Gemmatimonas aurantiaca (DSM 14586, JCM 11422, T-27)

Name: Gemmatimonas aurantiaca (DSM 14586, JCM 11422, T-27)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5788

Type strain

Strain Designation T-27

Culture col. no. DSM 14586 JCM 11422 T-27 NBRC 100505

NCBI tax ID(s) 379066 173480

Special Collections DSMZ JCM

Links

Gemmatimonas aurantiaca T-27 is a mesophilic prokaryote that was isolated from sludge from laboratory reactor.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 111713

JCM 11422,DSM 14586,NBRC 100505

@ref 20215

Last LPSN update 2025-12-16 09:48:09

Domain Pseudomonadati

Phylum Gemmatimonadota

Class Gemmatimonadia

Order Gemmatimonadales

Family Gemmatimonadaceae

Genus Gemmatimonas

Species Gemmatimonas aurantiaca

Full scientific name Gemmatimonas aurantiaca Zhang et al. 2003

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	93.885

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
5395	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
5395	positive	growth	28	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	97.9

Observation

67770

Observationquinones: MK-9

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	adipate degradation	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	gluconeogenesis	100	8 of 8
66794	aspartate and asparagine metabolism	100	9 of 9
66794	palmitate biosynthesis	100	22 of 22
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	enterobactin biosynthesis	100	3 of 3
66794	kanosamine biosynthesis II	100	2 of 2
66794	cardiolipin biosynthesis	100	7 of 7
66794	denitrification	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	phenylalanine metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	d-mannose degradation	88.89	8 of 9
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	NAD metabolism	83.33	15 of 18
66794	proline metabolism	81.82	9 of 11
66794	purine metabolism	80.85	76 of 94
66794	3-chlorocatechol degradation	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	hydrogen production	80	4 of 5
66794	alanine metabolism	79.31	23 of 29
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	methionine metabolism	76.92	20 of 26
66794	pyrimidine metabolism	75.56	34 of 45
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	peptidoglycan biosynthesis	73.33	11 of 15
66794	histidine metabolism	72.41	21 of 29
66794	heme metabolism	71.43	10 of 14
66794	reductive acetyl coenzyme A pathway	71.43	5 of 7
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	tyrosine metabolism	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	tryptophan metabolism	71.05	27 of 38
66794	glycolysis	70.59	12 of 17
66794	starch degradation	70	7 of 10
66794	leucine metabolism	69.23	9 of 13
66794	vitamin B1 metabolism	69.23	9 of 13
66794	formaldehyde oxidation	66.67	2 of 3
66794	arginine metabolism	66.67	16 of 24
66794	valine metabolism	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	lipid metabolism	64.52	20 of 31
66794	lysine metabolism	64.29	27 of 42
66794	glutathione metabolism	64.29	9 of 14
66794	pentose phosphate pathway	63.64	7 of 11
66794	vitamin B6 metabolism	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	non-pathway related	60.53	23 of 38
66794	vitamin K metabolism	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	arachidonate biosynthesis	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	cellulose degradation	60	3 of 5
66794	citric acid cycle	57.14	8 of 14
66794	cysteine metabolism	55.56	10 of 18
66794	urea cycle	53.85	7 of 13
66794	oxidative phosphorylation	52.75	48 of 91
66794	glycine metabolism	50	5 of 10
66794	ethanol fermentation	50	1 of 2
66794	4-hydroxyphenylacetate degradation	50	5 of 10
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	isoleucine metabolism	50	4 of 8
66794	quinate degradation	50	1 of 2
66794	coenzyme M biosynthesis	50	5 of 10
66794	polyamine pathway	47.83	11 of 23
66794	phenol degradation	45	9 of 20
66794	degradation of hexoses	44.44	8 of 18
66794	vitamin B12 metabolism	44.12	15 of 34
66794	degradation of sugar alcohols	43.75	7 of 16
66794	androgen and estrogen metabolism	43.75	7 of 16
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	ascorbate metabolism	40.91	9 of 22
66794	gallate degradation	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	factor 420 biosynthesis	40	2 of 5
66794	creatinine degradation	40	2 of 5
66794	bacilysin biosynthesis	40	2 of 5
66794	degradation of pentoses	39.29	11 of 28
66794	arachidonic acid metabolism	38.89	7 of 18
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	cholesterol biosynthesis	36.36	4 of 11
66794	cyanate degradation	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	allantoin degradation	33.33	3 of 9
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	methanogenesis from CO2	33.33	4 of 12
66794	sulfate reduction	30.77	4 of 13
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	aclacinomycin biosynthesis	28.57	2 of 7
66794	chlorophyll metabolism	27.78	5 of 18
66794	d-xylose degradation	27.27	3 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	metabolism of disaccharids	27.27	3 of 11
66794	carotenoid biosynthesis	27.27	6 of 22
66794	vitamin E metabolism	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	lactate fermentation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	degradation of sugar acids	24	6 of 25
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Engineered	#Bioreactor
#Engineered	#Laboratory
#Environmental	#Terrestrial

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
5395	sludge from laboratory reactor	Japan	JPN	Asia
67770	Laboratory-scale anaerobic-aerobic sequential batch reactor operated under EBPR conditions

Taxonmaps

69479

Global distribution of 16S sequence AB072735 (>99% sequence identity) for Gemmatimonas aurantiaca subclade from Microbeatlas

Aquatic Samples	1743
Soil Samples	654
Animal Samples	127
Plant Samples	82
Total Samples	2606

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5395	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	ASM1030v1 assembly for Gemmatimonas aurantiaca T-27	complete	GCA_000010305	379066.3	643692024	379066	97.22

Genome browser: GCA_000010305

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Gemmatimonas aurantiaca gene for 16S rRNA, partial sequence	AB072735	1446		379066

GC content

@ref	GC-content (mol%)	Method
67770	66	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Gemmatimonas aurantiaca T-27
NCBI: GCA_000010305

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	88.20	no
125439	motility	BacteriaNetⓘ	yes	58.80	no
125439	gram_stain	BacteriaNetⓘ	negative	83.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Gemmatimonas aurantiaca T-27 T-27
NCBI: GCA_000010305.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	93.89	no
125438	anaerobic	anaerobicⓘ	no	88.28	no
125438	aerobic	aerobicⓘ	yes	66.56	no
125438	spore-forming	spore-formingⓘ	no	76.67	no
125438	thermophilic	thermophileⓘ	no	94.47	yes
125438	flagellated	motile2+ⓘ	yes	52.98	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	A widely distributed hydrogenase oxidises atmospheric H₂ during bacterial growth.	Islam ZF, Welsh C, Bayly K, Grinter R, Southam G, Gagen EJ, Greening C.	ISME J	10.1038/s41396-020-0713-4	2020
Phylogeny	N2O Reduction by Gemmatimonas aurantiaca and Potential Involvement of Gemmatimonadetes Bacteria in N2O Reduction in Agricultural Soils.	Oshiki M, Toyama Y, Suenaga T, Terada A, Kasahara Y, Yamaguchi T, Araki N	Microbes Environ	10.1264/jsme2.ME21090	2022
Metabolism	Consumption of N2O and other N-cycle intermediates by Gemmatimonas aurantiaca strain T-27.	Chee-Sanford J, Tian D, Sanford R	Microbiology (Reading)	10.1099/mic.0.000847	2019
Metabolism	Nitrous Oxide Reduction by an Obligate Aerobic Bacterium, Gemmatimonas aurantiaca Strain T-27.	Park D, Kim H, Yoon S	Appl Environ Microbiol	10.1128/AEM.00502-17	2017
Cultivation	A hidden pitfall in the preparation of agar media undermines microorganism cultivability.	Tanaka T, Kawasaki K, Daimon S, Kitagawa W, Yamamoto K, Tamaki H, Tanaka M, Nakatsu CH, Kamagata Y	Appl Environ Microbiol	10.1128/AEM.02741-14	2014
Metabolism	Carotenoids of Gemmatimonas aurantiaca (Gemmatimonadetes): identification of a novel carotenoid, deoxyoscillol 2-rhamnoside, and proposed biosynthetic pathway of oscillol 2,2'-dirhamnoside.	Takaichi S, Maoka T, Takasaki K, Hanada S	Microbiology (Reading)	10.1099/mic.0.034249-0	2009
Phylogeny	Roseisolibacter agri gen. nov., sp. nov., a novel slow-growing member of the under-represented phylum Gemmatimonadetes.	Pascual J, Foesel BU, Geppert A, Huber KJ, Boedeker C, Luckner M, Wanner G, Overmann J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002619	2018
Phylogeny	Longimicrobium terrae gen. nov., sp. nov., an oligotrophic bacterium of the under-represented phylum Gemmatimonadetes isolated through a system of miniaturized diffusion chambers.	Pascual J, Garcia-Lopez M, Bills GF, Genilloud O	Int J Syst Evol Microbiol	10.1099/ijsem.0.000974	2016
Phylogeny	Characterization of the microaerophilic, bacteriochlorophyll a-containing bacterium Gemmatimonas phototrophica sp. nov., and emended descriptions of the genus Gemmatimonas and Gemmatimonas aurantiaca.	Zeng Y, Selyanin V, Lukes M, Dean J, Kaftan D, Feng F, Koblizek M	Int J Syst Evol Microbiol	10.1099/ijs.0.000272	2015
Phylogeny	Gemmatimonas aurantiaca gen. nov., sp. nov., a gram-negative, aerobic, polyphosphate-accumulating micro-organism, the first cultured representative of the new bacterial phylum Gemmatimonadetes phyl. nov.	Zhang H, Sekiguchi Y, Hanada S, Hugenholtz P, Kim H, Kamagata Y, Nakamura K	Int J Syst Evol Microbiol	10.1099/ijs.0.02520-0	2003

References

#5395	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14586
#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 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#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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Gemmatimonas aurantiaca (DSM 14586, JCM 11422, T-27)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Observation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000010305

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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