Archive BacDiveID:10.13145/bacdive2871.20230509.8.1

Strain identifier

BacDive ID: 2871

Type strain:

Species: Butyricicoccus pullicaecorum

Strain Designation: 25-3

Strain history: <- E. Moore, CCUG <- V. Eeckhaut, Lab. Microbiology, Ghent Univ., Belgium {2006}

NCBI tax ID(s): 1121128 (strain), 501571 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 16766

BacDive-ID: 2871

DSM-Number: 23266

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, coccus-shaped

description: Butyricicoccus pullicaecorum 25-3 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from cecal content .

NCBI tax id

NCBI tax id	Matching level
1121128	strain
501571	species

strain history

@ref: 16766
history: <- E. Moore, CCUG <- V. Eeckhaut, Lab. Microbiology, Ghent Univ., Belgium {2006}

doi: 10.13145/bacdive2871.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/bacillota
domain: Bacteria
phylum: Bacillota
class: Clostridia
order: Eubacteriales
family: Oscillospiraceae
genus: Butyricicoccus
species: Butyricicoccus pullicaecorum
full scientific name: Butyricicoccus pullicaecorum Eeckhaut et al. 2008

@ref: 16766

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Oscillospiraceae

genus: Butyricicoccus

species: Butyricicoccus pullicaecorum

full scientific name: Butyricicoccus pullicaecorum Eeckhaut et al. 2008

strain designation: 25-3

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell shape	motility	confidence
32584	positive	1.2-1.5 µm	coccus-shaped	no
69480	positive				99.719

colony morphology

@ref: 60513
incubation period: 2 days

pigmentation

@ref: 32584
production: yes

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
16766	CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)	yes	https://mediadive.dsmz.de/medium/110	Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
16766	PY + X MEDIUM (DSMZ Medium 104b)	yes	https://mediadive.dsmz.de/medium/104b	Name: PY + X MEDIUM (DSMZ Medium 104b) Composition: Yeast extract 10.0 g/l D-Glucose 5.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Sodium resazurin 0.0005 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
16766	positive	growth	37	mesophilic
32584	positive	growth	42	thermophilic
32584	positive	optimum	42	thermophilic
60513	positive	growth	37	mesophilic

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
16766	anaerobe
32584	anaerobe
60513	anaerobe
69480	anaerobe	100

spore formation

@ref	spore formation	confidence
32584	no
69481	no	100
69480	no	95.291

observation

@ref: 32584
observation: aggregates in chains

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
32584	17057	cellobiose	+	carbon source
32584	17234	glucose	+	carbon source
32584	17306	maltose	+	carbon source
32584	37684	mannose	+	carbon source
32584	17814	salicin	+	carbon source
32584	17992	sucrose	+	carbon source
32584	27082	trehalose	+	carbon source
32584	4853	esculin	+	hydrolysis

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent	sampling date
16766	cecal content (4-week-old broiler chicken)	Maldegem	Belgium	BEL	Europe
60513	Chicken feces,4-week old broiler	Gent	Belgium	BEL	Europe	2006-11-24

isolation source categories

Cat1	Cat2	Cat3
#Host	#Birds	#Chicken
#Host Body Product	#Gastrointestinal tract	#Caecal content

taxonmaps

@ref: 69479
File name: preview.99_5147.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_341;96_2504;97_3058;98_3838;99_5147&stattab=map
Last taxonomy: Butyricicoccus pullicaecorum subclade
16S sequence: EU410376
Sequence Identity:
Total samples: 29097
soil counts: 391
aquatic counts: 195
animal counts: 28431
plant counts: 80

Safety information

risk assessment

@ref: 16766
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 16766
description: Butyricicoccus pullicaecorum strain 25-3 16S ribosomal RNA gene, partial sequence
accession: EU410376
length: 1482
database: ena
NCBI tax ID: 501571

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Butyricicoccus pullicaecorum DSM 23266	GCA_900167005	scaffold	ncbi	1121128
66792	Butyricicoccus pullicaecorum DSM 23266 strain DSM 23266	1121128.3	wgs	patric	1121128
66792	Butyricicoccus pullicaecorum DSM 23266	2585428076	draft	img	1121128

GC content

@ref	GC-content	method
16766	54.5	high performance liquid chromatography (HPLC)
32584	54.5

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	no	89.07	yes
flagellated	no	96.398	no
gram-positive	yes	91.343	yes
anaerobic	yes	99.544	yes
aerobic	no	97.778	yes
halophile	no	86.296	no
spore-forming	no	75.731	yes
thermophile	no	92.932	no
glucose-util	yes	90.058	no
glucose-ferment	yes	67.018	no

External links

@ref: 16766

culture collection no.: DSM 23266, CCUG 55265, LMG 24109

straininfo link

@ref: 72395
straininfo: 354037

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	19060061	Butyricicoccus pullicaecorum gen. nov., sp. nov., an anaerobic, butyrate-producing bacterium isolated from the caecal content of a broiler chicken.	Eeckhaut V, Van Immerseel F, Teirlynck E, Pasmans F, Fievez V, Snauwaert C, Haesebrouck F, Ducatelle R, Louis P, Vandamme P	Int J Syst Evol Microbiol	10.1099/ijs.0.65730-0	2008	Anaerobiosis, Animals, Butyrates/metabolism, Chickens/microbiology, Fermentation, Gastrointestinal Contents/microbiology, Gram-Positive Endospore-Forming Rods/classification/genetics/metabolism/*physiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity	Metabolism
Genetics	25007784	Safety assessment of the butyrate-producing Butyricicoccus pullicaecorum strain 25-3(T), a potential probiotic for patients with inflammatory bowel disease, based on oral toxicity tests and whole genome sequencing.	Steppe M, Van Nieuwerburgh F, Vercauteren G, Boyen F, Eeckhaut V, Deforce D, Haesebrouck F, Ducatelle R, Van Immerseel F	Food Chem Toxicol	10.1016/j.fct.2014.06.024	2014	Aminoglycosides/pharmacology, Animals, Anti-Infective Agents/pharmacology, Butyrates/metabolism, Consumer Product Safety, DNA, Bacterial/genetics, Drug Resistance, Multiple, Bacterial/genetics, Female, Food Safety, Genome, Bacterial, Gram-Positive Bacteria/genetics, Inflammatory Bowel Diseases/therapy, Microbial Sensitivity Tests, Probiotics/administration & dosage, Rats, Rats, Wistar, Sequence Analysis, DNA, Toxicity Tests, Trimethoprim/pharmacology, Virulence Factors	Transcriptome
Metabolism	25999470	Interindividual differences in response to treatment with butyrate-producing Butyricicoccus pullicaecorum 25-3T studied in an in vitro gut model.	Geirnaert A, Wang J, Tinck M, Steyaert A, Van den Abbeele P, Eeckhaut V, Vilchez-Vargas R, Falony G, Laukens D, De Vos M, Van Immerseel F, Raes J, Boon N, Van de Wiele T	FEMS Microbiol Ecol	10.1093/femsec/fiv054	2015	Adult, Base Sequence, Butyrates/metabolism, Clostridium/genetics/metabolism, Colon/microbiology, Dysbiosis/prevention & control, Feces/microbiology, Humans, In Vitro Techniques, Inflammatory Bowel Diseases/microbiology/therapy, Male, Microbiota/genetics, Probiotics/*therapeutic use, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Young Adult	Pathogenicity
Phylogeny	27334534	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	Bacterial Typing Techniques, Base Composition, Butyrates/metabolism, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Eubacterium/classification/genetics/isolation & purification, Fatty Acids/chemistry, Feces/microbiology, Humans, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA	Pathogenicity
	27708624	The Probiotic Butyricicoccus pullicaecorum Reduces Feed Conversion and Protects from Potentially Harmful Intestinal Microorganisms and Necrotic Enteritis in Broilers.	Eeckhaut V, Wang J, Van Parys A, Haesebrouck F, Joossens M, Falony G, Raes J, Ducatelle R, Van Immerseel F	Front Microbiol	10.3389/fmicb.2016.01416	2016
Metabolism	28548573	Inulin-type fructan degradation capacity of Clostridium cluster IV and XIVa butyrate-producing colon bacteria and their associated metabolic outcomes.	Moens F, De Vuyst L	Benef Microbes	10.3920/BM2016.0142	2017	Butyrates/metabolism, Carbon Dioxide/metabolism, Colon/metabolism/microbiology, Eubacterium/metabolism, Faecalibacterium prausnitzii/metabolism, Fermentation/physiology, Formates/metabolism, Fructose/metabolism, Humans, Hydrogen/metabolism, Inulin/metabolism, Lactic Acid/metabolism, Oligosaccharides/*metabolism	Pathogenicity
	30417112	Butyrate Producers as Potential Next-Generation Probiotics: Safety Assessment of the Administration of Butyricicoccus pullicaecorum to Healthy Volunteers.	Boesmans L, Valles-Colomer M, Wang J, Eeckhaut V, Falony G, Ducatelle R, Van Immerseel F, Raes J, Verbeke K	mSystems	10.1128/mSystems.00094-18	2018

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
16766	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23266)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-23266
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
32584	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	28799	28776041
60513	Curators of the CCUG	Culture Collection University of Gothenburg (CCUG) (CCUG 55265)	https://www.ccug.se/strain?id=55265
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
72395	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID354037.1	StrainInfo: A central database for resolving microbial strain identifiers