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296 protocols using bhi broth

1

Anaerobic Culture of Oral Pathogens

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Wild-type P. gingivalis strain ATCC33277 and Fusobacterium nucleatum strain ATCC10953 were grown on blood agar anaerobically at 37°C as described previously (Gawron et al. 2014 (link)). Bacteria were next inoculated into brain–heart infusion (BHI) broth (Becton Dickinson) containing 0.5 mg/mL L-cysteine, 10 µg/mL hemin and 0.5 µg/mL vitamin K. Following anaerobic (85% N2, 10% CO2 and 5% H2) overnight (o/n) culture, bacteria were resuspended in fresh BHI broth at optical density (OD)600nm = 0.1 and cultured for an additional 20 h. After centrifugation and washing, bacteria were suspended in PBS to obtain a final concentration of 109 colony-forming units (CFU)/mL and used for cell infection. GFs were treated with dimethyl sulfoxide (DMSO) (BioShop) or HDACi: SAHA (Abcam), ITF2357 (Italfarmaco), MS-275 (TargetMol) or a panel of selective HDACi synthesized at Italfarmaco: HDAC3/6i, HDAC6i(a), HDAC6i(b) or HDAC8(i). Details of HDACi specificity are shown in Appendix Table 2. After 30 min incubation with HDACi, cells were stimulated with TNFα (BioLegend) or infected with P. gingivalis or F. nucleatum at the indicated multiplicity of infection (MOI). In some experiments, protein synthesis was blocked with cycloheximide (TargetMol) before TNFα stimulation.
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2

Listeria monocytogenes Culturing Protocol

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L. monocytogenes EGD was maintained as a frozen glycerol stock and cultured in brain heart infusion (BHI) broth (Becton Dickinson, Franklin Lakes, NJ) or on BHI broth containing 1.5% agar.
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3

Isolation and Characterization of Cefazolin-Resistant Klebsiella pneumoniae Strains

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PSC-derived Kp strains (Kp-P1 and Kp-P5) isolated from the MLNs of GF mice transplanted with human stool from patients with PSC at Keio University were used. Cefazolin-resistant Kp-P1 was produced by culturing Kp-P1 in 200 μL of brain heart infusion broth (BHI broth) (Becton Dickinson) containing cefazolin (128, 64, 32, 16, 8, 4, 2, 1 μg/mL) in a 96-well plate at 37 °C for 24–48 h. Bacterial species were preserved in BHI broth containing 40% glycerol, snap-frozen, and stored at −80 °C until use. The frozen stock was thawed, applied to deoxycholate-hydrogen sulfide-lactose agar (Nissui), and incubated at 37 °C overnight. The colonies were cultured in 10 mL of BHI broth at 37 °C for 15–20 h. To prepare the bacteria, they were collected by centrifugation (2000 × g, 10 min, 4 °C) and dissolved in phosphate-buffered saline (PBS).
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4

Culturing L. monocytogenes EGD

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L. monocytogenes EGD was maintained as a frozen glycerol stock and cultured in brain heart infusion (BHI) broth (Becton Dickinson, Franklin Lakes, NJ, USA) or on BHI broth containing 1.5% agar.
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5

Listeria monocytogenes Strain Maintenance

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Listeria monocytogenes strain EGD, an LLO deletion mutant (Δhly), and an LLO-complemented strain (Δhly::hly) were used in this study [15 ]. The L. monocytogenes strains were maintained in frozen glycerol stocks and cultured overnight in brain-heart infusion (BHI) broth (Becton Dickinson, Franklin Lakes, NJ, USA) at 37°C with shaking, or on BHI broth containing 1.5% agar.
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6

Cultivation of Oral Microorganism Strains

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Oral microorganism strains, E. faecalis (ATCC 19433) and P. gingivalis (ATCC 33277) were obtained from State Key Laboratory of Oral Diseases, Sichuan University, Chengdu, China. E. faecalis were cultivated in brain heart infusion broth (BHI broth, Becton, Dickinson and Company, US) and BHI agar plate, while P. gingivalis were cultivated in BHI broth and blood agar plate supplemented with 0.0005% hemin, 0.0001% vitamin K. Both strains were incubated anaerobically (N2 80%; H2 10%; CO2 10%) at 37 °C.
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7

Conjugative Transfer of Prophages in E. coli and K. pneumoniae

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Sodium azide-resistant E. coli J53 was used as a receptor, and the prophage-containing K. pneumoniae strains 19051, 675920, 721005, and 911021 were used as donors for the conjugative transfer experiments. Small amounts (10–20 μl) of donor and recipient glycerol bacteria were inoculated in 3 ml of brain heart infusion (BHI) broth (BD Biosciences, San Jose, CA, United States). After culture overnight, the donor bacteria were mixed with the recipient bacteria, centrifuged, resuspended in 80 μl of BHI broth, supplemented with a resuspended bacterial solution at the surface of a filter (filter size 1 cm2, pore size 0.45 μm), and the filter was adhered to BHI (BD Biosciences) agar plates. The cells were fully absorbed by the filter and cultured at 37°C for 12–18 h. The bacteria were then washed from the filter and spotted on to the BHI agar plates containing 200 μg/ml sodium azide and 50 μg/ml amikacin to select conjugons harboring the prophage.
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8

Antimicrobial Activity Screening of P. xiamenensis

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Secretion of antimicrobials by P. xiamenensis was assessed by diffusion assay on agar. Soft agar (0.8%) was prepared using Brain Heart Infusion (BHI) broth (BD, Sparks, MD, USA) or Tryptic Soy Broth (TSB, BD). The bacterial strains E. piscicida, S. epidermidis, A. hydrophila, and P. aeruginosa were incorporated into 4 mL of soft agar and overlaid onto pre-solidified respective agar media. P. xiamenensis was grown either in marine agar or broth. E. piscicida was grown on BHI broth medium while other strains were propagated on Tryptic Soy Broth (TSB; BD, Reno-Sparks, NV, USA) medium. Briefly, overnight cultures were inoculated into fresh respective mediums, 1% v/v, and allowed to grow to 0.4 OD595. At the appropriate density, 200 µL was retrieved and suspended into 4 mL of soft agar prepared by the respective media for each strain. The suspensions were overlaid onto pre-solidified agar and allowed to solidify. Then, complete round plugs were removed and filled with P. xiamenensis suspended in marine agar in a similar procedure. The P. xiamenensis suspension (1 mL) was poured into the well and allowed to solidify. Marine soft agar alone, or chloramphenicol-treated (50 µg/mL), were used as negative and positive controls, respectively. Plates were incubated> 24 h for pink color development, and the diffusion zones were compared.
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9

Culturing Enterococcus and Porphyromonas

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E. faecalis ATCC 29212 was cultivated in brain heart infusion (BHI) broth (BD Biosciences, Sparks, MD, USA), and P. endodontalis ATCC 35406 was cultured in BHI broth supplemented with hemin (1 μg/ml) and vitamin K (0.2 μg/ml) at 37 °C in an anaerobic condition (5% H2, 10% CO2, 85% N2).
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10

Cocktail of S. aureus Strains

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A cocktail of three strains of S. aureus was used: CECT976 (SEA producer) and CECT4466 (SED producer), from the Spanish Type Culture Collection, and CTC1008, as a meat isolate from the IRTA culture collection. Each strain was independently grown in Brain Heart Infusion (BHI) broth (Becton Dickinson, Sparks, MD, USA) at 37 °C for 24 h. The cultures were cryopreserved at −80 °C with 20% glycerol until use. Thawed cultures of each strain were mixed at equal concentrations before being inoculated on DCH.
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