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1

Microbial Strain Collection Management

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The following strains were used in this study: Staphylococcus aureus ATCC 6538, biofilm-producing reference strain [58 (link)], S. aureus ATCC 43300 (Methicillin resistant S. aureus-MRSA), Pseudomonas aeruginosa ATCC 9027, P. aeruginosa DSM 102273 (multidrug resistant). The strains were stored in the private collection of the Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina (Messina, Italy). They were stored at −70 °C in Microbanks™ (Pro-lab Diagnostics, Neston, UK).
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2

Bacterial Isolation from Toothbrush and Sputum

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The toothbrush’s head was detached and underwent five cycles of sonication (30 sec each) in 5 ml BHI (Brain Heart Infusion) medium before incubation for 24 h at 37°C with shaking. Saliva and sputum samples were treated with 0.5–1 ml Sputolysin (Calbiochem) and incubated for 40 min at 37°C with shaking. Each sample (100 µl) was plated on Columbia blood (5% sheep blood), McConkey, Mannitol Salt and Sabouraud agar plates (BD Difco), and incubated at 37°C for 48 h. All plates were kept at RT for five additional days to recover small variant colonies and slow-growing strains. Isolated colonies were identified using MALDI-TOF-MS [24] and/or Vitek2 (Biomerieux). Isolates were stored in Microbanks (ProLab Diagnostics) at – 80°C.
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3

Isolation of Campylobacter from Meat and Milk

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Isolation of Campylobacter spp. from meat and milk was conducted in compliance with the EN ISO 10272-1:2006 method with slight modification. Briefly, meat and cheese (25 g) were homogenized for 2 min in a stomacher with 225 mL buffered peptone water (Oxoid Limited, Basingstoke, United Kingdom) in the sterile plastic bags. Then, 10 mL of the homogenate solution and 10 ml of raw milk was added to 90 mL of Bolton broth containing the Bolton broth selective supplement and 5% laked horse blood (Oxoid Limited, Basingstoke, United Kingdom) and incubated at 42 °C for 48 h under microaerobic conditions (Generbox microaer-BioMerieux, Marcy l’Etoile, France). Next, the bacterial suspension was spread onto CCDA plates (Oxoid Limited, Basingstoke, United Kingdom) and then incubated at 42 °C for 48 h under microaerobic conditions. Characteristic growth from the CCDA plates was transferred to a blood plate (Columbia agar containing 5% cattle blood, Oxoid Limited, Basingstoke, United Kingdom) and incubated overnight at 42 °C. Colonies suspected as Campylobacter spp. were examined for cell morphology, motility, and oxidase reactions. Putative Campylobacter colonies were frozen at −80 in Microbanks (Pro-Lab Diagnostics, Birkenhead, United Kingdom) until species differentiation using polymerase chain reaction (PCR).
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4

Isolation of Campylobacter from Water Samples

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Isolation of Campylobacter spp. from water samples was performed according to International Organization for Standardisation (2019) . We filtered 100 ml of water sample through 0.45μm filters (Merc Millipore, Burlington, USA) and then each filter was transferred to 90 ml of Bolton broth (Oxoid Limited, Basingstoke, United Kingdom). The broth was incubated at 41°C in a microaerophilic atmosphere (Generbox microaer-BioMerieux, Marcy l’Etoile, France) for 48 hours and after preincubation 10μl of culture was performed on a solid CCDA medium (Oxoid Limited, Basingstoke, United Kingdom). Characteristic growth from the CCDA plates was transferred to a blood plate (Columbia agar containing 5% cattle blood, Oxoid Limited, Basingstoke, United Kingdom) and incubated overnight at 41°C. Colonies suspected as Campylobacter spp. were examined for cell morphology, motility, and oxidase reactions. Putative Campylobacter colonies were frozen at -80 in Microbanks (Pro-Lab Diagnostics, Birkenhead, United Kingdom) until species differentiation.
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5

Antibacterial Activity of R. montana Extracts

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The antibacterial activity of R. montana extracts was tested against the following strains: S. aureus ATCC 6538, S. aureus ATCC 43300, S. aureus 815, S. aureus 74CCH, S. epidermidis ATCC 35984, Escherichia coli ATCC 25922, E. coli ATCC 10536, E. coli DSM 105388, Pseudomonas aeruginosa ATCC 9027, and P. aeruginosa DSM 102273 [59 (link)]. The strains were stored in the private collection of the Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina (Italy). They were stored at −70 °C in Microbanks™ (Pro-lab Diagnostics, Neston, UK). All reagents were purchased from Sigma-Aldrich (Milan, Italy), unless otherwise specified in the text.
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6

Microbiome Sampling from Nasal Lavage and Saliva

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Nasal lavage was performed as described by Mainzet al. [12 (link)] by inserting 10 mL of sterile isotonic saline into each nostril [14 (link)]. The saliva was recovered by the unstimulated method, spitting in a sterile tube, while the sputum was collected by natural expectoration or by tracheal cannula (when the patient was unable to expectorate). The head of the toothbrush was detached and underwent five cycles of sonication (30 s each) in 5 mL of brain heart infusion medium before incubation for 24 h at 37°C with shaking. Saliva and sputum samples were treated with 0.5–1 mL of Sputolysin (Calbiochem, California, USA) and incubated for 40 min at 37°C with shaking. An aliquot of each sample was plated on Columbia blood (5% sheep blood), McConkey, and Mannitol Salt agar plates (BD Difco, USA) and incubated at 37°C for 48 h. All plates were kept at room temperature for an additional 5 days to recover small variant colonies and slow-growing strains. Isolated colonies were identified using MALDI-TOF-MS [15 (link)] and/or Vitek2 (Biomerieux, USA). Isolates were stored in Microbanks (ProLab Diagnostics, USA) at −80°C.
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7

Fungal Species Identification and Susceptibility

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Sixteen Candida spp. (C. albicans, C. glabrata, C. krusei, C. parapsilosis, C. tropicalis, C. valida, C. lusitaniae, C. norvegensis), 15 non-Candida spp. clinical strains (C. neoformans, S. cerevisiae, Kloekera japonica, P. carsonii, Sporobolomyces salmonicolor), and five dermatophyte clinical isolates (T. mentagrophytes, M. canis, M. gypseum) were tested (Table 2). C. albicans ATCC 90028 and C. glabrata ATCC 90030 were also included.
Yeast identification was conducted by the API ID32C system (BioMérieux, Rome, Italy). Then, strains were maintained at –80 °C in Microbanks™ (Pro-Lab Diagnostics, Neston, UK) and cultured twice on Sabouraud dextrose agar (SDA, Oxoid, Milan, Italy) at 35 °C for 72 h before the assays. Dermatophyte identification was carried out by macroscopic and microscopic observations of the colonies and reproductive structures after 15 days of incubation on Mycobiotic agar at 25 °C (Merck, KGAA, Darmstadt, Germany) [23 (link),24 (link)]. Molds were stored in SDA at 4 °C until use. For susceptibility testing, non-germinated conidial suspensions were prepared as previously described [23 (link)].
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8

Cryptococcosis Isolate Characterization

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Seven C. neoformans sensu lato clinical isolates from HIV-infected patients with cryptococcosis, admitted to Amedeo di Savoia Hospital (Turin, Italy) between January 2013 and December 2014, were tested. Yeast isolates were identified by the API ID32C identification systems (BioMérieux, Rome, Italy). Then, they were stored at − 80 °C in Microbanks™ (Pro-Lab Diagnostics, Neston, UK), and sub-cultured at least twice on Sabouraud dextrose agar (SDA, Oxoid, Milan, Italy) at 35 °C for 72 h before testing.
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9

Probiotic Strains Inhibit Pseudomonas Infection

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The probiotic strains tested in this study were L. reuteri DSM20016 and B. longum subsp. infantis DSM20088 (Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany) [53 (link),61 (link)]. The pathogen strain used was P. aeruginosa American Type Culture Collections (ATCC 9027). The L. reuteri and B. longum strains were grown in De Man, Rogosa, and Sharpe broth (MRSB, Oxoid, Milan, Italy) with and without the addition of 0.05% cysteine for 24–48 h at 37 °C under 5% CO2 conditions. P. aeruginosa was grown in tryptic soy broth (TSB, Oxoid) at 37 °C for 24 h in aerobic conditions. The strains were stored at −70 °C in Microbanks™ (Pro-lab Diagnostics, Neston, UK). All reagents were purchased from Sigma-Aldrich (Milan, Italy) unless otherwise specified in the text.
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10

Isolation and Identification of Thermotolerant Campylobacter

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A total of 1,720 samples were processed during the whole project and Campylobacter was recovered from carcass samples after the enrichment and the enumeration phases, according to parts 1 and 2, respectively, of the NF EN ISO 10272 standard procedure [20 , 21 ]. The isolates were cultured on Columbia blood agar and incubated at 42°C for 48 h in a microaerophilic atmosphere. After a preliminary phenotypic characterization, suspected colonies were confirmed as thermotolerant Campylobacter and identified to species level using a multiplex PCR, as described previously by Di Giannatale et al. [22 (link)]. Genomic DNA was extracted using a Wizard genomic DNA purification kit (Promega, Madison, WI, USA). Isolates were stored in a Microbank (Pro-Lab Diagnostics Canada, Richmond Hill, ON, Canada) at 80°C until further analysis.
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