Endomicrobium proavitum (DSM 29378, JCM 30189, Rsa215)

Name: Endomicrobium proavitum (DSM 29378, JCM 30189, Rsa215)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132651

Type strain

Strain Designation Rsa215

Culture col. no. DSM 29378 JCM 30189 Rsa215 JCM 32103

NCBI tax ID(s) 1408281

Special Collections DSMZ JCM

History <- A. Brune, MPI, Marburg, Germany; Rsa215 <- H. Zheng A. Brune; Max Planck Inst. for Terrestrial Microbiol., Germany; Rsa215.

Links

Endomicrobium proavitum Rsa215 is a mesophilic prokaryote that was isolated from filtered gut homogenate of starch-fed termite Reticulitermes santonensis .

mesophilic genome sequence

Name and taxonomic classification

SI-ID 405635

JCM 32103,DSM 29378

@ref 20215

Last LPSN update 2026-02-09 11:31:46

Domain Bacteria

Phylum Elusimicrobiota

Class Endomicrobiia

Order Endomicrobiales

Family Endomicrobiaceae

Genus Endomicrobium

Species Endomicrobium proavitum

Full scientific name Endomicrobium proavitum Zheng et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	93.423

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24440	OMIZ-PAT (DSMZ Medium 1494)		Medium recipe at MediaDive	Name: . OMIZ-PAT Medium (modified) (DSMZ Medium 1494) Composition: (NH4)6Mo7O24 x 4 H2O 12.4 g/l Yeast extract 3.0 g/l Fe SO4 x 7 H2O 2.78015 g/l D-Glucose 2.0 g/l D-Mannose 2.0 g/l D-Arabinose 2.0 g/l L-Fucose 2.0 g/l D-Trehalose 2.0 g/l D-Sucrose 2.0 g/l L-Rhamnose 2.0 g/l NH4Cl 1.6 g/l Glutathione 1.5366 g/l Ascorbic acid 1.0 g/l NaHCO3 1.0 g/l Ethanol 1.0 g/l KCl 0.968 g/l D-Maltose 0.8 g/l D-glucuronic acid 0.8 g/l D-Mannitol 0.8 g/l D-galacturonic acid 0.8 g/l D-Fructose 0.8 g/l L-Glutamine 0.68 g/l L-Histidine 0.62 g/l NaVO3 0.61 g/l D 0.56 g/l Pyruvic acid 0.55 g/l L-Serine 0.525 g/l Fumaric acid 0.5 g/l HCl 0.3646 g/l L-Cysteine HCl 0.35 g/l L-Glutamic acid 0.3 g/l Formic acid 0.3 g/l ZnSO4 x 7 H2O 0.287 g/l MgSO4 x 7 H2O 0.25 g/l DL-carnitine 0.2 g/l N-Acetylglucosamine 0.2 g/l Citric acid 0.2 g/l L-Lysine HCl 0.182 g/l L-Arginine 0.175 g/l L-Ornithine HCl 0.17 g/l L-Phenylalanine 0.165 g/l CaCl2 x H2O 0.15 g/l L-Methionine 0.15 g/l L-Asparagine 0.15 g/l NaH2PO4 x H2O 0.14 g/l L-Leucine 0.131 g/l L-Isoleucine 0.131 g/l NiSO4 x 6 H2O 0.131 g/l L-Threonine 0.12 g/l L-Aspartic acid 0.118 g/l SnCl2 x 2 H2O 0.118 g/l L-Valine 0.117 g/l L-Proline 0.115 g/l L-Tryptophan 0.102 g/l Nicotinic acid 0.1 g/l Folinic acid 0.1 g/l L-Tyrosine 0.09 g/l NaOH 0.079994 g/l Glycine 0.075 g/l Nicotinamide 0.05 g/l Folic acid 0.05 g/l D-(+)-biotin 0.05 g/l Vitamine B12 0.05 g/l Choline chloride 0.05 g/l Myo-inositol 0.05 g/l L-Alanine 0.045 g/l Hemin 0.026076 g/l N-acetylmuramic acid 0.025 g/l Na2SeO3 0.0173 g/l MnSO4 x H2O 0.0169 g/l Riboflavine 0.01 g/l 2-Mercaptoethanesulfonic acid 0.01 g/l Phenol red 0.01 g/l Putrescine 2 HCl 0.005 g/l Pyridoxal hydrochloride 0.005 g/l Pyridoxal phosphate 0.005 g/l Calcium D-(+)-pantothenate 0.005 g/l Thiamine HCl 0.005 g/l Thiamin pyrophosphate 0.005 g/l Thymidine 0.0024 g/l N-(2-acetamido)-2-aminoethanesulfonic acid 0.0018 g/l Hypoxanthine 0.0014 g/l Uracil 0.0011 g/l Flavin adenine dinucleotide 0.001 g/l ß-nicotinamide adenine dinucleotide 0.001 g/l Coenzym A 0.001 g/l CuSO4 0.000789 g/l Cholesterol Asialofetuin 2-Mercaptoethanol Isovaleric acid Valeric acid 2-Methylbutyric acid Isobutyric acid DL-alpha-lipoic acid Rabbit serum Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
24440	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	anaerobe	93.222

Spore formation

@ref	Spore formation	Confidence
125439		96.4
125438		93.185

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	suberin monomers biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	palmitate biosynthesis	90.91	20 of 22
66794	chorismate metabolism	88.89	8 of 9
66794	methylglyoxal degradation	80	4 of 5
66794	threonine metabolism	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	ppGpp biosynthesis	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	sulfopterin metabolism	75	3 of 4
66794	pyrimidine metabolism	73.33	33 of 45
66794	NAD metabolism	72.22	13 of 18
66794	photosynthesis	71.43	10 of 14
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	starch degradation	70	7 of 10
66794	flavin biosynthesis	66.67	10 of 15
66794	d-mannose degradation	66.67	6 of 9
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	valine metabolism	66.67	6 of 9
66794	lipid A biosynthesis	66.67	6 of 9
66794	alanine metabolism	65.52	19 of 29
66794	purine metabolism	64.89	61 of 94
66794	glycolysis	64.71	11 of 17
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	gluconeogenesis	62.5	5 of 8
66794	glutamate and glutamine metabolism	60.71	17 of 28
66794	hydrogen production	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	serine metabolism	55.56	5 of 9
66794	urea cycle	53.85	7 of 13
66794	vitamin B1 metabolism	53.85	7 of 13
66794	phenylalanine metabolism	53.85	7 of 13
66794	biotin biosynthesis	50	2 of 4
66794	methionine metabolism	50	13 of 26
66794	glycine metabolism	50	5 of 10
66794	cysteine metabolism	50	9 of 18
66794	kanosamine biosynthesis II	50	1 of 2
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	butanoate fermentation	50	2 of 4
66794	lysine metabolism	45.24	19 of 42
66794	histidine metabolism	44.83	13 of 29
66794	polyamine pathway	43.48	10 of 23
66794	citric acid cycle	42.86	6 of 14
66794	oxidative phosphorylation	42.86	39 of 91
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	tyrosine metabolism	42.86	6 of 14
66794	arginine metabolism	41.67	10 of 24
66794	arachidonate biosynthesis	40	2 of 5
66794	lipid metabolism	38.71	12 of 31
66794	leucine metabolism	38.46	5 of 13
66794	isoprenoid biosynthesis	38.46	10 of 26
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	non-pathway related	36.84	14 of 38
66794	proline metabolism	36.36	4 of 11
66794	vitamin B6 metabolism	36.36	4 of 11
66794	sphingosine metabolism	33.33	2 of 6
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	formaldehyde oxidation	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	L-lactaldehyde degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	tryptophan metabolism	31.58	12 of 38
66794	propionate fermentation	30	3 of 10
66794	coenzyme M biosynthesis	30	3 of 10
66794	ubiquinone biosynthesis	28.57	2 of 7
66794	degradation of hexoses	27.78	5 of 18
66794	pentose phosphate pathway	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	metabolism of disaccharids	27.27	3 of 11
66794	degradation of aromatic, nitrogen containing compounds	25	3 of 12
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	sulfate reduction	23.08	3 of 13
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	molybdenum cofactor biosynthesis	22.22	2 of 9
66794	nitrate assimilation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Arthropoda	#Insecta
#Host Body-Site	#Gastrointestinal tract	#Stomach

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
24440	filtered gut homogenate (0.22 µm pore size) of starch-fed termite Reticulitermes santonensis (Isoptera: Rhinotermitidae)	Reticulitermes santonensis	Saint-Georges-d'Oléron	France	FRA	Europe
67770	Hindgut of the termite Reticulitermes santonensis	Reticulitermes santonensis

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM102754v1 assembly for Endomicrobium proavitum Rsa215	complete	GCA_001027545	1408281.4	2639763091	1408281	96.53

GC content

@ref	GC-content (mol%)	Method
24440	39.3	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Endomicrobium proavitum Rsa215
NCBI: GCA_001027545

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.40	no
125439	motility	BacteriaNetⓘ	no	72.00	no
125439	gram_stain	BacteriaNetⓘ	negative	72.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	80.00	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Endomicrobium proavitum Rsa215
NCBI: GCA_001027545.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	93.42	no
125438	anaerobic	anaerobicⓘ	yes	93.22	no
125438	aerobic	aerobicⓘ	no	95.92	no
125438	spore-forming	spore-formingⓘ	no	93.19	no
125438	thermophilic	thermophileⓘ	no	82.99	yes
125438	flagellated	motile2+ⓘ	no	78.95	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Complete Genome Sequence of Endomicrobium proavitum, a Free-Living Relative of the Intracellular Symbionts of Termite Gut Flagellates (Phylum Elusimicrobia).	Zheng H, Brune A	Genome Announc	10.1128/genomeA.00679-15	2015
Phylogeny	Endomicrobium proavitum, the first isolate of Endomicrobia class. nov. (phylum Elusimicrobia)--an ultramicrobacterium with an unusual cell cycle that fixes nitrogen with a Group IV nitrogenase.	Zheng H, Dietrich C, Radek R, Brune A	Environ Microbiol	10.1111/1462-2920.12960	2015

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 )
#24440	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29378
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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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Endomicrobium proavitum (DSM 29378, JCM 30189, Rsa215)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_001027545

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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