Megasphaera massiliensis (DSM 26228, CSUR P245, NP3)

Name: Megasphaera massiliensis (DSM 26228, CSUR P245, NP3)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132967

Type strain

Strain Designation NP3

Culture col. no. DSM 26228 CSUR P245 NP3

NCBI tax ID(s) 1232428

Special Collections DSMZ Cadoret human gut

Links

Megasphaera massiliensis NP3 is a mesophilic prokaryote that was isolated from feces of a 32-year-old HIV-infected human patient.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 403381

DSM 26228

@ref 20215

Last LPSN update 2025-12-16 10:01:39

Domain Bacillati

Phylum Bacillota

Class Negativicutes

Order Veillonellales

Family Veillonellaceae

Genus Megasphaera

Species Megasphaera massiliensis

Full scientific name Megasphaera massiliensis Padmanabhan et al. 2016

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24755	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
24755	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

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
24755	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	anaerobe	90.4

Spore formation

@ref	Spore formation	Confidence
125439		98.1

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
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
68367	4853 ChEBI	esculin	+	hydrolysis	from API 20A
68367	5291 ChEBI	gelatin	-	hydrolysis	from API 20A
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
68367	62345 ChEBI	L-rhamnose	+	builds acid from	from API 20A
68367	17716 ChEBI	lactose	-	builds acid from	from API 20A
68367	17306 ChEBI	maltose	+	builds acid from	from API 20A
68367	6731 ChEBI	melezitose	-	builds acid from	from API 20A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68367	16634 ChEBI	raffinose	-	builds acid from	from API 20A
68367	17814 ChEBI	salicin	-	builds acid from	from API 20A
68367	30911 ChEBI	sorbitol	-	builds acid from	from API 20A
68367	17992 ChEBI	sucrose	-	builds acid from	from API 20A
68367	27082 ChEBI	trehalose	-	builds acid from	from API 20A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68367	27897 ChEBI	tryptophan	-	energy source	from API 20A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
68367	16199 ChEBI	urea	-	hydrolysis	from API 20A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A
68367	35581 ChEBI	indole		from API 20A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A
68367	35581 ChEBI	indole	-	from API 20A

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-fucosidase	-	3.2.1.51	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
68367	beta-glucosidase	+	3.2.1.21	from API 20A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68367	gelatinase	-		from API 20A
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
68367	urease	-	3.5.1.5	from API 20A

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
24755	-	-	+	+	-	-	+	-	+	-	-	+	-	-	-	-	-	-	+	-	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
24755	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Infection	#Disease
#Infection	#Patient
#Host	#Human
#Host Body Product	#Gastrointestinal tract

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
24755	feces of a 32-year-old HIV-infected human patient	Marseille (patient residence)	France	FRA	Europe

Taxonmaps

69479

Global distribution of 16S sequence JX424772 (>99% sequence identity) for Megasphaera massiliensis subclade from Microbeatlas

Aquatic Samples	623
Soil Samples	125
Animal Samples	12545
Plant Samples	60
Total Samples	13353

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24755	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Megasphaera_massiliensis assembly for Megasphaera massiliensis NP3	scaffold	GCA_000455225	1232428.4	2547132182	1232428	50.03

Genome browser: GCA_000455225

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24755	Megasphaera massiliensis strain NP3 16S ribosomal RNA gene, partial sequence	JX424772	1519		1232428

GC content

@ref	GC-content (mol%)	Method
24755	50.2	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Megasphaera massiliensis NP3
NCBI: GCA_000455225

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.10	no
125439	motility	BacteriaNetⓘ	no	75.30	no
125439	gram_stain	BacteriaNetⓘ	negative	74.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	90.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Megasphaera massiliensis NP3
NCBI: GCA_000455225.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	85.92	no
125438	anaerobic	anaerobicⓘ	yes	86.27	no
125438	aerobic	aerobicⓘ	no	89.91	no
125438	spore-forming	spore-formingⓘ	no	77.19	no
125438	thermophilic	thermophileⓘ	no	89.91	no
125438	flagellated	motile2+ⓘ	no	84.84	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Microbial short-chain fatty acids modulate CD8⁺ T cell responses and improve adoptive immunotherapy for cancer.	Luu M, Riester Z, Baldrich A, Reichardt N, Yuille S, Busetti A, Klein M, Wempe A, Leister H, Raifer H, Picard F, Muhammad K, Ohl K, Romero R, Fischer F, Bauer CA, Huber M, Gress TM, Lauth M, Danhof S, Bopp T, Nerreter T, Mulder IE, Steinhoff U, Hudecek M, Visekruna A.	Nat Commun	10.1038/s41467-021-24331-1	2021
Genetics	Biochemical and genome sequence analyses of Megasphaera sp. strain DISK18 from dental plaque of a healthy individual reveals commensal lifestyle.	Nallabelli N, Patil PP, Pal VK, Singh N, Jain A, Patil PB, Grover V, Korpole S.	Sci Rep	10.1038/srep33665	2016
Phylogeny	Description of Megasphaera jansseni sp. nov., a novel short- and medium-chain fatty acid-producing species isolated from faeces of a wild boar (Sus scrofa), and a taxonomic note on the family Veillonellaceae.	Heng YC, Lee JKY, Silvaraju S, Kittelmann S.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006937	2025
Genetics	Non-contiguous finished genome sequence and description of Megasphaera massiliensis sp. nov.	Padmanabhan R, Lagier JC, Dangui NP, Michelle C, Couderc C, Raoult D, Fournier PE.	Stand Genomic Sci	10.4056/sigs.4077819	2013
	Megasphaera lornae sp. nov., Megasphaera hutchinsoni sp. nov., and Megasphaera vaginalis sp. nov.: novel bacteria isolated from the female genital tract.	Srinivasan S, Beamer MA, Fiedler TL, Austin MN, Sizova MV, Strenk SM, Agnew KJ, Gowda GAN, Raftery D, Epstein SS, Fredricks DN, Hillier SL.	Int J Syst Evol Microbiol	10.1099/ijsem.0.004702	2019

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 )
#24755	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 26228
#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) .
#68367	Automatically annotated from API 20A .
#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 )

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Megasphaera massiliensis (DSM 26228, CSUR P245, NP3)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20A

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000455225

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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