Ramlibacter tataouinensis (DSM 14655, TTB310, CIP 108695)

Name: Ramlibacter tataouinensis (DSM 14655, TTB310, CIP 108695)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2987

Type strain

Strain Designation TTB310

Culture col. no. DSM 14655 TTB310 CIP 108695 ATCC BAA-407 LMG 21543

NCBI tax ID(s) 94132

Special Collections DSMZ CIP

History DSMZ <- T. Heulin; TTB310 CIP <- 2005, T. Heulin, Saint-Paul-Lez-Durance, France: strain TTB310

Links

Ramlibacter tataouinensis TTB310 is a Gram-negative, rod-shaped bacterium that was isolated from sub-desert soil.

Gram-negative rod-shaped genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 88869

LMG 21543,ATCC BAA-407,DSM 14655,CIP 108695

@ref 20215

Last LPSN update 2026-05-29 08:25:36

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Comamonadaceae

Genus Ramlibacter

Species Ramlibacter tataouinensis

Full scientific name Ramlibacter tataouinensis Heulin et al. 2003

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
123435	negative	rod-shaped
125438	negative			97.8

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
5464	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
5464	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
36407	MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati		Distilled water make up to (1000.000 ml);R2A agar (18.200 g)
123435	CIP Medium 566	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
5464	positive	growth	30
36407	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.257

Spore formation

@ref	Spore formation	Confidence
125439		90.312

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
123435	17632 ChEBI	nitrate	-	reduction
123435	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
123435	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
123435	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
123435	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
123435	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	resorcinol degradation	100	2 of 2
66794	formaldehyde oxidation	100	3 of 3
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	Entner Doudoroff pathway	100	10 of 10
66794	benzoyl-CoA degradation	100	7 of 7
66794	gallate degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	ethanol fermentation	100	2 of 2
66794	L-lactaldehyde degradation	100	3 of 3
66794	butanoate fermentation	100	4 of 4
66794	palmitate biosynthesis	100	22 of 22
66794	valine metabolism	100	9 of 9
66794	coenzyme A metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	folate polyglutamylation	100	1 of 1
66794	lactate fermentation	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	taurine degradation	100	1 of 1
66794	phenylalanine metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	4-hydroxymandelate degradation	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	citric acid cycle	85.71	12 of 14
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	photosynthesis	85.71	12 of 14
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	vitamin B1 metabolism	84.62	11 of 13
66794	leucine metabolism	84.62	11 of 13
66794	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
66794	alanine metabolism	82.76	24 of 29
66794	glycolysis	82.35	14 of 17
66794	methionine metabolism	80.77	21 of 26
66794	glycogen metabolism	80	4 of 5
66794	methylglyoxal degradation	80	4 of 5
66794	3-phenylpropionate degradation	80	12 of 15
66794	peptidoglycan biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	propionate fermentation	80	8 of 10
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	cysteine metabolism	77.78	14 of 18
66794	NAD metabolism	77.78	14 of 18
66794	purine metabolism	77.66	73 of 94
66794	tryptophan metabolism	76.32	29 of 38
66794	sulfopterin metabolism	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	isoleucine metabolism	75	6 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	pentose phosphate pathway	72.73	8 of 11
66794	proline metabolism	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	degradation of sugar acids	72	18 of 25
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	4-hydroxyphenylacetate degradation	70	7 of 10
66794	phenol degradation	70	14 of 20
66794	sulfate reduction	69.23	9 of 13
66794	urea cycle	69.23	9 of 13
66794	lipid metabolism	67.74	21 of 31
66794	IAA biosynthesis	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	d-mannose degradation	66.67	6 of 9
66794	pyrimidine metabolism	66.67	30 of 45
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	oxidative phosphorylation	65.93	60 of 91
66794	vitamin B6 metabolism	63.64	7 of 11
66794	ketogluconate metabolism	62.5	5 of 8
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	non-pathway related	60.53	23 of 38
66794	vitamin K metabolism	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	starch degradation	60	6 of 10
66794	lipoate biosynthesis	60	3 of 5
66794	arginine metabolism	58.33	14 of 24
66794	tyrosine metabolism	57.14	8 of 14
66794	lysine metabolism	57.14	24 of 42
66794	allantoin degradation	55.56	5 of 9
66794	d-xylose degradation	54.55	6 of 11
66794	degradation of pentoses	53.57	15 of 28
66794	arachidonic acid metabolism	50	9 of 18
66794	pantothenate biosynthesis	50	3 of 6
66794	ribulose monophosphate pathway	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	ascorbate metabolism	50	11 of 22
66794	carnitine metabolism	50	4 of 8
66794	quinate degradation	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	degradation of sugar alcohols	50	8 of 16
66794	androgen and estrogen metabolism	50	8 of 16
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	sphingosine metabolism	50	3 of 6
66794	selenocysteine biosynthesis	50	3 of 6
66794	glycine metabolism	50	5 of 10
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	metabolism of disaccharids	45.45	5 of 11
66794	degradation of hexoses	44.44	8 of 18
66794	nitrate assimilation	44.44	4 of 9
66794	arachidonate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	vitamin B12 metabolism	35.29	12 of 34
66794	polyamine pathway	34.78	8 of 23
66794	cyanate degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	carotenoid biosynthesis	31.82	7 of 22
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	myo-inositol biosynthesis	30	3 of 10
66794	coenzyme M biosynthesis	30	3 of 10
66794	cholesterol biosynthesis	27.27	3 of 11
66794	vitamin E metabolism	25	1 of 4
66794	alginate biosynthesis	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	daunorubicin biosynthesis	22.22	2 of 9

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
123435	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Desert
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
5464	sub-desert soil	Tataouine	Tunisia	TUN	Africa
123435	Environment, Sub-desert soil	Tataouine	Tunisia	TUN	Africa	1999

Taxonmaps

69479

Global distribution of 16S sequence AF144383 (>99% sequence identity) for Ramlibacter tataouinensis subclade from Microbeatlas

Aquatic Samples	673
Soil Samples	3799
Animal Samples	342
Plant Samples	532
Total Samples	5346

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5464	1	Risk group (German classification) According to TRBA 466
123435	1	Risk group (French 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	ASM21570v1 assembly for Ramlibacter tataouinensis TTB310	complete	GCA_000215705	365046.3	650716081	365046	99.62

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5464	Ramlibacter tataouinensis TTB310 16S ribosomal RNA gene, partial sequence	AF144383	1437		365046

GC content

5464

GC-content (mol%)70

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM21570v1 assembly for Ramlibacter tataouinensis TTB310
BV-BRC: 365046.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.26	no
125439	gram_stain	BacteriaNetⓘ	negative	70.91	no
125439	motility	BacteriaNetⓘ	yes	61.13	no
125439	spore_formation	BacteriaNetⓘ	no	90.31	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Ramlibacter tataouinensis TTB310 TTB310
NCBI: GCA_000215705.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.80	no
125438	anaerobic	anaerobicⓘ	no	95.35	no
125438	aerobic	aerobicⓘ	yes	86.99	no
125438	spore-forming	spore-formingⓘ	no	87.67	no
125438	thermophilic	thermophileⓘ	no	95.59	no
125438	flagellated	motile2+ⓘ	yes	70.62	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Light on the cell cycle of the non-photosynthetic bacterium Ramlibacter tataouinensis.	De Luca G, Fochesato S, Lavergne J, Forest KT, Barakat M, Ortet P, Achouak W, Heulin T, Vermeglio A	Sci Rep	10.1038/s41598-019-52927-7	2019
Metabolism	The cyst-dividing bacterium Ramlibacter tataouinensis TTB310 genome reveals a well-stocked toolbox for adaptation to a desert environment.	De Luca G, Barakat M, Ortet P, Fochesato S, Jourlin-Castelli C, Ansaldi M, Py B, Fichant G, Coutinho PM, Voulhoux R, Bastien O, Marechal E, Henrissat B, Quentin Y, Noirot P, Filloux A, Mejean V, DuBow MS, Barras F, Barbe V, Weissenbach J, Mihalcescu I, Vermeglio A, Achouak W, Heulin T	PLoS One	10.1371/journal.pone.0023784	2011
Cultivation	A morphological transition in the pleomorphic bacterium Ramlibacter tataouinensis TTB310.	Gommeaux M, Barakat M, Lesourd M, Thiery J, Heulin T	Res Microbiol	10.1016/j.resmic.2005.05.010	2005
Pathogenicity	Production and Characterization of a Novel Exopolysaccharide from Ramlibacter tataouinensis.	Jivkova D, Sathiyanarayanan G, Harir M, Hertkorn N, Schmitt-Kopplin P, Sanhaji G, Fochesato S, Berthomieu C, Heyraud A, Achouak W, Santaella C, Heulin T	Molecules	10.3390/molecules27217172	2022
Phylogeny	Ramlibacter pinisoli sp. nov., a novel bacterial species isolated from pine garden soil.	Akter S, N A M K, Lee SY, Moon SK, Choi C, Balusamy SR, Siddiqi MZ, Ashrafudoulla M, Rahman MS, Huq MA	Int J Syst Evol Microbiol	10.1099/ijsem.0.004486	2020
Phylogeny	Ramlibacter humi sp. nov., isolated from tropical forest soil.	Zhang XJ, Feng GD, Yao Q, Wang YH, Yang SZ, Zhu HH	Int J Syst Evol Microbiol	10.1099/ijsem.0.003641	2019
Phylogeny	Ramlibacter monticola sp. nov., isolated from forest soil.	Chaudhary DK, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002314	2017
Phylogeny	Ramlibacter rhizophilus sp. nov., isolated from rhizosphere soil of national flower Mugunghwa from South Korea.	Yan ZF, Trinh H, Moya G, Lin P, Li CT, Kook M, Yi TH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002191	2017
Phylogeny	Ramlibacter solisilvae sp. nov., isolated from forest soil, and emended description of the genus Ramlibacter.	Lee HJ, Lee SH, Lee SS, Lee JS, Kim Y, Kim SC, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijs.0.058396-0	2014
Phylogeny	Ramlibacter ginsenosidimutans sp. nov., with ginsenoside-converting activity.	Wang L, An DS, Kim SG, Jin FX, Kim SC, Lee ST, Im WT	J Microbiol Biotechnol	10.4014/jmb.1106.06041	2012
Phylogeny	Ramlibacter tataouinensis gen. nov., sp. nov., and Ramlibacter henchirensis sp. nov., cyst-producing bacteria isolated from subdesert soil in Tunisia.	Heulin T, Barakat M, Christen R, Lesourd M, Sutra L, De Luca G, Achouak W	Int J Syst Evol Microbiol	10.1099/ijs.0.02482-0	2003

References

#5464	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14655
#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 )
#36407	; Curators of the CIP;
#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 )
#68382	Automatically annotated from API zym .
#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 .
#123435	Collection of Institut Pasteur ; Curators of the CIP; CIP 108695
#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 )

Content

About us

Ramlibacter tataouinensis (DSM 14655, TTB310, CIP 108695)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000215705

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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