Gemmata obscuriglobus (DSM 5831, UQM 2246)

Name: Gemmata obscuriglobus (DSM 5831, UQM 2246)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11936

Type strain

Culture col. no. DSM 5831 UQM 2246

NCBI tax ID(s) 214688 114

Special Collections DSMZ

History DSMZ <- P.D. Franzmann, Dept. Microbiol., Univ. Queensland

Links

Gemmata obscuriglobus DSM 5831 is a bacterium that was isolated from water of edge of dam.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 48015

DSM 5831,ACM 2246

@ref 20215

Last LPSN update 2026-05-29 08:27:40

Domain Bacteria

Phylum Planctomycetota

Class Planctomycetia

Order Gemmatales

Family Gemmataceae

Genus Gemmata

Species Gemmata obscuriglobus

Full scientific name Gemmata obscuriglobus Franzmann and Skerman 1985

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	91.994

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
2331	STALEY'S MAINTENANCE MEDIUM (DSMZ Medium 629)		Medium recipe at MediaDive	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	Growth	Type	Temperature (°C)
2331	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	90.832

Spore formation

@ref	Spore formation	Confidence
125439		92.152

Compound production

2331

Compoundbuds

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	kanosamine biosynthesis II	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	glycine betaine biosynthesis	100	5 of 5
66794	adipate degradation	100	2 of 2
66794	lipoate biosynthesis	100	5 of 5
66794	butanoate fermentation	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	ethanol fermentation	100	2 of 2
66794	starch degradation	100	10 of 10
66794	coenzyme A metabolism	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	lactate fermentation	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	phenylalanine metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	valine metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	NAD metabolism	88.89	16 of 18
66794	chorismate metabolism	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	heme metabolism	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	selenocysteine biosynthesis	83.33	5 of 6
66794	proline metabolism	81.82	9 of 11
66794	threonine metabolism	80	8 of 10
66794	hydrogen production	80	4 of 5
66794	gallate degradation	80	4 of 5
66794	methanofuran biosynthesis	80	4 of 5
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	glutathione metabolism	78.57	11 of 14
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	purine metabolism	76.6	72 of 94
66794	degradation of sugar acids	76	19 of 25
66794	CMP-KDO biosynthesis	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	alanine metabolism	72.41	21 of 29
66794	tyrosine metabolism	71.43	10 of 14
66794	citric acid cycle	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	pyrimidine metabolism	71.11	32 of 45
66794	glycolysis	70.59	12 of 17
66794	isoprenoid biosynthesis	69.23	18 of 26
66794	vitamin B1 metabolism	69.23	9 of 13
66794	sulfate reduction	69.23	9 of 13
66794	lipid metabolism	67.74	21 of 31
66794	lysine metabolism	66.67	28 of 42
66794	4-hydroxymandelate degradation	66.67	6 of 9
66794	octane oxidation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	1,4-dihydroxy-6-naphthoate biosynthesis	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	cyanate degradation	66.67	2 of 3
66794	IAA biosynthesis	66.67	2 of 3
66794	metabolism of disaccharids	63.64	7 of 11
66794	vitamin B6 metabolism	63.64	7 of 11
66794	tryptophan metabolism	63.16	24 of 38
66794	non-pathway related	63.16	24 of 38
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	cysteine metabolism	61.11	11 of 18
66794	degradation of pentoses	60.71	17 of 28
66794	coenzyme M biosynthesis	60	6 of 10
66794	glycine metabolism	60	6 of 10
66794	propionate fermentation	60	6 of 10
66794	glycogen metabolism	60	3 of 5
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	arginine metabolism	58.33	14 of 24
66794	oxidative phosphorylation	58.24	53 of 91
66794	methionine metabolism	57.69	15 of 26
66794	nitrate assimilation	55.56	5 of 9
66794	phosphatidylethanolamine bioynthesis	53.85	7 of 13
66794	urea cycle	53.85	7 of 13
66794	phenylpropanoid biosynthesis	53.85	7 of 13
66794	polyamine pathway	52.17	12 of 23
66794	histidine metabolism	51.72	15 of 29
66794	ribulose monophosphate pathway	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	quinate degradation	50	1 of 2
66794	catecholamine biosynthesis	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	vitamin E metabolism	50	2 of 4
66794	myo-inositol biosynthesis	50	5 of 10
66794	sphingosine metabolism	50	3 of 6
66794	d-xylose degradation	45.45	5 of 11
66794	cholesterol biosynthesis	45.45	5 of 11
66794	ascorbate metabolism	45.45	10 of 22
66794	phenol degradation	45	9 of 20
66794	degradation of hexoses	44.44	8 of 18
66794	aclacinomycin biosynthesis	42.86	3 of 7
66794	methanogenesis from CO2	41.67	5 of 12
66794	carotenoid biosynthesis	40.91	9 of 22
66794	arachidonate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	3-phenylpropionate degradation	40	6 of 15
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	sulfoquinovose degradation	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	peptidoglycan biosynthesis	33.33	5 of 15
66794	arachidonic acid metabolism	33.33	6 of 18
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	chlorophyll metabolism	27.78	5 of 18
66794	carnitine metabolism	25	2 of 8
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	vitamin B12 metabolism	20.59	7 of 34

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Environmental	#Aquatic

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
2331	water of edge of dam	Queensland, Boonah, Moroon Dam	Australia	AUS	Australia and Oceania

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
2331	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM806509v1 assembly for Gemmata obscuriglobus DSM 5831	complete	GCA_008065095	114.15	8001766011	114	95.16
66792	ASM314949v1 assembly for Gemmata obscuriglobus DSM 5831	complete	GCA_003149495	114.8	2836862175	114	90.34
66792	ASM90153838v1 assembly for Gemmata obscuriglobus UQM 2246	chromosome	GCA_901538385	214688.28	8001755273	214688	81.38
66792	ASM17177v1 assembly for Gemmata obscuriglobus UQM 2246	contig	GCA_000171775	214688.27	641736268	214688	0

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	G.obscuriglobus 16S rRNA gene	X85248	1438	114
20218	Gemmata obscuriglobus (strain DSM 5831T) 16S rRNA gene, partial	AJ231191	1446	114
20218	G.obscuriglobus 16S small subunit rRNA gene	X54522	1491	114
20218	G.obscuriglobus gene for 16S rRNA	X56305	1491	114
124043	Gemmata obscuriglobus UQM 2246 partial 16S rRNA gene, strain JC673	LR898467	1360	214688

GC content

@ref	GC-content (mol%)	Method
2331	67	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM806509v1 assembly for Gemmata obscuriglobus DSM 5831
BV-BRC: 114.15

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	gram_stain	BacteriaNetⓘ	negative	71.38	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	90.83	no
125439	motility	BacteriaNetⓘ	yes	43.63	no
125439	spore_formation	BacteriaNetⓘ	no	92.15	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Gemmata obscuriglobus UQM 2246
PATRIC: 214688.28

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	91.99	no
125438	anaerobic	anaerobicⓘ	no	87.21	no
125438	spore-forming	spore-formingⓘ	no	74.47	no
125438	aerobic	aerobicⓘ	yes	73.51	no
125438	thermophilic	thermophileⓘ	no	91.43	yes
125438	flagellated	motile2+ⓘ	no	58.12	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Determining the bacterial cell biology of Planctomycetes.	Boedeker C, Schuler M, Reintjes G, Jeske O, van Teeseling MC, Jogler M, Rast P, Borchert D, Devos DP, Kucklick M, Schaffer M, Kolter R, van Niftrik L, Engelmann S, Amann R, Rohde M, Engelhardt H, Jogler C.	Nat Commun	10.1038/ncomms14853	2017
	Chromatin organization and radio resistance in the bacterium Gemmata obscuriglobus.	Lieber A, Leis A, Kushmaro A, Minsky A, Medalia O.	J Bacteriol	10.1128/jb.01513-08	2009
Metabolism	Planctomycetes do possess a peptidoglycan cell wall.	Jeske O, Schuler M, Schumann P, Schneider A, Boedeker C, Jogler M, Bollschweiler D, Rohde M, Mayer C, Engelhardt H, Spring S, Jogler C.	Nat Commun	10.1038/ncomms8116	2015
	Prokaryotic membrane coat - like proteins: An update.	Ferrelli ML, Pidre ML, Garcia-Dominguez R, Alberca LN, Del Saz-Navarro D, Santana-Molina C, Devos DP.	J Struct Biol	10.1016/j.jsb.2023.107987	2023
	Effects of pesticide application on soil bacteria community structure in a cabbage-based agroecosystem in Ghana.	Peprah S, Addo-Fordjour P, Fei-Baffoe B, Boampong K, Avicor SW, Damsere-Derry J.	PLoS One	10.1371/journal.pone.0323936	2025
Phylogeny	Kolteria novifilia, a novel planctomycetotal strain from the volcanic habitat of Panarea divides by unusual lateral budding.	Kallscheuer N, Boedeker C, Wiegand S, Kohn T, Heuer A, Overmann J, Peters S, Jogler M, Rohde M, Jogler C.	J Bacteriol	10.1128/jb.00337-24	2025
	Gemmata algarum, a Novel Planctomycete Isolated from an Algal Mat, Displays Antimicrobial Activity.	Kumar G, Kallscheuer N, Kashif M, Ahamad S, Jagadeeshwari U, Pannikurungottu S, Haufschild T, Kabuu M, Sasikala C, Jogler C, Ramana CV.	Mar Drugs	10.3390/md22010010	2023
Metabolism	Sterol synthesis is essential for viability in the planctomycete bacterium Gemmata obscuriglobus.	Gudde LR, Hulce M, Largen AH, Franke JD.	FEMS Microbiol Lett	10.1093/femsle/fnz019	2019
Genetics	Paralogization and New Protein Architectures in Planctomycetes Bacteria with Complex Cell Structures.	Mahajan M, Yee B, Hagglund E, Guy L, Fuerst JA, Andersson SGE.	Mol Biol Evol	10.1093/molbev/msz287	2020
Genetics	Assembly of a complete genome sequence for Gemmata obscuriglobus reveals a novel prokaryotic rRNA operon gene architecture.	Franke JD, Blomberg WR, Todd RT, Thomas RW, Selmecki AM.	Antonie Van Leeuwenhoek	10.1007/s10482-018-1102-0	2018
Pathogenicity	Development of a chemically-defined minimal medium for studies on growth and protein uptake of Gemmata obscuriglobus.	Mishek HP, Stock SA, Florick JDE, Blomberg WR, Franke JD.	J Microbiol Methods	10.1016/j.mimet.2017.12.010	2018
	Escherichia coli Culture Filtrate Enhances the Growth of Gemmata spp.	Kabore OD, Aghnatios R, Godreuil S, Drancourt M.	Front Microbiol	10.3389/fmicb.2019.02552	2019
	Adequacy of planctomycetes as supplementary food source for Daphnia magna.	Marinho MC, Lage OM, Catita J, Antunes SC.	Antonie Van Leeuwenhoek	10.1007/s10482-017-0997-1	2018
	The Evolutionary History and Modern Diversity of Triterpenoid Cyclases.	McShea HS, Viens RA, Olagunju BO, Giner JL, Welander PV.	Mol Biol Evol	10.1093/molbev/msaf203	2025
Enzymology	A geranylgeranyl reductase homolog required for cholesterol production in Myxococcota.	Lee AK, Welander PV.	J Bacteriol	10.1128/jb.00495-24	2025
Metabolism	Essentiality of sterol synthesis genes in the planctomycete bacterium Gemmata obscuriglobus.	Rivas-Marin E, Stettner S, Gottshall EY, Santana-Molina C, Helling M, Basile F, Ward NL, Devos DP.	Nat Commun	10.1038/s41467-019-10983-7	2019
	Development of Genetic Tools for the Manipulation of the Planctomycetes.	Rivas-Marin E, Canosa I, Santero E, Devos DP.	Front Microbiol	10.3389/fmicb.2016.00914	2016
	Gemmata species: Planctomycetes of medical interest.	Aghnatios R, Drancourt M.	Future Microbiol	10.2217/fmb-2015-0001	2016
Metabolism	Towards understanding the molecular mechanism of the endocytosis-like process in the bacterium Gemmata obscuriglobus.	Fuerst JA, Sagulenko E.	Biochim Biophys Acta	10.1016/j.bbamcr.2013.10.002	2014
Enzymology	Methods for detecting Gemmata spp. bacteremia in the microbiology laboratory.	Christen JR, Edmond E, Drancourt M.	BMC Res Notes	10.1186/s13104-017-3119-2	2018
Phylogeny	Evolutionary Remodeling of the Cell Envelope in Bacteria of the Planctomycetes Phylum.	Mahajan M, Seeger C, Yee B, Andersson SGE.	Genome Biol Evol	10.1093/gbe/evaa159	2020
	A bacterial tubulovesicular network.	Acehan D, Santarella-Mellwig R, Devos DP.	J Cell Sci	10.1242/jcs.137596	2014
	Sewage sludge fertilization affects microbial community structure and its resistome in agricultural soils.	Serwecinska L, Font-Najera A, Strapagiel D, Lach J, Toloczko W, Boldak M, Urbaniak M.	Sci Rep	10.1038/s41598-024-71656-0	2024
	Natural Products Biosynthesis by Streptomyces netropsis IMV Ac-5025 under Exogenous Sterol Action.	Loboda M, Biliavska L, Iutynska G, Newitt J, Mariychuk R.	Antibiotics (Basel)	10.3390/antibiotics13020146	2024
	Making heads or tails of the HU proteins in the planctomycete Gemmata obscuriglobus.	Yee B, Sagulenko E, Fuerst JA.	Microbiology (Reading)	10.1099/mic.0.047605-0	2011
Phylogeny	Serine/threonine kinases and E2-ubiquitin conjugating enzymes in Planctomycetes: unexpected findings.	Arcas A, Cases I, Rojas AM.	Antonie Van Leeuwenhoek	10.1007/s10482-013-9993-2	2013
Metabolism	Nested bacterial boxes: nuclear and other intracellular compartments in planctomycetes.	Fuerst JA, Sagulenko E.	J Mol Microbiol Biotechnol	10.1159/000346544	2013
	Nuclear Pore-Like Structures in a Compartmentalized Bacterium.	Sagulenko E, Nouwens A, Webb RI, Green K, Yee B, Morgan G, Leis A, Lee KC, Butler MK, Chia N, Pham UT, Lindgreen S, Catchpole R, Poole AM, Fuerst JA.	PLoS One	10.1371/journal.pone.0169432	2017
Phylogeny	The PVC superphylum: exceptions to the bacterial definition?	Fuerst JA.	Antonie Van Leeuwenhoek	10.1007/s10482-013-9986-1	2013
	Advancing biomonitoring of eDNA studies with the Anaconda R package: Integrating soil and One Health perspectives in the face of evolving traditional agriculture practices.	Stenger PL, Leopold A, Dinh K, Mournet P, Robert N, Drouin J, Wamejonengo J, Russet S, Ibanez T, Maggia L, Carriconde F.	PLoS One	10.1371/journal.pone.0311986	2025
	Phylogenetic Revisit to a Review on Predatory Bacteria.	Kamada S, Wakabayashi R, Naganuma T.	Microorganisms	10.3390/microorganisms11071673	2023
Genetics	Unusual Genomic and Biochemical Features of Paenarthrobacter lasiusi sp. nov-A Novel Bacterial Species Isolated from Lasius niger Anthill Soil.	Dymova AA, Kovalev MA, Silantyev AS, Borzykh AA, Osipova PJ, Poddubko SV, Mitkevich VA, Karpov DS, Kostina NV.	Int J Mol Sci	10.3390/ijms26010067	2024
Genetics	Principles of bacterial genome organization, a conformational point of view.	Ponndara S, Kortebi M, Boccard F, Bury-Mone S, Lioy VS.	Mol Microbiol	10.1111/mmi.15290	2025
	Intratumoral Microbiota: Insights from Anatomical, Molecular, and Clinical Perspectives.	Lombardo C, Fazio R, Sinagra M, Gattuso G, Longo F, Lombardo C, Salmeri M, Zanghi GN, Loreto CAE.	J Pers Med	10.3390/jpm14111083	2024
	Structural studies of planctomycete Gemmata obscuriglobus support cell compartmentalisation in a bacterium.	Sagulenko E, Morgan GP, Webb RI, Yee B, Lee KC, Fuerst JA.	PLoS One	10.1371/journal.pone.0091344	2014
	Tumor microbiome - an integral part of the tumor microenvironment.	Ciernikova S, Sevcikova A, Stevurkova V, Mego M.	Front Oncol	10.3389/fonc.2022.1063100	2022
Metabolism	Co-culture models illustrate the digestion of Gemmata spp. by phagocytes.	Kabore OD, Loukil A, Godreuil S, Drancourt M.	Sci Rep	10.1038/s41598-018-31667-0	2018
Pathogenicity	Broad-spectrum antibiotic resistance of Planctomycetes organisms determined by Etest.	Cayrou C, Raoult D, Drancourt M.	J Antimicrob Chemother	10.1093/jac/dkq290	2010
	Roles of cysteine in the structure and metabolic function of Mycobacterium tuberculosis CYP142A1.	Lu Y, Sun L, Pang J, Li C, Wang X, Hu X, Li G, Li X, Zhang Y, Wang H, Yang X, You X.	RSC Adv	10.1039/d2ra04257f	2022
	Species-Specific Effects of Planktonic Bacteria on the Predator-Induced Life-History Defense of Daphnia: Based on Hierarchical Cluster Analysis and Structural Equation Model.	Liu Q, Ding Z, Gu L, Sun Y, Zhang L, Yang Z.	Appl Environ Microbiol	10.1128/aem.01432-22	2022
	Protein uptake by bacteria: An endocytosis-like process in the planctomycete Gemmata obscuriglobus.	Fuerst JA, Sagulenko E.	Commun Integr Biol	10.4161/cib.3.6.13061	2010
Metabolism	Evolutionary gradient of predicted nuclear localization signals (NLS)-bearing proteins in genomes of family Planctomycetaceae.	Guo M, Yang R, Huang C, Liao Q, Fan G, Sun C, Lee SM.	BMC Microbiol	10.1186/s12866-017-0981-y	2017
Metabolism	Spatially segregated transcription and translation in cells of the endomembrane-containing bacterium Gemmata obscuriglobus.	Gottshall EY, Seebart C, Gatlin JC, Ward NL.	Proc Natl Acad Sci U S A	10.1073/pnas.1409187111	2014
Phylogeny	The differential distribution of bacteria between cancerous and noncancerous ovarian tissues in situ.	Wang Q, Zhao L, Han L, Fu G, Tuo X, Ma S, Li Q, Wang Y, Liang D, Tang M, Sun C, Wang Q, Song Q, Li Q.	J Ovarian Res	10.1186/s13048-019-0603-4	2020
Genetics	Draft genome of Gemmata massiliana sp. nov, a water-borne Planctomycetes species exhibiting two variants.	Aghnatios R, Cayrou C, Garibal M, Robert C, Azza S, Raoult D, Drancourt M.	Stand Genomic Sci	10.1186/s40793-015-0103-0	2015
	Peptide-Mediated Gene Transfer into Marine Purple Photosynthetic Bacteria.	Higuchi-Takeuchi M, Miyamoto T, Foong CP, Goto M, Morisaki K, Numata K.	Int J Mol Sci	10.3390/ijms21228625	2020
	Evolution of endonuclease IV protein family: an in silico analysis.	Kanchan S, Sharma P, Chowdhury S.	3 Biotech	10.1007/s13205-019-1696-6	2019
Enzymology	Planctomycetes DNA in febrile aplastic patients with leukemia, rash, diarrhea, and micronodular pneumonia.	Drancourt M, Prebet T, Aghnatios R, Edouard S, Cayrou C, Henry M, Blaise D, Raoult D.	J Clin Microbiol	10.1128/jcm.01207-14	2014
	Sterol Synthesis in Diverse Bacteria.	Wei JH, Yin X, Welander PV.	Front Microbiol	10.3389/fmicb.2016.00990	2016
Metabolism	Answers to naysayers regarding microbial extracellular vesicles.	Coelho C, Casadevall A.	Biochem Soc Trans	10.1042/bst20180252	2019
	Electron tomography of the nucleoid of Gemmata obscuriglobus reveals complex liquid crystalline cholesteric structure.	Yee B, Sagulenko E, Morgan GP, Webb RI, Fuerst JA.	Front Microbiol	10.3389/fmicb.2012.00326	2012
Genetics	Identification of proteins likely to be involved in morphogenesis, cell division, and signal transduction in Planctomycetes by comparative genomics.	Jogler C, Waldmann J, Huang X, Jogler M, Glockner FO, Mascher T, Kolter R.	J Bacteriol	10.1128/jb.01325-12	2012
	Non-essentiality of canonical cell division genes in the planctomycete Planctopirus limnophila.	Rivas-Marin E, Peeters SH, Claret Fernandez L, Jogler C, van Niftrik L, Wiegand S, Devos DP.	Sci Rep	10.1038/s41598-019-56978-8	2020
	The Subcellular Proteome of a Planctomycetes Bacterium Shows That Newly Evolved Proteins Have Distinct Fractionation Patterns.	Seeger C, Dyrhage K, Mahajan M, Odelgard A, Lind SB, Andersson SGE.	Front Microbiol	10.3389/fmicb.2021.643045	2021
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Enzymology	Polyketide genes in the marine sponge Plakortis simplex: a new group of mono-modular type I polyketide synthases from sponge symbionts.	Della Sala G, Hochmuth T, Costantino V, Teta R, Gerwick W, Gerwick L, Piel J, Mangoni A.	Environ Microbiol Rep	10.1111/1758-2229.12081	2013
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Phylogeny	Genomic evolution of 11 type strains within family Planctomycetaceae.	Guo M, Zhou Q, Zhou Y, Yang L, Liu T, Yang J, Chen Y, Su L, Xu J, Chen J, Liu F, Chen J, Dai W, Ni P, Fang C, Yang R.	PLoS One	10.1371/journal.pone.0086752	2014
Genetics	Massive expansion of Ubiquitination-related gene families within the Chlamydiae.	Domman D, Collingro A, Lagkouvardos I, Gehre L, Weinmaier T, Rattei T, Subtil A, Horn M.	Mol Biol Evol	10.1093/molbev/msu227	2014
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Metabolism	Genomic Evidence that Methanotrophic Endosymbionts Likely Provide Deep-Sea Bathymodiolus Mussels with a Sterol Intermediate in Cholesterol Biosynthesis.	Takishita K, Takaki Y, Chikaraishi Y, Ikuta T, Ozawa G, Yoshida T, Ohkouchi N, Fujikura K.	Genome Biol Evol	10.1093/gbe/evx082	2017
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Enzymology	Isolation of Gemmata-like and Isosphaera-like planctomycete bacteria from soil and freshwater.	Wang J, Jenkins C, Webb RI, Fuerst JA.	Appl Environ Microbiol	10.1128/aem.68.1.417-422.2002	2002
Genetics	Analysis of genome content evolution in pvc bacterial super-phylum: assessment of candidate genes associated with cellular organization and lifestyle.	Kamneva OK, Knight SJ, Liberles DA, Ward NL.	Genome Biol Evol	10.1093/gbe/evs113	2012
Genetics	Genome-wide influence of indel Substitutions on evolution of bacteria of the PVC superphylum, revealed using a novel computational method.	Kamneva OK, Liberles DA, Ward NL.	Genome Biol Evol	10.1093/gbe/evq071	2010
Phylogeny	Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges.	Siegl A, Kamke J, Hochmuth T, Piel J, Richter M, Liang C, Dandekar T, Hentschel U.	ISME J	10.1038/ismej.2010.95	2011
Metabolism	Evolutionary acquisition and loss of saxitoxin biosynthesis in dinoflagellates: the second "core" gene, sxtG.	Orr RJ, Stuken A, Murray SA, Jakobsen KS.	Appl Environ Microbiol	10.1128/aem.03279-12	2013
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Metabolism	Vesicular transport mediates the uptake of cytoplasmic proteins into mitochondria in Drosophila melanogaster.	Chen PL, Huang KT, Cheng CY, Li JC, Chan HY, Lin TY, Su MP, Yang WY, Chang HC, Wang HD, Chen CH.	Nat Commun	10.1038/s41467-020-16335-0	2020
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Metabolism	Mannosylglucosylglycerate biosynthesis in the deep-branching phylum Planctomycetes: characterization of the uncommon enzymes from Rhodopirellula baltica.	Cunha S, d'Avo AF, Mingote A, Lamosa P, da Costa MS, Costa J.	Sci Rep	10.1038/srep02378	2013
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Metabolism	The 2-methylcitrate cycle is implicated in the detoxification of propionate in Toxoplasma gondii.	Limenitakis J, Oppenheim RD, Creek DJ, Foth BJ, Barrett MP, Soldati-Favre D.	Mol Microbiol	10.1111/mmi.12139	2013
Metabolism	Steroids as Environmental Compounds Recalcitrant to Degradation: Genetic Mechanisms of Bacterial Biodegradation Pathways.	Olivera ER, Luengo JM.	Genes (Basel)	10.3390/genes10070512	2019
Enzymology	Isolation and molecular identification of planctomycete bacteria from postlarvae of the giant tiger prawn, Penaeus monodon.	Fuerst JA, Gwilliam HG, Lindsay M, Lichanska A, Belcher C, Vickers JE, Hugenholtz P.	Appl Environ Microbiol	10.1128/aem.63.1.254-262.1997	1997
Metabolism	A novel sterol desaturase-like protein promoting dealkylation of phytosterols in Tetrahymena thermophila.	Tomazic ML, Najle SR, Nusblat AD, Uttaro AD, Nudel CB.	Eukaryot Cell	10.1128/ec.00259-10	2011
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Metabolism	Highly divergent genes for methanopterin-linked C1 transfer reactions in Lake Washington, assessed via metagenomic analysis and mRNA detection.	Kalyuzhnaya MG, Bowerman S, Nercessian O, Lidstrom ME, Chistoserdova L.	Appl Environ Microbiol	10.1128/aem.71.12.8846-8854.2005	2005
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Metabolism	The N-terminal amphipathic helix of the topological specificity factor MinE is associated with shaping membrane curvature.	Shih YL, Huang KF, Lai HM, Liao JH, Lee CS, Chang CM, Mak HM, Hsieh CW, Lin CC.	PLoS One	10.1371/journal.pone.0021425	2011
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Metabolism	Extracellular membrane vesicles in the three domains of life and beyond.	Gill S, Catchpole R, Forterre P.	FEMS Microbiol Rev	10.1093/femsre/fuy042	2019
Phylogeny	Comparative analysis of bacterial diversity in freshwater sediment of a shallow eutrophic lake by molecular and improved cultivation-based techniques.	Tamaki H, Sekiguchi Y, Hanada S, Nakamura K, Nomura N, Matsumura M, Kamagata Y.	Appl Environ Microbiol	10.1128/aem.71.4.2162-2169.2005	2005
Metabolism	Bioinformatic analyses of integral membrane transport proteins encoded within the genome of the planctomycetes species, Rhodopirellula baltica.	Paparoditis P, Vastermark A, Le AJ, Fuerst JA, Saier MH.	Biochim Biophys Acta	10.1016/j.bbamem.2013.08.007	2014
Genetics	Complete genome sequence of the marine planctomycete Pirellula sp. strain 1.	Glockner FO, Kube M, Bauer M, Teeling H, Lombardot T, Ludwig W, Gade D, Beck A, Borzym K, Heitmann K, Rabus R, Schlesner H, Amann R, Reinhardt R.	Proc Natl Acad Sci U S A	10.1073/pnas.1431443100	2003
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	Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements.	Makarova KS, Wolf YI, van der Oost J, Koonin EV.	Biol Direct	10.1186/1745-6150-4-29	2009
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	Compilation of small ribosomal subunit RNA structures.	Neefs JM, Van de Peer Y, De Rijk P, Chapelle S, De Wachter R.	Nucleic Acids Res	10.1093/nar/21.13.3025	1993
	A census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial IQ, extroverts and introverts.	Galperin MY.	BMC Microbiol	10.1186/1471-2180-5-35	2005
	A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems.	Zhang D, Iyer LM, Aravind L.	Nucleic Acids Res	10.1093/nar/gkr036	2011
Metabolism	Steroids, triterpenoids and molecular oxygen.	Summons RE, Bradley AS, Jahnke LL, Waldbauer JR.	Philos Trans R Soc Lond B Biol Sci	10.1098/rstb.2006.1837	2006
	Compilation of 5S rRNA and 5S rRNA gene sequences.	Specht T, Wolters J, Erdmann VA.	Nucleic Acids Res	10.1093/nar/18.suppl.2215	1990
	Calpain chronicle--an enzyme family under multidisciplinary characterization.	Sorimachi H, Hata S, Ono Y.	Proc Jpn Acad Ser B Phys Biol Sci	10.2183/pjab.87.287	2011
Cultivation	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
	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
Enzymology	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
Enzymology	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
Phylogeny	Gemmata obscuriglobus, a new genus and species of the budding bacteria.	Franzmann PD, Skerman VB	Antonie Van Leeuwenhoek	10.1007/BF02342136	1984
	Tautonia plasticadhaerens sp. nov., a novel species in the family Isosphaeraceae isolated from an alga in a hydrothermal area of the Eolian Archipelago.	Jogler C, Wiegand S, Boedeker C, Heuer A, Peeters SH, Jogler M, Jetten MSM, Rohde M, Kallscheuer N.	Antonie Van Leeuwenhoek	10.1007/s10482-020-01424-3	2020
Phylogeny	Zavarzinella formosa gen. nov., sp. nov., a novel stalked, Gemmata-like planctomycete from a Siberian peat bog.	Kulichevskaya IS, Baulina OI, Bodelier PL, Rijpstra WI, Damste JS, Dedysh SN.	Int J Syst Evol Microbiol	10.1099/ijs.0.002378-0	2009
Phylogeny	Tuwongella immobilis gen. nov., sp. nov., a novel non-motile bacterium within the phylum Planctomycetes.	Seeger C, Butler MK, Yee B, Mahajan M, Fuerst JA, Andersson SGE.	Int J Syst Evol Microbiol	10.1099/ijsem.0.002271	2017
	Telmatocola sphagniphila gen. nov., sp. nov., a novel dendriform planctomycete from northern wetlands.	Kulichevskaya IS, Serkebaeva YM, Kim Y, Rijpstra WI, Damste JS, Liesack W, Dedysh SN.	Front Microbiol	10.3389/fmicb.2012.00146	2012
Phylogeny	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

References

#2331	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5831
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#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 )
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Gemmata obscuriglobus (DSM 5831, UQM 2246)

Name and taxonomic classification

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Physiology and metabolism

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