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19 protocols using luria bertani lb

1

E. coli Strains for Experimental Infection

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E. coli DH5α (BLP-positive, E. coli K-12 derivative) bacteria were stored in our laboratory. The E. coli JE5505 (BLP-negative, E. coli K-12 derivative) strain was obtained from The Coli Genetic Stock Center (CGSC) of Yale University (New Haven, CT; CGSC number 6672). Although the E. coli JE5505 strain lacks BLP, its normal physiological properties of growth and multiplication are not impaired (54 (link)). According to previously reported studies, E. coli DH5α was referenced for E. coli JE5505 during experimental infection (13 (link), 55 (link)). To determine the number of CFU in the bacterial suspension used in this study, 1 mL of bacterial suspension (1 × 107 CFU/mL) was seeded in 100 mL of Luria-Bertani (LB; Oxoid, Basingstoke, UK) broth and incubated with shaking at 37°C for 12 h (optical density at 600 nm [OD600] value of approximately 0.9 in the log phase). Thereafter, the cultured bacterial suspension was serially diluted and plated on LB agar plates and incubated at 37°C for 12 h. The colony counting technique was used to determine the total number of CFU (approximately 1 × 108 CFU/mL). At least eight independent experiments were performed, and the results of CFU counting were consistent. C57BL/6J mice were provided by the Model Animal Research Center of Nanjing University, Nanjing, China.
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2

Cultivation of Pseudomonas aeruginosa PAO1

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Pseudomonas aeruginosa strain PAO1 (Holloway1C Stanier131) was obtained from the National Collection of Industrial, Food and Marine Bacteria (NCIMB), United Kingdom. PAO1 was grown in Luria-Bertani (LB, Oxoid) broth and on nutrient agar (Oxoid) at 37°C.
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3

Bacterial Growth Conditions for Antibacterial Assays

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Bacterial strains were grown in Mueller Hinton (MH) (non-biofilm forming C. striatum, S. epidermidis, E. coli, K. pneumoniae, P. aeruginosa, S. aureus and clinical isolates CI1–5) and Luria Bertani (LB) (biofilm forming S. aureus ATCC 1167) media (Oxoid, Basingstoke, Hampshire, MA, USA) at 37 °C in aerobic conditions. To obtain a bacterial suspension suitable for antibacterial assays, fresh colonies of each strain, grown on MH and LB agar, were inoculated in MH and LB media, and incubated at 37 °C overnight. The bacterial suspension was resuspended in a fresh medium and further incubated at 37 °C until bacterial growth reached the exponential phase. Serial dilutions were performed to achieve the necessary bacterial load for the tests (1 × 106 CFU/mL).
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4

Carbapenem-Resistant E. coli Outbreak

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On July 1, 2012, one strain of E. coli was isolated from a sputum sample from a pneumonia patient presenting with expiratory dyspnea in the geriatrics department at a hospital in Beijing. This strain showed resistance to carbapenems. Since then, carbapenem-resistant E. coli strains were frequently isolated in four wards of the geriatric and neurology departments until December 28, 2013. A total of 45 strains were included in the study. Some of the E. coli strains were collected from the same patient on different days. The bacterial strains were cultured on Luria-Bertani (LB) (Oxoid, Wesel, Germany) plates at 37°C for 24 h.
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5

Microbial Growth and Antibiotic Susceptibility

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Tryptic soy broth (Oxoid, UK) was used for the proliferation of S. aureus and S. epidermidis strains. TSB medium with 1% glucose (TSBG) was used for staphylococcal biofilm formation [59 (link),62 (link)]. Luria–Bertani (LB, Oxoid, UK) medium was used for E. coli cultivation. Calcium-adjusted Mueller–Hinton Broth (CAMHB, Oxoid, UK) was chosen for the antimicrobial susceptibility test (AST) [10 (link),63 (link),64 (link),65 (link)]. The antibiotics ampicillin (100 µg/mL), kanamycin (50 µg/mL), chloramphenicol (10 µg/mL) and erythromycin (10 µg/mL) were used for selection of the constructed bacterial strains. Tilmicosin and oxacillin were purchased from MedChemExpress China and Sangon Biotech (Shanghai, China) Co., Ltd., respectively.
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6

Bacterial Culture and Preparation

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Methicillin-resistant Staphylococcus aureus (MRSA; clinical isolates LUH14616 [16 (link)] and Mu50, ATCC 700699), Enterococcus faecalis (ATCC 29212), Pseudomonas aeruginosa (PAO1; ATCC BAA47), Escherichia coli (ATCC 35218) and a clinical isolate of Acinetobacter baumannii were used. The clinical isolate of A. baumannii was kindly provided by Drs. Jan Sinnige (Regional Laboratory for Medical Microbiology and Public Health Haarlem, Haarlem, the Netherlands). Bacteria were stored in Luria-Bertani (LB; Oxoid, Ltd., Basingstoke, UK) medium supplemented with 15% (v/v) glycerol at − 80 °C. LB agar plates were used to grow the inoculae at 37 °C and 5% CO2 overnight. To create a mid-log phase growth culture, bacteria were cultured in LB medium at 37 °C, shaken at 200 rpm. The bacterial culture was centrifuged at 3600×g for 5 min and the pellet was re-suspended in PBS to the desired bacterial concentration, based on the optical density at 600 nm.
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7

Fecal and Luminal Microbial Enumeration

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Fecal samples from both groups of mice and luminal samples from jejunum, cecum and colon of the MC mice were suspended in sterile saline supplemented with 0.1% of peptone. NCFM of all fecal and luminal samples were counted on MRS agar (Oxoid Ltd) after anaerobic incubation at 37 °C for 48 h. Additionally, fecal samples collected twice a week and all luminal samples were screened for absence of contamination by plating on Luria-Bertani (LB; Oxoid Ltd) agar incubated at 37 °C for 48 h under aerobic and anaerobic atmosphere.
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8

Phenotypic Characterization of Klebsiella pneumoniae

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A total of ten K. pneumoniae clinical isolates were obtained from the strain collection at the Bacterial Molecular Genetics research group, Universidad El Bosque, Bogotá, Colombia. Control strains consisting of previously characterized K. pneumoniae isolates, the LM21 gfp strain [27] (link), and mutants lacking genes relevant to biofilm formation [28] (link) were also included. Unless otherwise indicated, all strains were grown at 37 °C in bacterial culture media Luria Bertani (LB; Oxoid) or Mueller-Hinton (MH; Oxoid), with agitation at 180 rpm, overnight for 16 hours. Media were supplemented with antibiotics (Sigma-Aldrich) when necessary: Meropenem (MER), amikacin (AMK), ciprofloxacin (CIP), trimethoprim-sulfamethoxazole (TS); the latter prepared at a 1:19 combination of two antibiotics that inhibit two steps in the synthesis of tetrahydrofolate. LB agar, supplemented with Congo red (Sigma-Aldrich), Coomassie blue (Sigma-Aldrich), and calcofluor (fluorescent brightener 28; Sigma-Aldrich), was used to assess colony morphology [29, (link)30] (link).
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9

Cultivation of M. smegmatis mc 2 155

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M. smegmatis mc 2 155 cells from the ATCC were routinely cultivated in Luria-Bertani (LB, Oxoid Ltd., England) broth with 0.05% Tween 80 or on LB agar at 37°C. TBSSB was synthesized and confirmed as described previously [8] .
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10

Antagonistic Effects of Novel Bacillus DFMs

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A total of 4 proprietary Bacillus DFM combinations from a set of >500 novel DFMs were selected for this study based on their antagonistic effect against a set of bacterial pathogens including Salmonella, Staphylococcus aureus, E. coli, among others. Samples of 1 g of each lyophilized DFM combination were grown individually in 9 mL of Luria-Bertani (LB, ThermoFisher Scientific, Waltham, MA) broth at 37°C for 24 h. Overnight cultures were used for agar-well diffusion assay, as described below, and were serially diluted in 9 mL of BPW and plated aerobically onto LB agar plates (ThermoFisher Scientific, Waltham, MA) at 37°C for 24 h for enumeration.
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