Archive BacDiveID:10.13145/bacdive132651.20251217.10

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BacDive ID 132651

Type strain

Strain Designation Rsa215

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

NCBI tax ID(s) 1408281

Links

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For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 24440

BacDive-ID: 132651

DSM-Number: 29378

keywords: genome sequence, mesophilic

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

NCBI tax id

NCBI tax id: 1408281
Matching level: species

strain history

@ref	history
24440	<- A. Brune, MPI, Marburg, Germany; Rsa215 <- H. Zheng
67770	A. Brune; Max Planck Inst. for Terrestrial Microbiol., Germany; Rsa215.

doi: 10.13145/bacdive132651.20251217.10

Name and taxonomic classification

LPSN

@ref: 20215
description: kingdom/pseudomonadati
keyword: phylum/elusimicrobiota
phylum: Elusimicrobiota
class: Endomicrobiia
order: Endomicrobiales
family: Endomicrobiaceae
genus: Endomicrobium
species: Endomicrobium proavitum
full scientific name: Endomicrobium proavitum Zheng et al. 2018

@ref: 24440

domain: Bacteria

phylum: Elusimicrobia

class: Endomicrobia

order: Endomicrobiales

family: Endomicrobiaceae

genus: Endomicrobium

species: Endomicrobium proavitum

full scientific name: Endomicrobium proavitum Zheng et al. 2018

strain designation: Rsa215

type strain: no

Morphology

cell morphology

@ref: 125438
gram stain: negative
confidence: 93.423

Culture and growth conditions

culture medium

@ref: 24440
name: OMIZ-PAT (DSMZ Medium 1494)
growth: yes
link: https://mediadive.dsmz.de/medium/1494
composition: 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
24440	positive	growth	30
67770	positive	growth	30

Physiology and metabolism

oxygen tolerance

@ref: 125438
oxygen tolerance: anaerobe
confidence: 93.222

spore formation

@ref	spore formation	confidence
125439	no	96.4
125438	no	93.185

Isolation, sampling and environmental information

isolation

@ref	sample type	host species	geographic location	country	origin.country	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

isolation source categories

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

Sequence information

Genome sequences

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

GC content

@ref: 24440
GC-content: 39.3
method: sequence analysis

Genome-based predictions

predictions

@ref	model	trait	description	prediction	confidence	training_data
125438	gram-positive	gram-positive	Positive reaction to Gram-staining	no	93.423	no
125438	anaerobic	anaerobic	Ability to grow under anoxygenic conditions (including facultative anaerobes)	yes	93.222	no
125438	aerobic	aerobic	Ability to grow under oxygenic conditions (including facultative aerobes)	no	95.92	no
125438	spore-forming	spore-forming	Ability to form endo- or exospores	no	93.185	no
125438	thermophile	thermophilic	Ability to grow at temperatures above or equal to 45°C	no	82.992	yes
125438	motile2+	flagellated	Ability to perform flagellated movement	no	78.95	no
125439	BacteriaNet	spore_formation	Ability to form endo- or exospores	no	96.4
125439	BacteriaNet	motility	Ability to perform movement	no	72
125439	BacteriaNet	gram_stain	Reaction to gram-staining	negative	72.3
125439	BacteriaNet	oxygen_tolerance	Oxygenic conditions needed for growth	obligate anaerobe	80

Literature

@ref: 24440

culture collection no.: DSM 29378, JCM 30189, JCM 32103

straininfo link

@ref: 126262
straininfo: 405635

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	26119974	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	Acetylene/metabolism, Animals, Bacteria/classification/genetics/isolation & purification/metabolism, Cell Cycle/genetics, Isoptera/microbiology, Nitrogen/metabolism, Nitrogen Fixation/genetics, Nitrogenase/*genetics/metabolism, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Symbiosis/genetics	Metabolism
Genetics	26184928	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

Reference

@id	authors	title	doi/url	catalogue	journal	pubmed
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	10.1099/ijsem.0.004332
24440	Curators of the DSMZ		https://www.dsmz.de/collection/catalogue/details/culture/DSM-29378	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (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)	https://diaspora-project.de/progress.html#genomes
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	10.1093/nar/gkaa1025		Nucleic Acids Res. 49: D498-D508 2020	33211880
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann	Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets	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	https://github.com/GenomeNet/deepG
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	10.1093/database/baaf059

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Archive

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

Morphology

cell morphology

Culture and growth conditions

culture medium

culture temp

Physiology and metabolism

oxygen tolerance

spore formation

Isolation, sampling and environmental information

isolation

isolation source categories

Sequence information

Genome sequences

GC content

Genome-based predictions

predictions

Literature

straininfo link

literature

Reference

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