Agathobacter rectalis (DSM 17629, NCIMB 14373, A1-86)

Name: Agathobacter rectalis (DSM 17629, NCIMB 14373, A1-86)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5441

Type strain

Strain Designation A1-86

Culture col. no. DSM 17629 NCIMB 14373 A1-86

NCBI tax ID(s) 657318 39491

Special Collections DSMZ

History DSMZ <- S. Duncan; A1-86

Links

Agathobacter rectalis A1-86 is an anaerobe bacterium that was isolated from faecal sample, adult female.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 397561

NCIMB 14373,DSM 17629

@ref 20215

Last LPSN update 2026-05-29 08:26:10

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Lachnospiraceae

Genus Agathobacter

Species Agathobacter rectalis

Full scientific name Agathobacter rectalis (Hauduroy et al. 1937) Rosero et al. 2016

Synonyms (2)

Eubacterium rectale
"Bacteroides rectalis"

BacDive ID	Other strains from **Agathobacter rectalis** (2)	Type strain
162023	A. rectalis JCM 17463, ATCC 33656, CIP 105953, DSM 3377, ... (type strain)
164025	A. rectalis JCM 31336

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7093	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

@ref	Growth	Type	Temperature (°C)
7093	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
7093	anaerobe
125438	anaerobe	93.804
125439	anaerobe	98.936

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

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
68380	alanine arylamidase	-	3.4.11.2	from API rID32A
68380	alkaline phosphatase	-	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	+	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
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
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

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
7093	-	-	+	+	-	+	+/-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
7093	-	-	+	+	-	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
7093	-	-	+	+/-	-	+/-	-	+	-	-	-	-	-	-	not determinedn.d.	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-
7093	-	-	+	+	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-
7093	-	-	+	+	-	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7093	faecal sample, adult female	Aberdeen, Scotland	United Kingdom	GBR	Europe

Taxonmaps

69479

Global distribution of 16S sequence AJ270475 (>99% sequence identity) for [Eubacterium] rectale subclade from Microbeatlas

Aquatic Samples	1562
Soil Samples	291
Animal Samples	68496
Plant Samples	68
Total Samples	70417

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7093	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	Eubacterium rectale DSM 17629	complete		657318.4		657318	96.6
66792	ASM20993v1 assembly for Agathobacter rectalis DSM 17629	chromosome	GCA_000209935	657318.12	650377936	657318	67.72

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7093	Butyrate-producing bacterium A1-86 16S rRNA gene	AJ270475	1506		105829

GC content

7093

GC-content (mol%)41.2

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM20993v1 assembly for Agathobacter rectalis DSM 17629
BV-BRC: 657318.12

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	98.94	no
125439	gram_stain	BacteriaNetⓘ	variable	59.40	no
125439	motility	BacteriaNetⓘ	yes	54.72	no
125439	spore_formation	BacteriaNetⓘ	yes	46.88	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Eubacterium rectale DSM 17629
PATRIC: 657318.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	73.10	no
125438	anaerobic	anaerobicⓘ	yes	93.80	yes
125438	spore-forming	spore-formingⓘ	no	57.79	no
125438	aerobic	aerobicⓘ	no	95.72	yes
125438	thermophilic	thermophileⓘ	no	92.51	yes
125438	flagellated	motile2+ⓘ	yes	74.11	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Soy sauce-like seasoning enhances the growth of Agathobacter rectalis and the production of butyrate, propionate, and lactate.	Hayashi K, Uchida R, Horiba T, Kawaguchi T, Gomi K, Goto Y.	Biosci Microbiota Food Health	10.12938/bmfh.2023-103	2024
Metabolism	Sulfoglycolysis sustains Eubacterium rectale in low-fiber diets.	Sharma M, Pudlo N, Jarva MA, Kaur A, John A, Burchill L, Lingford JP, Epa R, Abayakoon P, Scott NE, Turkenburg JP, Davies GJ, Martens EC, Goddard-Borger ED, Williams SJ.	J Biol Chem	10.1016/j.jbc.2025.108320	2025
	A Gnotobiotic Mouse Model with Divergent Equol-Producing Phenotypes: Potential for Determining Microbial-Driven Health Impacts of Soy Isoflavone Daidzein.	Leonard LM, Simpson AMR, Li S, Reddivari L, Cross TL.	Nutrients	10.3390/nu16071079	2024
	A metagenome-level analysis of a microbial community fermenting ultra-filtered milk permeate.	Walters KA, Mohan G, Myers KS, Ingle AT, Donohue TJ, Noguera DR.	Front Bioeng Biotechnol	10.3389/fbioe.2023.1173656	2023
	Sulfoquinovose is a select nutrient of prominent bacteria and a source of hydrogen sulfide in the human gut.	Hanson BT, Dimitri Kits K, Loffler J, Burrichter AG, Fiedler A, Denger K, Frommeyer B, Herbold CW, Rattei T, Karcher N, Segata N, Schleheck D, Loy A.	ISME J	10.1038/s41396-021-00968-0	2021
	Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties.	Shetty SA, Kostopoulos I, Geerlings SY, Smidt H, de Vos WM, Belzer C.	ISME J	10.1038/s41396-022-01255-2	2022
	Sialidases and fucosidases of Akkermansia muciniphila are crucial for growth on mucin and nutrient sharing with mucus-associated gut bacteria.	Shuoker B, Pichler MJ, Jin C, Sakanaka H, Wu H, Gascuena AM, Liu J, Nielsen TS, Holgersson J, Nordberg Karlsson E, Juge N, Meier S, Morth JP, Karlsson NG, Abou Hachem M.	Nat Commun	10.1038/s41467-023-37533-6	2023
	Inter-species Metabolic Interactions in an In-vitro Minimal Human Gut Microbiome of Core Bacteria.	Shetty SA, Kuipers B, Atashgahi S, Aalvink S, Smidt H, de Vos WM.	NPJ Biofilms Microbiomes	10.1038/s41522-022-00275-2	2022
Enzymology	Degradation of the low-calorie sugar substitute 5-ketofructose by different bacteria.	Schiessl J, Kosciow K, Garschagen LS, Hoffmann JJ, Heymuth J, Franke T, Deppenmeier U.	Appl Microbiol Biotechnol	10.1007/s00253-021-11168-3	2021
Metabolism	Molecular Evolution of the Oxygen-Binding Hemerythrin Domain.	Alvarez-Carreno C, Becerra A, Lazcano A.	PLoS One	10.1371/journal.pone.0157904	2016
Phylogeny	Opinions 100, 101 and 102.	Arahal DR	Int J Syst Evol Microbiol	10.1099/ijsem.0.004390	2020
Metabolism	Molecular details of a starch utilization pathway in the human gut symbiont Eubacterium rectale.	Cockburn DW, Orlovsky NI, Foley MH, Kwiatkowski KJ, Bahr CM, Maynard M, Demeler B, Koropatkin NM	Mol Microbiol	10.1111/mmi.12859	2014
Metabolism	Fermentation RS3 derived from sago and rice starch with Clostridium butyricum BCC B2571 or Eubacterium rectale DSM 17629.	Purwani EY, Purwadaria T, Suhartono MT	Anaerobe	10.1016/j.anaerobe.2011.09.007	2011
Phylogeny	Proposal of a neotype strain (A1-86) for Eubacterium rectale. Request for an opinion.	Duncan SH, Flint HJ	Int J Syst Evol Microbiol	10.1099/ijs.0.2008/004580-0	2008

References

#7093	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17629
#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) .
#68380	Automatically annotated from API rID32A .
#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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Agathobacter rectalis (DSM 17629, NCIMB 14373, A1-86)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000209935

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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