Name: Parabacteroides chinchillae ST166
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 24336

Type strain:

Species: Parabacteroides chinchillae

Strain Designation: ST166

Culture col. no.: DSM 29073, CCUG 62154, JCM 17104

Strain history: M. Kitahara ST166.

NCBI tax ID(s): 871327 (species)

SI-ID 401567

DSM 29073, CCUG 62154

Special Collections

Section

Parabacteroides chinchillae ST166 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from faeces of Chinchilla lanigera.

Gram-negative
rod-shaped
anaerobe
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	*Tannerellaceae*
	Genus	*Parabacteroides*
	Species	**Parabacteroides chinchillae**
	Full Scientific Name (LPSN)	Parabacteroides chinchillae Kitahara et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #31031]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %94.908

[Ref.: #31031]	Cell length	8.5 µm

[Ref.: #31031]	Cell width	1.2 µm

[Ref.: #31031]	Cell shape	rod-shaped

[Ref.: #31031]	Motility	no

[Ref.: #20719]	Incubation period	1-2 days

[Ref.: #62787]	Incubation period	2 days

[Ref.: #31031]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #20719]

Culture medium

CHOPPED MEAT MEDIUM (DSMZ Medium 78)

[Ref.: #20719]

Culture medium growth

[Ref.: #20719]

Culture medium link

Medium recipe at MediaDive

[Ref.: #20719]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #20719]	growth	37 °C
[Ref.: #31031]	optimum	37 °C
[Ref.: #62787]	growth	37 °C
[Ref.: #67770]	growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #20719]	Oxygen tolerance	anaerobe
[Ref.: #31031]	Oxygen tolerance	anaerobe
[Ref.: #62787]	Oxygen tolerance	anaerobe

[Ref.: #31031]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %93.292
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

[Ref.: #67770]

Observation

quinones: MK-9, MK-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]	arginine ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #31031]	esculin ChEBI	+	hydrolysis
[Ref.: #31031]	glucose ChEBI	+	carbon source
[Ref.: #68380]	L-glutamate ChEBI	+	degradation	* from API rID32A
[Ref.: #31031]	lactose ChEBI	+	carbon source
[Ref.: #31031]	maltose ChEBI	+	carbon source
[Ref.: #31031]	mannose ChEBI	+	carbon source
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #31031]	raffinose ChEBI	+	carbon source
[Ref.: #31031]	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.: #31031]	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.: #31031]	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]	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-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]	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]	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.: #20719]	12472	-	-	+	+	-	+	+/-	-	-	+	+/-	+/-	+	+	-	-	+	+	-	+	+/-	+	-	+/-	+	+	+	+	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	vitamin B6 metabolism	81.82	9 of 11
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	NAD metabolism	72.22	13 of 18
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	purine metabolism	71.28	67 of 94
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	UDP-GlcNAc biosynthesis	66.67	2 of 3
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	lipid metabolism	54.84	17 of 31
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	sphingosine metabolism	50	3 of 6
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	degradation of sugar alcohols	50	8 of 16
[Ref.: #66794]	polyamine pathway	47.83	11 of 23
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	cysteine metabolism	44.44	8 of 18
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	degradation of sugar acids	40	10 of 25
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	oxidative phosphorylation	38.46	35 of 91
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	vitamin B12 metabolism	38.24	13 of 34
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	L-lactaldehyde degradation	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	23.53	4 of 17
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	glutathione 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.: #20719]	Sample type/isolated from	faeces of Chinchilla lanigera
[Ref.: #20719]	Host species	Chinchilla lanigera
[Ref.: #20719]	Country	Japan
[Ref.: #20719]	Country ISO 3 Code	JPN
[Ref.: #20719]	Continent	Asia

[Ref.: #62787]	Sample type/isolated from	Feces,Chichilla lanigera
[Ref.: #62787]	Country	Japan
[Ref.: #62787]	Country ISO 3 Code	JPN
[Ref.: #62787]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Feces of a chinchilla
* marker position based on {}

Isolation sources categories

#Host	#Mammals	#Rodentia (Other)
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB574482 (>99% sequence identity) for Parabacteroides chinchillae from Microbeatlas

Aquatic Samples	50
Soil Samples	27
Animal Samples	2465
Plant Samples	8
Total Samples	2550

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

[Ref.: #20719]

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.: #20719]	Parabacteroides chinchillae gene for 16S rRNA, partial sequence	AB574482	1489	GenBank ENA	871327 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Parabacteroides chinchillae DSM 29073	GCA_900108035	contig	GenBank ENA	871327 tax ID	*
[Ref.: #66792]	Parabacteroides chinchillae strain DSM 29073	871327.5	wgs	PATRIC	871327 tax ID	*
[Ref.: #66792]	Parabacteroides chinchillae DSM 29073	2693429876	draft	JGI IMG/M	871327 tax ID	*

[Ref.: #31031]	GC-content	42.8 mol%
[Ref.: #67770]	GC-content	42.8 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Parabacteroides chinchillae strain DSM 29073 PATRIC: 871327.5
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Parabacteroides chinchillae strain DSM 29073 PATRIC: 871327.5
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	94.908	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	88.788	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	91.602	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	93.292	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	94.964	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	89	yes

Availability in culture collections External links

[Ref.: #20719]

Culture collection no.

DSM 29073, CCUG 62154, JCM 17104

[Ref.: #88262]

SI-ID 401567

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Parabacteroides pacaensis sp. nov. and Parabacteroides provencensis sp. nov., two new species identified from human gut microbiota.	Benabdelkader S, Naud S, Lo CI, Fadlane A, Traore SI, Aboudharam G, La Scola B	New Microbes New Infect	10.1016/j.nmni.2019.100642	2020	*
Phylogeny	Parabacteroides chinchillae sp. nov., isolated from chinchilla (Chincilla lanigera) faeces.	Kitahara M, Sakamoto M, Tsuchida S, Kawasumi K, Amao H, Benno Y, Ohkuma M	Int J Syst Evol Microbiol	10.1099/ijs.0.050146-0	2013	*

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 )

#20719

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29073

#31031

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 #27361 (see below)

#62787 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 62154

#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) .

#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 )

#88262

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-ID401567.1 )

#27361

IJSEM 3470 2013 ( DOI 10.1099/ijs.0.050146-0 , PubMed 23563230 )

* These data were automatically processed and therefore are not curated

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Parabacteroides chinchillae strain DSM 29073

Parabacteroides chinchillae strain DSM 29073

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Change proposal