Name: Barnesiella viscericola C46
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 12518

Type strain:

Species: Barnesiella viscericola

Strain Designation: C46

Culture col. no.: CCUG 55593, DSM 18177, JCM 13660

Strain history: M. Sakamoto <-- P. T. N. Lan C46.

NCBI tax ID(s): 880074 (strain), 397865 (species)

SI-ID 294005

JCM 13660, DSM 18177, CCUG 55593

Other strains from Barnesiella viscericola

B. viscericola JCM 13661

Section

Barnesiella viscericola C46 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from chicken caecum.

Gram-negative
rod-shaped
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	*Bacteroidota*
	Class	*Bacteroidia*
	Order	*Bacteroidales*
	Family	*Barnesiellaceae*
	Genus	*Barnesiella*
	Species	**Barnesiella viscericola**
	Full Scientific Name (LPSN)	Barnesiella viscericola Sakamoto et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31956]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #31956]	Cell length	6.35 µm

[Ref.: #31956]	Cell width	1.2 µm

[Ref.: #31956]	Cell shape	rod-shaped

[Ref.: #31956]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %91.408

[Ref.: #7411]	Incubation period	2-3 days

[Ref.: #60660]	Incubation period	2 days

[Ref.: #31956]

Pigment production

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7411]

Culture medium

COLUMBIA BLOOD AGAR (DSMZ Medium 429)

[Ref.: #7411]

Culture medium growth

[Ref.: #7411]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7411]

Culture medium composition

expand / minimize

[Ref.: #7411]

Culture medium

CHOPPED MEAT MEDIUM (DSMZ Medium 78)

[Ref.: #7411]

Culture medium growth

[Ref.: #7411]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7411]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7411]	growth	37 °C
[Ref.: #60660]	growth	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #7411]	Temperature range	mesophilic
[Ref.: #60660]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7411]	Oxygen tolerance	anaerobe
[Ref.: #31956]	Oxygen tolerance	anaerobe
[Ref.: #60660]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %99.999

[Ref.: #31956]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %100

[Ref.: #67770]

Observation

quinones: MK-11, MK-12

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31956]	acetate ChEBI	+	carbon source
[Ref.: #31956]	cellobiose ChEBI	+	carbon source
[Ref.: #68380]	D-mannose ChEBI	-	fermentation	* from API rID32A
[Ref.: #31956]	esculin ChEBI	+	hydrolysis
[Ref.: #31956]	glucose ChEBI	+	carbon source
[Ref.: #68380]	L-glutamate ChEBI	+	degradation	* from API rID32A
[Ref.: #31956]	maltose ChEBI	+	carbon source
[Ref.: #31956]	mannose ChEBI	+	carbon source
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #31956]	raffinose ChEBI	+	carbon source
[Ref.: #68380]	raffinose ChEBI	-	fermentation	* from API rID32A
[Ref.: #31956]	succinate ChEBI	+	carbon source
[Ref.: #31956]	sucrose ChEBI	+	carbon source
[Ref.: #68380]	tryptophan ChEBI	-	energy source	* from API rID32A
[Ref.: #68380]	urea ChEBI	-	hydrolysis	* from API rID32A
	Only first 10 entries are displayed. Click here to see all.

	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.: #31956]	alkaline phosphatase	+	3.1.3.1
[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.: #31956]	alpha-galactosidase	+	3.2.1.22
[Ref.: #68380]	alpha-galactosidase	+	3.2.1.22	* from API rID32A
[Ref.: #68380]	alpha-glucosidase	+	3.2.1.20	* 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-glucuronidase	-	3.2.1.31	* from API rID32A
[Ref.: #31956]	gelatinase	+
[Ref.: #68380]	glutamate decarboxylase	+	4.1.1.15	* from API rID32A
[Ref.: #68380]	glycin 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]	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.: #7411]	12231	-	+/-	+	+	-	+	+/-	-	-	+	-	-	+	+	-	-	+	-	-	+	-	-	-	-	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	pyrimidine metabolism	68.89	31 of 45
[Ref.: #66794]	purine metabolism	68.09	64 of 94
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	UDP-GlcNAc biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	glutamate and glutamine metabolism	64.29	18 of 28
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of hexoses	61.11	11 of 18
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	alanine metabolism	51.72	15 of 29
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	methionine metabolism	50	13 of 26
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	citric acid cycle	50	7 of 14
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	histidine metabolism	48.28	14 of 29
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	cysteine metabolism	44.44	8 of 18
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	tryptophan metabolism	42.11	16 of 38
[Ref.: #66794]	non-pathway related	42.11	16 of 38
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of pentoses	39.29	11 of 28
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	oxidative phosphorylation	37.36	34 of 91
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	glutathione metabolism	35.71	5 of 14
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	allantoin degradation	33.33	3 of 9
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	glycine metabolism	30	3 of 10
[Ref.: #66794]	Entner Doudoroff pathway	30	3 of 10
[Ref.: #66794]	tyrosine metabolism	28.57	4 of 14
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	degradation of sugar acids	24	6 of 25
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	heme metabolism	21.43	3 of 14
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #7411]	Sample type/isolated from	chicken caecum
[Ref.: #7411]	Country	Japan
[Ref.: #7411]	Country ISO 3 Code	JPN
[Ref.: #7411]	Continent	Asia

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

Isolation sources categories

#Host	#Birds	#Chicken
#Host Body-Site	#Gastrointestinal tract	#Large intestine

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB267809 (>99% sequence identity) for Barnesiella viscericola subclade from Microbeatlas

Aquatic Samples	558
Soil Samples	419
Animal Samples	12135
Plant Samples	119
Total Samples	13231

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

[Ref.: #7411]

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.: #7411]	Barnesiella viscericola gene for 16S ribosomal RNA, partial sequence	AB267809	1461	ENA	880074 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Barnesiella viscericola DSM 18177 C46, DSM 18177	GCA_000512915	complete	GenBank	880074 tax ID	*
[Ref.: #66792]	Barnesiella viscericola DSM 18177 strain C46, DSM 18177	880074.29	complete	PATRIC	880074 tax ID	*
[Ref.: #66792]	Barnesiella viscericola C46, DSM 18177	2509276067	complete	JGI IMG/M	880074 tax ID	*

[Ref.: #7411]	GC-content	52.0 mol%
[Ref.: #31956]	GC-content	52 mol%
[Ref.: #67770]	GC-content	52 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Barnesiella viscericola DSM 18177 C46, DSM 18177 NCBI: GCA_000512915.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Barnesiella viscericola DSM 18177 C46, DSM 18177 NCBI: GCA_000512915.1
[Ref.: #69480]	motile	no	92.884	yes
[Ref.: #69480]	flagellated	no	96.289	yes
[Ref.: #69480]	gram-positive	no	97.108	yes
[Ref.: #69480]	anaerobic	yes	99.171	yes
[Ref.: #69480]	halophile	no	81.04	no
[Ref.: #69480]	spore-forming	no	96.483	yes
[Ref.: #69480]	thermophile	no	96.145	no
[Ref.: #69480]	glucose-util	yes	87.207	no
[Ref.: #69480]	aerobic	no	98.809	yes
[Ref.: #69480]	glucose-ferment	yes	56.522	no

Availability in culture collections External links

[Ref.: #7411]

Culture collection no.

CCUG 55593, DSM 18177, JCM 13660

[Ref.: #81737]

SI-ID 294005

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Barnesiella viscericola gen. nov., sp. nov., a novel member of the family Porphyromonadaceae isolated from chicken caecum.	Sakamoto M, Lan PTN, Benno Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64709-0	2007	*
Pathogenicity	Arabinoxylan and Pectin Metabolism in Crohn's Disease Microbiota: An In Silico Study.	Sabater C, Calvete-Torre I, Ruiz L, Margolles A	Int J Mol Sci	10.3390/ijms23137093	2022	*

References

#7411

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18177

#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 )

#31956

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28212 (see below)

#60660 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55593

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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;

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#81737

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-ID294005.1 )

#28212

IJSEM 342 2007 ( DOI 10.1099/ijs.0.64709-0 , PubMed 17267976 )

* These data were automatically processed and therefore are not curated

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Barnesiella viscericola DSM 18177 C46, DSM 18177

Barnesiella viscericola DSM 18177 C46, DSM 18177

Change proposal

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