Seven bacterial strains were selected as the representative strains of the Pectobacterium species isolated in South Korea. The seven bacterial strains consisted of six species: Pca, Pod, Pbr, Pve, Ppv, and Ppa. Jee et al. (2020) (link) isolated five strains from potato (Solanum tuberosum), P. carotovorum JR1.1 from radish (Raphanus sativus), and P. odoriferum JK2.1 from kimchi cabbage (Brassica rapa subsp. pekinensis). The seven strains were cultivated in Luria-Bertani medium (BD, Franklin Lakes, NJ, USA) at 28°C for 16 h. Genomic DNA of seven Pectobacterium strains was extracted using the G-spin Genomic DNA Extraction Kit (Intron Biotechnology, Seongnam, Korea) according to the manufacturer’s instructions.
Luria bertani medium
Manufactured by BD
Sourced in United States, France, Japan
Luria-Bertani (LB) medium is a common culture medium used for the growth of bacteria, particularly Escherichia coli. It provides the essential nutrients required for bacterial growth and proliferation.
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Lab products found in correlation
Ampicillin, by Merck Group (4 mentions)
Bhi medium, by BD (4 mentions)
Tryptic soy broth (tsb), by BD (3 mentions)
Escherichia coli top10, by Thermo Fisher Scientific (3 mentions)
Mrs medium, by Thermo Fisher Scientific (2 mentions)
Kanamycin, by Thermo Fisher Scientific (2 mentions)
Restriction endonuclease, by New England Biolabs (2 mentions)
E coli top10, by Thermo Fisher Scientific (2 mentions)
Yeast extract, by BD (2 mentions)
3 3 diaminobenzidine (dab), by Merck Group (2 mentions)
Tween 80, by Merck Group (2 mentions)
Shuffle t7 competent e coli cells, by New England Biolabs (2 mentions)
Sucrose, by Merck Group (2 mentions)
Absolute ethanol, by Merck Group (2 mentions)
Isopropyl alcohol, by Merck Group (2 mentions)
G spin genomic dna extraction kit, by iNtRON Biotechnology (1 mentions)
Fusobacterium nucleatum, by American Type Culture Collection (1 mentions)
Vitamin k1, by Merck Group (1 mentions)
Fusobacterium nucleatum, by Merck Group (1 mentions)
Escherichia coli mg1655, by American Type Culture Collection (1 mentions)
68 protocols using luria bertani medium
1
Isolation and Characterization of Pectobacterium Strains
2
Anaerobic Culture of Fusobacterium nucleatum
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Fusobacterium nucleatum was purchased from American Type Culture Collection (ATCC, Manassas, VA, USA; #25586). WT Fusobacterium nucleatum and FadA−/− Fusobacterium nucleatum were cultured in Columbia blood agar with 5 μg/mL heme, 5% desalted sheep blood, and 1 μg/mL vitamin K1 (Sigma-Aldrich, St. Louis, MO, USA) in a 37 °C anaerobic glove box containing 85% N2, 10% H2 and 5% CO2 [30 (link)]. Escherichia coli (MG1655, ATCC, Manassas, VA, USA) was propagated in Luria Bertani medium (BD Biosciences, Franklin Lakes, NJ, USA) at 37 °C in an aerobic incubator.
3
Determining Antimicrobial Potential of Hydrolysates
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The following indicator bacteria were used to determine the minimum inhibitory concentrations (MICs) as described by Wiegand et al. [23 (link)] and Maky and Zendo [14 (link)] by using a broth microdilution assay. Weizmannia (Bacillus) coagulans JCM 2257T, Salmonella enterica serovar Typhimurium NBRC 13243T, Listeria innocua ATCC 33090T, Proteus vulgaris F24B [24 (link)] and Escherichia coli JM109 were cultivated in Tryptic Soy Broth (BD, Sparks, MD, USA) supplemented with 0.6% yeast extract. Enterococcus faecalis JCM 5803T was cultivated in MRS medium (Oxoid, Basingstoke, UK), while Pseudomonas putida ATCC 12633T was cultivated in Luria Bertani medium (BD). Briefly, the bacterial inhibition was assessed at an optical density at 620 nm using an Infinite F200 Pro microplate reader (Tecan, Männedorf, Switzerland) after the indicator strains were cultured with twofold serial dilutions of chicken hydrolysates and C25.
4
Isolation and Culture of Antibiotic-Resistant Helicobacter pylori
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The H. pylori reference strain 26695 (ATCC 700392) was obtained from the American Type Culture Collection (ATCC; Manassas, VA, USA). The antibiotic-resistant (metronidazole and clarithromycin) H. pylori strains V633, V1254, V1354 and V2356 were clinical isolates from previous studies (19 (link),20 (link)). H. pylori were grown on Brucella agar (BD Biosciences, Franklin Lakes, NJ, USA) supplemented with 5% sheep blood under microaerophilic conditions at 37°C for 48–72 h. Brucella blood agar plates containing H. pylori supplement SR0147E (Thermo Fisher Scientific Oxoid Ltd., Basingstoke, UK) were used to examine the H. pylori load in infected mice under same culture condition. Salmonella enterica serovar Typhimurium (ATCC 6994), Escherichia coli (ATCC 25922) and Streptococcus aureus (ATCC 25923) were obtained from the ATCC and Pseudomonas aeruginosa (BCRC 13984) was obtained from the Bioresource Collection and Research Centre (Hsinchu, Taiwan). These bacteria were grown in Luria-Bertani medium (BD Biosciences) at 37°C for 48–72 h. Human AGS cells (CRL-1739; ATCC, Manassas, VA, USA) were purchased from ATCC and were cultured in RPMI-1640 medium (Thermo Fisher Scientific, Inc., Waltham, MA, USA), supplemented with 10% fetal bovine serum (FBS; Thermo Fisher Scientific, Inc.), 100 U/ml penicillin and 100 µg/ml streptomycin.
5
Bacterial Cultivation and Bioreporter Assay
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Four Gram-negative pathogens—Pseudomonas aeruginosa PAO1, Acinetobacter baumannii, Serratia marcescens, and Providencia stuartii strains—were grown at 37 °C in LB medium (Difco Luria-Bertani medium, BD, France) with constant agitation at 120 rpm for 24 h. The E. coli K802NR strain was cultivated in LB medium supplemented with ampicillin (100 μg mL−1) followed by incubation at 30 °C. Overnight inocula were diluted into fresh LB medium to a density of approximately 107 cells mL−1 for re-growth at 30 °C to reach an optical density (OD) of 0.2. PAO-JP2 (pKD-rhlA), a lasI-rhlI double mutant of P. aeruginosa PAO1 that harbors pKD vector with rhlA promoter coupled upstream to the luxCDABE operon. This bioreporter was inoculated into 10 mL LB broth containing 300 µg mL−1 trimethoprim and grown overnight at 37 °C with agitation.
6
Bioremediation of Heavy Metals
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All chemicals used were of analytical grade. Stock solutions of Cadmium(II), Lead(II), Zinc(II), and Copper(II)) were prepared from their respective chloride salts (Sigma, St. Louis, MI, USA). Luria Bertani medium (trypton, yeast extract, sodium chloride), cobalt(II) nitrate (Co(NO3)2, iron(III) nitrate anhydrate (Fe(NO3)3·9H2O), silver nitrate (AgNO3), and nickel(II) nitrate (Ni(NO3)2) were purchased from BDH (Radnor, PA, USA). Hydrogen chloride (HCl), sodium hydroxide (NaOH), 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (Hepes) buffer, alginate acid, calcium chloride (CaCl2), and potassium dichromate (K2Cr4O7) were obtained from Sigma. All glassware used was cleaned by immersion in nitric acid (15%) for 24 h to remove trace elements, and sterilized by autoclaving at 121 °C for 20 min.
7
Isolation and Characterization of Bioactive Compounds
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Primary samples (liquiritigenin, naringenin, and hesperetin) and other compounds were all obtained from Shanghai Yuanye Bio-Technology Co., Ltd. (Shanghai, China). All media components were provided by Clontech Laboratories, Inc. (Los Angeles, CA, USA). Methylene blue, Luria–Bertani medium, and potato dextrose broth medium were purchased from BD-Pharmingen (San Diego, CA, USA). Other reagents were of analytical grade.
8
Bacterial Strains and Cultivation for Bioconversion
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The bacterial strains and plasmids used in this study are listed in Table 3 . Escherichia coli XL1-Blue was used for gene cloning and plasmid maintenance, and L. citreum CB2567 [45 (link)] was used as a major host for bioconversion of isoflavone glycosides. E. coli XL1-Blue was cultivated in Luria-Bertani medium (tryptone 10 g/L, yeast extract 5 g/L, and sodium chloride 10 g/L; BD, Franklin Lakes, NJ, USA) at 37 °C and 200 rpm. L. citreum was cultivated in MRS medium (proteose peptone no. 3 10 g/L, beef extract 10 g/L, yeast extract 5 g/L, dextrose 20 g/L, polysorbate 80 1 g/L, ammonium citrate 2 g/L, sodium acetate 5 g/L, magnesium sulfate 0.1 g/L, manganese sulfate 0.05 g/L, and dipotassium phosphate 2 g/L, purchased as premixed media from BD) at 30 °C with shaking at 200 rpm. Ampicillin (100 µg/mL) and chloramphenicol (Cm, 10 µg/mL) were used for the selection and cultivation of E. coli and L. citreum, respectively.
9
Aspergillus nidulans Strain Cultivation
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Aspergillus nidulans strains used in this study are described in Table 1 . Fungal strains were grown on solid or liquid minimal media (MM) [21 (link)]. Colony photographs were taken with a Pentax MX-1 digital camera (Ricoh Imaging Company LTD, Tokyo, Japan). Photomicrographs were taken using a Zeiss Lab A1 microscope (Carl Zeiss MicroImaging GmbH, Jena, Germany) equipped with AxioCam 105c (Carl Zeiss MicroImaging GmbH, Jena, Germany) and AxioVision (Rel. 4.9) digital imaging software (Carl Zeiss MicroImaging GmbH, Jena, Germany). Escherichia coli DH5α was grown in Luria-Bertani medium (BD, Sparks MD, USA) with ampicillin (100 μm/mL, Sigma-Aldrich, St. Louis MO, USA) for plasmid manipulation. For auxotrophic strains, uracil/uridine (Acros Organics, Geel, Belgium) or pyridoxine (Sigma-Aldrich, St. Louis MO, USA) were used for cultivation.
10
Screening for Tetracycline Resistance in Coastal Bacteria
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For screening of traI, 83 tetracycline-resistant strains of bacteria isolated from the sediment or seawater of a coastal aquaculture site in Japan were used (Supplementary Table 1 ). At the site, oxytetracycline and flumequine had been used (Nonaka et al., 2007 (link)). Theses environmental strains were cultured at 25°C in the brain heart infusion (BHI) medium (Becton, Dickinson and Company, Sparks, MD, USA) with 0.2% NaCl and 10 μg/ml of TC (Nakalai tesque, Kyoto, Japan). All of the strains were confirmed by PCR to have tet(M) (Nonaka et al., 2007 (link)), and strains 04Ya001, 04Ya016, 04Ya090, and 04Ya108 have previously been shown to transfer tet(M) to E. coli (Neela et al., 2009 (link)). E. coli W3110 obtained from the National BioResource Project (National Institute of Genetics, Japan) and its rifampicin-resistant derivative, W3110Rifr (Nonaka et al., 2012 (link)), were cultured at 37°C in the Luria-Bertani medium (BD) with or without 10 μg/ml (for liquid media) or 20 μg/ml (solid media) of TC and 100 μg/ml of rifampicin (Sigma-Aldrich, Saint-Louis, MO).
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