Archive BacDiveID:10.13145/bacdive11936.20230509.8.1

Strain identifier

BacDive ID: 11936

Type strain:

Species: Gemmata obscuriglobus

Strain history: <- P.D. Franzmann, Dept. Microbiol., Univ. Queensland

NCBI tax ID(s): 214688 (strain), 114 (species)

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

General

@ref: 2331

BacDive-ID: 11936

DSM-Number: 5831

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative

description: Gemmata obscuriglobus DSM 5831 is a mesophilic, Gram-negative bacterium that was isolated from water of edge of dam.

NCBI tax id

NCBI tax id	Matching level
114	species
214688	strain

strain history

@ref: 2331
history: <- P.D. Franzmann, Dept. Microbiol., Univ. Queensland

doi: 10.13145/bacdive11936.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/planctomycetota
domain: Bacteria
phylum: Planctomycetota
class: Planctomycetia
order: Gemmatales
family: Gemmataceae
genus: Gemmata
species: Gemmata obscuriglobus
full scientific name: Gemmata obscuriglobus Franzmann and Skerman 1985

@ref: 2331

domain: Bacteria

phylum: Planctomycetes

class: Planctomycetia

order: Planctomycetales

family: Gemmataceae

genus: Gemmata

species: Gemmata obscuriglobus

full scientific name: Gemmata obscuriglobus Franzmann and Skerman 1985 emend. Scheuner et al. 2014

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: negative
confidence: 99.962

Culture and growth conditions

culture medium

@ref: 2331
name: STALEY'S MAINTENANCE MEDIUM (DSMZ Medium 629)
growth: yes
link: https://mediadive.dsmz.de/medium/629
composition: Name: STALEY'S MAINTENANCE MEDIUM (DSMZ Medium 629) Composition: Agar 15.0 g/l Peptone 5.0 g/l MgSO4 x 7 H2O 0.594 g/l Yeast extract 0.5 g/l Nitrilotriacetic acid 0.2 g/l CaCl2 x 2 H2O 0.0667 g/l ZnSO4 x 7 H2O 0.001095 g/l FeSO4 x 7 H2O 0.0005 g/l Na-EDTA 0.00025 g/l (NH4)6Mo7O24 x 4 H2O 0.000185 g/l MnSO4 x H2O 0.000154 g/l Nicotinamide 9e-05 g/l Riboflavin 5e-05 g/l Calcium pantothenate 5e-05 g/l Thiamine-HCl x 2 H2O 5e-05 g/l CuSO4 x 5 H2O 3.92e-05 g/l Co(NO3)2 x 6 H2O 2.48e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Na2B4O7 x 10 H2O 1.77e-05 g/l Vitamin B12 1e-06 g/l Distilled water

culture temp

@ref: 2331
growth: positive
type: growth
temperature: 30
range: mesophilic

Physiology and metabolism

spore formation

@ref	spore formation	confidence
69481	no	91
69480	no	99.992

compound production

@ref: 2331
compound: buds

Isolation, sampling and environmental information

isolation

@ref: 2331
sample type: water of edge of dam
geographic location: Queensland, Boonah, Moroon Dam
country: Australia
origin.country: AUS
continent: Australia and Oceania

isolation source categories

Cat1: #Environmental
Cat2: #Aquatic

Safety information

risk assessment

@ref: 2331
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	G.obscuriglobus 16S rRNA gene	X85248	1438	ena	114
20218	Gemmata obscuriglobus (strain DSM 5831T) 16S rRNA gene, partial	AJ231191	1446	ena	114
20218	G.obscuriglobus 16S small subunit rRNA gene	X54522	1491	ena	114
20218	G.obscuriglobus gene for 16S rRNA	X56305	1491	ena	114

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Gemmata obscuriglobus UQM 2246 UQM 2246	GCA_901538385	chromosome	ncbi	214688
66792	Gemmata obscuriglobus DSM 5831	GCA_008065095	complete	ncbi	114
66792	Gemmata obscuriglobus DSM 5831	GCA_003149495	complete	ncbi	114
66792	Gemmata obscuriglobus UQM 2246	GCA_000171775	contig	ncbi	214688
66792	Gemmata obscuriglobus UQM 2246	214688.28	complete	patric	214688
66792	Gemmata obscuriglobus UQM 2246	214688.27	wgs	patric	214688
66792	Gemmata obscuriglobus strain DSM 5831	114.8	complete	patric	114
66792	Gemmata obscuriglobus strain DSM 5831	114.15	complete	patric	114
66792	Gemmata obscuriglobus DSM 5831	2836862175	complete	img	114
66792	Gemmata obscuriglobus UQM 2246	641736268	draft	img	214688

GC content

@ref: 2331
GC-content: 67
method: sequence analysis

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	91	no
motile	yes	57.832	no
gram-positive	no	96.227	no
anaerobic	no	95.076	no
aerobic	yes	84.662	no
halophile	no	94.846	no
spore-forming	no	84.141	no
glucose-util	yes	77.101	no
flagellated	no	89.997	no
thermophile	no	98.725	yes
glucose-ferment	no	88.677	no

External links

@ref: 2331

culture collection no.: DSM 5831, UQM 2246

straininfo link

@ref: 81150
straininfo: 48015

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	6486770	Gemmata obscuriglobus, a new genus and species of the budding bacteria.	Franzmann PD, Skerman VB	Antonie Van Leeuwenhoek	10.1007/BF02342136	1984	Australia, Bacteria/classification/isolation & purification/metabolism/ultrastructure, Fresh Water, Terminology as Topic, Water Microbiology	Enzymology
Enzymology	15693614	Archaea-like genes for C1-transfer enzymes in Planctomycetes: phylogenetic implications of their unexpected presence in this phylum.	Bauer M, Lombardot T, Teeling H, Ward NL, Amann RI, Glockner FO	J Mol Evol	10.1007/s00239-004-2643-6	2004	Amidohydrolases/chemistry/genetics, Amino Acid Sequence, Archaea/enzymology/genetics, Bacteria/enzymology/genetics, Catalysis, Conserved Sequence, Genes, Archaeal/genetics, Genes, Bacterial/genetics, Genome, Bacterial, Methylobacterium extorquens/chemistry/genetics, Molecular Sequence Data, *Phylogeny, Sequence Alignment	Genetics
Enzymology	20028524	Gene cloning and characterization of a novel esterase from activated sludge metagenome.	Zhang T, Han WJ	Microb Cell Fact	10.1186/1475-2859-8-67	2009	Amino Acid Sequence, Catalytic Domain, Cloning, Molecular, DNA, Bacterial/metabolism, Esterases/genetics/metabolism, Hydrogen-Ion Concentration, Metagenome, Molecular Sequence Data, Sequence Alignment, Sequence Homology, Amino Acid, Sewage/microbiology, Substrate Specificity, Temperature, Triglycerides/metabolism, Yarrowia/classification/enzymology	Metabolism
	23766281	Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry for the identification of environmental organisms: the Planctomycetes paradigm.	Cayrou C, Raoult D, Drancourt M	Environ Microbiol Rep	10.1111/j.1758-2229.2010.00176.x	2010
Cultivation	31406238	Improved culture of fastidious Gemmata spp. bacteria using marine sponge skeletons.	Kabore OD, Godreuil S, Drancourt M	Sci Rep	10.1038/s41598-019-48293-z	2019	Animal Shells/chemistry, Animals, Bacteria, Colony Count, Microbial, Culture Media/chemistry/pharmacology, Planctomycetales/*drug effects/growth & development, Porifera/chemistry	Pathogenicity
Phylogeny	32847778	Frigoriglobus tundricola gen. nov., sp. nov., a psychrotolerant cellulolytic planctomycete of the family Gemmataceae from a littoral tundra wetland.	Kulichevskaya IS, Ivanova AA, Naumoff DG, Beletsky AV, Rijpstra WIC, Sinninghe Damste JS, Mardanov AV, Ravin NV, Dedysh SN	Syst Appl Microbiol	10.1016/j.syapm.2020.126129	2020	Bacteria, Bacterial Typing Techniques, Base Composition, Cellulose/metabolism, Cold Temperature, DNA, Bacterial/chemistry/genetics, Fatty Acids/analysis, Genes, Bacterial, Genes, rRNA, Genome, Bacterial, Gram-Negative Aerobic Bacteria/classification/genetics/isolation & purification/physiology, Lipids/analysis, Metabolic Networks and Pathways/genetics, Phylogeny, Planctomycetales/classification/genetics, RNA, Ribosomal, 16S/genetics, Tundra, Wetlands, Xylans/metabolism	Metabolism

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
2331	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5831)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-5831
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	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		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates	Nucleic Acids Res. 49: D498-D508 2020	33211880
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
81150	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID48015.1	StrainInfo: A central database for resolving microbial strain identifiers