Ramlibacter henchirensis (DSM 14656, ATCC BAA-408, LMG 21542)

Name: Ramlibacter henchirensis (DSM 14656, ATCC BAA-408, LMG 21542)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2988

Type strain

Strain Designation TMB834

Culture col. no. DSM 14656 ATCC BAA-408 LMG 21542 TMB834 CIP 108694 1 more

NCBI tax ID(s) 204072

Special Collections DSMZ CIP

History DSMZ <- T. Heulin; TMB834 CIP <- 2005, T. Heulin, Saint-Paul-lez-Durance, France: strainTMB834

Links

Ramlibacter henchirensis TMB834 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 14230

LMG 21542,ATCC BAA-408,DSM 14656,CIP 108694

@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 henchirensis

Full scientific name Ramlibacter henchirensis Heulin et al. 2003

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility	Confidence
119872	negative	rod-shaped
125438	negative			98.333

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
5465	REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)	Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 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
5465	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)	Medium recipe at MediaDive	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water
36406	MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati		Distilled water make up to (1000.000 ml);R2A agar (18.200 g)
119872	CIP Medium 566	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
5465	positive	growth	30
36406	positive	growth	30
119872	positive	growth	25-37
119872	negative	growth	5
119872	negative	growth	10
119872	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.544

Spore formation

@ref	Spore formation	Confidence
125439		93.805
125438		93.218

Halophily

@ref	Salt	Tested relation	Concentration
119872	NaCl	growth	0 %
119872	NaCl	growth	2 %
119872	NaCl	growth	4 %
119872	NaCl	growth	6 %
119872	NaCl	growth	8 %
119872	NaCl	growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
119872	16947 ChEBI	citrate	-	carbon source
119872	4853 ChEBI	esculin	-	hydrolysis
119872	17632 ChEBI	nitrate	-	reduction
119872	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
119872	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
119872	alcohol dehydrogenase	-	1.1.1.1
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
119872	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
119872	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
119872	caseinase	-	3.4.21.50
119872	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
119872	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
119872	gelatinase	-
119872	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
119872	lipase	-
68382	lipase (C 14)	-		from API zym
119872	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
119872	ornithine decarboxylase	-	4.1.1.17
119872	oxidase	+
119872	protease	-
68382	trypsin	-	3.4.21.4	from API zym
119872	tryptophan deaminase	-
119872	tween esterase	-
119872	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

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
119872	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

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
5465	sub-desert soil	Tataouine	Tunisia	TUN	Africa
119872	Environment, Sub-desert soil	Tataouine	Tunisia	TUN	Africa	2001

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5465	1	Risk group (German classification) According to TRBA 466
119872	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	ASM468201v1 assembly for Ramlibacter henchirensis DSM 14656	contig	GCA_004682015	204072.3	2892993325	204072	77.44

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
5465	Ramlibacter henchirensis 16S ribosomal RNA gene, partial sequence	AF439400	1393		204072

GC content

5465

GC-content (mol%)70

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM468201v1 assembly for Ramlibacter henchirensis DSM 14656
BV-BRC: 204072.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.54	no
125439	gram_stain	BacteriaNetⓘ	negative	56.08	no
125439	motility	BacteriaNetⓘ	yes	44.70	no
125439	spore_formation	BacteriaNetⓘ	no	93.81	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Agrobacterium tumefaciens strain LMG 215
PATRIC: 358.159

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.33	no
125438	anaerobic	anaerobicⓘ	no	95.84	no
125438	spore-forming	spore-formingⓘ	no	93.22	no
125438	aerobic	aerobicⓘ	yes	84.26	no
125438	thermophilic	thermophileⓘ	no	99.25	yes
125438	flagellated	motile2+ⓘ	yes	71.38	no

Literature

Topic	Title	Authors	Journal	DOI	Year
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 alkalitolerans sp. nov., alkali-tolerant bacterium isolated from soil of ginseng.	Lee DH, Cha CJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.002342	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 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

#5465	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14656
#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 )
#36406	; 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) .
#68382	Automatically annotated from API zym .
#119872	Collection of Institut Pasteur ; Curators of the CIP; CIP 108694
#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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Ramlibacter henchirensis (DSM 14656, ATCC BAA-408, LMG 21542)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004682015

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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