Coprobacter secundus (CSUR P1909, DSM 100571, JCM 33965)

Name: Coprobacter secundus (CSUR P1909, DSM 100571, JCM 33965)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 160793

Type strain

Strain Designation GM3

Culture col. no. CSUR P1909 DSM 100571 JCM 33965 GM3

NCBI tax ID(s) 1686296

Special Collections DSMZ JCM Cadoret human gut

Links

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

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 400083

JCM 33965,DSM 100571

@ref 20215

Last LPSN update 2025-12-16 10:08:34

Domain Pseudomonadati

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Barnesiellaceae

Genus Coprobacter

Species Coprobacter secundus

Full scientific name Coprobacter secundus Shkoporov et al. 2015

Synonyms (1)

"Gabonia massiliensis"

BacDive ID	Other strains from **Coprobacter secundus** (1)	Type strain
140126	C. secundus 177, DSM 28864, VKM B-2857, JCM 33897 (type strain)

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	99.7
125438	negative	96.025

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
67730	FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a)		Medium recipe at MediaDive	Name: FASTIDIOUS ANAEROBE BROTH (DSMZ Medium 1203a) Composition: Fastidious Anaerobe Basal Broth 35.4 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
67730	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	anaerobe	94.3

Spore formation

@ref	Spore formation	Confidence
125439		98.8
125438		95

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

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

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68380	alpha-glucosidase	+	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	-		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	+	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

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
67730	-	-	+	+	-	+	-	-	-	+	-	-	-	+/-	-	-	+	-	-	+	-	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
67730	human stool specimen	Lebamba	Gabon	GAB	Africa
67770	Stool specimen from a healthy Gabonese male

Taxonmaps

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

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	Gabonia massiliensis assembly for Gabonia massiliensis GM3	scaffold	GCA_001403595	1686296.4	2681813420	1686296	65.21

Genome browser: GCA_001403595

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Porphyromonadaceae bacterium GM3 partial 16S rRNA gene, strain GM3	LN849789	1491		1686296

GC content

@ref	GC-content (mol%)	Method
67770	37.9	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Gabonia massiliensis GM3
NCBI: GCA_001403595

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.80	no
125439	motility	BacteriaNetⓘ	no	66.80	no
125439	gram_stain	BacteriaNetⓘ	negative	99.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	94.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Gabonia massiliensis GM3
NCBI: GCA_001403595.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.03	no
125438	anaerobic	anaerobicⓘ	yes	88.32	no
125438	aerobic	aerobicⓘ	no	92.12	no
125438	spore-forming	spore-formingⓘ	no	95.00	no
125438	thermophilic	thermophileⓘ	no	93.24	yes
125438	flagellated	motile2+ⓘ	no	88.00	no

Literature

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 .
#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 )

Rate our new design

Content

About us