Name: Endomicrobium proavitum Rsa215
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132651

Type strain:

Species: Endomicrobium proavitum

Strain Designation: Rsa215

Culture col. no.: DSM 29378, JCM 30189, JCM 32103

Strain history: A. Brune; Max Planck Inst. for Terrestrial Microbiol., Germany; Rsa215.

NCBI tax ID(s): 1408281 (species)

Section

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

mesophilic
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	07-12-2022 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Elusimicrobiota*
	Class	*Endomicrobiia*
	Order	*Endomicrobiales*
	Family	*Endomicrobiaceae*
	Genus	*Endomicrobium*
	Species	**Endomicrobium proavitum**
	Full Scientific Name (PNU)	Endomicrobium proavitum Zheng et al. 2018

Information on culture and growth conditions Culture and growth conditions

[Ref.: #24440]

Culture medium

OMIZ-PAT (DSMZ Medium 1494)

[Ref.: #24440]

Culture medium growth

[Ref.: #24440]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #24440]

Culture medium composition

expand / minimize

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

	Temperatures	Kind of temperature		Temperature
[Ref.: #24440]			growth	30 °C
[Ref.: #67770]			growth	30 °C

[Ref.: #24440]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

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

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

[Ref.: #24440]	Sample type/isolated from	filtered gut homogenate (0.22 µm pore size) of starch-fed termite Reticulitermes santonensis (Isoptera: Rhinotermitidae)
[Ref.: #24440]	Host species	Reticulitermes santonensis
[Ref.: #24440]	Geographic location (country and/or sea, region)	Saint-Georges-d'Oléron
[Ref.: #24440]	Country	France
[Ref.: #24440]	Country ISO 3 Code	FRA
[Ref.: #24440]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Hindgut of the termite Reticulitermes santonensis
[Ref.: #67770]	Host species	Reticulitermes santonensis
* marker position based on {}

Isolation sources categories

#Host	#Arthropoda	#Insecta
#Host Body-Site	#Gastrointestinal tract	#Stomach

What are isolation sources categories?

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Endomicrobium proavitum Rsa215	GCA_001027545	complete	GenBank	1408281 tax ID	*
[Ref.: #66792]	Endomicrobium proavitum strain Rsa215	1408281.4	complete	PATRIC	1408281 tax ID	*
[Ref.: #66792]	Endomicrobium proavitum Rsa215	2639763091	complete	JGI IMG/M	1408281 tax ID	*
[Ref.: #67770]	Endomicrobium proavitum strain Rsa215, complete genome	CP009498		ENA	1408281 tax ID
[Ref.: #66792]	Caulobacteraceae bacterium TE-Jun18-1	GCA_947484535	contig	PATRIC	1978230 tax ID	*

[Ref.: #24440]

GC-content

39.3 mol%

sequence analysis

Availability in culture collections External links

[Ref.: #24440]

Culture collection no.

DSM 29378, JCM 30189, JCM 32103

Literature:

Topic	Title	Authors	Journal	DOI	Year
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	*
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	*

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;

#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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