Name: Coprobacter secundus GM3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 160793

Type strain:

Species: Coprobacter secundus

Strain Designation: GM3

Culture col. no.: DSM 100571, JCM 33965, CSUR P1909

Strain history: DSM 100571 <-- S. Khelaifia, Timone Hosp., Marseille, France; GM3 <-- Unité de Recherche sur les Maladies Infectieuses et Tropicales É ergentes, France.

NCBI tax ID(s): 1686296 (species)

Other strains from Coprobacter secundus

C. secundus 177, DSM 28864, VKM B-2857, JCM ... (type strain)

Section

Coprobacter secundus GM3 is a mesophilic bacterium that was isolated from human stool specimen.

mesophilic
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	*Barnesiellaceae*
	Genus	*Coprobacter*
	Species	**Coprobacter secundus**
	Full Scientific Name (LPSN)	Coprobacter secundus Shkoporov et al. 2015

Synonym

"Gabonia massiliensis"

Information on culture and growth conditions Culture and growth conditions

[Ref.: #67730]

Culture medium

FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)

[Ref.: #67730]

Culture medium growth

[Ref.: #67730]

Culture medium link

Medium recipe at MediaDive

[Ref.: #67730]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #67730]			growth	37 °C
[Ref.: #67770]			growth	37 °C

[Ref.: #67730]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

	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.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[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.: #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-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.: #67730]	12493	-	-	+	+	-	+	-	-	-	+	-	-	-	+/-	-	-	+	-	-	+	-	-	-	-	+	-	-	-	-

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

[Ref.: #67730]	Sample type/isolated from	human stool specimen
[Ref.: #67730]	Geographic location (country and/or sea, region)	Lebamba
[Ref.: #67730]	Country	Gabon
[Ref.: #67730]	Country ISO 3 Code	GAB
[Ref.: #67730]	Continent	Africa

[Ref.: #67770]	Sample type/isolated from	Stool specimen from a healthy Gabonese male
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence LN849789 (>99% sequence identity) for Bacteroidales from Microbeatlas

Aquatic Samples	186
Soil Samples	38
Animal Samples	12866
Plant Samples	9
Total Samples	13099

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.: #67770]	Porphyromonadaceae bacterium GM3 partial 16S rRNA gene, strain GM3	LN849789	1491	ENA	1686296 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Gabonia massiliensis GM3	GCA_001403595	scaffold	GenBank	1686296 tax ID

[Ref.: #67770]

GC-content

37.9 mol%

genome sequence analysis

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Gabonia massiliensis GM3 NCBI: GCA_001403595.1
[Ref.: #69480]	flagellated	no	96.3	no
[Ref.: #69480]	gram-positive	no	97.798	no
[Ref.: #69480]	anaerobic	yes	99.07	no
[Ref.: #69480]	aerobic	no	95.582	no
[Ref.: #69480]	halophile	no	82.771	no
[Ref.: #69480]	spore-forming	no	94.923	no
[Ref.: #69480]	glucose-util	yes	87.654	no
[Ref.: #69480]	thermophile	no	97.223	no
[Ref.: #69480]	motile	no	91.091	no
[Ref.: #69480]	glucose-ferment	yes	58.35	no

Availability in culture collections External links

[Ref.: #67730]

Culture collection no.

DSM 100571, JCM 33965, CSUR P1909

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 )

#67730

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100571

#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) .

* These data were automatically processed and therefore are not curated

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Gabonia massiliensis GM3

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