Name: Agathobaculum butyriciproducens SR79
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 132618

Type strain:

Species: Agathobaculum butyriciproducens

Strain Designation: SR79

Culture col. no.: DSM 100391, KCTC 15532, JCM 30795

Strain history: <- BC Kim, KRIBB

NCBI tax ID(s): 1628085 (species)

SI-ID 397368

DSM 100391

Special Collections

Section

When using BacDive for research please cite our paper

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Oscillospiraceae*
	Genus	*Agathobaculum*
	Species	**Agathobaculum butyriciproducens**
	Full Scientific Name (LPSN)	Agathobaculum butyriciproducens Ahn et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43140]	Gram stain	positive
[Ref.: #67771]	Gram stain	positive

[Ref.: #43140]	Cell length	0.9-1.1 µm

[Ref.: #43140]	Cell width	0.6-0.7 µm

[Ref.: #43140]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #43140]	Motility	no
[Ref.: #67771]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24407]

Culture medium

PY + X MEDIUM (N2/CO2) (DSMZ Medium 104c)

[Ref.: #24407]

Culture medium growth

[Ref.: #24407]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24407]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #24407]	growth	37 °C
[Ref.: #43140]	optimum	37 °C
[Ref.: #43140]	growth	30-40 °C
[Ref.: #67770]	growth	37 °C
[Ref.: #67771]	growth	37 °C

	pH	Kind of pH		pH
[Ref.: #43140]			optimum	7
[Ref.: #43140]			growth	6-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43140]	Oxygen tolerance	obligate anaerobe
[Ref.: #67771]	Oxygen tolerance	anaerobe

[Ref.: #43140]	Type of spore	spore
[Ref.: #43140]	Ability of spore formation	no
[Ref.: #67771]	Ability of spore formation	no

[Ref.: #24407]

Name of produced compound

butyrate

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43140]		NaCl		maximum	1	%(w/v)
[Ref.: #43140]		NaCl		optimum	0.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43140]	cellobiose ChEBI	+	builds acid from
[Ref.: #43140]	D-arabinose ChEBI	+	builds acid from
[Ref.: #43140]	D-glucose ChEBI	+	builds acid from
[Ref.: #43140]	D-mannitol ChEBI	+	builds acid from
[Ref.: #43140]	D-mannose ChEBI	+	builds acid from
[Ref.: #43140]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #43140]	D-trehalose ChEBI	+	builds acid from
[Ref.: #43140]	D-xylose ChEBI	+	builds acid from
[Ref.: #43140]	esculin ferric citrate	+	hydrolysis
[Ref.: #43140]	gelatin ChEBI	-	hydrolysis
[Ref.: #43140]	glycerol ChEBI	-	builds acid from
[Ref.: #43140]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #43140]	L-tryptophan ChEBI	-	assimilation
[Ref.: #43140]	lactose ChEBI	+	builds acid from
[Ref.: #43140]	maltose ChEBI	+	builds acid from
[Ref.: #43140]	melezitose ChEBI	+	builds acid from
[Ref.: #43140]	raffinose ChEBI	-	builds acid from
[Ref.: #43140]	salicin ChEBI	+	builds acid from
[Ref.: #43140]	sucrose ChEBI	+	builds acid from
[Ref.: #43140]	urea ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #43140]	acetate ChEBI	yes
[Ref.: #43140]	butanol ChEBI	yes
[Ref.: #43140]	butyrate ChEBI	yes
[Ref.: #43140]	ethanol ChEBI	yes

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43140]

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

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	CO2 fixation in Crenarchaeota	100	9 of 9
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	vitamin B1 metabolism	92.31	12 of 13
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	vitamin B12 metabolism	79.41	27 of 34
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	C4 and CAM-carbon fixation	75	6 of 8
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	myo-inositol biosynthesis	70	7 of 10
[Ref.: #66794]	degradation of sugar alcohols	68.75	11 of 16
[Ref.: #66794]	purine metabolism	67.02	63 of 94
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	tetrahydrofolate metabolism	64.29	9 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	NAD metabolism	61.11	11 of 18
[Ref.: #66794]	oxidative phosphorylation	60.44	55 of 91
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	pyrimidine metabolism	60	27 of 45
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	histidine metabolism	55.17	16 of 29
[Ref.: #66794]	polyamine pathway	52.17	12 of 23
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	methionine metabolism	50	13 of 26
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	gluconeogenesis	50	4 of 8
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	non-pathway related	44.74	17 of 38
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	heme metabolism	42.86	6 of 14
[Ref.: #66794]	lipid metabolism	41.94	13 of 31
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	lysine metabolism	40.48	17 of 42
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	Entner Doudoroff pathway	40	4 of 10
[Ref.: #66794]	degradation of pentoses	39.29	11 of 28
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	glycine metabolism	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	pentose phosphate pathway	27.27	3 of 11
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
[Ref.: #66794]	glutathione metabolism	21.43	3 of 14
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #24407]	Sample type/isolated from	human faeces of a 23-years-old healthy Korean woman
[Ref.: #24407]	Country	Republic of Korea
[Ref.: #24407]	Country ISO 3 Code	KOR
[Ref.: #24407]	Continent	Asia

[Ref.: #43140]	Sample type/isolated from	human faeces samples of a 23-years-old healthy Korean woman

[Ref.: #67770]	Sample type/isolated from	Faeces of a healthy 23-year-old Korean female

[Ref.: #67771]	Sample type/isolated from	From human faeces of a 23-years-old healthy Korean woman
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #24407]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #24407]	Agathobaculum butyriciproducens strain SR79 16S ribosomal RNA gene, partial sequence	KP889099	1383	GenBank ENA	1628085 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Agathobaculum butyriciproducens strain DSM 100391	1628085.3	wgs	PATRIC	1628085 tax ID	*
[Ref.: #66792]	Agathobaculum butyriciproducens DSM 100391	2756170243	draft	JGI IMG/M	1628085 tax ID	*

[Ref.: #24407]	GC-content	52.9 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67771]	GC-content	52.9 mol%

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	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.: #125438]	gram-positive	gram-positiveⓘ	yes	72.424	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	yes	86.672	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	63.397	yes
[Ref.: #125438]	aerobic	aerobicⓘ	no	96.768	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	89.725	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	83.753	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Agathobaculum butyriciproducens DSM 100391 IMG: 2756170243
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	63.6
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	68.1
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	variable	67.4
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	aerobe	83.1

Availability in culture collections External links

[Ref.: #24407]

Culture collection no.

DSM 100391, KCTC 15532, JCM 30795

[Ref.: #90932]

SI-ID 397368

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 )

#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 )

#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 .

#90932

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID397368.1 )

#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 .

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Agathobaculum butyriciproducens in external resources:
SILVA
BRENDA
PANGAEA
GBIF

Agathobaculum butyriciproducens strain DSM 100391

Agathobaculum butyriciproducens DSM 100391

Change proposal

Change proposal