Name: Parabacteroides merdae T4-1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 12499

Type strain:

Species: Parabacteroides merdae

Strain Designation: T4-1

Culture col. no.: DSM 19495, ATCC 43184, CCUG 38734, CIP 104202, JCM 9497, VPI T4-1, NCTC 13052

Strain history: CIP <- 1994, ATCC <- L.V. Moore, VPI: strain T4-1 <- W.E.C. Moore

NCBI tax ID(s): 411477 (strain), 46503 (species)

SI-ID 41698

ATCC 43184, CIP 104202, JCM 9497, CCUG 38734, NCTC 13052, DSM 19495, VTT E-062953

Special Collections

Other strains from Parabacteroides merdae

Section

Parabacteroides merdae T4-1 is an anaerobe, Gram-negative, rod-shaped human pathogen that was isolated from human faeces.

Gram-negative
rod-shaped
anaerobe
human pathogen
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 merdae**
	Full Scientific Name (LPSN)	Parabacteroides merdae (Johnson et al. 1986) Sakamoto and Benno 2006

Synonym

Bacteroides merdae

Information on morphological and physiological properties Morphology

[Ref.: #120896]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %93.856

[Ref.: #120896]	Cell shape	rod-shaped

[Ref.: #120896]	Motility	no

[Ref.: #8118]

Incubation period

1-2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8118]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #8118]

Culture medium growth

[Ref.: #8118]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8118]

Culture medium composition

expand / minimize

[Ref.: #8118]

Culture medium

CHOPPED MEAT MEDIUM (DSMZ Medium 78)

[Ref.: #8118]

Culture medium growth

[Ref.: #8118]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8118]

Culture medium composition

expand / minimize

[Ref.: #34044]

Culture medium

MEDIUM 20 - for Anaerobic bacteria

[Ref.: #34044]

Culture medium growth

[Ref.: #34044]

Culture medium composition

expand / minimize

[Ref.: #120896]

Culture medium

CIP Medium 20

[Ref.: #120896]

Culture medium growth

[Ref.: #120896]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #8118]	growth	37 °C
[Ref.: #34044]	growth	37 °C
[Ref.: #54425]	growth	37 °C
[Ref.: #67770]	growth	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #8118]	Oxygen tolerance	anaerobe
[Ref.: #54425]	Oxygen tolerance	anaerobe

[Ref.: #69480]

Ability of spore formation

no Confidence in %93.833

[Ref.: #67770]

Observation

quinones: MK-9, MK-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]	arginine ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #68380]	D-mannose ChEBI	+	fermentation	* from API rID32A
[Ref.: #120896]	nitrate ChEBI	-	reduction
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #120896]	nitrite ChEBI	-	reduction
[Ref.: #68380]	raffinose ChEBI	+	fermentation	* from API rID32A
[Ref.: #68380]	tryptophan ChEBI	-	energy source	* from API rID32A
[Ref.: #68380]	urea ChEBI	-	hydrolysis	* from API rID32A

	Metabolite production	Metabolite	Production
[Ref.: #120896]		indole ChEBI	no
[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.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #68380]	alanine arylamidase	+	3.4.11.2	* from API rID32A
[Ref.: #68380]	alkaline phosphatase	+	3.1.3.1	* from API rID32A, API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68380]	alpha-fucosidase	-	3.2.1.51	* from API rID32A, API zym
[Ref.: #68380]	alpha-galactosidase	+	3.2.1.22	* from API rID32A
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68380]	alpha-glucosidase	+	3.2.1.20	* from API rID32A
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68380]	arginine dihydrolase	-	3.5.3.6	* from API rID32A
[Ref.: #68380]	beta-galactosidase	+	3.2.1.23	* from API rID32A, API zym
[Ref.: #68380]	beta-Galactosidase 6-phosphate	-		* from API rID32A
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #120896]	catalase	-	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	-		* from API zym
[Ref.: #68380]	glutamyl-glutamate 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, API zym
[Ref.: #68380]	leucyl glycin arylamidase	+	3.4.11.1	* from API rID32A
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68380]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API rID32A, API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #120896]	oxidase	-
[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.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68380]	tryptophan deaminase	-	4.1.99.1	* from API rID32A
[Ref.: #120896]	urease	-	3.5.1.5
[Ref.: #68380]	urease	-	3.5.1.5	* from API rID32A
[Ref.: #68382]	valine arylamidase	-		* from API zym
	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.: #8118]	12277	-	-	+	+	-	+	+	+	+/-	+	+	+	-	-	-	-	+	+	-	+	+	+	-	+	+	+	+	+	-
[Ref.: #8118]	12276	-	-	+	+	-	+	+/-	+/-	-	+	+	+	+	-	-	-	+	+	-	+	+	+	-	+/-	+	+/-	+	+	-

API® zym:

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

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #120896]	7838	-	+	-	-	-	+	-	-	-	-	-	+	-	+	-	-	-	+	-	-

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

[Ref.: #8118]	Sample type/isolated from	human faeces
[Ref.: #8118]	Country	USA
[Ref.: #8118]	Country ISO 3 Code	USA
[Ref.: #8118]	Continent	North America

[Ref.: #54425]	Sample type/isolated from	Human feces
[Ref.: #54425]	Geographic location (country and/or sea, region)	Texas
[Ref.: #54425]	Country	USA
[Ref.: #54425]	Country ISO 3 Code	USA
[Ref.: #54425]	Continent	North America

[Ref.: #67770]	Sample type/isolated from	Human feces

[Ref.: #120896]	Sample type/isolated from	Human, Feces
[Ref.: #120896]	Geographic location (country and/or sea, region)	Texas
[Ref.: #120896]	Country	United States of America
[Ref.: #120896]	Country ISO 3 Code	USA
[Ref.: #120896]	Continent	North America
[Ref.: #120896]	Isolation date	1972
* 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 EU136685 (>99% sequence identity) for Parabacteroides merdae subclade from Microbeatlas

Aquatic Samples	11747
Soil Samples	3196
Animal Samples	284785
Plant Samples	969
Total Samples	300697

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

[Ref.: #8118]	Pathogenicity (human)	yes, in single cases
[Ref.: #8118]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120896]	Biosafety level	2	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #8118]	B.merdae 16S rRNA (ATCC 43184T)	X83954	1405	GenBank ENA	411477 tax ID
[Ref.: #8118]	Parabacteroides merdae ATCC 43184 16S ribosomal RNA, partial sequence	NR_119166	1405	GenBank ENA	411477 tax ID
[Ref.: #20218]	Parabacteroides merdae gene for 16S ribosomal RNA, partial sequence, strain: JCM 9497	AB238928	1492	GenBank ENA	46503 tax ID	*
[Ref.: #20218]	Bacteroides merdae 16S-23S ribosomal RNA intergenic spacer region, partial sequence	AY153427	431	GenBank ENA	411477 tax ID	*
[Ref.: #20218]	Parabacteroides merdae strain JCM9497 16S ribosomal RNA gene, partial sequence	EU136685	2023	GenBank ENA	46503 tax ID	*
[Ref.: #20218]	Bacteroides merdae 16S ribosomal RNA gene, partial sequence	U50416	62	GenBank ENA	411477 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Parabacteroides merdae ATCC 43184	411477.87	complete	PATRIC	411477 tax ID	*
[Ref.: #66792]	Parabacteroides merdae ATCC 43184	411477.4	wgs	PATRIC	411477 tax ID	*
[Ref.: #66792]	Parabacteroides merdae strain NCTC13052	46503.89	wgs	PATRIC	46503 tax ID	*
[Ref.: #66792]	Parabacteroides merdae NCTC 13052	2811995281	draft	JGI IMG/M	46503 tax ID	*
[Ref.: #66792]	Parabacteroides merdae ATCC 43184	640963016	draft	JGI IMG/M	411477 tax ID	*
[Ref.: #66792]	Parabacteroides merdae ATCC 43184	GCA_000154105	scaffold	GenBank ENA	411477 tax ID	*

[Ref.: #8118]	GC-content	44 mol%
[Ref.: #8118]	GC-content	45.3 mol%	sequence analysis
[Ref.: #67770]	GC-content	44 mol%	thermal denaturation, midpoint method (Tm)

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: Parabacteroides merdae ATCC 43184 ATCC 43184 NCBI: GCA_025151215.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	93.856	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	88.37	no
[Ref.: #69480]	aerobic	aerobicⓘ	no	94.206	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	93.833	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	92.37	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	88	no

Availability in culture collections External links

[Ref.: #8118]

Culture collection no.

DSM 19495, ATCC 43184, CCUG 38734, CIP 104202, JCM 9497, VPI T4-1, NCTC 13052

[Ref.: #81718]

SI-ID 41698

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Parabacteroides pekinense sp. nov.: a new bacterium isolated from the stool of a healthy man living in China.	Li Z, Zhou X, Xu W, Chen R, Zhao B, Wu C	New Microbes New Infect	10.1016/j.nmni.2022.100973	2022	*
Phylogeny	Parabacteroides massiliensis sp. nov., a new bacterium isolated from a fresh human stool specimen.	Bellali S, Lo CI, Naud S, Fonkou MDM, Armstrong N, Raoult D, Fournier PE, Fenollar F	New Microbes New Infect	10.1016/j.nmni.2019.100602	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 chartae sp. nov., an obligately anaerobic species from wastewater of a paper mill.	Tan HQ, Li TT, Zhu C, Zhang XQ, Wu M, Zhu XF	Int J Syst Evol Microbiol	10.1099/ijs.0.038000-0	2011	*
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	*
Phylogeny	Reclassification of Bacteroides distasonis, Bacteroides goldsteinii and Bacteroides merdae as Parabacteroides distasonis gen. nov., comb. nov., Parabacteroides goldsteinii comb. nov. and Parabacteroides merdae comb. nov.	Sakamoto M, Benno Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64192-0	2006	*
Phylogeny	"Bacteroides goldsteinii sp. nov." isolated from clinical specimens of human intestinal origin.	Song Y, Liu C, Lee J, Bolanos M, Vaisanen ML, Finegold SM	J Clin Microbiol	10.1128/JCM.43.9.4522-4527.2005	2005	*
Enzymology	Detection of Bacteroides fragilis in clinical specimens by polymerase chain reaction amplification of the neuraminidase gene.	Jotwani R, Kato N, Kato H, Watanabe K, Ueno K	Curr Microbiol	10.1007/BF00298376	1995	*

References

#8118

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19495

#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 )

#34044 ; Curators of the CIP;
#54425 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 38734

#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 .

#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 .

#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) .

#81718

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-ID41698.1 )

#120896 Collection of Institut Pasteur ; Curators of the CIP; CIP 104202
* These data were automatically processed and therefore are not curated

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Parabacteroides merdae ATCC 43184 ATCC 43184

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