Name: Beggiatoa leptomitoformis D-402
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133124

Type strain:

Species: Beggiatoa leptomitoformis

Strain Designation: D-402

Culture col. no.: DSM 14946, UNIQEM U 779

Strain history: <- G. A. Dubinina, Russian Academy of Sciences, Inst. of Microbiology, Moscow, Russia; D-402 <- A.S. Savichev {1981}

NCBI tax ID(s): 288004 (species)

SI-ID 397716

DSM 14946

Other strains from Beggiatoa leptomitoformis

B. leptomitoformis D-401, DSM 14945

Section

Beggiatoa leptomitoformis D-402 is a chemolithoautotroph, mesophilic, Gram-negative bacterium that was isolated from freshwater spring contaminated with residential and agricultural wastewater.

Gram-negative
motile
chemolithoautotroph
mesophilic
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	*Gammaproteobacteria*
	Order	*Beggiatoales*
	Family	*Beggiatoaceae*
	Genus	*Beggiatoa*
	Species	**Beggiatoa leptomitoformis**
	Full Scientific Name (LPSN)	Beggiatoa leptomitoformis Dubinina et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #25176]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #25176]	Cell length	3.5-4.0 µm

[Ref.: #25176]	Cell width	1.0-2.5 µm

[Ref.: #25176]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5613]

Culture medium

EGGC (DSMZ Medium 1191)

[Ref.: #5613]

Culture medium growth

[Ref.: #5613]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5613]

Culture medium composition

expand / minimize

[Ref.: #25176]

Culture medium

agar medium

[Ref.: #25176]

Culture medium growth

[Ref.: #25176]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #5613]	growth	25 °C
[Ref.: #25176]	growth	8.0-35.0 °C
[Ref.: #25176]	optimum	28 °C

[Ref.: #5613]	Temperature range	mesophilic
[Ref.: #25176]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #25176]			optimum	7.5-7.8
[Ref.: #25176]			growth	6.0-8.2

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25176]

Nutrition type

chemolithoautotroph

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.981

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25176]		NaCl	maximum	0.3	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25176]	acetate ChEBI	+	growth
[Ref.: #25176]	aconitate ChEBI	+	growth
[Ref.: #25176]	alanine ChEBI	+	nitrogen source
[Ref.: #25176]	alanine ChEBI	+	growth
[Ref.: #25176]	ammonium ChEBI	+	nitrogen source
[Ref.: #25176]	arabinose ChEBI	+	growth
[Ref.: #25176]	arginine ChEBI	+	growth
[Ref.: #25176]	asparagine ChEBI	+	growth
[Ref.: #25176]	aspartate ChEBI	+	nitrogen source
[Ref.: #25176]	butanol ChEBI	+	growth
[Ref.: #25176]	casein hydrolysate	+	nitrogen source
[Ref.: #25176]	cysteine ChEBI	+	nitrogen source
[Ref.: #25176]	cystine ChEBI	+	nitrogen source
[Ref.: #25176]	D-fructose ChEBI	+	growth
[Ref.: #25176]	dimethyl sulfide ChEBI	+	oxidation
[Ref.: #25176]	dimethyl sulfoxide ChEBI	+	oxidation
[Ref.: #25176]	elemental sulfur ChEBI	+	growth
[Ref.: #25176]	ethanol ChEBI	+	growth
[Ref.: #25176]	formate ChEBI	+	growth
[Ref.: #25176]	galactose ChEBI	+	growth
[Ref.: #25176]	glucose ChEBI	+	growth
[Ref.: #25176]	glutamate ChEBI	+	nitrogen source
[Ref.: #25176]	histidine ChEBI	+	growth
[Ref.: #25176]	lactate ChEBI	+	growth
[Ref.: #25176]	lactose ChEBI	+	growth
[Ref.: #25176]	malate ChEBI	+	growth
[Ref.: #25176]	maltose ChEBI	+	growth
[Ref.: #25176]	methanol ChEBI	+	growth
[Ref.: #25176]	methionine ChEBI	+	nitrogen source
[Ref.: #25176]	nitrate ChEBI	+	nitrogen source
[Ref.: #25176]	peptone	+	nitrogen source
[Ref.: #25176]	peptone	+	growth
[Ref.: #25176]	phenylalanine ChEBI	+	growth
[Ref.: #25176]	pyruvate ChEBI	+	growth
[Ref.: #25176]	raffinose ChEBI	+	growth
[Ref.: #25176]	ribose ChEBI	+	growth
[Ref.: #25176]	serine ChEBI	+	nitrogen source
[Ref.: #25176]	serine ChEBI	+	growth
[Ref.: #25176]	sorbose ChEBI	+	growth
[Ref.: #25176]	starch ChEBI	+	hydrolysis
[Ref.: #25176]	succinate ChEBI	+	growth
[Ref.: #25176]	sucrose ChEBI	+	growth
[Ref.: #25176]	sulfide ChEBI	+	growth
[Ref.: #25176]	tetrathionate ChEBI	+	growth
[Ref.: #25176]	thioacetamide ChEBI	+	oxidation
[Ref.: #25176]	thiodiglycol ChEBI	+	oxidation
[Ref.: #25176]	thiosulfate ChEBI	+	growth
[Ref.: #25176]	trithionate ChEBI	+	growth
[Ref.: #25176]	tryptophan ChEBI	+	growth
[Ref.: #25176]	valine ChEBI	+	growth
[Ref.: #25176]	xylose ChEBI	+	growth
[Ref.: #25176]	yeast extract	+	growth
	Only first 10 entries are displayed. Click here to see all.

	Antibiotica	Metabolite	Antibiotic resistance	Concentration
[Ref.: #25176]		neomycin ChEBI	yes	10	µg/mL
[Ref.: #25176]		rifampicin ChEBI	yes	100	µg/mL

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #25176]		catalase	-	1.11.1.6
[Ref.: #25176]		cytochrome oxidase	+	1.9.3.1

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #25176]

Fatty acid	Percentage
C18:1	46.1
C16:1	32.9
C16:0	15.5
C12:0	2.3
C14:0	2.2
C12:0 3OH	1.1

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

[Ref.: #25176]	Sample type/isolated from	freshwater spring contaminated with residential and agricultural wastewater
[Ref.: #25176]	Geographic location (country and/or sea, region)	Moscow region
[Ref.: #25176]	Country	Russia
[Ref.: #25176]	Country ISO 3 Code	RUS
[Ref.: #25176]	Continent	Europe
[Ref.: #25176]	Enrichment culture	agar medium
[Ref.: #25176]	Enrichment culture composition	containing the following (g l-1 distilled water): NaNO3 (0.62); NaH2PO4 (0.125); CaCl2.2H2O (0.03); Na2SO4 (0.5); KCl (0.125);MgCl2.6H2O (0.05); agar (Difco; 15.0); pH 7.2.; Prior to inoculation, the following components were added to 1 litre of the medium as sterile solutions: trace elements and vitamins [16, 17], 1 ml; NaHCO3 , 0.125 g; Na2S2O3.5H2O, 1.0g; sodium lactate, 0.5 g

[Ref.: #5613]	Sample type/isolated from	sulfur mat in a freshwater spring contaminated with residential and agricultural wastewater
[Ref.: #5613]	Geographic location (country and/or sea, region)	Moscow region
[Ref.: #5613]	Country	Russia
[Ref.: #5613]	Country ISO 3 Code	RUS
[Ref.: #5613]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	-
#Engineered	#Waste	#Wastewater
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Spring

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY583996 (>99% sequence identity) for Beggiatoa leptomitoformis subclade from Microbeatlas

Aquatic Samples	268
Soil Samples	50
Animal Samples	49
Plant Samples	4
Total Samples	371

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

[Ref.: #5613]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #5613]	Beggiatoa leptomitoformis strain D-402 16S ribosomal RNA gene, partial sequence	AY583996	1416	ENA	288004 tax ID
[Ref.: #25176]	Beggiatoa sp. 402 16S ribosomal RNA gene, partial sequence	AY583996.1	1416	GenBank	288004 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Beggiatoa leptomitoformis D-402	GCA_001305575	complete	GenBank	288004 tax ID	*
[Ref.: #66792]	Beggiatoa leptomitiformis strain D-402	319938.3	complete	PATRIC	288004 tax ID	*
[Ref.: #66792]	Beggiatoa leptomitoformis D-402	2654588010	complete	JGI IMG/M	288004 tax ID	*

[Ref.: #5613]

GC-content

42.1 mol%

thermal denaturation, midpoint method (Tm)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Beggiatoa leptomitoformis D-402 NCBI: GCA_001305575.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Beggiatoa leptomitoformis D-402 NCBI: GCA_001305575.1
[Ref.: #69480]	motile	no	78.344	yes
[Ref.: #69480]	flagellated	no	85.748	no
[Ref.: #69480]	gram-positive	no	99.168	yes
[Ref.: #69480]	anaerobic	no	91.459	no
[Ref.: #69480]	aerobic	no	74.049	no
[Ref.: #69480]	halophile	no	91.544	no
[Ref.: #69480]	spore-forming	no	93.561	no
[Ref.: #69480]	glucose-util	no	50.772	yes
[Ref.: #69480]	thermophile	no	92.907	yes
[Ref.: #69480]	glucose-ferment	no	88.756	no
[Ref.: #69480]	motile	no	78.344	yes
[Ref.: #69480]	flagellated	no	85.748	no
[Ref.: #69480]	gram-positive	no	99.168	yes
[Ref.: #69480]	anaerobic	no	91.459	no
[Ref.: #69480]	aerobic	no	74.049	no
[Ref.: #69480]	halophile	no	91.544	no
[Ref.: #69480]	spore-forming	no	93.561	no
[Ref.: #69480]	glucose-util	no	50.772	yes
[Ref.: #69480]	thermophile	no	92.907	yes
[Ref.: #69480]	glucose-ferment	no	88.756	no
[Ref.: #69480]	motile	no	78.344	yes
[Ref.: #69480]	flagellated	no	85.748	no
[Ref.: #69480]	gram-positive	no	99.168	yes
[Ref.: #69480]	anaerobic	no	91.459	no
[Ref.: #69480]	aerobic	no	74.049	no
[Ref.: #69480]	halophile	no	91.544	no
[Ref.: #69480]	spore-forming	no	93.561	no
[Ref.: #69480]	glucose-util	no	50.772	yes
[Ref.: #69480]	thermophile	no	92.907	yes
[Ref.: #69480]	glucose-ferment	no	88.756	no

Availability in culture collections External links

[Ref.: #5613]

Culture collection no.

DSM 14946, UNIQEM U 779

[Ref.: #91372]

SI-ID 397716

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Comparative Genomics of Beggiatoa leptomitoformis Strains D-401 and D-402(T) with Contrasting Physiology but Extremely High Level of Genomic Identity.	Rudenko TS, Tarlachkov SV, Shatskiy ND, Grabovich MY	Microorganisms	10.3390/microorganisms8060928	2020	*
Genetics	Genomics and Biochemistry of Metabolic Pathways for the C1 Compounds Utilization in Colorless Sulfur Bacterium Beggiatoa leptomitoformis D-402.	Orlova MV, Tarlachkov SV, Kulinchenko EI, Dubinina GA, Tutukina MN, Grabovich MY	Indian J Microbiol	10.1007/s12088-018-0737-x	2018	*
Genetics	Complete Genome Sequence of the Freshwater Bacterium Beggiatoa leptomitoformis Strain D-401.	Fomenkov A, Sun Z, Vincze T, Dubinina G, Orlova M, Tarlachkov SV, Anton BP, Grabovich MY, Roberts RJ	Genome Announc	10.1128/genomeA.00311-18	2018	*
Phylogeny	Beggiatoa leptomitoformis sp. nov., the first freshwater member of the genus capable of chemolithoautotrophic growth.	Dubinina G, Savvichev A, Orlova M, Gavrish E, Verbarg S, Grabovich M	Int J Syst Evol Microbiol	10.1099/ijsem.0.001584	2017	*
Genetics	Complete Genome Sequence of the Freshwater Colorless Sulfur Bacterium Beggiatoa leptomitoformis [corrected] Neotype Strain D-402T.	Fomenkov A, Vincze T, Grabovich MY, Dubinina G, Orlova M, Belousova E, Roberts RJ	Genome Announc	10.1128/genomeA.01436-15	2015	*

References

#5613

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14946

#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 )

#25176

G. S. Dubinina, A.,Orlova, M.,Gavrish, E.,Verbarg, S.,Grabovich, M.: Beggiatoa leptomitoformis sp. nov., the first freshwater member of the genus capable of chemolithoautotrophic growth. IJSEM 67: 197 - 204 2017 ( DOI 10.1099/ijsem.0.001584 , PubMed 27902215 )

#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) .

#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 .

#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 )

#91372

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-ID397716.1 )

* These data were automatically processed and therefore are not curated

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