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11 protocols using erythromycin

1

Detailed Bacterial Culture Protocol

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All strains used in this study are listed in Supplementary Table 2.
For cloning purposes, selective media was prepared using LB broth or LB-agar using appropriate antibiotics at the following concentrations, 10 μg/ml chloramphenicol (Amersco), 10 µg/ml, 10 μg/ml spectinomycin (Tivan biotech), 10 µg/ml kanamycin (A.G scientific), 1 µg/ml erythromycin (Amresco) + 25 µg/ml lincomycin (Sigma-Aldrich) .MSgg was prepared as described previously [23] (link). Briefly, 5 mM potassium phosphate, 100 mM MOPS (pH 7), 2 mM MgCl2, 50 μM MnCl2, 50 μM FeCl3, 700 μM CaCl2, 1 μM ZnCl2, 2 μM thiamine, 0.5% glycerol, 0.5% glutamate, Threonine (50 μg ml−1), Tryptophan (50 μg ml−1), and PhenylAlanine (50 μg ml−1).
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2

Cultivation and Characterization of A. baumannii

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A. baumannii ATCC 17978 (70 (link)) was obtained from the American Type Culture Collection (ATCC) and is designated the WT strain in all analyses. Bacterial strains and plasmids are summarized in Table 3, and primers are listed in Table 4. All bacterial strains used in the study were grown in LB broth or on LB agar plates and incubated under aerobic conditions overnight (ON) (16 to 20 h) at 37°C unless otherwise stated. Antibiotic concentrations used for selection purposes were 100 µg/ml ampicillin and 25 µg/ml erythromycin, unless otherwise stated, and were purchased from AMRESCO and Sigma-Aldrich, respectively.
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3

Evaluating Antibiotic Resistance in Bacteria

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For testing antibiotic resistance, bacterial strains were inoculated (1%, v v‐1) in MRS broth supplemented with different antibiotics at various final concentrations (1, 2, 4, 8, 16, 32, 64, 128, 256, 512 and 1024 μg ml‐1), including ampicillin, vancomycin, gentamicin, erythromycin, chloramphenicol and penicillin (Amresco, USA). The MICs of a given antibiotic was visually evaluated as the lowest concentration at which no growth was observed following a 24 h incubation period at 37oC. Interpretation for susceptibility status was based on the criteria adopted by European Food Safety Authority in the assessment of bacterial resistance to antibiotics (European Food Safety Authority, 2008). The possible presence of genes responsible for resistance to gentamicin [aac(6′)‐aph(2′)‐Ia], chloramphenicol (catpIP501) and vancomycin (vanA and vanB) was investigated for the four isolates by PCR assays. Primers and protocols were described by Maietti and colleagues (2007).
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4

Bacterial Growth Media Preparation

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The strains were routinely manipulated in LB broth (Difco, Falcon BD, Corning, NY, USA) or MSgg medium (5 mM potassium phosphate, 100 mM MOPS pH 7, 2 mM MgCl2, 50 μM MnCl2, 50 μM FeCl3, 700 μM CaCl2, 1 μM ZnCl2, 50 μM FeCl3. 2 μM thiamine, 0.5% glycerol, 0.5% glutamate, 50 μg ml−1 threonine, tryptophan and phenylalanine; Branda et al., 2001 (link)).
Selective media for cloning purposes were prepared with LB or LB-agar using antibiotics at the following final concentrations: 100 μg ml−1 ampicillin, 10 μg ml−1 kanamycin from AG Scientific (San-Diego, California, USA), 10 μg ml−1 chloramphenicol, 10 μg ml−1 tetracycline, 100 μg ml−1 spectinomycin from Amersco (Dallas, Texas, USA) and 1 μg ml−1 erythromycin (Amresco, Dallas, Texas, USA) + 25 μg ml−1 lincomycin (Sigma Aldrich, St. Louis, Missouri, USA for MLS.
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5

Bacterial Strain Preparation and Culture

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All strains used in this study are listed in Supplementary Table 3.
Selective media for cloning purposes were prepared with LB broth or LB-agar using antibiotics at the following final concentrations: 10 μg/ml chloramphenicol (Amersco), 10 µg/ml, 10 μg/ml spectinomycin (Tivan biotech), 10 µg/ml tetracycline (Amresco), 1 µg/ml erythromycin (Amresco) + 25 µg/ml lincomycin (Sigma). Starter cultures of all strains was prepared using LB (Luria- Bertani) broth (Difco). B4 (0.4% yeast extract, (Difco), 0.5% D-glucose and 0.25% calcium acetate (Sigma Aldrich)) was prepared as described previously55 (link).
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6

Detailed Reagent Acquisition for Mouse Colitis Study

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Reagent grade dextran sulfate sodium salt (DSS, M.W. 36–50 kDa, Ref = 160110) was purchased from MP Biomedicals (Solon, OH). Duoset ELISA kits for mouse Lcn2 and keratinocyte-derived chemokine CXCL1 (KC), serum amyloid A (SAA) and biotinylated murine Lcn2 antibody were obtained from R&D Systems (Minneapolis, MN). Hydrogen peroxide (H2O2), myeloperoxidase (MPO), hexadecyl trimethyl ammonium bromide, RNAlater®, TRI Reagent®, iron-free enterobactin (Ent), dimethyl sulfoxide, glucose, sodium taurocholate, glycocholate, lithocholate and deoxycholate were procured from Sigma-Aldrich (St. Louis, MO). Guaiacol (2-methoxyphenol) were obtained from Alfa Aesar (Ward Hill, MA). Erythromycin was purchased from Amresco (Solon, OH). The iron atomic absorption (AA) standard was purchased from RICCA Chemical Company. SYBR® Green mix and qScript cDNA synthesis kit were procured from Quanta Biosciences. Mouse recombinant (rec)-Lcn2 (free from endotoxin, siderophore, and iron) was obtained from Cell Signaling. All other chemicals used in the present study were reagent grade and procured from Sigma.
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7

Bacterial Strain Cultivation and Antibiotic Selection

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All B. thuringiensis strains are isogenic derivatives of AW43, a derivative of B. thuringiensis serovar kurstaki strain HD73 (57 (link)). All B. subtilis strains are derivatives of 168 or PY79 (58 (link)). The strains and genotypes can be found in Table 3. All B. thuringiensis strains were grown in or on LB medium at 30°C unless otherwise specified. Liquid cultures of B. thuringiensis were grown with agitation in a roller drum. B. thuringiensis strains containing episomal plasmids were grown in LB medium containing erythromycin (erm, 10 μg/mL; Amresco). E. coli strains were grown at 37°C using LB-ampicillin (amp, 100 μg/mL; Amresco) or LB-chloramphenicol (cam, 10 μg/mL; Amresco) medium. B. subtilis strains were grown on LB with antibiotics (cam, 10 μg/mL; spectinomycin [spec], 100 μg/mL [Amresco]; or erm, 10 μg/mL). The β-galactosidase chromogenic indicator 5-bromo-4-chloro-3-indolyl β-d-galactopyranoside (X-Gal; Research Products International) was used at a concentration of 100 μg/mL. IPTG (Research Products International) and xylose (Acros) were used at the concentrations indicated in the figure legends. Cefoxitin (Sigma-Aldrich) was used at the concentrations listed in the figure legends.
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8

Bacterial Strain Cultivation and Media Preparation

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All strains used in this study are listed in Supplementary Table 1.
For cloning purposes, selective media was prepared using LB broth or LB-agar using appropriate antibiotics at the following concentrations, 10 μg/ml chloramphenicol (Amersco), 10 µg/ml, 10 μg/ml spectinomycin (Tivan biotech), 10 µg/ml kanamycin (A.G scientific), 1 µg/ml erythromycin (Amresco) + 25 µg/ml lincomycin (Sigma-Aldrich) .MSgg was prepared as described previously [32] . Briefly, 5 mM potassium phosphate, 100 mM MOPS (pH 7), 2 mM MgCl2, 50 M MnCl2, 50 M FeCl3, 700 M CaCl2, 1 M ZnCl2, 2 M thiamine, 0.5% glycerol, 0.5% glutamate, Threonine (50 g ml-1), Tryptophan (50 g ml-1), and PhenylAlanine (50 g ml-1).
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9

Bacillus subtilis Biofilm Culture Protocols

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The strains were routinely manipulated in LB broth (Difco) or MSgg medium (5 mM potassium phosphate, 100 mM MOPS pH 7, 2 mM MgCl 2 , 50 mM MnCl 2 , 50 mM FeCl 3 for liquid or 125 mM FeCl 3 for solid medium, 700 mM CaCl 2 , 1 mM ZnCl 2 , 2 mM thiamine, 0.5% glycerol, 0.5% glutamate, 50 mg ml 21 threonine, tryptophan and phenylalanine). The solid medium contained 1.5% bacto agar (Difco). Note that the iron concentration in the solid MSgg medium was 2.5-fold higher compared with the original recipe (Branda et al., 2001) , as it improved the overall morphology development. Biofilm media were often modified as indicated in the legends for each figure.
Selective media were prepared with LB or LB-agar using antibiotics at the following final concentrations: 100 mg ml 21 ampicillin (AG Scientific), 10 mg ml 21 kanamycin (AG Scientific), 10 mg ml 21 chloramphenicol (Amresco), 10 mg ml 21 tetracycline (Amresco), 100 mg ml 21 spectinomycin (Tivan Biotech) and 1 mg ml 21 erythromycin (Amresco) 1 25 mg ml 21 lincomycin (Sigma Aldrich) for MLS.
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10

Growth Media and Cultivation Protocols for Lactic Acid Bacteria

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All strains and plasmids used in this study are listed in Supplementary file 3. Standard laboratory culture medium was used for routine growth of bacteria as follows: Lactiplantibacillus spp., Lacticaseibacillus spp., Levilactobacillus brevis, Ligilactobacillus murinus, and Pediococcus pentosaceus, MRS (BD, Franklin Lakes, NJ, USA); Lactococcus lactis and Streptococcus agalactiae, M17 (BD) with 2% w/v glucose; Enterococcus faecalis, and Enterococcus faecium, BHI (BD); and Escherichia coli, LB (Teknova, Hollister, CA, USA). Bacterial strains were incubated without shaking except for E. coli (250 RPM) and at either 30 or 37 °C. Where indicated, strains were grown in filter-sterilized MRS (De MAN et al., 1960 (link)) lacking beef extract with either 110 mM glucose [gMRS] or 110 mM mannitol [mMRS], or a chemically defined minimal medium (Supplementary file 4) with 125 mM glucose [gCDM] or 125 mM mannitol [mCDM] for 18 hr (Aumiller et al., 2021 (link)). riboflavin (1 mg/L) was routinely added to the CDM. When indicated, culture medium was supplemented with 20 μg/mL of the quinone 1,4-dihydroxy-2-naphthoic acid (DHNA) (Alfa Aesar, Haverhill, MA, USA), 1.25 mM ferric ammonium citrate (C6H8FeNO7) (1.25 mM) (VWR, Radnor, PA, USA), riboflavin (Sigma-Aldrich, St. Louis, MO, USA), or 5 μg/mL erythromycin (VWR).
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