Amedibacillus dolichus (DSM 3991, ATCC 29143, VPI C9-20)

Name: Amedibacillus dolichus (DSM 3991, ATCC 29143, VPI C9-20)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5424

Type strain

Culture col. no. DSM 3991 ATCC 29143 VPI C9-20 JCM 10413

NCBI tax ID(s) 428127 31971

Special Collections DSMZ JCM

History DSMZ <- ATCC <- L.V. Holdeman, VPI C9-20 JCM <-- DSM 3991 <-- ATCC 29143 <-- L. Holdeman VPI C9-20.

Links

Amedibacillus dolichus DSM 3991 is an anaerobe bacterium that was isolated from human faeces.

anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 39376

ATCC 29143,DSM 3991,JCM 10413

@ref 20215

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

Domain Bacteria

Phylum Bacillota

Class Erysipelotrichia

Order Erysipelotrichales

Family Erysipelotrichaceae

Genus Amedibacillus

Species Amedibacillus dolichus

Full scientific name Amedibacillus dolichus (Moore et al. 1976) Ikeyama et al. 2020

Synonyms (2)

Eubacterium dolichum
"Absiella dolichum"

Morphology

Cell morphology

@ref	Motility	Confidence
125438		90.562

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1561	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)
1561	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
1561	anaerobe
125439	anaerobe	98.635

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	alpha-glucosidase	-	3.2.1.20	from API rID32A
68380	arginine dihydrolase	+	3.5.3.6	from API rID32A
68380	beta-galactosidase	-	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	-	3.2.1.21	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
1561	-	+	-	-	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Host species
1561	human faeces	Homo sapiens
67770	Human feces	Homo sapiens

Taxonmaps

69479

Global distribution of 16S sequence L34682 (>99% sequence identity) for Amedibacillus dolichus subclade from Microbeatlas

Aquatic Samples	861
Soil Samples	239
Animal Samples	41686
Plant Samples	118
Total Samples	42904

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1561	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	ASM15428v1 assembly for Amedibacillus dolichus DSM 3991	scaffold	GCA_000154285	428127.7	641380446	428127	71.29

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	[Eubacterium] dolichum strain ATCC 29143 16S ribosomal RNA gene, partial sequence	L34682	1486		428127
20218	Eubacterium dolichum gene for 16S ribosomal RNA, partial sequence, strain: JCM 10413	AB649277	1490		31971

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM15428v1 assembly for Amedibacillus dolichus DSM 3991
NCBI: GCA_000154285

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	98.64	no
125439	gram_stain	BacteriaNetⓘ	variable	51.51	no
125439	motility	BacteriaNetⓘ	yes	63.39	no
125439	spore_formation	BacteriaNetⓘ	yes	49.82	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Eubacterium dolichum DSM 3991
PATRIC: 428127.7

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	84.23	no
125438	anaerobic	anaerobicⓘ	yes	89.67	yes
125438	spore-forming	spore-formingⓘ	no	67.51	no
125438	aerobic	aerobicⓘ	no	99.60	yes
125438	thermophilic	thermophileⓘ	no	90.90	yes
125438	flagellated	motile2+ⓘ	no	90.56	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Disease-associated microbiome signature species in the gut.	Li J, Li J, O'Toole PW.	PNAS Nexus	10.1093/pnasnexus/pgae352	2024
Phylogeny	Genome-Based Reclassification of Strain KIST612, Previously Classified as Eubacterium limosum, into a New Strain of Eubacterium callanderi.	Kim JY, Kang B, Oh S, Gil Y, Choi IG, Chang IS.	J Microbiol Biotechnol	10.4014/jmb.2304.04011	2023
	Siderophore-harboring gut bacteria and fecal siderophore genes for predicting the responsiveness of fecal microbiota transplantation for active ulcerative colitis.	Yan J, Zhou G, Ren R, Zhang X, Zhang N, Wang Z, Peng L, Yang Y.	J Transl Med	10.1186/s12967-024-05419-w	2024
	Intestinal microbiology and urinary tract infection associated risk in long-term aged care residents.	Miller SJ, Carpenter L, Taylor SL, Wesselingh SL, Choo JM, Shoubridge AP, Papanicolas LE, Rogers GB, GRACE Investigator Group.	Commun Med (Lond)	10.1038/s43856-024-00583-y	2024
	Alterations in lung and gut microbiota reduce diversity in patients with nontuberculous mycobacterial pulmonary disease.	Choi JY, Shim B, Park Y, Kang YA.	Korean J Intern Med	10.3904/kjim.2023.097	2023
	To Feed or to Stick? Genomic Analysis Offers Clues for the Role of a Molecular Machine in Endospore Formers.	Stragier P.	J Bacteriol	10.1128/jb.00187-22	2022
Phylogeny	Distinct gut microbiomes in Thai patients with colorectal polyps.	Intarajak T, Udomchaiprasertkul W, Khoiri AN, Sutheeworapong S, Kusonmano K, Kittichotirat W, Thammarongtham C, Cheevadhanarak S.	World J Gastroenterol	10.3748/wjg.v30.i27.3336	2024
Pathogenicity	Identification of Clostridium innocuum hypothetical protein that is cross-reactive with C. difficile anti-toxin antibodies.	Cherny KE, Balaji A, Mukherjee J, Goo YA, Hauser AR, Ozer E, Satchell KJF, Bachta KER, Kochan TJ, Mitra SD, Kociolek LK.	Anaerobe	10.1016/j.anaerobe.2022.102555	2022
Phylogeny	Description of a new member of the family Erysipelotrichaceae: Dakotella fusiforme gen. nov., sp. nov., isolated from healthy human feces.	Ghimire S, Wongkuna S, Scaria J	PeerJ	10.7717/peerj.10071	2020
Phylogeny	Amedibacterium intestinale gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium dolichum Moore et al. 1976 (Approved Lists 1980) as Amedibacillus dolichus gen. nov., comb. nov.	Ikeyama N, Toyoda A, Morohoshi S, Kunihiro T, Murakami T, Mori H, Iino T, Ohkuma M, Sakamoto M	Int J Syst Evol Microbiol	10.1099/ijsem.0.004215	2020

References

#1561	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 3991
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Amedibacillus dolichus (DSM 3991, ATCC 29143, VPI C9-20)

Name and taxonomic classification

Morphology

Cell 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_000154285

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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