Clostridium methylpentosum (DSM 5476, ATCC 43829, R2)

Name: Clostridium methylpentosum (DSM 5476, ATCC 43829, R2)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2743

Type strain

Strain Designation R2

Culture col. no. DSM 5476 ATCC 43829 R2

NCBI tax ID(s) 537013 84026

Special Collections DSMZ

History <- ATCC; ATCC 43829 <- E. Canale-Parola, Department of Microbiology, University of Massachusetts, Amherst, USA; R2

Links

Clostridium methylpentosum R2 is an anaerobe bacterium that was isolated from human faeces.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 42073

ATCC 43829,DSM 5476

@ref 20215

Last LPSN update 2026-02-09 11:18:21

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Clostridiaceae

Genus Clostridium

Species Clostridium methylpentosum

Full scientific name Clostridium methylpentosum Himelbloom and Canale-Parola 1989

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	96.5

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
2178	CLOSTRIDIUM METHYLPENTOSUM MEDIUM (DSMZ Medium 492)		Medium recipe at MediaDive	Name: CLOSTRIDIUM METHYLPENTOSUM MEDIUM (DSMZ Medium 492) Composition: L-Rhamnose 1.99005 g/l L-Cysteine HCl x H2O 0.995025 g/l NaHCO3 0.995025 g/l NaCl 0.895522 g/l KH2PO4 0.895522 g/l NH4Cl 0.895522 g/l CaCl2 x 2 H2O 0.0199005 g/l MnCl2 x 4 H2O 0.0199005 g/l MgSO4 x 7 H2O 0.0199005 g/l CoCl2 x 6 H2O 0.00497512 g/l FeSO4 x 7 H2O 0.00497512 g/l ZnSO4 x 7 H2O 0.00199005 g/l CuSO4 x H2O 0.00199005 g/l Sodium resazurin 0.000497512 g/l Pyridoxine hydrochloride 9.95025e-05 g/l (DL)-alpha-Lipoic acid 4.97512e-05 g/l p-Aminobenzoic acid 4.97512e-05 g/l Calcium D-(+)-pantothenate 4.97512e-05 g/l Nicotinic acid 4.97512e-05 g/l Riboflavin 4.97512e-05 g/l Thiamine HCl 4.97512e-05 g/l Folic acid 1.99005e-05 g/l Biotin 1.99005e-05 g/l Vitamin B12 9.95025e-07 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
2178	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
2178	anaerobe
125438	anaerobe	93.906
125439	anaerobe	95.2

Spore formation

@ref	Spore formation	Confidence
125439		99.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	cardiolipin biosynthesis	100	7 of 7
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	starch degradation	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	vitamin B1 metabolism	84.62	11 of 13
66794	threonine metabolism	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	photosynthesis	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	glycolysis	76.47	13 of 17
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	glutamate and glutamine metabolism	67.86	19 of 28
66794	serine metabolism	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	degradation of hexoses	66.67	12 of 18
66794	enterobactin biosynthesis	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	gluconeogenesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	methylglyoxal degradation	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	oxidative phosphorylation	59.34	54 of 91
66794	pyrimidine metabolism	57.78	26 of 45
66794	methionine metabolism	57.69	15 of 26
66794	propanol degradation	57.14	4 of 7
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	cysteine metabolism	55.56	10 of 18
66794	purine metabolism	55.32	52 of 94
66794	tryptophan metabolism	55.26	21 of 38
66794	histidine metabolism	55.17	16 of 29
66794	vitamin B6 metabolism	54.55	6 of 11
66794	leucine metabolism	53.85	7 of 13
66794	flavin biosynthesis	53.33	8 of 15
66794	non-pathway related	52.63	20 of 38
66794	alanine metabolism	51.72	15 of 29
66794	phenylmercury acetate degradation	50	1 of 2
66794	suberin monomers biosynthesis	50	1 of 2
66794	tetrahydrofolate metabolism	50	7 of 14
66794	ethanol fermentation	50	1 of 2
66794	Entner Doudoroff pathway	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	adipate degradation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	biotin biosynthesis	50	2 of 4
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	quinate degradation	50	1 of 2
66794	degradation of pentoses	50	14 of 28
66794	butanoate fermentation	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	arginine metabolism	50	12 of 24
66794	polyamine pathway	47.83	11 of 23
66794	lysine metabolism	47.62	20 of 42
66794	isoprenoid biosynthesis	46.15	12 of 26
66794	urea cycle	46.15	6 of 13
66794	proline metabolism	45.45	5 of 11
66794	citric acid cycle	42.86	6 of 14
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	vitamin B12 metabolism	41.18	14 of 34
66794	propionate fermentation	40	4 of 10
66794	factor 420 biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
66794	d-xylose degradation	36.36	4 of 11
66794	pentose phosphate pathway	36.36	4 of 11
66794	lipid metabolism	35.48	11 of 31
66794	sphingosine metabolism	33.33	2 of 6
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	lipid A biosynthesis	33.33	3 of 9
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	nitrate assimilation	33.33	3 of 9
66794	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	degradation of aromatic, nitrogen containing compounds	33.33	4 of 12
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	ascorbate metabolism	31.82	7 of 22
66794	sulfate reduction	30.77	4 of 13
66794	myo-inositol biosynthesis	30	3 of 10
66794	glycine metabolism	30	3 of 10
66794	tyrosine metabolism	28.57	4 of 14
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	metabolism of disaccharids	27.27	3 of 11
66794	CMP-KDO biosynthesis	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	phenylpropanoid biosynthesis	23.08	3 of 13
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	heme metabolism	21.43	3 of 14

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
2178	human faeces	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence Y18181 (>99% sequence identity) for [Clostridium] methylpentosum subclade from Microbeatlas

Aquatic Samples	270
Soil Samples	154
Animal Samples	36917
Plant Samples	94
Total Samples	37435

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2178	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	ASM15865v1 assembly for [Clostridium] methylpentosum DSM 5476	scaffold	GCA_000158655	537013.3	643886206	537013	24.44

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
2178	Clostridium methylpentosum 16S rRNA gene, partial, strain DSM 5476	Y18181	1435		537013

GC content

2178

GC-content (mol%)46.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: [Clostridium] methylpentosum DSM 5476
NCBI: GCA_000158655

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.50	no
125439	motility	BacteriaNetⓘ	no	85.10	no
125439	gram_stain	BacteriaNetⓘ	negative	96.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	95.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: [Clostridium] methylpentosum DSM 5476 DSM 5476
NCBI: GCA_000158655.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	71.38	no
125438	anaerobic	anaerobicⓘ	yes	93.91	yes
125438	aerobic	aerobicⓘ	no	98.07	yes
125438	spore-forming	spore-formingⓘ	no	53.40	no
125438	thermophilic	thermophileⓘ	no	85.99	yes
125438	flagellated	motile2+ⓘ	no	85.63	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Fermented soybean meal using Bacillus subtilis and Aspergillus oryzae positively enhances cecal microbial composition and broiler performance.	Akhirini N, Suprayogi WPS, Saraswati PN, Ratriyanto A, Irawan A.	Anim Biosci	10.5713/ab.250400	2025
	GLP-1 Responses to a Single Meal Fortified With Oyster Mushroom Powder in Adults With Impaired Glucose Tolerance Depend on the Gut Microbiota Composition Before the Meal.	Klumpen L, Donkers A, Seel W, Dicks L, Holst JJ, Stehle P, Simon MC, Ellinger S.	Mol Nutr Food Res	10.1002/mnfr.70159	2025
	Plant Heteropolysaccharides as Potential Anti-Diabetic Agents: A Review.	He D, Cui C.	Curr Issues Mol Biol	10.3390/cimb47070533	2025
	Study on characteristics of gut flora composition of pregnant women with preeclampsia	Li G, Niu H, Xie M, Yang M, Li M, Hao Y, Zhang J.	BMC Pregnancy Childbirth		2025
Enzymology	Feeding amylolytic and fibrolytic exogenous enzymes in feedlot diets: effects on ruminal parameters, nitrogen balance and microbial diversity of Nellore cattle.	Ferreira IM, Mantovani HC, Viquez-Umana F, Granja-Salcedo YT, E Silva LFC, Koontz A, Holder V, Pettigrew JE, Rodrigues AA, Rodrigues AN, de Abreu MJI, de Almeida STR, Vidigal PMP, Siqueira GR, de Resende FD.	J Anim Sci Biotechnol	10.1186/s40104-025-01226-5	2025
	Gut infection and dysbiosis are hallmarks of severe SARS-CoV-2 variants.	Nagaraj SK, Joy CM, Shiraz R, Narayan R, Kaur S, Khatun O, Dubey S, Ng J, Mishra N, Tripathi S.	Npj Viruses	10.1038/s44298-025-00158-1	2025
	Lactobacillus salivarius and Berberine Alleviated Yak Calves' Diarrhea via Accommodating Oxidation Resistance, Inflammatory Factors, and Intestinal Microbiota.	He Q, Lu S, Wang J, Xu C, Qu W, Nawaz S, Ataya FS, Wu Y, Li K.	Animals (Basel)	10.3390/ani14162419	2024
	Decreased Lactococcus lactis and Propionic Acid in Feces of Patients with Moyamoya Disease: Possible Implications of Immune Dysregulation.	Otomo M, Tashiro R, Tokuno H, Kanoke A, Tominaga K, Nagai A, Aikawa T, Ando D, Sakata H, Sato T, Abe T, Endo H, Niizuma K, Tominaga T.	Cerebrovasc Dis	10.1159/000545478	2025
	Systematic review of bidirectional interaction between gut microbiome, miRNAs, and human pathologies.	Drago L, De La Motte LR, Deflorio L, Sansico DF, Salvatici M, Micaglio E, Biazzo M, Giarritiello F.	Front Microbiol	10.3389/fmicb.2025.1540943	2025
	The Prebiotic Effect of Kaempferol in Regulating Bile Acid Metabolism.	Li X, Huang G, Khan I, Ding Z, Hsiao WLW, Liu Z.	Food Sci Nutr	10.1002/fsn3.70023	2025
	Exploring the gut microbiota of healthy captive Asian elephants from various locations in Yunnan, China.	Wang Y, Wang Y, Zhou J, Bao M, Shah T, Yang S, Zheng J, Li Q, Hou Y, Wang B, Yuan R.	Front Microbiol	10.3389/fmicb.2024.1403930	2024
	Gut Microbiome rewiring via fecal transplants: Uncovering therapeutic avenues in Alzheimer's disease models.	Upadhyay P, Kumar S, Tyagi A, Tyagi AR, Barbhuyan T, Gupta S.	BMC Neurosci	10.1186/s12868-025-00953-9	2025
	Geranylgeraniol and Green Tea Polyphenols Mitigate Negative Effects of a High-Fat Diet on Skeletal Muscle and the Gut Microbiome in Male C57BL/6J Mice.	Shen CL, Elmassry MM, Grue K, Joiner HE, Jacobo AU, Hamood A, Chung E.	Metabolites	10.3390/metabo12100913	2022
	Dietary low levels of Eucommia ulmoides leaf extracts: effects on antioxidant capacity, immunity, and cecal microbiota in lipopolysaccharide-challenged broilers.	Zhang J, Chai L, Guo Y, Han J, Yang G.	Front Microbiol	10.3389/fmicb.2025.1662502	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
	Integrating the serum proteomic and fecal metaproteomic to analyze the impacts of overweight/obesity on IBD: a pilot investigation.	Yan P, Sun Y, Luo J, Liu X, Wu J, Miao Y.	Clin Proteomics	10.1186/s12014-023-09396-y	2023
	Gut microbiota, physical activity and/or metabolic markers in healthy individuals - towards new biomarkers of health.	Myhrstad MCW, Ruud E, Gaundal L, Gjovaag T, Rud I, Retterstol K, Ulven SM, Holven KB, Koehler K, Telle-Hansen VH.	Front Nutr	10.3389/fnut.2024.1438876	2024
	Membrane-bound pyrophosphatase of human gut microbe Clostridium methylpentosum confers improved salt tolerance in Escherichia coli, Saccharomyces cerevisiae and tobacco.	Yang Y, Liu Y, Yuan H, Liu X, Gao Y, Gong M, Zou Z.	Mol Membr Biol	10.1080/09687688.2017.1370145	2016
	Comparative time-series analyses of gut microbiome profiles in genetically and chemically induced lupus-prone mice and the impacts of fecal transplantation.	Chatthanathon P, Leelahavanichkul A, Cheibchalard T, Wilantho A, Hirankarn N, Somboonna N.	Sci Rep	10.1038/s41598-024-77672-4	2024
Metabolism	Gut Microbiome Profiles and Associated Metabolic Pathways in HIV-Infected Treatment-Naïve Patients.	do Nascimento WM, Machiavelli A, Ferreira LGE, Cruz Silveira L, de Azevedo SSD, Bello G, Smith DP, Mezzari MP, Petrosino JF, Delgado Duarte RT, Zarate-Blades CR, Pinto AR.	Cells	10.3390/cells10020385	2021
	Development of a Protocol for Anaerobic Preparation and Banking of Fecal Microbiota Transplantation Material: Evaluation of Bacterial Richness in the Cultivated Fraction.	Bosch B, Hartikainen A, Ronkainen A, Scheperjans F, Arkkila P, Satokari R.	Microorganisms	10.3390/microorganisms11122901	2023
	Intestinal fatty acid binding protein is associated with cardiac function and gut dysbiosis in chronic heart failure.	Nendl A, Raju SC, Broch K, Mayerhofer CCK, Holm K, Halvorsen B, Lappegard KT, Moscavitch S, Hov JR, Seljeflot I, Troseid M, Awoyemi A.	Front Cardiovasc Med	10.3389/fcvm.2023.1160030	2023
	Trimethylamine Oxidation into the Proatherogenic Trimethylamine N-Oxide Is Higher in Coronary Heart Disease Men: From the CORDIOPREV Study.	Garcia-Fernandez H, Alcala-Diaz JF, Quintana-Navarro GM, Lopez-Moreno J, Luque-Cordoba D, Ruiz-Diaz Narvaez E, Arenas-de Larriva AP, Gutierrez-Mariscal FM, Torres-Pena JD, Rodriguez-Cano D, Luque RM, Priego-Capote F, Lopez-Miranda J, Camargo A.	World J Mens Health	10.5534/wjmh.230366	2025
Genetics	Host origin of microbiota drives functional recovery and Clostridioides difficile clearance in mice.	Millard SA, Vendrov KC, Young VB, Seekatz AM.	mBio	10.1128/mbio.01108-25	2025
	Effects of glucose oxidase on growth performance, clinical symptoms, serum parameters, and intestinal health in piglets challenged by enterotoxigenic Escherichia coli.	Wang W, Xie R, Cao Q, Ye H, Zhang C, Dong Z, Feng D, Zuo J.	Front Microbiol	10.3389/fmicb.2022.994151	2022
Phylogeny	Metataxonomics and Metabolomics Profiles in Metabolic Dysfunction-Associated Fatty Liver Disease Patients on a "Navelina" Orange-Enriched Diet.	Calabrese FM, Aloisio Caruso E, De Nunzio V, Celano G, Pinto G, Cofano M, Sallustio S, Iacobellis I, Apa CA, Santamaria M, Calasso M, Giannelli G, De Angelis M, Notarnicola M.	Nutrients	10.3390/nu16203543	2024
	The Use of Fecal Microbiota Transplant in Overcoming and Modulating Resistance to Anti-PD-1 Therapy in Patients with Skin Cancer.	Vongsavath T, Rahmani R, Tun KM, Manne V.	Cancers (Basel)	10.3390/cancers16030499	2024
Transcriptome	1-Deoxynojirimycin containing Morus alba leaf-based food modulates the gut microbiome and expression of genes related to obesity.	Jaiswal V, Lee MJ, Chun JL, Park M, Lee HJ.	BMC Vet Res	10.1186/s12917-024-03961-9	2024
	Gut-brain axis in post-traumatic stress disorder: microbial - mediated mechanisms and new therapeutic approaches - A narrative review.	Pan J, Lin S, Qian Q, Fu S, Liu X.	Front Pharmacol	10.3389/fphar.2025.1621678	2025
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
	Deciphering the Physiological Responses to the Intake of Plant-Based Meat Analogues: On the Track of Microbiota and Biomarkers in Serum and Urine.	Sanchez-Terron G, Martinez R, Morcuende D, Estevez M.	J Agric Food Chem	10.1021/acs.jafc.5c02799	2025
Pathogenicity	The Influence of Probiotic Supplementation on the Obesity Indexes, Neuroinflammatory and Oxidative Stress Markers, Gut Microbial Diversity, and Working Memory in Obese Thai Children.	Khongtan S, Sivamaruthi BS, Thangaleela S, Kesika P, Bharathi M, Sirilun S, Choeisoongnern T, Peerajan S, Sittiprapaporn P, Chaiyasut C.	Foods	10.3390/foods12213890	2023
Pathogenicity	Protection of Alzheimer's disease progression by a human-origin probiotics cocktail.	Prajapati SK, Wang S, Mishra SP, Jain S, Yadav H.	Sci Rep	10.1038/s41598-024-84780-8	2025
	Systematic review of donor and recipient predictive biomarkers of response to faecal microbiota transplantation in patients with ulcerative colitis.	Rees NP, Shaheen W, Quince C, Tselepis C, Horniblow RD, Sharma N, Beggs AD, Iqbal TH, Quraishi MN.	EBioMedicine	10.1016/j.ebiom.2022.104088	2022
	Effects of dietary supplementation of a blend of Saccharomyces cerevisiae, multiple live probiotic bacteria, and their fermentation products on performance, health, and rumen bacterial community of newly weaned beef steers during a 56-d receiving period.	Treon E, Sidney T, Taiwo G, Idowu M, Leal Y, Ologunagba D, Ogunade IM.	Transl Anim Sci	10.1093/tas/txad143	2024
	Dietary Supplementation With Lactobacillus plantarum Ameliorates Compromise of Growth Performance by Modulating Short-Chain Fatty Acids and Intestinal Dysbiosis in Broilers Under Clostridium perfringens Challenge.	Wang B, Zhou Y, Mao Y, Gong L, Li X, Xu S, Wang F, Guo Q, Zhang H, Li W.	Front Nutr	10.3389/fnut.2021.706148	2021
Phylogeny	Effects of Polymannuronic Acid on the Intestinal Microbiota in Mice after Long-Term Intragastric Administration.	Zhang E, Wei Q, Li X, Song S.	Mar Drugs	10.3390/md22030125	2024
	Effects of high intake of cod or salmon on gut microbiota profile, faecal output and serum concentrations of lipids and bile acids in overweight adults: a randomised clinical trial.	Bratlie M, Hagen IV, Helland A, Erchinger F, Midttun O, Ueland PM, Rosenlund G, Sveier H, Mellgren G, Hausken T, Gudbrandsen OA.	Eur J Nutr	10.1007/s00394-020-02417-8	2021
	Seasonal Influence on Rumen Microbiota, Rumen Fermentation, and Enteric Methane Emissions of Holstein and Jersey Steers under the Same Total Mixed Ration.	Islam M, Kim SH, Son AR, Ramos SC, Jeong CD, Yu Z, Kang SH, Cho YI, Lee SS, Cho KK, Lee SS.	Animals (Basel)	10.3390/ani11041184	2021
	Gut Microbiota Composition and Metabolic Potential of Long-Living People in China.	Zhang S, Ning R, Zeng B, Deng F, Kong F, Guo W, Zhao J, Li Y.	Front Aging Neurosci	10.3389/fnagi.2022.820108	2022
	Bank1 deficiency reshapes the gut microbiota of lupus mice towards an anti-inflammatory composition.	Galicia G, Botia-Sanchez M, Toro-Dominguez D, Garcia AL, Valera JR, Gomez Hernandez G, Fernandez RM, Carmona N, Luque G, Morell M, Varela N, Perez-Cozar F, Margolles A, Aguilera M, Alarcon-Riquelme ME.	Front Immunol	10.3389/fimmu.2025.1586025	2025
	Stool preparation under anaerobic conditions contributes to retention of obligate anaerobes: potential improvement for fecal microbiota transplantation.	Shimizu H, Arai K, Asahara T, Takahashi T, Tsuji H, Matsumoto S, Takeuchi I, Kyodo R, Yamashiro Y.	BMC Microbiol	10.1186/s12866-021-02325-9	2021
	Immunoglobulin A Targets a Unique Subset of the Microbiota in Inflammatory Bowel Disease.	Shapiro JM, de Zoete MR, Palm NW, Laenen Y, Bright R, Mallette M, Bu K, Bielecka AA, Xu F, Hurtado-Lorenzo A, Shah SA, Cho JH, LeLeiko NS, Sands BE, Flavell RA, Clemente JC.	Cell Host Microbe	10.1016/j.chom.2020.12.003	2021
Genetics	Investigating the modulatory effects of Moringa oleifera on the gut microbiota of chicken model through metagenomic approach.	Soundararajan S, Selvakumar J, Maria Joseph ZM, Gopinath Y, Saravanan V, Santhanam R.	Front Vet Sci	10.3389/fvets.2023.1153769	2023
Genetics	Integrated Analysis of Gut Microbiome and Lipid Metabolism in Mice Infected with Carbapenem-Resistant Enterobacteriaceae.	Zhang N, Peng Y, Zhao L, He P, Zhu J, Liu Y, Liu X, Liu X, Deng G, Zhang Z, Feng M.	Metabolites	10.3390/metabo12100892	2022
	Intestinal microbiota has important effect on severity of hand foot and mouth disease in children.	Shen C, Xu Y, Ji J, Wei J, Jiang Y, Yang Y, Yang M, Huang H, Zou R, Fang C, Zeng F, Yang F, Wang X, Yuan J, Li J, Wang X, Yang H, Gong S, Wang H, Xia H, Ma J, Liu Y.	BMC Infect Dis	10.1186/s12879-021-06748-7	2021
	Differential Fecal Microbiome Dysbiosis after Equivalent Traumatic Brain Injury in Aged Versus Young Adult Mice.	Davis BT, Islam MBAR, Das P, Gilbert JA, Ho KJ, Schwulst SJ.	J Exp Neurol	10.33696/neurol.2.044	2021
	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	Integrated analysis of multi-tissues lipidome and gut microbiome reveals microbiota-induced shifts on lipid metabolism in pigs.	Xie C, Zhu X, Xu B, Niu Y, Zhang X, Ma L, Yan X.	Anim Nutr	10.1016/j.aninu.2022.04.011	2022
	The Impact of Lactobacillus plantarum on the Gut Microbiota of Mice with DSS-Induced Colitis.	Zhang F, Li Y, Wang X, Wang S, Bi D.	Biomed Res Int	10.1155/2019/3921315	2019
Genetics	Dietary Emulsifier Sodium Stearoyl Lactylate Alters Gut Microbiota in vitro and Inhibits Bacterial Butyrate Producers.	Elmen L, Zlamal JE, Scott DA, Lee RB, Chen DJ, Colas AR, Rodionov DA, Peterson SN.	Front Microbiol	10.3389/fmicb.2020.00892	2020
	Screening for chronic prostatitis pathogens using high-throughput next-generation sequencing.	Wu Y, Jiang H, Tan M, Lu X.	Prostate	10.1002/pros.23971	2020
	Repairing gut barrier by traditional Chinese medicine: roles of gut microbiota.	Zhou Y, Zhang D, Cheng H, Wu J, Liu J, Feng W, Peng C.	Front Cell Infect Microbiol	10.3389/fcimb.2024.1389925	2024
	Metagenomic Analysis Reveals New Microbiota Related to Fiber Digestion in Pigs.	Liu G, Li P, Hou L, Niu Q, Pu G, Wang B, Du T, Kim SW, Niu P, Li Q, Huang R.	Front Microbiol	10.3389/fmicb.2021.746717	2021
	A Novel Plant-Based Nutraceutical Combined with Exercise Can Revert Oxidative Status in Plasma and Liver in a Diet-Induced-Obesity Animal Model.	Guzman-Carrasco A, Kapravelou G, Lopez-Jurado M, Bermudez F, Andres-Leon E, Terron-Camero LC, Prados J, Melguizo C, Porres JM, Martinez R.	Antioxidants (Basel)	10.3390/antiox13030274	2024
Metabolism	Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation.	Wlodarska M, Luo C, Kolde R, d'Hennezel E, Annand JW, Heim CE, Krastel P, Schmitt EK, Omar AS, Creasey EA, Garner AL, Mohammadi S, O'Connell DJ, Abubucker S, Arthur TD, Franzosa EA, Huttenhower C, Murphy LO, Haiser HJ, Vlamakis H, Porter JA, Xavier RJ.	Cell Host Microbe	10.1016/j.chom.2017.06.007	2017
	Effects of supplemental xylanase and xylooligosaccharides on production performance and gut health variables of broiler chickens.	Singh AK, Mishra B, Bedford MR, Jha R.	J Anim Sci Biotechnol	10.1186/s40104-021-00617-8	2021
Genetics	Comparative Genomic Analysis Reveals Novel Microcompartment-Associated Metabolic Pathways in the Human Gut Microbiome.	Ravcheev DA, Moussu L, Smajic S, Thiele I.	Front Genet	10.3389/fgene.2019.00636	2019
Metabolism	Alterations in the Gut Microbiome and Cecal Metabolome During Klebsiella pneumoniae-Induced Pneumosepsis.	Wu T, Xu F, Su C, Li H, Lv N, Liu Y, Gao Y, Lan Y, Li J.	Front Immunol	10.3389/fimmu.2020.01331	2020
	Senolytic Combination of Dasatinib and Quercetin Alleviates Intestinal Senescence and Inflammation and Modulates the Gut Microbiome in Aged Mice.	Saccon TD, Nagpal R, Yadav H, Cavalcante MB, Nunes ADC, Schneider A, Gesing A, Hughes B, Yousefzadeh M, Tchkonia T, Kirkland JL, Niedernhofer LJ, Robbins PD, Masternak MM.	J Gerontol A Biol Sci Med Sci	10.1093/gerona/glab002	2021
Pathogenicity	Fecal Microbiota Composition Drives Immune Activation in HIV-infected Individuals.	Neff CP, Krueger O, Xiong K, Arif S, Nusbacher N, Schneider JM, Cunningham AW, Armstrong A, Li S, McCarter MD, Campbell TB, Lozupone CA, Palmer BE.	EBioMedicine	10.1016/j.ebiom.2018.03.024	2018
Genetics	Disorganized Gut Microbiome Contributed to Liver Cirrhosis Progression: A Meta-Omics-Based Study.	Shao L, Ling Z, Chen D, Liu Y, Yang F, Li L.	Front Microbiol	10.3389/fmicb.2018.03166	2018
	Meta-analysis of the Parkinson's disease gut microbiome suggests alterations linked to intestinal inflammation.	Romano S, Savva GM, Bedarf JR, Charles IG, Hildebrand F, Narbad A.	NPJ Parkinsons Dis	10.1038/s41531-021-00156-z	2021
	Evolutionary and Functional Relationships of the dha Regulon by Genomic Context Analysis.	Martins-Pinheiro M, Lima WC, Asif H, Oller CA, Menck CF.	PLoS One	10.1371/journal.pone.0150772	2016
	Influence of the microbiome, diet and genetics on inter-individual variation in the human plasma metabolome.	Chen L, Zhernakova DV, Kurilshikov A, Andreu-Sanchez S, Wang D, Augustijn HE, Vich Vila A, Lifelines Cohort Study, Weersma RK, Medema MH, Netea MG, Kuipers F, Wijmenga C, Zhernakova A, Fu J.	Nat Med	10.1038/s41591-022-02014-8	2022
Pathogenicity	Eukaryotic and Prokaryotic Microbiota Interactions.	Kodio A, Menu E, Ranque S.	Microorganisms	10.3390/microorganisms8122018	2020
	A combination of Lactobacillus mali APS1 and dieting improved the efficacy of obesity treatment via manipulating gut microbiome in mice.	Chen YT, Yang NS, Lin YC, Ho ST, Li KY, Lin JS, Liu JR, Chen MJ.	Sci Rep	10.1038/s41598-018-23844-y	2018
Metabolism	Haem iron reshapes colonic luminal environment: impact on mucosal homeostasis and microbiome through aldehyde formation.	Martin OCB, Olier M, Ellero-Simatos S, Naud N, Dupuy J, Huc L, Tache S, Graillot V, Leveque M, Bezirard V, Helies-Toussaint C, Estrada FBY, Tondereau V, Lippi Y, Naylies C, Peyriga L, Canlet C, Davila AM, Blachier F, Ferrier L, Boutet-Robinet E, Gueraud F, Theodorou V, Pierre FHF.	Microbiome	10.1186/s40168-019-0685-7	2019
Pathogenicity	Antrodia cinnamomea reduces obesity and modulates the gut microbiota in high-fat diet-fed mice.	Chang CJ, Lu CC, Lin CS, Martel J, Ko YF, Ojcius DM, Wu TR, Tsai YH, Yeh TS, Lu JJ, Lai HC, Young JD.	Int J Obes (Lond)	10.1038/ijo.2017.149	2018
	Automated analysis of genomic sequences facilitates high-throughput and comprehensive description of bacteria.	Hitch TCA, Riedel T, Oren A, Overmann J, Lawley TD, Clavel T.	ISME Commun	10.1038/s43705-021-00017-z	2021
	Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified.	De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A, Serrazzanetti DI, Cristofori F, Guerzoni ME, Gobbetti M, Francavilla R.	PLoS One	10.1371/journal.pone.0076993	2013
Phylogeny	Host contributes to longitudinal diversity of fecal microbiota in swine selected for lean growth.	Lu D, Tiezzi F, Schillebeeckx C, McNulty NP, Schwab C, Shull C, Maltecca C.	Microbiome	10.1186/s40168-017-0384-1	2018
	Differential responses of cecal microbiota to fishmeal, Eimeria and Clostridium perfringens in a necrotic enteritis challenge model in chickens.	Stanley D, Wu SB, Rodgers N, Swick RA, Moore RJ.	PLoS One	10.1371/journal.pone.0104739	2014
Genetics	Metagenomic analysis of mother-infant gut microbiome reveals global distinct and shared microbial signatures.	Wang S, Zeng S, Egan M, Cherry P, Strain C, Morais E, Boyaval P, Ryan CA, M Dempsey E, Ross RP, Stanton C.	Gut Microbes	10.1080/19490976.2021.1911571	2021
	Molecular and evolutionary analysis of NEAr-iron Transporter (NEAT) domains.	Honsa ES, Maresso AW, Highlander SK.	PLoS One	10.1371/journal.pone.0104794	2014
Pathogenicity	Ganoderma lucidum reduces obesity in mice by modulating the composition of the gut microbiota.	Chang CJ, Lin CS, Lu CC, Martel J, Ko YF, Ojcius DM, Tseng SF, Wu TR, Chen YY, Young JD, Lai HC.	Nat Commun	10.1038/ncomms8489	2015
Genetics	Genomic and functional analyses of Rhodococcus equi phages ReqiPepy6, ReqiPoco6, ReqiPine5, and ReqiDocB7.	Summer EJ, Liu M, Gill JJ, Grant M, Chan-Cortes TN, Ferguson L, Janes C, Lange K, Bertoli M, Moore C, Orchard RC, Cohen ND, Young R.	Appl Environ Microbiol	10.1128/aem.01952-10	2011
Metabolism	ABC transporters involved in export of cell surface glycoconjugates.	Cuthbertson L, Kos V, Whitfield C.	Microbiol Mol Biol Rev	10.1128/mmbr.00009-10	2010
Phylogeny	Harryflintia acetispora gen. nov., sp. nov., isolated from chicken caecum.	Petzoldt D, Breves G, Rautenschlein S, Taras D.	Int J Syst Evol Microbiol	10.1099/ijsem.0.001317	2016
Genetics	Massilioclostridium coli gen. nov., sp. nov., a new member of the Clostridiaceae family isolated from the left colon of a 27-year-old woman.	Lo CI, Mailhe M, Ricaboni D, Vitton V, Benezech A, Michelle C, Armstrong N, Bittar F, Fournier PE, Raoult D, Lagier JC.	New Microbes New Infect	10.1016/j.nmni.2017.01.004	2017
Phylogeny	Paludicola psychrotolerans gen. nov., sp. nov., a novel psychrotolerant chitinolytic anaerobe of the family Ruminococcaceae.	Li Y, Zhang LL, Liu L, Tian YQ, Liu XF, Li WJ, Dai YM	Int J Syst Evol Microbiol	10.1099/ijsem.0.002260	2017
Metabolism	Clostridium methylpentosum sp. nov.: a ring-shaped intestinal bacterium that ferments only methylpentoses and pentoses.	Himelbloom BH, Canale-Parola E	Arch Microbiol	10.1007/BF00406553	1989

References

#2178	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5476
#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 )
#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 .
#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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Clostridium methylpentosum (DSM 5476, ATCC 43829, R2)

Name and taxonomic classification

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