Strain identifier
BacDive ID: 133124
Type strain:
Species: Beggiatoa leptomitoformis
Strain Designation: D-402
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)
General
@ref: 5613
BacDive-ID: 133124
DSM-Number: 14946
keywords: genome sequence, 16S sequence, Bacteria, chemolithoautotroph, mesophilic, Gram-negative, motile
description: Beggiatoa leptomitoformis D-402 is a chemolithoautotroph, mesophilic, Gram-negative bacterium that was isolated from freshwater spring contaminated with residential and agricultural wastewater.
NCBI tax id
- NCBI tax id: 288004
- Matching level: species
strain history
- @ref: 5613
- history: <- G. A. Dubinina, Russian Academy of Sciences, Inst. of Microbiology, Moscow, Russia; D-402 <- A.S. Savichev {1981}
doi: 10.13145/bacdive133124.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Beggiatoales
- family: Beggiatoaceae
- genus: Beggiatoa
- species: Beggiatoa leptomitoformis
- full scientific name: Beggiatoa leptomitoformis Dubinina et al. 2017
@ref: 5613
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Thiotrichales
family: Beggiatoaceae
genus: Beggiatoa
species: Beggiatoa leptomitoformis
full scientific name: Beggiatoa leptomitoformis Dubinina et al. 2017
strain designation: D-402
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | motility | confidence |
---|---|---|---|---|---|
25176 | negative | 3.5-4.0 µm | 1.0-2.5 µm | yes | |
69480 | negative | 100 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
5613 | EGGC (DSMZ Medium 1191) | yes | https://mediadive.dsmz.de/medium/1191 | Name: EGGC (DSMZ Medium 1191) Composition: Agar 15.0 g/l Glucose 0.6 g/l Casamino acids 0.3 g/l Na-acetate 0.3 g/l Na2HPO4 0.248 g/l NaH2PO4 0.0308 g/l (NH4)2SO4 0.01 g/l MgSO4 x 7 H2O 0.005 g/l KCl 0.005 g/l Thiamine-HCl x 2 H2O 0.0025 g/l Nicotinic acid 0.0025 g/l Pyridoxine hydrochloride 0.0025 g/l Calcium pantothenate 0.0025 g/l CaCl2 x 2 H2O 0.002 g/l CaCO3 0.002 g/l Riboflavin 0.0005 g/l FeCl3 x 6 H2O 5e-05 g/l Vitamin B12 5e-05 g/l Folic acid 1e-05 g/l Biotin 5e-06 g/l Demineralized water |
25176 | agar medium | yes | 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 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
5613 | positive | growth | 25 | mesophilic |
25176 | positive | growth | 8.0-35.0 | |
25176 | positive | optimum | 28 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
25176 | positive | growth | 6.0-8.2 |
25176 | positive | optimum | 7.5-7.8 |
Physiology and metabolism
nutrition type
- @ref: 25176
- type: chemolithoautotroph
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.981 |
halophily
- @ref: 25176
- salt: NaCl
- tested relation: maximum
- concentration: 0.3 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
25176 | 30089 | acetate | + | growth |
25176 | 22210 | aconitate | + | growth |
25176 | 16449 | alanine | + | nitrogen source |
25176 | 16449 | alanine | + | growth |
25176 | 28938 | ammonium | + | nitrogen source |
25176 | 22599 | arabinose | + | growth |
25176 | 29016 | arginine | + | growth |
25176 | 22653 | asparagine | + | growth |
25176 | 35391 | aspartate | + | nitrogen source |
25176 | 28885 | butanol | + | growth |
25176 | casein hydrolysate | + | nitrogen source | |
25176 | 15356 | cysteine | + | nitrogen source |
25176 | 17376 | cystine | + | nitrogen source |
25176 | 15824 | D-fructose | + | growth |
25176 | 17437 | dimethyl sulfide | + | oxidation |
25176 | 28262 | dimethyl sulfoxide | + | oxidation |
25176 | 33403 | elemental sulfur | + | growth |
25176 | 16236 | ethanol | + | growth |
25176 | 15740 | formate | + | growth |
25176 | 28260 | galactose | + | growth |
25176 | 17234 | glucose | + | growth |
25176 | 29987 | glutamate | + | nitrogen source |
25176 | 27570 | histidine | + | growth |
25176 | 24996 | lactate | + | growth |
25176 | 17716 | lactose | + | growth |
25176 | 25115 | malate | + | growth |
25176 | 17306 | maltose | + | growth |
25176 | 17790 | methanol | + | growth |
25176 | 16811 | methionine | + | nitrogen source |
25176 | 17632 | nitrate | + | nitrogen source |
25176 | peptone | + | nitrogen source | |
25176 | peptone | + | growth | |
25176 | 28044 | phenylalanine | + | growth |
25176 | 15361 | pyruvate | + | growth |
25176 | 16634 | raffinose | + | growth |
25176 | 33942 | ribose | + | growth |
25176 | 17822 | serine | + | nitrogen source |
25176 | 17822 | serine | + | growth |
25176 | 27922 | sorbose | + | growth |
25176 | 28017 | starch | + | hydrolysis |
25176 | 30031 | succinate | + | growth |
25176 | 17992 | sucrose | + | growth |
25176 | 15138 | sulfide | + | growth |
25176 | 15226 | tetrathionate | + | growth |
25176 | 32497 | thioacetamide | + | oxidation |
25176 | 75184 | thiodiglycol | + | oxidation |
25176 | 16094 | thiosulfate | + | growth |
25176 | 15987 | trithionate | + | growth |
25176 | 27897 | tryptophan | + | growth |
25176 | 27266 | valine | + | growth |
25176 | 18222 | xylose | + | growth |
25176 | yeast extract | + | growth |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is resistant | resistance conc. |
---|---|---|---|---|---|
25176 | 28077 | rifampicin | yes | yes | 100 µg/mL |
25176 | 7507 | neomycin | yes | yes | 10 µg/mL |
enzymes
@ref | value | activity | ec |
---|---|---|---|
25176 | catalase | - | 1.11.1.6 |
25176 | cytochrome oxidase | + | 1.9.3.1 |
fatty acid profile
fatty acids
@ref fatty acid percentage 25176 C12:0 2.3 25176 C12:0 3OH 1.1 25176 C14:0 2.2 25176 C16:0 15.5 25176 C16:1 32.9 25176 C18:1 46.1 - type of FA analysis: whole cell analysis
- incubation medium: See reference
- agar/liquid: agar
- software version: Sherlock 6.1
- library/peak naming table: ANAER 6
- system: MIS MIDI
- method/protocol: Sasser 1990
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | enrichment culture | enrichment culture composition |
---|---|---|---|---|---|---|---|
25176 | freshwater spring contaminated with residential and agricultural wastewater | Moscow region | Russia | RUS | Europe | agar medium | 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 |
5613 | sulfur mat in a freshwater spring contaminated with residential and agricultural wastewater | Moscow region | Russia | RUS | Europe |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Contamination | |
#Engineered | #Waste | #Wastewater |
#Environmental | #Aquatic | #Freshwater |
#Environmental | #Aquatic | #Spring |
taxonmaps
- @ref: 69479
- File name: preview.99_6494.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16706;96_2716;97_3337;98_4790;99_6494&stattab=map
- Last taxonomy: Beggiatoa leptomitoformis subclade
- 16S sequence: AY583996
- Sequence Identity:
- Total samples: 371
- soil counts: 50
- aquatic counts: 268
- animal counts: 49
- plant counts: 4
Safety information
risk assessment
- @ref: 5613
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
25176 | Beggiatoa sp. 402 16S ribosomal RNA gene, partial sequence | AY583996.1 | 1416 | nuccore | 288004 |
5613 | Beggiatoa leptomitoformis strain D-402 16S ribosomal RNA gene, partial sequence | AY583996 | 1416 | ena | 288004 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Beggiatoa leptomitoformis D-402 | GCA_001305575 | complete | ncbi | 288004 |
66792 | Beggiatoa leptomitiformis strain D-402 | 319938.3 | complete | patric | 288004 |
66792 | Beggiatoa leptomitoformis D-402 | 2654588010 | complete | img | 288004 |
GC content
- @ref: 5613
- GC-content: 42.1
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 78.344 | yes |
motile | no | 78.344 | yes |
motile | no | 78.344 | yes |
flagellated | no | 85.748 | no |
flagellated | no | 85.748 | no |
flagellated | no | 85.748 | no |
gram-positive | no | 99.168 | yes |
gram-positive | no | 99.168 | yes |
gram-positive | no | 99.168 | yes |
anaerobic | no | 91.459 | no |
anaerobic | no | 91.459 | no |
anaerobic | no | 91.459 | no |
aerobic | no | 74.049 | no |
aerobic | no | 74.049 | no |
aerobic | no | 74.049 | no |
halophile | no | 91.544 | no |
halophile | no | 91.544 | no |
halophile | no | 91.544 | no |
spore-forming | no | 93.561 | no |
spore-forming | no | 93.561 | no |
spore-forming | no | 93.561 | no |
glucose-util | no | 50.772 | yes |
glucose-util | no | 50.772 | yes |
glucose-util | no | 50.772 | yes |
thermophile | no | 92.907 | yes |
thermophile | no | 92.907 | yes |
thermophile | no | 92.907 | yes |
glucose-ferment | no | 88.756 | no |
glucose-ferment | no | 88.756 | no |
glucose-ferment | no | 88.756 | no |
External links
@ref: 5613
culture collection no.: DSM 14946, UNIQEM U 779
straininfo link
- @ref: 91372
- straininfo: 397716
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Genetics | 26659680 | 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 | ||
Phylogeny | 27902215 | 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 | Bacterial Typing Techniques, Base Composition, Beggiatoa/*classification/genetics/isolation & purification, *Chemoautotrophic Growth, DNA, Bacterial/genetics, Fatty Acids/chemistry, Fresh Water/*microbiology, Nucleic Acid Hybridization, Oxidation-Reduction, *Phylogeny, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA, Sulfides/chemistry | Transcriptome |
Genetics | 29700149 | 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 | ||
Genetics | 30262951 | 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 | 32575621 | 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 | Physiology |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
5613 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14946) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14946 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
25176 | G. S. Dubinina, A.,Orlova, M.,Gavrish, E.,Verbarg, S.,Grabovich, M. | 10.1099/ijsem.0.001584 | Beggiatoa leptomitoformis sp. nov., the first freshwater member of the genus capable of chemolithoautotrophic growth | IJSEM 67: 197-204 2017 | 27902215 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | 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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | 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 | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
91372 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID397716.1 | StrainInfo: A central database for resolving microbial strain identifiers |