Name: Ramlibacter henchirensis TMB834
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 2988

Type strain:

Species: Ramlibacter henchirensis

Strain Designation: TMB834

Culture col. no.: DSM 14656, ATCC BAA-408, LMG 21542, CIP 108694

Strain history: CIP <- 2005, T. Heulin, Saint-Paul-lez-Durance, France: strainTMB834

NCBI tax ID(s): 204072 (species)

SI-ID 14230

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

Special Collections

DSMZ
CIP

Section

Ramlibacter henchirensis TMB834 is a Gram-negative bacterium that was isolated from sub-desert soil.

Gram-negative
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Comamonadaceae*
	Genus	*Ramlibacter*
	Species	**Ramlibacter henchirensis**
	Full Scientific Name (LPSN)	Ramlibacter henchirensis Heulin et al. 2003

Information on morphological and physiological properties Morphology

[Ref.: #119872]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %98.333

[Ref.: #119872]	Cell shape	rod-shaped

[Ref.: #119872]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5465]

Culture medium

REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

[Ref.: #36406]

Culture medium

MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati

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Culture medium growth

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Culture medium composition

expand / minimize

[Ref.: #119872]

Culture medium

CIP Medium 566

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #5465]		growth	30 °C
[Ref.: #36406]		growth	30 °C
[Ref.: #119872]		growth	25-37 °C
[Ref.: #119872]	no	growth	5 °C
[Ref.: #119872]	no	growth	10 °C
[Ref.: #119872]	no	growth	41 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]	Ability of spore formation	no Confidence in %93.218
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Salt	Tested relation		Salt conc.
[Ref.: #119872]	NaCl	no	growth	0	%
[Ref.: #119872]	NaCl	no	growth	2	%
[Ref.: #119872]	NaCl	no	growth	4	%
[Ref.: #119872]	NaCl	no	growth	6	%
[Ref.: #119872]	NaCl	no	growth	8	%
[Ref.: #119872]	NaCl	no	growth	10	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #119872]	citrate ChEBI	-	carbon source
[Ref.: #119872]	esculin ChEBI	-	hydrolysis
[Ref.: #119872]	nitrate ChEBI	-	reduction
[Ref.: #119872]	nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #119872]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #119872]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #119872]	amylase	-
[Ref.: #119872]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #119872]	caseinase	-	3.4.21.50
[Ref.: #119872]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #119872]	DNase	-
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #119872]	gelatinase	-
[Ref.: #119872]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #119872]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #119872]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #119872]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #119872]	oxidase	+
[Ref.: #119872]	protease	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #119872]	tryptophan deaminase	-
[Ref.: #119872]	tween esterase	-
[Ref.: #119872]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #119872]	11395	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #5465]	Sample type/isolated from	sub-desert soil
[Ref.: #5465]	Geographic location (country and/or sea, region)	Tataouine
[Ref.: #5465]	Country	Tunisia
[Ref.: #5465]	Country ISO 3 Code	TUN
[Ref.: #5465]	Continent	Africa

[Ref.: #119872]	Sample type/isolated from	Environment, Sub-desert soil
[Ref.: #119872]	Geographic location (country and/or sea, region)	Tataouine
[Ref.: #119872]	Country	Tunisia
[Ref.: #119872]	Country ISO 3 Code	TUN
[Ref.: #119872]	Continent	Africa
[Ref.: #119872]	Isolation date	2001
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Desert
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #5465]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #119872]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #5465]	Ramlibacter henchirensis 16S ribosomal RNA gene, partial sequence	AF439400	1393	GenBank ENA	204072 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Ramlibacter henchirensis DSM 14656	GCA_004682015	contig	GenBank ENA	204072 tax ID	*
[Ref.: #66792]	Ramlibacter henchirensis strain DSM 14656	204072.3	wgs	PATRIC	204072 tax ID	*
[Ref.: #66792]	Ramlibacter henchirensis DSM 14656	2892993325	draft	JGI IMG/M	204072 tax ID	*

[Ref.: #5465]

GC-content

70 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Agrobacterium vitis strain V80/94 PATRIC: 373.65
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Agrobacterium tumefaciens strain LMG 215 PATRIC: 358.159
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	98.333	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.844	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	93.218	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	84.26	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	99.25	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	71.38	no

Availability in culture collections External links

[Ref.: #5465]

Culture collection no.

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

[Ref.: #72510]

SI-ID 14230

Literature:

Only first 10 entries are displayed. Click here to see all.

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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: 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: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#72510

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID14230.1 )

#119872 Collection of Institut Pasteur ; Curators of the CIP; CIP 108694
* These data were automatically processed and therefore are not curated

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Agrobacterium vitis strain V80/94

Agrobacterium tumefaciens strain LMG 215

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