Agathobaculum butyriciproducens (DSM 100391, KCTC 15532, SR79)

Name: Agathobaculum butyriciproducens (DSM 100391, KCTC 15532, SR79)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132618

Type strain

Strain Designation SR79

Culture col. no. DSM 100391 KCTC 15532 SR79 JCM 30795

NCBI tax ID(s) 1628085

Special Collections DSMZ JCM KCTC Literature strains

History <- S. Ahn, KCTC, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea; SR79 <- S. Ahn {2014} B.-C. Kim; KCTC, South Korea; SR79. <- BC Kim, KRIBB

Links

Agathobaculum butyriciproducens SR79 is an obligate anaerobe, Gram-positive, rod-shaped bacterium that was isolated from human faeces of a 23-years-old healthy Korean woman.

Gram-positive rod-shaped obligate anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 397368

KCTC 15532,DSM 100391

@ref 20215

Last LPSN update 2026-02-09 11:31:45

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Oscillospiraceae

Genus Agathobaculum

Species Agathobaculum butyriciproducens

Full scientific name Agathobaculum butyriciproducens Ahn et al. 2016

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
43140	positive	0.9-1.1 µm	0.6-0.7 µm	rod-shaped
67771				rod-shaped
67771	positive

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24407	PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c)		Medium recipe at MediaDive	Name: PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c) Composition: Yeast extract 10.0 g/l D-Glucose 5.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l Na2CO3 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Sodium resazurin 0.0005 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
24407	positive	growth	37
43140	positive	optimum	37
43140	positive	growth	30-40
67770	positive	growth	37
67771	positive	growth	37

Culture pH

@ref	Ability	Type	PH
43140	positive	optimum	7
43140	positive	growth	6-8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
43140	obligate anaerobe
67771	anaerobe

Spore formation

@ref	Type of spore	Spore formation
43140	spore
67771

Compound production

24407

Compoundbutyrate

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43140	NaCl	positive	maximum	1 %(w/v)
43140	NaCl	positive	optimum	0.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43140	17057 ChEBI	cellobiose	+	builds acid from
43140	17108 ChEBI	D-arabinose	+	builds acid from
43140	17634 ChEBI	D-glucose	+	builds acid from
43140	16899 ChEBI	D-mannitol	+	builds acid from
43140	16024 ChEBI	D-mannose	+	builds acid from
43140	17924 ChEBI	D-sorbitol	-	builds acid from
43140	16551 ChEBI	D-trehalose	+	builds acid from
43140	65327 ChEBI	D-xylose	+	builds acid from
43140		esculin ferric citrate	+	hydrolysis
43140	5291 ChEBI	gelatin	-	hydrolysis
43140	17754 ChEBI	glycerol	-	builds acid from
43140	62345 ChEBI	L-rhamnose	+	builds acid from
43140	16828 ChEBI	L-tryptophan	-	assimilation
43140	17716 ChEBI	lactose	+	builds acid from
43140	17306 ChEBI	maltose	+	builds acid from
43140	6731 ChEBI	melezitose	+	builds acid from
43140	16634 ChEBI	raffinose	-	builds acid from
43140	17814 ChEBI	salicin	+	builds acid from
43140	17992 ChEBI	sucrose	+	builds acid from
43140	16199 ChEBI	urea	-	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite
43140	30089 ChEBI	acetate
43140	28885 ChEBI	butanol
43140	17968 ChEBI	butyrate
43140	16236 ChEBI	ethanol

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	CO2 fixation in Crenarchaeota	100	9 of 9
66794	adipate degradation	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	palmitate biosynthesis	100	22 of 22
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	vitamin B1 metabolism	92.31	12 of 13
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	flavin biosynthesis	80	12 of 15
66794	glycine betaine biosynthesis	80	4 of 5
66794	starch degradation	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	vitamin B12 metabolism	79.41	27 of 34
66794	serine metabolism	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	phenylalanine metabolism	76.92	10 of 13
66794	glycogen biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	ppGpp biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	photosynthesis	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	myo-inositol biosynthesis	70	7 of 10
66794	degradation of sugar alcohols	68.75	11 of 16
66794	purine metabolism	67.02	63 of 94
66794	acetoin degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	molybdenum cofactor biosynthesis	66.67	6 of 9
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	glutamate and glutamine metabolism	64.29	18 of 28
66794	isoleucine metabolism	62.5	5 of 8
66794	alanine metabolism	62.07	18 of 29
66794	NAD metabolism	61.11	11 of 18
66794	oxidative phosphorylation	60.44	55 of 91
66794	propionate fermentation	60	6 of 10
66794	pyrimidine metabolism	60	27 of 45
66794	glycogen metabolism	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	citric acid cycle	57.14	8 of 14
66794	d-mannose degradation	55.56	5 of 9
66794	tryptophan metabolism	55.26	21 of 38
66794	histidine metabolism	55.17	16 of 29
66794	polyamine pathway	52.17	12 of 23
66794	kanosamine biosynthesis II	50	1 of 2
66794	methionine metabolism	50	13 of 26
66794	pantothenate biosynthesis	50	3 of 6
66794	cysteine metabolism	50	9 of 18
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	phenylmercury acetate degradation	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	gluconeogenesis	50	4 of 8
66794	quinate degradation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	leucine metabolism	46.15	6 of 13
66794	isoprenoid biosynthesis	46.15	12 of 26
66794	urea cycle	46.15	6 of 13
66794	arginine metabolism	45.83	11 of 24
66794	vitamin B6 metabolism	45.45	5 of 11
66794	proline metabolism	45.45	5 of 11
66794	non-pathway related	44.74	17 of 38
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	tyrosine metabolism	42.86	6 of 14
66794	heme metabolism	42.86	6 of 14
66794	lipid metabolism	41.94	13 of 31
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	lysine metabolism	40.48	17 of 42
66794	factor 420 biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	Entner Doudoroff pathway	40	4 of 10
66794	degradation of pentoses	39.29	11 of 28
66794	sulfate reduction	38.46	5 of 13
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	metabolism of disaccharids	36.36	4 of 11
66794	lipid A biosynthesis	33.33	3 of 9
66794	cyanate degradation	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	nitrate assimilation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	glycine metabolism	30	3 of 10
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	pentose phosphate pathway	27.27	3 of 11
66794	d-xylose degradation	27.27	3 of 11
66794	biotin biosynthesis	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	alginate biosynthesis	25	1 of 4
66794	ascorbate metabolism	22.73	5 of 22
66794	glutathione metabolism	21.43	3 of 14

Fatty acid profile

Metadata FA analysis

@ref

43140

Fatty acid	Percentage
C16:0	21.6
cis9-C18:1	14.1
cyc9,10-C19:1	14
C14:0	11.8

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
24407	human faeces of a 23-years-old healthy Korean woman	Republic of Korea	KOR	Asia
43140	human faeces samples of a 23-years-old healthy Korean woman
67770	Faeces of a healthy 23-year-old Korean female
67771	From human faeces of a 23-years-old healthy Korean woman	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence KP889099 (>99% sequence identity) for Eubacteriales from Microbeatlas

Aquatic Samples	757
Soil Samples	133
Animal Samples	56625
Plant Samples	65
Total Samples	57580

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24407	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM309653v1 assembly for Agathobaculum butyriciproducens DSM 100391	scaffold	GCA_003096535	1628085.3	2756170243	1628085	66.38

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24407	Agathobaculum butyriciproducens strain SR79 16S ribosomal RNA gene, partial sequence	KP889099	1383		1628085

GC content

@ref	GC-content (mol%)	Method
24407	52.9	high performance liquid chromatography (HPLC)
67771	52.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Agathobaculum butyriciproducens DSM 100391
IMG: 2756170243

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	63.60	no
125439	motility	BacteriaNetⓘ	yes	68.10	no
125439	gram_stain	BacteriaNetⓘ	variable	67.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	83.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Agathobaculum butyriciproducens strain DSM 100391
PATRIC: 1628085.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	72.42	yes
125438	anaerobic	anaerobicⓘ	yes	86.67	yes
125438	spore-forming	spore-formingⓘ	no	63.40	yes
125438	aerobic	aerobicⓘ	no	96.77	yes
125438	thermophilic	thermophileⓘ	no	89.73	yes
125438	flagellated	motile2+ⓘ	no	83.75	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Agathobaculum butyriciproducens gen. nov. sp. nov., a strict anaerobic, butyrate-producing gut bacterium isolated from human faeces and reclassification of Eubacterium desmolans as Agathobaculum desmolans comb. nov.	Ahn S, Jin TE, Chang DH, Rhee MS, Kim HJ, Lee SJ, Park DS, Kim BC	Int J Syst Evol Microbiol	10.1099/ijsem.0.001195	2016

References

#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 )
#24407	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100391
#43140	Sharon Ahn, Tae-Eun Jin, Dong-Ho Chang, Moon-Soo Rhee, Hyun Ju Kim, Sang Jun Lee, Doo-Sang Park and Byoung-Chan Kim: Agathobaculum butyriciproducens gen. nov. sp. nov., a strict anaerobic, butyrate-producing gut bacterium isolated from human faeces and reclassification of Eubacterium desmolans as Agathobaculum desmolans comb. nov.. IJSEM 66: 3656 - 3661 2016 ( DOI 10.1099/ijsem.0.001195 , PubMed 27334534 )
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Agathobaculum butyriciproducens (DSM 100391, KCTC 15532, SR79)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Halophily

Metabolite utilization

Metabolite production

Pathway annotation

Fatty acid profile

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003096535

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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