Clostridium merdae (DSM 103669, Marseille-P2953)

Name: Clostridium merdae (DSM 103669, Marseille-P2953)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140416

Type strain

Culture col. no. DSM 103669 Marseille-P2953

NCBI tax ID(s) 1958780

Special Collections DSMZ Cadoret human gut

Links

Clostridium merdae DSM 103669 is a mesophilic bacterium that was isolated from stool sample from patient.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 397331

DSM 103669

@ref 43023

Domain Bacteria

Phylum Firmicutes

Class Clostridia

Order Anaeroplasmatales

Family Clostridiaceae

Genus Clostridium

Species Clostridium merdae

Full scientific name Clostridium merdae Ndongo et al. 2017

Type strain no

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
43023	CMC MEDIUM (N2/CO2) (DSMZ Medium 110a)		Medium recipe at MediaDive	Name: CMC MEDIUM (N2/CO2) (DSMZ Medium 110a) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Yeast extract 5.0 g/l K2HPO4 5.0 g/l D-Glucose 4.0 g/l Na2CO3 1.5 g/l Cellobiose 1.0 g/l Maltose 1.0 g/l Starch 1.0 g/l L-Cysteine HCl x H2O 0.5 g/l Sodium resazurin 0.0005 g/l NaOH Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
43023	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	96.7

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
43023	stool sample from patient	Marseille	France	FRA	Europe

Taxonmaps

69479

Global distribution of 16S sequence LT732642 (>99% sequence identity) for Clostridium merdae from Microbeatlas

Aquatic Samples	53
Soil Samples	74
Animal Samples	587
Plant Samples	80
Total Samples	794

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	PRJEB20369 assembly for Clostridium merdae Marseille-P2953	contig	GCA_900176635	1958780.3	2791355326	1958780	75.44

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
43023	Clostridium merdae partial 16S rRNA gene, type strain Marseille-P2953T	LT732642	1482		1958780

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Clostridium merdae Marseille-P2953
NCBI: GCA_900176635

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	63.30	no
125439	motility	BacteriaNetⓘ	yes	60.60	no
125439	gram_stain	BacteriaNetⓘ	variable	71.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.70	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Three Novel Clostridia Isolates Produce n-Caproate and iso-Butyrate from Lactate: Comparative Genomics of Chain-Elongating Bacteria.	Liu B, Popp D, Muller N, Strauber H, Harms H, Kleinsteuber S.	Microorganisms	10.3390/microorganisms8121970	2020
Metabolism	Unravelling lactate-acetate and sugar conversion into butyrate by intestinal Anaerobutyricum and Anaerostipes species by comparative proteogenomics.	Shetty SA, Boeren S, Bui TPN, Smidt H, de Vos WM.	Environ Microbiol	10.1111/1462-2920.15269	2020
	The Isolate Caproiciproducens sp. 7D4C2 Produces n-Caproate at Mildly Acidic Conditions From Hexoses: Genome and rBOX Comparison With Related Strains and Chain-Elongating Bacteria.	Esquivel-Elizondo S, Bagci C, Temovska M, Jeon BS, Bessarab I, Williams RBH, Huson DH, Angenent LT.	Front Microbiol	10.3389/fmicb.2020.594524	2020
Metabolism	Identification of novel autoinducer-2 receptors in Clostridia reveals plasticity in the binding site of the LsrB receptor family.	Torcato IM, Kasal MR, Brito PH, Miller ST, Xavier KB.	J Biol Chem	10.1074/jbc.ra118.006938	2019
	Taxonogenomic description of four new Clostridium species isolated from human gut: 'Clostridium amazonitimonense', 'Clostridium merdae', 'Clostridium massilidielmoense' and 'Clostridium nigeriense'.	Alou MT, Ndongo S, Fregere L, Labas N, Andrieu C, Richez M, Couderc C, Baudoin JP, Abrahao J, Brah S, Diallo A, Sokhna C, Cassir N, La Scola B, Cadoret F, Raoult D	New Microbes New Infect	10.1016/j.nmni.2017.11.003	2017
Phylogeny	'Collinsella phocaeensis' sp. nov., 'Clostridium merdae' sp. nov., 'Sutterella massiliensis' sp. nov., 'Sutturella timonensis' sp. nov., 'Enorma phocaeensis' sp. nov., 'Mailhella massiliensis' gen. nov., sp. nov., 'Mordavella massiliensis' gen. nov., sp. nov. and 'Massiliprevotella massiliensis' gen. nov., sp. nov., 9 new species isolated from fresh stool samples of healthy French patients.	Ndongo S, Cadoret F, Dubourg G, Delerce J, Fournier PE, Raoult D, Lagier JC	New Microbes New Infect	10.1016/j.nmni.2017.02.005	2017

References

#43023	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 103669
#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) .
#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 .
#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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Clostridium merdae (DSM 103669, Marseille-P2953)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_900176635

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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