Name: Parabacteroides johnsonii M-165
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 12498

Type strain:

Species: Parabacteroides johnsonii

Strain Designation: M-165

Culture col. no.: DSM 18315, CIP 109537, JCM 13406, CCUG 54943

Strain history: M. Sakamoto <-- M. Kitahara M-165.

NCBI tax ID(s): 537006 (strain), 387661 (species)

Section

Parabacteroides johnsonii M-165 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from human faeces.

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	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Bacteroidia*
	Order	*Bacteroidales*
	Family	*Tannerellaceae*
	Genus	*Parabacteroides*
	Species	**Parabacteroides johnsonii**
	Full Scientific Name (PNU)	Parabacteroides johnsonii Sakamoto et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #31881]	Gram stain	negative
[Ref.: #31881]	Cell length	1.7-2.5 µm
[Ref.: #31881]	Cell width	0.8 µm
[Ref.: #31881]	Cell shape	rod-shaped
[Ref.: #31881]	Motility	no

[Ref.: #7499]	Incubation period	1-2 days

[Ref.: #60403]	Incubation period	2 days

[Ref.: #31881]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7499]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #7499]

Culture medium growth

[Ref.: #7499]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #7499]

Culture medium composition

expand / minimize

[Ref.: #7499]

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

[Ref.: #7499]

Culture medium growth

[Ref.: #7499]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #7499]

Culture medium composition

expand / minimize

[Ref.: #34705]

Culture medium

MEDIUM 20 - for Anaerobic bacteria

[Ref.: #34705]

Culture medium growth

[Ref.: #34705]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7499]	growth	37 °C
[Ref.: #34705]	growth	37 °C
[Ref.: #60403]	growth	37 °C
[Ref.: #67770]	growth	37 °C

[Ref.: #7499]	Temperature range	mesophilic
[Ref.: #34705]	Temperature range	mesophilic
[Ref.: #60403]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #7499]	Oxygen tolerance	anaerobe
[Ref.: #31881]	Oxygen tolerance	anaerobe
[Ref.: #60403]	Oxygen tolerance	anaerobe

[Ref.: #31881]

Ability of spore formation

[Ref.: #67770]

Observation

quinones: MK-9, MK-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31881]	arabinose ChEBI	+	carbon source
[Ref.: #68380]	arginine ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #68367]	cellobiose ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	D-glucose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68367]	D-mannitol ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	D-mannose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68380]	D-mannose ChEBI	+	fermentation	* from API rID32A
[Ref.: #68367]	D-xylose ChEBI	+	builds acid from	* from API 20A
[Ref.: #31881]	esculin ChEBI	+	hydrolysis
[Ref.: #68367]	esculin ChEBI	+	hydrolysis	* from API 20A
[Ref.: #68367]	gelatin ChEBI	-	hydrolysis	* from API 20A
[Ref.: #31881]	glucose ChEBI	+	carbon source
[Ref.: #68367]	glycerol ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	L-arabinose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68380]	L-glutamate ChEBI	+	degradation	* from API rID32A
[Ref.: #31881]	lactose ChEBI	+	carbon source
[Ref.: #68367]	lactose ChEBI	+	builds acid from	* from API 20A
[Ref.: #31881]	maltose ChEBI	+	carbon source
[Ref.: #31881]	mannose ChEBI	+	carbon source
[Ref.: #68367]	melezitose ChEBI	+	builds acid from	* from API 20A
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #31881]	raffinose ChEBI	+	carbon source
[Ref.: #31881]	rhamnose ChEBI	+	carbon source
[Ref.: #68367]	salicin ChEBI	-	builds acid from	* from API 20A
[Ref.: #68367]	sorbitol ChEBI	-	builds acid from	* from API 20A
[Ref.: #31881]	sucrose ChEBI	+	carbon source
[Ref.: #68367]	sucrose ChEBI	+	builds acid from	* from API 20A
[Ref.: #31881]	trehalose ChEBI	+	carbon source
[Ref.: #68380]	tryptophan ChEBI	-	energy source	* from API rID32A
[Ref.: #68380]	urea ChEBI	-	hydrolysis	* from API rID32A, API 20A
[Ref.: #31881]	xylose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite
[Ref.: #68380]		indole ChEBI	* 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.: #31881]	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.: #31881]	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-glucosidase	+	3.2.1.21	* from API rID32A, API 20A
[Ref.: #31881]	catalase	+	1.11.1.6
[Ref.: #68367]	gelatinase	-		* from API 20A
[Ref.: #68380]	glutamate decarboxylase	+	4.1.1.15	* 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]	tryptophan deaminase	-	4.1.99.1	* from API rID32A
[Ref.: #68380]	urease	-	3.5.1.5	* from API rID32A, API 20A
	Only first 10 entries are displayed. Click here to see all.

API® 20A:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Indole productionIND	Urease/urea hydrolysisURE	Acid from D-glucoseGLU	Acid from D-mannitolMAN	Acid from lactoseLAC	Acid from sucroseSAC	Acid from maltoseMAL	Acid from salicinSAL	Acid from D-xyloseXYL	Acid from L-arabinoseARA	Gelatinase/gelatin hydrolysisGEL	Esculin hydrolysis/beta-glucosidaseESC	Acid from glycerolGLY	Acid from cellobioseCEL	Acid from D-mannoseMNE	Acid from melezitoseMLZ	Acid from raffinoseRAF	Acid from sorbitolSOR	Acid from L-rhamnoseRHA	Acid from trehaloseTRE	CatalaseCAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
[Ref.: #7499]	1778	not determinedn.d.	-	+	-	+	+	+/-	-	+	+	-	+	-	-	+	+	+/-	-	+/-	+/-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

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.: #7499]	10954	-	-	+	+	-	+	+	+	+/-	+	+	+	+	-	-	-	+	+	-	+	+/-	+	-	+/-	+	+	+	+/-	+/-
[Ref.: #7499]	10953	-	-	+	+	-	+	+	+	-	+	+	+/-	+	-	-	-	+	+	-	+	+	+	+	+	+	+	+	+	+

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

[Ref.: #7499]	Sample type/isolated from	human faeces
[Ref.: #7499]	Country	Japan
[Ref.: #7499]	Country ISO 3 Code	JPN
[Ref.: #7499]	Continent	Asia

[Ref.: #60403]	Sample type/isolated from	Human feces

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

Isolation sources categories

#Host	#Human	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB261128 (>99% sequence identity) for Parabacteroides johnsonii subclade from Microbeatlas

Aquatic Samples	2276
Soil Samples	461
Animal Samples	67348
Plant Samples	159
Total Samples	70244

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

[Ref.: #7499]

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.: #7499]	Parabacteroides johnsonii gene for 16S ribosomal RNA, partial sequence	AB261128	1492	ENA	537006 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Parabacteroides johnsonii DSM 18315 DSM 18315	GCA_000156495	scaffold	GenBank	537006 tax ID
[Ref.: #66792]	Parabacteroides johnsonii DSM 18315	537006.5	wgs	PATRIC	537006 tax ID	*
[Ref.: #66792]	Parabacteroides johnsonii DSM 18315	642979358	draft	JGI IMG/M	537006 tax ID	*
[Ref.: #66792]	Parabacteroides johnsonii DSM 18315 DSM 18315	GCA_025151045	complete	GenBank	537006 tax ID	*
[Ref.: #66792]	Parabacteroides johnsonii DSM 18315	537006.36	complete	PATRIC	537006 tax ID	*

[Ref.: #7499]	GC-content	47.6 mol%
[Ref.: #7499]	GC-content	45.2 mol%	sequence analysis
[Ref.: #67770]	GC-content	47.6 mol%	high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #7499]

Culture collection no.

DSM 18315, CIP 109537, JCM 13406, CCUG 54943

[Ref.: #20218]

Associated Passport(s) in StrainInfo

690163, 900549, 681034

Literature:

	Title	Authors	Journal	DOI	Year
Phylogeny	Parabacteroides acidifaciens sp. nov., isolated from human faeces.	Wang YJ, Xu XJ, Zhou N, Sun Y, Liu C, Liu SJ, You X	Int J Syst Evol Microbiol	10.1099/ijsem.0.003230	2019	*
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	*
Phylogeny	Parabacteroides johnsonii sp. nov., isolated from human faeces.	Sakamoto M, Kitahara M, Benno Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64588-0	2007	*
	A 2.08 A resolution structure of HLB5, a novel cellulase from the anaerobic gut bacterium Parabacteroides johnsonii DSM 18315.	Chang C, Brooke C, Piao H, Mack J, Babnigg G, Joachimiak A, Hess M	Protein Sci	10.1002/pro.3582	2019	*

References

#7499

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18315

#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 )

#31881

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 #28141 (see below)

#34705 ; Curators of the CIP;
#60403 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 54943

#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;

#68367

Automatically annotated from API 20A .

#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 .

#28141

IJSEM 293 2007 ( DOI 10.1099/ijs.0.64588-0 , PubMed 17267966 )

* These data were automatically processed and therefore are not curated

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