Holdemanella biformis (DSM 3989, ATCC 27806, KCTC 5969)

Name: Holdemanella biformis (DSM 3989, ATCC 27806, KCTC 5969)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5417

Type strain

Culture col. no. DSM 3989 ATCC 27806 KCTC 5969 CCUG 28091 VPI C17-5 1 more

NCBI tax ID(s) 518637 1735

Special Collections DSMZ CCUG JCM KCTC

Links

Holdemanella biformis DSM 3989 is an anaerobe, mesophilic, coccus-shaped prokaryote that was isolated from human faeces.

coccus-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 39186

KCTC 5969,ATCC 27806,CCUG 28091,DSM 3989

@ref 20215

Last LPSN update 2025-12-16 09:48:04

Domain Bacillati

Phylum Bacillota

Class Erysipelotrichia

Order Erysipelotrichales

Family Erysipelotrichaceae

Genus Holdemanella

Species Holdemanella biformis

Full scientific name Holdemanella biformis (Eggerth 1935) De Maesschalck et al. 2014

Synonyms (2)

"Bacteroides biformis"
Eubacterium biforme

Morphology

Cell morphology

@ref	Cell shape	Motility
67771	coccus-shaped
67771
125438

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1559	CHOPPED MEAT MEDIUM (DSMZ Medium 78)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78; with strain-specific modifications) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) Yeast extract 5.0 g/l K2HPO4 5.0 g/l Tween 80 1.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
1559	positive	growth	37	mesophilic
49093	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic
67771	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
1559	anaerobe
49093	anaerobe
67771	anaerobe
125439	facultative anaerobe

Spore formation

67771

Spore formationno

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	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	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	alpha-glucosidase	-	3.2.1.20	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	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine 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	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

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	ribulose monophosphate pathway	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	L-lactaldehyde degradation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	teichoic acid biosynthesis	100	1 of 1
66794	butanoate fermentation	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	glycogen biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	peptidoglycan biosynthesis	93.33	14 of 15
66794	vitamin B1 metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
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	flavin biosynthesis	80	12 of 15
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	palmitate biosynthesis	77.27	17 of 22
66794	acetate fermentation	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	ppGpp biosynthesis	75	3 of 4
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	photosynthesis	71.43	10 of 14
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	purine metabolism	71.28	67 of 94
66794	glycolysis	70.59	12 of 17
66794	phenylalanine metabolism	69.23	9 of 13
66794	alanine metabolism	68.97	20 of 29
66794	methane metabolism	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	pyrimidine metabolism	64.44	29 of 45
66794	pentose phosphate pathway	63.64	7 of 11
66794	gluconeogenesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	oxidative phosphorylation	60.44	55 of 91
66794	glycogen metabolism	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	factor 420 biosynthesis	60	3 of 5
66794	Entner Doudoroff pathway	60	6 of 10
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	histidine metabolism	55.17	16 of 29
66794	metabolism of disaccharids	54.55	6 of 11
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	selenocysteine biosynthesis	50	3 of 6
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	methionine metabolism	50	13 of 26
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	lactate fermentation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	ethanol fermentation	50	1 of 2
66794	CMP-KDO biosynthesis	50	2 of 4
66794	non-pathway related	47.37	18 of 38
66794	vitamin B6 metabolism	45.45	5 of 11
66794	CO2 fixation in Crenarchaeota	44.44	4 of 9
66794	lipid A biosynthesis	44.44	4 of 9
66794	valine metabolism	44.44	4 of 9
66794	cysteine metabolism	44.44	8 of 18
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	tyrosine metabolism	42.86	6 of 14
66794	glutathione metabolism	42.86	6 of 14
66794	isoprenoid biosynthesis	42.31	11 of 26
66794	tryptophan metabolism	42.11	16 of 38
66794	methylglyoxal degradation	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	degradation of hexoses	38.89	7 of 18
66794	lipid metabolism	38.71	12 of 31
66794	leucine metabolism	38.46	5 of 13
66794	isoleucine metabolism	37.5	3 of 8
66794	ketogluconate metabolism	37.5	3 of 8
66794	d-xylose degradation	36.36	4 of 11
66794	tetrahydrofolate metabolism	35.71	5 of 14
66794	lysine metabolism	35.71	15 of 42
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	degradation of pentoses	32.14	9 of 28
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	sulfate reduction	30.77	4 of 13
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	glycine metabolism	30	3 of 10
66794	coenzyme M biosynthesis	30	3 of 10
66794	reductive acetyl coenzyme A pathway	28.57	2 of 7
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	ascorbate metabolism	27.27	6 of 22
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	proline metabolism	27.27	3 of 11
66794	carnitine metabolism	25	2 of 8
66794	catecholamine biosynthesis	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	nitrate assimilation	22.22	2 of 9
66794	arginine metabolism	20.83	5 of 24

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
1559	-	-	-	+/-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	+/-	-	-	-	-	-	-
1559	-	-	-	+	-	-	+/-	-	-	-	-	-	+	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Host	#Human
#Host Body Product	#Gastrointestinal tract

Isolation

@ref	Sample type
1559	human faeces
49093	Human feces
67770	Human feces
67771	From human faeces.

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1559	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
67770	ASM15665v1 assembly for Holdemanella biformis DSM 3989	scaffold	GCA_000156655	518637.5	642979360	518637	41.11

Genome browser: GCA_000156655

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
1559	[Eubacterium] biforme DSM 3989 16S ribosomal RNA gene, partial sequence	M59230	1487		518637

GC content

@ref	GC-content (mol%)	Method
1559	32	thermal denaturation, midpoint method (Tm)
67770	33.8
67771	32.0	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Holdemanella biformis DSM 3989
NCBI: GCA_000156655

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	75.00	no
125439	motility	BacteriaNetⓘ	no	50.90	no
125439	gram_stain	BacteriaNetⓘ	positive	80.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	97.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Eubacterium biforme DSM 3989
PATRIC: 518637.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	81.45	yes
125438	anaerobic	anaerobicⓘ	yes	85.25	yes
125438	spore-forming	spore-formingⓘ	no	73.59	no
125438	aerobic	aerobicⓘ	no	97.98	yes
125438	thermophilic	thermophileⓘ	no	95.49	yes
125438	flagellated	motile2+ⓘ	no	92.97	yes

Literature

Title	Authors	Journal	DOI	Year
Coarse-grained model of serial dilution dynamics in synthetic human gut microbiome.	Mahajan T, Maslov S.	PLoS Comput Biol	10.1371/journal.pcbi.1013222	2025
The microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids.	Mannochio-Russo H, Charron-Lamoureux V, van Faassen M, Lamichhane S, Goncalves Nunes WD, Deleray V, Ayala AV, Tanaka Y, Patan A, Vittali K, Rajkumar P, El Abiead Y, Zhao HN, Gomes PWP, Mohanty I, Lee C, Sund A, Sharma M, Liu Y, Pattynama D, Walker GT, Norton GJ, Khatib L, Andalibi MS, Wang CX, Ellis RJ, Moore DJ, Iudicello JE, Franklin D, Letendre S, Chin L, Walker C, Renwick S, Zemlin J, Meehan MJ, Song X, Kasper D, Burcham Z, Kim JJ, Kadakia S, Raffatellu M, Bode L, Chu H, Zengler K, Wang M, Siegel D, Knight R, Dorrestein PC.	Cell	10.1016/j.cell.2025.05.015	2025
An oxidation resistant pediocin PA-1 derivative and penocin A display effective anti-Listeria activity in a model human gut environment.	Kuniyoshi TM, O'Connor PM, Lawton E, Thapa D, Mesa-Pereira B, Abulu S, Hill C, Ross RP, Oliveira RPS, Cotter PD.	Gut Microbes	10.1080/19490976.2021.2004071	2022
The Impact of Producing Type and Dietary Crude Protein on Animal Performances and Microbiota Together with Greenhouse Gases Emissions in Growing Pigs.	Seradj AR, Balcells J, Sarri L, Fraile LJ, de la Fuente Oliver G.	Animals (Basel)	10.3390/ani10101742	2020
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
Intestinal microbial communities and Holdemanella isolated from HIV+/- men who have sex with men increase frequencies of lamina propria CCR5⁺ CD4⁺ T cells.	Yamada E, Martin CG, Moreno-Huizar N, Fouquier J, Neff CP, Coleman SL, Schneider JM, Huber J, Nusbacher NM, McCarter M, Campbell TB, Lozupone CA, Palmer BE.	Gut Microbes	10.1080/19490976.2021.1997292	2021
Single-strain behavior predicts responses to environmental pH and osmolality in the gut microbiota.	Ng KM, Pannu S, Liu S, Burckhardt JC, Hughes T, Van Treuren W, Nguyen J, Naqvi K, Nguyen B, Clayton CA, Pepin DM, Collins SR, Tropini C.	mBio	10.1128/mbio.00753-23	2023
Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model.	Cuisiniere T, Hajjar R, Oliero M, Calve A, Fragoso G, Rendos HV, Gerkins C, Taleb N, Gagnon-Konamna M, Dagbert F, Loungnarath R, Sebajang H, Schwenter F, Wassef R, Ratelle R, De Broux E, Richard C, Santos MM.	Microbiome	10.1186/s40168-025-02101-1	2025
Clostridium butyricum-altered lung microbiome is associated with enhanced anti-influenza effects via G-protein-coupled receptor120.	Hagihara M, Yamashita M, Ariyoshi T, Minemura A, Yoshida C, Higashi S, Oka K, Takahashi M, Ota A, Maenaka A, Iwasaki K, Hirai J, Shibata Y, Umemura T, Mori T, Kato H, Asai N, Mikamo H.	iScience	10.1016/j.isci.2025.113502	2025
Genome sequence and description of Traorella massiliensis gen. nov., sp. nov., a new bacterial genus isolated from human left colon.	Bonnet M, Mailhe M, Ricaboni D, Labas N, Richez M, Vitton V, Benezech A, Fournier PE, Million M, Raoult D, Khelaifia S.	New Microbes New Infect	10.1016/j.nmni.2019.100520	2019
Absicoccus porci gen. nov., sp. nov., a member of the family Erysipelotrichaceae isolated from pig faeces.	Shin Y, Paek J, Kim H, Kook JK, Kim JS, Kim SH, Chang YH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003803	2020
Faecalibaculum rodentium gen. nov., sp. nov., isolated from the faeces of a laboratory mouse.	Chang DH, Rhee MS, Ahn S, Bang BH, Oh JE, Lee HK, Kim BC	Antonie Van Leeuwenhoek	10.1007/s10482-015-0583-3	2015
Faecalicoccus acidiformans gen. nov., sp. nov., isolated from the chicken caecum, and reclassification of Streptococcus pleomorphus (Barnes et al. 1977), Eubacterium biforme (Eggerth 1935) and Eubacterium cylindroides (Cato et al. 1974) as Faecalicoccus pleomorphus comb. nov., Holdemanella biformis gen. nov., comb. nov. and Faecalitalea cylindroides gen. nov., comb. nov., respectively, within the family Erysipelotrichaceae.	De Maesschalck C, Van Immerseel F, Eeckhaut V, De Baere S, Cnockaert M, Croubels S, Haesebrouck F, Ducatelle R, Vandamme P	Int J Syst Evol Microbiol	10.1099/ijs.0.064626-0	2014

References

#1559	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3989
#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 )
#49093	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 28091
#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;
#68380	Automatically annotated from API rID32A .
#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 )

Rate our new design

Content

About us

Holdemanella biformis (DSM 3989, ATCC 27806, KCTC 5969)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000156655

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media