Name: Amedibacillus dolichus DSM 3991
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5424

Type strain:

Species: Amedibacillus dolichus

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

Strain history: DSM 3991 <-- ATCC 29143 <-- L. Holdeman VPI C9-20.

NCBI tax ID(s): 428127 (strain), 31971 (species)

SI-ID 39376

ATCC 29143, DSM 3991, JCM 10413

Section

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

anaerobe
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Erysipelotrichia*
	Order	*Erysipelotrichales*
	Family	*Erysipelotrichaceae*
	Genus	*Amedibacillus*
	Species	**Amedibacillus dolichus**
	Full Scientific Name (LPSN)	Amedibacillus dolichus (Moore et al. 1976) Ikeyama et al. 2020

	Synonym	"Absiella* dolichum"*
	Synonym	Eubacterium dolichum

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1561]

Culture medium

CHOPPED MEAT MEDIUM (DSMZ Medium 78)

[Ref.: #1561]

Culture medium growth

[Ref.: #1561]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1561]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #1561]			growth	37 °C
[Ref.: #67770]			growth	37 °C

[Ref.: #1561]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #1561]

Oxygen tolerance

anaerobe

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]	arginine ChEBI	+	hydrolysis	* from API rID32A
[Ref.: #68380]	D-mannose ChEBI	-	fermentation	* from API rID32A
[Ref.: #68380]	L-glutamate ChEBI	+	degradation	* from API rID32A
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #68380]	raffinose ChEBI	-	fermentation	* from API rID32A
[Ref.: #68380]	tryptophan ChEBI	-	energy source	* from API rID32A
[Ref.: #68380]	urea ChEBI	-	hydrolysis	* from API rID32A

	Metabolite production	Metabolite	Production
[Ref.: #68380]		indole ChEBI	no	* from API rID32A

	Physiological tests	Metabolite	Indole test
[Ref.: #68380]		indole ChEBI	-	* from API rID32A

	Enzyme	Enzyme activity	EC number
[Ref.: #68380]	alanine arylamidase	-	3.4.11.2	* from API rID32A
[Ref.: #68380]	alkaline phosphatase	-	3.1.3.1	* from API rID32A
[Ref.: #68380]	alpha-arabinosidase	-	3.2.1.55	* from API rID32A
[Ref.: #68380]	alpha-fucosidase	-	3.2.1.51	* from API rID32A
[Ref.: #68380]	alpha-galactosidase	-	3.2.1.22	* from API rID32A
[Ref.: #68380]	alpha-glucosidase	-	3.2.1.20	* from API rID32A
[Ref.: #68380]	arginine dihydrolase	+	3.5.3.6	* from API rID32A
[Ref.: #68380]	beta-galactosidase	-	3.2.1.23	* from API rID32A
[Ref.: #68380]	beta-Galactosidase 6-phosphate	-		* from API rID32A
[Ref.: #68380]	beta-glucosidase	-	3.2.1.21	* from API rID32A
[Ref.: #68380]	beta-glucuronidase	-	3.2.1.31	* from API rID32A
[Ref.: #68380]	glutamate decarboxylase	+	4.1.1.15	* from API rID32A
[Ref.: #68380]	glutamyl-glutamate arylamidase	-		* from API rID32A
[Ref.: #68380]	glycin arylamidase	-		* from API rID32A
[Ref.: #68380]	histidine arylamidase	-		* from API rID32A
[Ref.: #68380]	L-arginine arylamidase	-		* from API rID32A
[Ref.: #68380]	leucine arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68380]	leucyl glycin arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68380]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API rID32A
[Ref.: #68380]	phenylalanine arylamidase	-		* from API rID32A
[Ref.: #68380]	proline-arylamidase	-	3.4.11.5	* from API rID32A
[Ref.: #68380]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API rID32A
[Ref.: #68380]	serine arylamidase	-		* from API rID32A
[Ref.: #68380]	tryptophan deaminase	-	4.1.99.1	* from API rID32A
[Ref.: #68380]	tyrosine arylamidase	-		* from API rID32A
[Ref.: #68380]	urease	-	3.5.1.5	* from API rID32A
	Only first 10 entries are displayed. Click here to see all.

API® rID32A:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Urease/urea hydrolysisURE	Arginine dihydrolaseADH (Arg)	alpha-Galactosidasealpha GAL	beta-Galactosidasebeta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha-Glucosidasealpha GLU	beta-Glucosidasebeta GLU	alpha-Arabinosidasealpha ARA	beta-Glucuronidasebeta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	Fermentation of D-mannoseMNE	Fermentation of raffinoseRAF	Glutamate decarboxylaseGDC	alpha-Fucosidasealpha FUC	Reduction of nitrateNIT	Indole productionIND	Alkaline phosphatasePAL	L-arginine arylamidaseArgA	Proline arylamidaseProA	Leucyl glycin arylamidaseLGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	Pyrrolidonyl arylamidasePyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
[Ref.: #1561]	12553	-	+	-	-	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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

[Ref.: #1561]	Sample type/isolated from	human faeces

[Ref.: #67770]	Sample type/isolated from	Human feces
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #1561]

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.: #20218]	Eubacterium dolichum gene for 16S ribosomal RNA, partial sequence, strain: JCM 10413	AB649277	1490	ENA	31971 tax ID	*
[Ref.: #20218]	[Eubacterium] dolichum strain ATCC 29143 16S ribosomal RNA gene, partial sequence	L34682	1486	ENA	428127 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Amedibacillus dolichus DSM 3991	GCA_000154285	scaffold	GenBank	428127 tax ID
[Ref.: #66792]	Eubacterium dolichum DSM 3991	428127.7	wgs	PATRIC	428127 tax ID	*
[Ref.: #66792]	Amedibacillus dolichus DSM 3991	641380446	draft	JGI IMG/M	428127 tax ID	*

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Eubacterium dolichum DSM 3991 PATRIC: 428127.7
[Ref.: #69480]	gram-positive	yes	95.11	no
[Ref.: #69480]	anaerobic	yes	97.939	yes
[Ref.: #69480]	halophile	no	66.226	no
[Ref.: #69480]	spore-forming	no	84.733	no
[Ref.: #69480]	glucose-util	yes	87.765	no
[Ref.: #69480]	aerobic	no	98.685	no
[Ref.: #69480]	flagellated	no	97.908	no
[Ref.: #69480]	thermophile	no	97.926	no
[Ref.: #69480]	motile	no	92.7	no
[Ref.: #69480]	glucose-ferment	yes	73.972	no

Availability in culture collections External links

[Ref.: #1561]

Culture collection no.

DSM 3991, ATCC 29143, VPI C9-20, JCM 10413

[Ref.: #74912]

SI-ID 39376

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 )

#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) .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#74912

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-ID39376.1 )

* These data were automatically processed and therefore are not curated

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Eubacterium dolichum DSM 3991

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