Name: Phocaeicola paurosaccharolyticus WK042
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 1625

Type strain:

Species: Phocaeicola paurosaccharolyticus

Strain Designation: WK042

Culture col. no.: DSM 21004, JCM 15092

Strain history: A. Ueki WK042.

NCBI tax ID(s): 1236498 (strain), 732242 (species)

SI-ID 397244

DSM 21004

Special Collections

Section

Phocaeicola paurosaccharolyticus WK042 is an anaerobe, Gram-negative, rod-shaped bacterium that was isolated from rice-straw residue from a methanogenic fermenter treating cattle waste.

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	*Bacteroidaceae*
	Genus	*Phocaeicola*
	Species	**Phocaeicola paurosaccharolyticus**
	Full Scientific Name (LPSN)	Phocaeicola paurosaccharolyticus (Ueki et al. 2011) García-López et al. 2020

Synonym

Bacteroides paurosaccharolyticus

Information on morphological and physiological properties Morphology

[Ref.: #29851]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %91.713

[Ref.: #29851]	Cell length	3.15 µm

[Ref.: #29851]	Cell width	0.75 µm

[Ref.: #29851]	Cell shape	rod-shaped

[Ref.: #29851]	Motility	no

[Ref.: #29851]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #9078]

Culture medium

CHOPPED MEAT MEDIUM (DSMZ Medium 78)

[Ref.: #9078]

Culture medium growth

[Ref.: #9078]

Culture medium link

Medium recipe at MediaDive

[Ref.: #9078]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #9078]	growth	30 °C
[Ref.: #29851]	growth	10-40 °C
[Ref.: #29851]	optimum	35 °C
[Ref.: #67770]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #29851]			optimum	7.7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #9078]	Oxygen tolerance	anaerobe
[Ref.: #29851]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %93.738

[Ref.: #29851]	Ability of spore formation	no
[Ref.: #69480]	Ability of spore formation	no Confidence in %91.96

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29851]		NaCl		growth	<2	%
[Ref.: #29851]		NaCl		optimum	1	%

[Ref.: #67770]

Observation

quinones: MK-11

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29851]	acetate ChEBI	+	carbon source
[Ref.: #29851]	arabinose ChEBI	+	carbon source
[Ref.: #68380]	arginine ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #68380]	D-mannose ChEBI	+	fermentation	* from API rID32A
[Ref.: #29851]	dextrin ChEBI	+	carbon source
[Ref.: #29851]	esculin ChEBI	+	hydrolysis
[Ref.: #29851]	glucose ChEBI	+	carbon source
[Ref.: #29851]	glycogen ChEBI	+	carbon source
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #29851]	maltose ChEBI	+	carbon source
[Ref.: #29851]	mannose ChEBI	+	carbon source
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #29851]	propionate ChEBI	+	carbon source
[Ref.: #29851]	pyruvate ChEBI	+	carbon source
[Ref.: #29851]	rhamnose ChEBI	+	carbon source
[Ref.: #29851]	succinate ChEBI	+	carbon source
[Ref.: #68380]	tryptophan ChEBI	-	energy source	* from API rID32A
[Ref.: #68380]	urea ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #29851]	xylose ChEBI	+	carbon source
	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.: #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.: #9078]	12383	-	-	+	+	-	+	+	+	+	+	+	+/-	-	+	-	-	+	-	-	+	-	-	-	-	+	-	-	-	-

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

[Ref.: #9078]	Sample type/isolated from	rice-straw residue from a methanogenic fermenter treating cattle waste
[Ref.: #9078]	Geographic location (country and/or sea, region)	Hokkaido
[Ref.: #9078]	Country	Japan
[Ref.: #9078]	Country ISO 3 Code	JPN
[Ref.: #9078]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Methanogenic reactor treating waste from cattle farms
* marker position based on {}

Isolation sources categories

#Engineered	#Bioreactor	-
#Engineered	#Waste	-
#Host	#Mammals	#Bovinae (Cow, Cattle)
#Host	#Plants	#Herbaceous plants (Grass,Crops)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB298727 (>99% sequence identity) for Phocaeicola paurosaccharolyticus subclade from Microbeatlas

Aquatic Samples	6726
Soil Samples	823
Animal Samples	16180
Plant Samples	270
Total Samples	23999

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

[Ref.: #9078]

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.: #9078]	Bacteroides paurosaccharolyticus JCM 15092 gene for 16S rRNA, partial sequence	AB298727	1472	GenBank ENA	1236498 tax ID
[Ref.: #20218]	Bacteroides paurosaccharolyticus gene for 16S ribosomal RNA, partial sequence	AB547645	1493	GenBank ENA	1236498 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Phocaeicola paurosaccharolyticus JCM 15092 JCM 15092	GCA_000613805	contig	GenBank ENA	1236498 tax ID
[Ref.: #66792]	Bacteroides paurosaccharolyticus JCM 15092	1236498.4	wgs	PATRIC	1236498 tax ID	*
[Ref.: #66792]	Bacteroides paurosaccharolyticus JCM 15092	2585427865	draft	JGI IMG/M	1236498 tax ID	*

[Ref.: #9078]	GC-content	41.0 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29851]	GC-content	41 mol%
[Ref.: #67770]	GC-content	37.1 mol%	genome sequence analysis
[Ref.: #67770]	GC-content	41 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 Diaspora project based on: Bacteroides paurosaccharolyticus JCM 15092 PATRIC: 1236498.4
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	91.713	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	93.738	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	91.96	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	95.009	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	95.873	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	no	88.5	yes

Availability in culture collections External links

[Ref.: #9078]

Culture collection no.

DSM 21004, JCM 15092

[Ref.: #71271]

SI-ID 397244

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Bacteroides paurosaccharolyticus sp. nov., isolated from a methanogenic reactor treating waste from cattle farms.	Ueki A, Abe K, Ohtaki Y, Kaku N, Watanabe K, Ueki K	Int J Syst Evol Microbiol	10.1099/ijs.0.022566-0	2010	*

References

#9078

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21004

#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 )

#29851

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 #26225 (see below)

#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) .

#71271

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-ID397244.1 )

#26225

IJSEM 448 2011 ( DOI 10.1099/ijs.0.022566-0 , PubMed 20348319 )

* These data were automatically processed and therefore are not curated

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Bacteroides paurosaccharolyticus JCM 15092

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