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113 protocols using neomycin sulfate

1

Neomycin Treatments on Larval Zebrafish

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A 1 mM Neomycin sulfate (EMD Millipore Corp., Burlington, MA, USA) stock solution was made in 25 mL of E3 (embryo medium) and diluted in 35 × 10 mm Petri dishes containing 30 mL E3 to make 50, 100, 200, 300, and 400 µM concentrations for each treatment round. These concentrations are consistent with those previously used as single treatments on larval zebrafish [5 (link),13 (link),22 (link)]. Timeline One involved neomycin treatments every six hours for a total of seven treatments, while Timeline Two entailed treatments every twelve hours for a total of four treatments (Figure 1A). Both timelines were repeated three times at all neomycin concentrations. All treatments were carried out in Petri dishes containing 18–25 larvae and incubated for 25 min at 28.5 °C before being returned to Petri dishes with fresh E3.
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2

Lipid Standards Acquisition Protocol

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Sigma (Taufkirchen, Germany) was the supplier of all reagents unless otherwise specified. Chloroform and methanol, both HPLC-grade, as well as neomycin sulfate and gentamycin sulfate were obtained from Merck (Darmstadt, Germany). Avanti Polar Lipids (Alabaster, AL, USA) was the source for the lipid standards.
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3

Biomolecular Immobilization on CMD-Gold

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PBS solution, acetate buffer, BSA, neomycin sulfate, ethanolamine-HCl, N-hydroxysuccinimide (NHS), and N-ethyl- N-(3-diethylaminopropyl) carbodiimide (EDC) were purchased from Merck (Darmstadt, Germany). Carboxymethyl dextran (CMD) low density-modified gold surface chips were supplied from BioNavis Company (Tampere-region, Finland).
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4

Antimicrobial Cocktail Administration in Mice

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Mice were treated with antimicrobials in drinking water. Antibiotics used were ampicillin (0.5 mg/ml) (Sigma Aldrich; St. Louis, MO), gentamicin sulfate (0.5 mg/ml) (Corning; Manassas, VA), metronidazole (0.5 mg/ml) (Spectrum Chemical, Gardena, CA), neomycin sulfate (0.5 mg/ml) (EMD Millipore; Billerica, MA), and vancomycin (0.25 mg/ml) (VWR Life Science). All of the antimicrobials were dissolved in non-acidified autoclaved reverse osmosis drinking water. Antimicrobial water was changed every week.
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5

Antibiotic-Loaded Composite Spheres Synthesis

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All reagents used for the synthesis of antibiotic-loaded composite spheres were purchased from Sigma-Aldrich (Merck Group, Darmstadt, Germany), namely poly(3-hydroxybutyric acid-co-3-hydroxyvaleric acid)—P(3HB-3HV) with 8 mol% polyhydroxyvalerate content, high purity chitosan (CS) with ≤40 mol% acetylation degree, polyvinyl alcohol (PVA) with 87–89% hydrolysis degree, bacitracin (Bac) produced by Bacillus licheniformis with ≥60,000 U/g (potency), neomycin sulfate (Neo), kanamycin sulfate (Kan) and chloroform.
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6

Lipid Extraction and Quantification

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Unless otherwise specified, all chemicals were obtained from Sigma (Taufkirchen, Germany). HPLC-grade methanol and chloroform, gentamycin sulfate, and neomycin sulfate were purchased from Merck (Darmstadt, Germany). The lipid standards were purchased from Avanti Polar Lipids (Alabaster, AL, USA).
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7

Antibiotic-Induced Gut Microbiome Modification

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To create an MD mouse model, broad-spectrum antibiotics (ampicillin, 1 g/L; neomycin sulfate, 1 g/L; metronidazole, 1 g/L; vancomycin, 0.5 g/L; Sigma, USA) were added to the drinking water for 3 weeks to eliminate the intestinal flora, as described previously.11 (link) During this time, weight and food intake were recorded. At 2 days after antibiotic water was discontinued, to create the MD+KLA group, K. pneumoniae was administered.
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8

Gut Microbiome Modulation Protocol

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The main regents used in this study, Trp, indole, IPA, IAld, Ficz, CH223191, metronidazole, ampicillin, vancomycin, and neomycin sulfate, were purchased from Sigma-Aldrich (St. Louis, MO, USA). The specific primary antibodies of AhR and Cyp1a1 were bought from Affinity Biosciences (OH, USA). Phosphorylation (p-) of p65 and IκB, p65, IκB, and β-actin were obtained from Cell Signaling Technology (CST; Boston, USA). The occludin and claudin-3 were bought from Bioss (Beijing, China). MPO activity assay kit was purchased from Nanjing Jiancheng Bioengineering Institute (Nanjing, China). TNF-α and IL-1β enzyme linked immunosorbent assay (ELISA) kits were bought from Biolegend, Inc. (San Diego, CA, USA). indole and IAld ELISA kits were bought from Hnybio (Shanghai, China), and the IPA ELISA kit was obtained from Shyqbio (Shanghai, China). L. reuteri CNCM I-5022 was obtained from the Collection Nationale de Cultures de Microorganisms (CNCM) of the Institut Pasteur. E.coli CVCC1418 was obtained from the China Veterinary Culture Collection Center (CVCC).
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9

Antibiotic Sensitivity of Multidrug-Resistant Salmonella

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Multidrug-resistant Salmonella (ATCC 700408) was obtained from the American Type Culture Collection (Manassas, VA). Silver nitrate, sodium borohydride, sodium citrate, NaOH, tetracycline hydrochloride (TET), neomycin sulfate (NEO), kanamycin sulfate (KAN), tryptic soy broth (TSB), and tryptic soy agar (TSA) were purchased from Sigma-Aldrich (St. Louis, MO). Penicillin G sodium salt (PEN) and nitric acid (trace metal grade, 67%–70%) were from Fisher Scientific (Houston, TX). Ampicillin sodium salt (AMP) was from Research Products International Corp (Prospect, IL), and enoxacin hydrochloride (ENO) was from MP Biomedicals LLC (Solon, OH). The structures of the antibiotics are shown in Figure SI 1.
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10

Antibiotic-Induced Gut Dysbiosis Promotes Tumor Development in APCMin Mice

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Mice were given the following antibiotics in autoclaved drinking water: ampicillin (1g/l; Sigma), vancomycin (500 mg/l; Henry Schein, Inc.) neomycin sulfate (1g/l; Sigma), and metronidazole (1g/l; Sigma; solubilized with 15 ml of 0.1N acetic acid/liter). Fresh antibiotics were supplied every three days. Mice were kept on antibiotics for the indicated time and killed for tumor and tissue analysis. Mice were administered IDENs resuspended in PBS by gavage or intravenous injection as described previously39 (link). In some experiments, neutralizing antibody (200 µg/mouse) for IL-17A (MAB421 R&D Systems) or control IgG was injected once every week for eight weeks. ApcMin/+ and ApcMin/+/MyD88−/− littermates were euthanized at 3−4 months of age or when the first signs of morbidity appeared. The intestinal tract was removed immediately after euthanasia. The small intestine and colon were examined, and tumors were counted and measured using a stereomicroscope. Most polyps were adenomas, identified by their appearance as grossly visible, preinvasive lesions that were common in the small intestine of APCMin/+ mice. Colonic lesions that displayed a focally invasive phenotype were categorized as tumors. Five-µm sections of paraffin-embedded specimens were cut and stained with H&E for histology analyses.
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