Berryella intestinalis (DSM 104960, 68-1-3, JCM 34389)

Name: Berryella intestinalis (DSM 104960, 68-1-3, JCM 34389)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159448

Type strain

Strain Designation 68-1-3

Culture col. no. DSM 104960 68-1-3 JCM 34389

NCBI tax ID(s) 1531429

Special Collections DSMZ JCM Pig DZIF

History DSMZ <- T. Looft, USDA-ARS-NADC; 68-1-3 JCM <-- B. Abt; DSMZ, Germany; DSM 104960 (=68-1-3) <-- T. Looft; ARS, USDA, USA.

Links

Berryella intestinalis 68-1-3 is a bacterium that was isolated from intestinal tract of a three month-old healthy pig.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 401089

JCM 34389,DSM 104960

@ref 20215

Last LPSN update 2026-05-29 08:44:11

Domain Bacteria

Phylum Actinomycetota

Class Coriobacteriia

Order Eggerthellales

Family Eggerthellaceae

Genus Berryella

Species Berryella intestinalis

Full scientific name Berryella intestinalis Wylensek et al. 2021

Morphology

Cell morphology

@ref	Motility	Confidence	Gram stain
125438		91
125439		95.024	negative

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
66271	CHOPPED MEAT MEDIUM (DSMZ Medium 78)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 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
66271	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)		Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

Culture temp

@ref	Growth	Type	Temperature (°C)
66271	positive	growth	37
67770	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate anaerobe	95.215

Spore formation

@ref	Spore formation	Confidence
125439		99.877

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
66271	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	-	+	-	+	+	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Suidae (Pig,Swine)
#Host Body-Site	#Gastrointestinal tract	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
66271	intestinal tract (ileal lumen) of a three month-old healthy pig	Ames, Iowa	USA	USA	North America	42.0308	-93.6318 42.0308/-93.6318
67770	Ileal content of a pig in Ames	Iowa	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence MN537474 (>99% sequence identity) for Berryella intestinalis subclade from Microbeatlas

Aquatic Samples	105
Soil Samples	269
Animal Samples	8287
Plant Samples	35
Total Samples	8696

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM81482v1 assembly for Berryella intestinalis 68-1-3	complete	GCA_000814825	1531429.3	2634166451	1531429	98.08

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66271	Berryella intestinalis strain 68-1-3 16S ribosomal RNA gene, partial sequence	MN537474	1389		2652296

GC content

@ref	GC-content (mol%)	Method
67770	63.6	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM81482v1 assembly for Berryella intestinalis 68-1-3
NCBI: GCA_000814825

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	95.22	no
125439	gram_stain	BacteriaNetⓘ	negative	95.02	no
125439	spore_formation	BacteriaNetⓘ	no	99.88	no
125439	motility	BacteriaNetⓘ	yes	71.07	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Berryella intestinalis 68-1-3
NCBI: GCA_000814825.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	81.80	no
125438	anaerobic	anaerobicⓘ	yes	88.43	no
125438	aerobic	aerobicⓘ	no	93.63	no
125438	spore-forming	spore-formingⓘ	no	82.55	no
125438	thermophilic	thermophileⓘ	no	87.41	yes
125438	flagellated	motile2+ⓘ	no	91.00	no

Literature

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 )
#66271	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 104960
#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 .
#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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