau F.	Microorganisms	10.3390/microorganisms9112284	2021
	A Polyclonal Aptamer Library for the Specific Binding of the Gut Bacterium Roseburia intestinalis in Mixtures with Other Gut Microbiome Bacteria and Human Stool Samples.	Xing H, Zhang Y, Kramer M, Kissmann AK, Amann V, Raber HF, Weil T, Stieger KR, Knippschild U, Henkel M, Andersson J, Rosenau F.	Int J Mol Sci	10.3390/ijms23147744	2022
	Draft Genome Sequence of Amycolatopsis decaplanina Strain DSM 44594T.	Kaur N, Kumar S, Bala M, Raghava GP, Mayilraj S.	Genome Announc	10.1128/genomea.00138-13	2013
Pathogenicity	Exposure to concentrated ambient PM2.5 alters the composition of gut microbiota in a murine model.	Wang W, Zhou J, Chen M, Huang X, Xie X, Li W, Cao Q, Kan H, Xu Y, Ying Z.	Part Fibre Toxicol	10.1186/s12989-018-0252-6	2018
Metabolism	Restriction-modification mediated barriers to exogenous DNA uptake and incorporation employed by Prevotella intermedia.	Johnston CD, Skeete CA, Fomenkov A, Roberts RJ, Rittling SR.	PLoS One	10.1371/journal.pone.0185234	2017
	Identification of Prevotella Oralis as a possible target antigen in children with Enthesitis related arthritis.	Stoll ML, Duck LW, Chang MH, Colbert RA, Nigrovic PA, Thompson SD, Elson CO.	Clin Immunol	10.1016/j.clim.2020.108463	2020
Metabolism	Analysis of the microbial community of the biocathode of a hydrogen-producing microbial electrolysis cell.	Croese E, Pereira MA, Euverink GJ, Stams AJ, Geelhoed JS.	Appl Microbiol Biotechnol	10.1007/s00253-011-3583-x	2011
	The application of rumen simulation technique (RUSITEC) for studying dynamics of the bacterial community and metabolome in rumen fluid and the effects of a challenge with Clostridium perfringens.	Wetzels SU, Eger M, Burmester M, Kreienbrock L, Abdulmawjood A, Pinior B, Wagner M, Breves G, Mann E.	PLoS One	10.1371/journal.pone.0192256	2018
Enzymology	Detection of unculturable bacteria in periodontal health and disease by PCR.	Harper-Owen R, Dymock D, Booth V, Weightman AJ, Wade WG.	J Clin Microbiol	10.1128/jcm.37.5.1469-1473.1999	1999
	Selenobaculum gbiensis gen. nov. sp. nov., a new bacterium isolated from the gut microbiota of a patient with Crohn's disease.	Yeo S, Park H, Kim H, Ryu CB, Huh CS.	Sci Rep	10.1038/s41598-023-42017-0	2023
Phylogeny	Mucinivorans hirudinis gen. nov., sp. nov., an anaerobic, mucin-degrading bacterium isolated from the digestive tract of the medicinal leech Hirudo verbana.	Nelson MC, Bomar L, Maltz M, Graf J	Int J Syst Evol Microbiol	10.1099/ijs.0.000052	2015
Phylogeny	Acetobacteroides hydrogenigenes gen. nov., sp. nov., an anaerobic hydrogen-producing bacterium in the family Rikenellaceae isolated from a reed swamp.	Su XL, Tian Q, Zhang J, Yuan XZ, Shi XS, Guo RB, Qiu YL	Int J Syst Evol Microbiol	10.1099/ijs.0.063917-0	2014