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5 protocols using bacteriological agar

1

Preparation of Cell Culture Media

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Bacteriological agar, casein peptone, and yeast extract powder were purchased from Becton Dickinson (Franklin Lakes, NJ, USA). Citric acid hydrate, D-(+)-glucose anhydrous, sodium dodecyl sulfate (SDS), sodium dihydrogen phosphate anhydrous, sodium hydroxide, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and carboxymethyl cellulose (CMC, C5678) were purchased from Sigma-Aldrich (St. Louis, MO, USA). Avicel-plus® CM 2159 was obtained from FMC Biopolymers, USA. Roswell Park Memorial Institute (RPMI) 1640 medium, fetal bovine serum (FBS) and penicillin-streptomycin was obtained from Merck Millipore (Burlington, VT, USA).
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2

Culturing Probiotic Bacteria from Human Gut

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Major bacterial species/genus that inhabit the human small intestine consist of Bifidobacterium, Bacteroides, Lactobacillus, Clostridium, Fusobacterium and Enterobacteria (34 (link)). In this study, the two commensal, well-characterized, human derived probiotic Gram-positive strains Lactobacillus rhamnosus GG and Bifidobacterium bifidum VPI 1124 were used. L. rhamnosus and B. bifidum overnight cultures were grown on test tubes containing complete brain heart infusion media (BHI), consisting of BHI (Becton, Dickinson and Company, Franklin Lakes, NJ) supplemented with 0.5% Dextrose, 0.05% L-Cysteine and 0.1% Bacteriological Agar (Becton, Dickinson and Company, Franklin Lakes, NJ) for 48 h. L. rhamnosus was cultured at 37 °C with 5% CO2, and B. bifidum was cultures at 37 °C anaerobically using BD GasPack EZ anaerobe pouch systems (Becton, Dickinson and Company, Franklin Lakes, NJ).
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3

Conidia Removal Assay for Entomopathogenic Fungus

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Conidia removal by the insect was determined after exposing Xyleborus affinis females to B. bassiana CHE-CNRCB 44 strain at a concentration of 1 × 109 conidia mL−1. After exposure, beetles were transferred to 2 mL Eppendorf tubes with diet for 12 h. For the evaluation at time 0, insects were immediately placed in tubes without diet. Insects were removed from tubes with or without diet and individually transferred to 1.5 mL Eppendorf tubes containing 150 μL of 0.05% Tween 80. Tubes were then gently shaken for one minute and 10 μL was diluted to 1:1000, after which 30 µL was placed in a selective medium for B. bassiana (SMBb) (39 g L−1 potato dextrose agar; BD Bioxon, Guadalajara, Mexico), supplemented with 2.5 g L−1 bacteriological agar (BD Bioxon Mexico), 80 mg L−1 tetracycline (Sigma-Aldrich, St. Louis, MO, USA), 25 mg L−1 cycloheximide (Sigma-Aldrich), 80 mg L−1 streptomycin (Sigma-Aldrich), 80 mg L−1 penicillin (Sigma-Aldrich), and 1 mg L−1 benomyl (Robust R; Promotora Técnica Industrial, Morelos, Mexico) [26 (link),27 (link),28 (link)]. The inoculum was distributed using Drigalski rods, and Petri dishes were incubated at 25 °C ± 2 °C for 72 h, after which colony-forming units (CFU) were determined. A control group was kept for 12 h in a humid chamber after exposure. All bioassays were performed in triplicate.
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4

Synthesis and Biodegradation of Alginate-Acrylate Copolymer

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For the synthesis of the copolymer we used sodium alginate (sodium polymanuronate) (Golden Bell® CA, USA) USP grade, ethyl acrylate (EA; Sigma-Aldrich, St. Louis, MO, USA), and as initiator α,α,′-Azoisobutyronitrile (AIBN; Sigma-Aldrich, St. Louis, MO, USA) with a purity of 98%.
For biodegradation tests, we used as a culture medium dextrose and potato agar (DPA BD Bioxon, Edo. de Mex., México), bacteriological agar (BD Bioxon, Edo. de Mex., México), trisodium citrate pentahydrate (Merck, Edo. de Mex., México), monophasic anhydrous potassium phosphate (Merck, Edo. de Mex., México), monobasic anhydrous potassium phosphate (J,T, Baker, Phillipsburg, NJ, USA), copper (II) pentahydrate sulfate (Sigma-Aldrich, St. Louis, MO, USA), manganese sulfate monohydrate, anhydrous orthoboric acid (JT Baker, Phillipsburg, NJ, USA), chloroform (Sigma-Aldrich, St. Louis, MO, USA), magnesium sulfate heptahydrate (Merck), sucrose (Sigma-Aldrich, St. Louis, MO, USA) and glycerol 99.5% purity (Sigma-Aldrich, St. Louis, MO, USA).
The fungus Alternaria spp. isolated in our laboratory was used for the biodegradation.
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5

Bacterial Primer Specificity Validation

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In order to test the specificity of the designed primers, a reference cultured bacterial strain was selected from every clade targeted by a primer set, and obtained from culture collections or private laboratories (see Table 1 for details). Liquid cultures were grown at the appropriate temperature (Table 1) in an orbital shaking incubator at 140 rpm. Solid media were prepared by the addition of 1% bacteriological agar (BDH Prolabo). Where needed (Pandoraea pnomenusa B-356, Burkholderia xenovorans LB400 and Rhodococcus globerulus P6), a carbon source was supplied to the media as biphenyl crystals, added as solid to the liquid medium (0.1% w/v) or a few crystals on the lids of inverted agar plates.
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