Parabacteroides johnsonii (DSM 18315, CIP 109537, JCM 13406)

Name: Parabacteroides johnsonii (DSM 18315, CIP 109537, JCM 13406)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 12498

Type strain

Strain Designation M-165

Culture col. no. DSM 18315 CIP 109537 JCM 13406 CCUG 54943 M-165

NCBI tax ID(s) 537006 387661

Special Collections DSMZ CCUG JCM CIP Literature strains

History <- M. Sakamoto; M-165 <- M. Kitahara M. Sakamoto <-- M. Kitahara M-165. CIP <- 2007, DSMZ <- M. Sakamoto, Bioresources Cent., Saitama, Japan: strain M-165

Links

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

Gram-negative rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 293991

JCM 13406,DSM 18315,CIP 109537,CCUG 54943

@ref 20215

Last LPSN update 2025-12-16 09:49:51

Domain Pseudomonadati

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Tannerellaceae

Genus Parabacteroides

Species Parabacteroides johnsonii

Full scientific name Parabacteroides johnsonii Sakamoto et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31881	negative	1.7-2.5 µm	0.8 µm	rod-shaped
120361	negative			rod-shaped
125439	negative				98.6
125438	negative				93.023

Colony morphology

@ref	Incubation period
7499	1-2 days
60403	2 days

Pigmentation

31881

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7499	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
7499	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)	Medium recipe at MediaDive	Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water
34705	MEDIUM 20 - for Anaerobic bacteria		Agar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
120361	CIP Medium 137	Medium recipe at CIP
120361	CIP Medium 20	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7499	positive	growth	37	mesophilic
34705	positive	growth	37	mesophilic
60403	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
7499	anaerobe
31881	anaerobe
60403	anaerobe
120361	anaerobe
125439	obligate anaerobe	99.5

Spore formation

@ref	Spore formation	Confidence
31881
125439		99.3
125438		93.243

Observation

67770

Observationquinones: MK-9, MK-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31881	22599 ChEBI	arabinose	+	carbon source
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68367	17057 ChEBI	cellobiose	-	builds acid from	from API 20A
68367	17634 ChEBI	D-glucose	+	builds acid from	from API 20A
68367	16899 ChEBI	D-mannitol	-	builds acid from	from API 20A
68380	16024 ChEBI	D-mannose	+	fermentation	from API rID32A
68367	16024 ChEBI	D-mannose	+	builds acid from	from API 20A
68367	65327 ChEBI	D-xylose	+	builds acid from	from API 20A
31881	4853 ChEBI	esculin	+	hydrolysis
68367	4853 ChEBI	esculin	+	hydrolysis	from API 20A
68367	5291 ChEBI	gelatin	-	hydrolysis	from API 20A
31881	17234 ChEBI	glucose	+	carbon source
68367	17754 ChEBI	glycerol	-	builds acid from	from API 20A
68367	30849 ChEBI	L-arabinose	+	builds acid from	from API 20A
68380	29985 ChEBI	L-glutamate	+	degradation	from API rID32A
31881	17716 ChEBI	lactose	+	carbon source
68367	17716 ChEBI	lactose	+	builds acid from	from API 20A
31881	17306 ChEBI	maltose	+	carbon source
31881	37684 ChEBI	mannose	+	carbon source
68367	6731 ChEBI	melezitose	+	builds acid from	from API 20A
120361	17632 ChEBI	nitrate	-	reduction
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
120361	16301 ChEBI	nitrite	-	reduction
31881	16634 ChEBI	raffinose	+	carbon source
31881	26546 ChEBI	rhamnose	+	carbon source
68367	17814 ChEBI	salicin	-	builds acid from	from API 20A
68367	30911 ChEBI	sorbitol	-	builds acid from	from API 20A
31881	17992 ChEBI	sucrose	+	carbon source
68367	17992 ChEBI	sucrose	+	builds acid from	from API 20A
31881	27082 ChEBI	trehalose	+	carbon source
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
68367	16199 ChEBI	urea	-	hydrolysis	from API 20A
31881	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A
120361	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
31881	alkaline phosphatase	+	3.1.3.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	+	3.2.1.55	from API rID32A
68382	alpha-chymotrypsin	+	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
31881	alpha-galactosidase	+	3.2.1.22
68382	alpha-galactosidase	+	3.2.1.22	from API zym
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68382	beta-galactosidase	+	3.2.1.23	from API zym
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68382	beta-glucosidase	-	3.2.1.21	from API zym
68380	beta-glucosidase	+	3.2.1.21	from API rID32A
68367	beta-glucosidase	+	3.2.1.21	from API 20A
68382	beta-glucuronidase	-	3.2.1.31	from API zym
31881	catalase	+	1.11.1.6
120361	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	-		from API zym
68382	esterase lipase (C 8)	-		from API zym
68367	gelatinase	-		from API 20A
68380	glutamate decarboxylase	+	4.1.1.15	from API rID32A
68380	glycin arylamidase	+		from API rID32A
68380	histidine arylamidase	+		from API rID32A
68380	L-arginine arylamidase	+		from API rID32A
68382	leucine arylamidase	+	3.4.11.1	from API zym
68380	leucine arylamidase	+	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	+	3.4.11.1	from API rID32A
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68380	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API rID32A
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
120361	oxidase	-
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68382	trypsin	-	3.4.21.4	from API zym
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
120361	urease	-	3.5.1.5
68380	urease	-	3.5.1.5	from API rID32A
68367	urease	-	3.5.1.5	from API 20A
68382	valine arylamidase	-		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
120361	-	+	-	-	-	+	-	-	-	+	+	-	+	+	-	-	-	+	-	-

API 20A

@ref	IND	URE	GLU	MAN	LAC	SAC	MAL	SAL	XYL	ARA	GEL	ESC	GLY	CEL	MNE	MLZ	RAF	SOR	RHA	TRE	CAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
7499	not determinedn.d.	-	+	-	+	+	+/-	-	+	+	-	+	-	-	+	+	+/-	-	+/-	+/-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
7499	-	-	+	+	-	+	+	+	+/-	+	+	+	+	-	-	-	+	+	-	+	+/-	+	-	+/-	+	+	+	+/-	+/-
7499	-	-	+	+	-	+	+	+	-	+	+	+/-	+	-	-	-	+	+	-	+	+	+	+	+	+	+	+	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
7499	human faeces	Japan	JPN	Asia
60403	Human feces
67770	Human feces
120361	Human, Faeces	Japan	JPN	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7499	1	Risk group (German classification) According to TRBA 466
120361	2	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2515104v1 assembly for Parabacteroides johnsonii DSM 18315	complete	GCA_025151045	537006.36	8119248302	537006	97.6
67770	ASM15649v1 assembly for Parabacteroides johnsonii DSM 18315	scaffold	GCA_000156495	537006.5	642979358	537006

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7499	Parabacteroides johnsonii gene for 16S ribosomal RNA, partial sequence	AB261128	1492		537006

GC content

@ref	GC-content (mol%)	Method
7499	47.6
7499	45.2	sequence analysis
67770	47.6	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Parabacteroides johnsonii DSM 18315
NCBI: GCA_025151045

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.30	no
125439	motility	BacteriaNetⓘ	no	76.90	no
125439	gram_stain	BacteriaNetⓘ	negative	98.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	99.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Parabacteroides johnsonii DSM 18315 DSM 18315
NCBI: GCA_025151045.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	93.02	yes
125438	anaerobic	anaerobicⓘ	yes	86.45	no
125438	aerobic	aerobicⓘ	no	90.84	yes
125438	spore-forming	spore-formingⓘ	no	93.24	yes
125438	thermophilic	thermophileⓘ	no	92.87	no
125438	flagellated	motile2+ⓘ	no	89.50	yes

Literature

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Genetics	The estrobolome: Estrogen-metabolizing pathways of the gut microbiome and their relation to breast cancer.	Larnder AH, Manges AR, Murphy RA.	Int J Cancer	10.1002/ijc.35427	2025
Enzymology	Isolation and screening of wood-decaying fungi for lignocellulolytic enzyme production and bioremediation processes.	Civzele A, Mezule L.	Front Fungal Biol	10.3389/ffunb.2024.1494182	2024
Enzymology	Fungal Ligninolytic Enzymes and Their Application in Biomass Lignin Pretreatment.	Civzele A, Stipniece-Jekimova AA, Mezule L.	J Fungi (Basel)	10.3390/jof9070780	2023
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Pathogenicity	Microbiota-derived bile acids antagonize the host androgen receptor and drive anti-tumor immunity.	Jin WB, Xiao L, Jeong M, Han SJ, Zhang W, Yano H, Shi H, Arifuzzaman M, Lyu M, Wang D, Tang YA, Qiao S, JRI IBD Live Cell Bank Consortium, Yang X, Yang HS, Fu J, Sonnenberg GF, Collins N, Artis D, Guo CJ.	Cell	10.1016/j.cell.2025.02.029	2025
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Phylogeny	Parabacteroides faecalis sp. nov. Isolated from Swine Faeces.	Bak JE, Oh BS, Ryu SW, Yu SY, Choi WJ, Kim JS, Lee JS, Park SH, Kang SW, Lee J, Lee MK, Yun CS, Jung WY, Kim JE, Cho ES, Kim HB, Kim JK, Lee JH, Lee JH.	Curr Microbiol	10.1007/s00284-023-03190-7	2023
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Phylogeny	Acinetobacter kookii sp. nov., isolated from soil.	Choi JY, Ko G, Jheong W, Huys G, Seifert H, Dijkshoorn L, Ko KS.	Int J Syst Evol Microbiol	10.1099/ijs.0.047969-0	2013
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

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 )
#28141	IJSEM 293 2007 ( DOI 10.1099/ijs.0.64588-0 , PubMed 17267966 )
#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
#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 .
#68382	Automatically annotated from API zym .
#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 .
#120361	Collection of Institut Pasteur ; Curators of the CIP; CIP 109537
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Parabacteroides johnsonii (DSM 18315, CIP 109537, JCM 13406)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 20A

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

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Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_025151045

16S sequences

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