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161 protocols using peptone

1

Freeze-Dried Starter Culture Preparation

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The commercial starters (BOX-57—Carnobacterium divergens, C. maltoaromaticum and L. sakei; LAK-23—L. sakei; and FP-50—C. divergens, C. maltoaromaticum) were freeze-dried in a foil pouch. F-106 (Lacticaseibacillus casei) was derived from the Collection of the Department of Agricultural Food, Environmental, and Animal Sciences of the University of Udine and was grown in de Man, Rogosa and Sharpe (MRS) broth (Oxoid, Italy). After its growth, the strain was harvested by centrifugation at 8000× g for 10 min and then diluted in peptone water. The commercial starters were thawed, homogenized, and diluted in sterile peptone water (NaCl 0.6%, peptone, Oxoid, 0.1%, and distilled water 1 L) at the time of use. To evaluate the load of each starter, dilutions were performed in sterile peptone water, and 0.1 mL of each dilution was inoculated in the de Man, Rogosa and Sharpe (MRS) medium (Oxoid, Italy) by the double layer method for the LAB and in TSM agar (tryptic soy medium with 5% glucose, 2% NaCl, and pH 8, Oxoid, Italy) in a jar prepared for anaerobic reaction with a gas-packing anaerobic system (BBL, Becton Dickinson, USA) for the carnobacteria. The plates were incubated at 37 °C for 48–72 h, and the grown colonies were counted. Each suspension contained, on average, approximately 11 Log CFU/g.
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2

Starter Culture Enumeration and Dilution

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The chosen starter was sold freeze-dried in a foil pouch. At the time of use, the starter was thawed, homogenized, and diluted in sterile peptone water (NaCl 0.6%; peptone, Oxoid, 0.1%, distilled water 1 L). To evaluate its load, dilutions were performed in sterile peptone water, and 0.1 mL of each dilution was inoculated in Petri dishes, to which de Man, Rogosa, and Sharpe (MRS) medium (Oxoid, Italy) was subsequently added by the double layer method. The plates were incubated at 37 °C for 48–72 h, and the grown colonies were counted. Each suspension contained on average approximately 11 log CFU/g. Then, the starter culture was diluted in natural water used to wash the fish before packaging at a level of approximately 7 log CFU/mL.
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3

Quantification of Aerobic and Anaerobic Bacteria in Salmon

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Ten grams of each salmon piece was mixed with 90 g of peptone water (1 g/l of peptone (Oxoid) and 8.5 g/l of NaCl (VWR, Belgium), and homogenised in a stomacher (IUL Masticator, Spain), and serially diluted (10-fold) before plating. Lyngby's Iron agar (Oxoid, Norway) supplemented with 0,04% l-cysteine (Sigma-Aldrich) was used for quantification of total aerobic counts and H2S -producing bacteria, and incubated at 22 °C for 72 ± 6 h [57 ], while MRS and M17 agar were used for quantification of LAB using anaerobic incubation at 25 °C for 2–5 d.
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4

High-Quality Genomic DNA Extraction from Saccharomyces cerevisiae

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Saccharomyces cerevisiae IMDO 050523 was grown in yeast extract-peptone-glucose medium that contained 10 g/L of yeast extract (Oxoid, Basingstoke, Hampshire, UK), 20 g/L of peptone (Oxoid), and 20 g/L of glucose (Avantor, Radnor, Pennsylvania, USA). High-molecular-mass DNA was extracted and purified using a Genomic tip 20/G kit following the manufacturer’s instructions (Qiagen, Hilden, Germany). The genomic DNA was finally collected with a glass rod to avoid shearing and was dissolved in 250 μL of nuclease-free water (Avantor) by incubation in a water bath at 55°C for 2 h. The DNA integrity was checked by agarose gel electrophoresis, the purity was assessed with a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, Massachusetts, USA), and the concentration was measured using a Qubit fluorometer (Thermo Fisher Scientific).
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5

Isolation and Characterization of Lactic Acid Bacteria from Cheese

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For isolation of lactic acid bacteria, 10 milliliters of cheese sample was homogenized with sterilized peptone physiological saline solution (1% peptone (Oxoid), 0.9% NaCl) for about 1-3 minutes aseptically. Appropriate serial dilution (10 -1 to 10 -6 ) was prepared. A volume of 0.1 milliliters of appropriate dilutions was spread plated on MRS (OXOID) agar media. Then the plates were incubated for 48hours in an anaerobic jar at 32oC. Typical LAB characteristics colonies were randomly picked up and purify by streaking two or three times on fresh MRS agar plates followed by macroscopic and microscopic examinations. The colonies displaying the general characteristics of lactic acid bacteria were chosen from each plate for the physiological and biochemical tests.
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6

Meat Inoculation with Lactic Acid Bacteria

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Lactobacillus sakei, Lactobacillus sakei subsp. carnosus, Lactococcus lactis ssp. lactis and Staphylococcus xylosus used in this experiment were obtained from the Italy branch supplier of Chr.
Hansen, Denmark. The lyophilised cultures were resuspended in peptone water [0.1% sodium chloride and 0.7% peptone (Oxoid, Italy)] and left for 1 h at room temperature to rehydrate. Subsequently, appropriate dilutions were made, and 1 ml of each dilution was placed in MRS agar (de Man-Rogosa-Sharpe agar, pH 6.2, Oxoid, Italy) and incubated at 30°C for 48-72 h in a microaerophilic conditions (gas pack anaerobic system, BBL, Becton Dickinson, USA). A suspension of 107 CFU/ml was used to directly inoculate the ground meat (hamburgers), and the final bacterial cell concentration was approximately 105 CFU/g hamburger.
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7

Yeast Culture Media Preparation

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Unless otherwise stated, all chemicals including solvents were reagent grade and purchased from Sigma-Aldrich, St. Louis, MO, USA. Water was deionized (DI) and biological impurities removed by a departmental purification system. yeast extractpeptonedextroseadenine (YPDA) medium was prepared by dissolving 10 g of yeast extract (No. BP9727, Fisher Scientific, Pittsburgh, PA, USA), 20 g of peptone (No. BP1422, Fisher Scientific), and 20 g of D-glucose (No. AC41095, Acros Organics, part of Fisher Scientific) in 1 L of water. Eighty milligrams of adenine (No. A8626, Sigma-Aldrich) was then added following sterilization of the medium by autoclaving.
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8

E. coli Strain and Media Preparation

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E. coli K‐12 strains, plasmids, and promoter fragments used in this study are listed in Table S1 and oligonucleotide primers are in Table S2. Strains were grown in lysogeny broth (LB) (Sigma), Lennox broth (2% (w/v) peptone (Oxoid), 1% (w/v) yeast extract (Oxoid) and 170 mM NaCl), minimal salts medium (Squire et al., 2009 (link)) (minimal salts with 0.4% glycerol, 10% Lennox broth, 20 mM fumarate), or M9 minimal salts media (Sigma), supplemented with 0.36% glucose, 2 mM MgSO4, 0.1 mM CaCl2, all with appropriate antibiotic supplements (ampicillin 100 µg/ml and tetracycline 15 µg/ml).
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9

Cultivation of Akkermansia muciniphila

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Akkermansia muciniphila MucT (ATTC BAA-835) was grown in a basal medium as described previously, except without the addition of rumen fluid (Derrien et al., 2004 (link)). The medium was supplemented with either hog gastric mucin (0.5 %, Type III; Sigma-Aldrich, St. Louis, MO, USA) purified by ethanol precipitation as described previously (Miller and Hoskins, 1981 (link)), or D-glucose (10 mM, Sigma–Aldrich). The medium with glucose was also supplemented with BactoTM casitone (BD, Sparks, MD, USA), BBLTM yeast extract (BD), tryptone (Oxoid Ltd, Basingstoke, Hampshire, England), peptone (Oxoid ltd) (2 g/l each) and L-threonine (Sigma–Aldrich) (2 mM). Incubations were performed in serum bottles sealed with butyl-rubber stoppers at 37°C under anaerobic conditions provided by a gas phase of 182 kPa (1.5 atm) N2/CO2. Growth was measured by following optical density at 600 nm (OD600) using a spectrophotometer.
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10

Purification of Nickel-Binding Proteins

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Nickel (Ni) Sepharose 6 FF and DEAE Sepharose FF were obtained from Pharmacia Biotech Inc. (Piscataway, NJ, USA). Phenylmethanesulfonyl fluoride (PMSF) and imidazole were purchased from Sigma (St. Louis, MO, USA). Peptone was purchased from OXOID (Basingstoke, Hampshire, UK), and yeast extract was purchased from Angel Yeast (Angel Yeast Co., Ltd, Yichang, China). Other reagents used in this research were analytical reagent grade or the highest grade commercially available.
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