biostudies-arrayexpressEmma HoldenSalmonella enterica subsp. enterica serovar Typhimuriumhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17304We used TraDIS-Xpress (a high throughput next generation TnSeq approach) to determine the essential genes required for survival of Salmonella in simulated decontamination protocols using heat treatment and essential oil preparations. We exposed planktonic cultures and established biofilms in parallel to 2 heat stresses (plus a 37ºC control) and 2 essential oil preparations (oil and nanoemulsions, plus an untreated control). DNA was extracted and sequenced to determine the essential genes for each treatment and find mechanisms of killing and mechansism of susceptibility for each treatment combination.biostudies-arrayexpressSequencing - DNA was sequenced on a NextSeq500 using the NextSeq 500/550 High Output Kit v2.5 with 75 cycles.Library Construction - Libraries were prepared following the protocol outlined by Holden et al 2022 (https://pubmed.ncbi.nlm.nih.gov/40952897/) to amplify and isolate DNA fragments containing the transposon. DNA fragment length was quantified using a Tapestation (Aligent)Sample Collection - For planktonic conditions, approximately 10^7 CFU/mL of transposon mutant library was added to 5 ml LB broth without salt supplemented with 1 mM IPTG in sterile 5 mL eppendorfs. A total of 1 µL (0.2 µL/mL) of essential oil or nanoemulsion was added to each tube. Tubes with essential oil, nanoemulsion and untreated controls were placed in a water bath at 54 ºC for 26 minutes, 56 ºC for 9 minutes or 37 ºC for 1 hour. After the treatments, media was removed to eliminate the presence of the essential oils, replaced with 1 mL of fresh LB, and incubated at 37 ºC for 4 hours to allow cells to recover and repopulate. Cells were then pelleted and stored at -20 ºC until DNA extraction. For biofilm conditions, a total of 30 sterile 5mm glass beads were placed in each well of a 6-Nucleic Acid Extraction - DNA was extracted using a Maxwell® Robot (Promega, UK) with Maxwell® RSC PureFood GMO and Authentication Kit AS1600 (Promega, UK), following manufacturer’s protocols. DNA concentration was measured using Qubit 2.0 Fluorometer (Thermo Fisher Scientific, UK) and normalised for library preparation.Growth Protocol - The transposon mutant library used in this work was previously described by Holden et al 2022 (https://pubmed.ncbi.nlm.nih.gov/36326671/). For planktonic conditions, approximately 10^7 CFU/mL of transposon mutant library was added to 5 ml LB broth without salt supplemented with 1 mM IPTG in sterile 5 mL eppendorfs. A total of 1 µL (0.2 µL/mL) of essential oil or nanoemulsion was added to each tube. Tubes with essential oil, nanoemulsion and untreated controls were placed in a water bath at 54 ºC for 26 minutes, 56 ºC for 9 minutes or 37 ºC for 1 hour. After the treatments, media was removed to eliminate the presence of the essential oils, replaced with 1 mL of fresh LB, and incubated at 37 ºC for 4 hours to allow cells to recover and repopulate. Cells were then pelleted aSample Treatment - The transposon mutant library used in this work was previously described by Holden et al 2022 (https://pubmed.ncbi.nlm.nih.gov/36326671/). For planktonic conditions, approximately 10^7 CFU/mL of transposon mutant library was added to 5 ml LB broth without salt supplemented with 1 mM IPTG in sterile 5 mL eppendorfs. A total of 1 µL (0.2 µL/mL) of essential oil or nanoemulsion was added to each tube. Tubes with essential oil, nanoemulsion and untreated controls were placed in a water bath at 54 ºC for 26 minutes, 56 ºC for 9 minutes or 37 ºC for 1 hour. After the treatments, media was removed to eliminate the presence of the essential oils, replaced with 1 mL of fresh LB, and incubated at 37 ºC for 4 hours to allow cells to recover and repopulate. Cells were then pelleted OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesData Transformation - QuaTraDIS (version 1.4) (https://github.com/quadram-institute-bioscience/QuaTradis) was used to map fastq files to a Salmonella Typhimurium reference genome (CP001363, modified to include the chromosomally-integrated tac promoter) and determine statistically significant differences in insertion frequencies between conditions. A set of default cut-offs for significance and number of reads were applied (q-value < 0.05, logFC ≥2, logCPM ≥4) to create a list of candidate genes.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNAMaxwell® RSC PureFood GMO and Authentication Kit AS1600 (Promega, UK)NextSeq 500DNA-seqSalmonella enterica subsp. enterica serovar TyphimuriumEmma HoldenfalseTraDIS-Xpress identifies essential genes for Salmonella survival following combined heat and essential oil treatments in planktonic cultures and established biofilmsWe used TraDIS-Xpress (a high throughput next generation TnSeq approach) to determine the essential genes required for survival of Salmonella in simulated decontamination protocols using heat treatment and essential oil preparations. We exposed planktonic cultures and established biofilms in parallel to 2 heat stresses (plus a 37ºC control) and 2 essential oil preparations (oil and nanoemulsions, plus an untreated control). DNA was extracted and sequenced to determine the essential genes for each treatment and find mechanisms of killing and mechansism of susceptibility for each treatment combination.2026-10-05T00:00:00Z2026-10-05T01:00:39.024Z2026-07-10T13:48:39.75ZE-MTAB-17304ERP201037EFO_0002944EFO_0004170EFO_0003789EFO_0002693EFO_0005518EFO_0003816EFO_0004184EFO_0003969