Gahan CGM, Hill C. Listeria monocytogenes: survival and adaptation in the gastrointestinal tract. Front Cell Infect Microbiol. 2014;4. https://doi.org/10.3389/fcimb.2014.00009.
NicAogáin K, O’Byrne CP. The role of stress and stress adaptations in determining the fate of the bacterial pathogen Listeria monocytogenes in the food chain. Front Microbiol. 2016;7. https://doi.org/10.3389/fmicb.2016.01865.
Bucur FI, Grigore-Gurgu L, Crauwels P, Riedel CU, Nicolau AI. Resistance of Listeria monocytogenes to stress conditions encountered in food and food processing environments. Front Microbiol. 2018;9. https://doi.org/10.3389/fmicb.2018.02700.
EFSA Panel on Biological Hazards (BIOHAZ), Ricci A, Allende A, Bolton D, Chemaly M, Davies R, et al. Listeria monocytogenes contamination of ready-to-eat foods and the risk for human health in the EU. EFSA J. 2018;16:e05134.
Article
Google Scholar
Buchanan RL, Gorris LGM, Hayman MM, Jackson TC, Whiting RC. A review of Listeria monocytogenes: an update on outbreaks, virulence, dose-response, ecology, and risk assessments. Food Control. 2017;75:1–13.
Article
Google Scholar
Chan YC, Wiedmann M. Physiology and genetics of Listeria monocytogenes survival and growth at cold temperatures. Crit Rev Food Sci Nutr. 2009;49:237–53.
Article
CAS
PubMed
Google Scholar
Muntean M-V, Marian O, Barbieru V, Cătunescu GM, Ranta O, Drocas I, et al. High pressure processing in food industry – characteristics and applications. Agriculture and Agricultural Science Procedia. 2016;10:377–83.
Article
Google Scholar
Woldemariam HW, Emire SA. High pressure processing of foods for microbial and Mycotoxins control: current trends and future prospects. Cogent Food Agric. 2019;5:1622184.
Article
CAS
Google Scholar
Ferreira M, Almeida A, Delgadillo I, Saraiva J, Cunha Â. Susceptibility of Listeria monocytogenes to high pressure processing: a review. Food Reviews International. 2016;32:377–99.
Article
Google Scholar
Wen J, Anantheswaran RC, Knabel SJ. Changes in barotolerance, thermotolerance, and cellular morphology throughout the life cycle of Listeria monocytogenes. Appl Environ Microbiol. 2009;75:1581–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ritz M, Tholozan JL, Federighi M, Pilet MF. Morphological and physiological characterization of Listeria monocytogenes subjected to high hydrostatic pressure. Appl Environ Microbiol. 2001;67:2240–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Duru IC, Andreevskaya M, Laine P, Rode TM, Ylinen A, Løvdal T, et al. Genomic characterization of the most barotolerant Listeria monocytogenes RO15 strain compared to reference strains used to evaluate food high pressure processing. BMC Genomics. 2020;21:455.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bruschi C, Komora N, Castro SM, Saraiva J, Ferreira VB, Teixeira P. High hydrostatic pressure effects on Listeria monocytogenes and L. innocua: evidence for variability in inactivation behaviour and in resistance to pediocin bacHA-6111-2. Food Microbiol. 2017;64:226–31.
Article
CAS
PubMed
Google Scholar
Koseki S, Mizuno Y, Yamamoto K. Predictive modelling of the recovery of Listeria monocytogenes on sliced cooked ham after high pressure processing. Int J Food Microbiol. 2007;119:300–7.
Article
CAS
PubMed
Google Scholar
Koseki S, Mizuno Y, Yamamoto K. Use of mild-heat treatment following high-pressure processing to prevent recovery of pressure-injured Listeria monocytogenes in milk. Food Microbiol. 2008;25:288–93.
Article
CAS
PubMed
Google Scholar
Tomasula PM, Renye JA, Van Hekken DL, Tunick MH, Kwoczak R, Toht M, et al. Effect of high-pressure processing on reduction of Listeria monocytogenes in packaged Queso Fresco. J Dairy Sci. 2014;97:1281–95.
Article
CAS
PubMed
Google Scholar
Valdramidis VP, Patterson MF, Linton M. Modelling the recovery of Listeria monocytogenes in high pressure processed simulated cured meat. Food Control. 2015;47:353–8.
Article
CAS
Google Scholar
Nakaura Y, Morimatsu K, Inaoka T, Yamamoto K. Listeria monocytogenes cells injured by high hydrostatic pressure and their recovery in nutrient-rich or -free medium during cold storage. High Press Res. 2019;39:324–33.
Article
CAS
Google Scholar
Bozoglu F, Alpas H, Kaletunç G. Injury recovery of foodborne pathogens in high hydrostatic pressure treated milk during storage. FEMS Immunol Med Microbiol. 2004;40:243–7.
Article
CAS
PubMed
Google Scholar
Liu G, Wang Y, Gui M, Zheng H, Dai R, Li P. Combined effect of high hydrostatic pressure and enterocin LM-2 on the refrigerated shelf life of ready-to-eat sliced vacuum-packed cooked ham. Food Control. 2012;24:64–71.
Article
CAS
Google Scholar
Evrendilek GA, Balasubramaniam VM. Inactivation of Listeria monocytogenes and Listeria innocua in yogurt drink applying combination of high pressure processing and mint essential oils. Food Control. 2011;22:1435–41.
Article
CAS
Google Scholar
Espina L, García-Gonzalo D, Laglaoui A, Mackey BM, Pagán R. Synergistic combinations of high hydrostatic pressure and essential oils or their constituents and their use in preservation of fruit juices. Int J Food Microbiol. 2013;161:23–30.
Article
CAS
PubMed
Google Scholar
Stratakos AC, Delgado-Pando G, Linton M, Patterson MF, Koidis A. Synergism between high-pressure processing and active packaging against Listeria monocytogenes in ready-to-eat chicken breast. Innov Food Sci Emerg Technol. 2015;27:41–7.
Article
CAS
Google Scholar
Bleoancă I, Saje K, Mihalcea L, Oniciuc E-A, Smole-Mozina S, Nicolau AI, et al. Contribution of high pressure and thyme extract to control Listeria monocytogenes in fresh cheese - a hurdle approach. Innov Food Sci Emerg Technol. 2016;38:7–14.
Article
CAS
Google Scholar
Komora N, Maciel C, Pinto CA, Ferreira V, Brandão TRS, Saraiva JMA, et al. Non-thermal approach to Listeria monocytogenes inactivation in milk: the combined effect of high pressure, pediocin PA-1 and bacteriophage P100. Food Microbiol. 2020;86:103315.
Article
CAS
PubMed
Google Scholar
Komora N, Bruschi C, Ferreira V, Maciel C, Brandão TRS, Fernandes R, et al. The protective effect of food matrices on Listeria lytic bacteriophage P100 application towards high pressure processing. Food Microbiol. 2018;76:416–25.
Article
CAS
PubMed
Google Scholar
Vannini L, Lanciotti R, Baldi D, Guerzoni ME. Interactions between high pressure homogenization and antimicrobial activity of lysozyme and lactoperoxidase. Int J Food Microbiol. 2004;94:123–35.
Article
CAS
PubMed
Google Scholar
Iucci L, Patrignani F, Vallicelli M, Guerzoni ME, Lanciotti R. Effects of high pressure homogenization on the activity of lysozyme and lactoferrin against Listeria monocytogenes. Food Control. 2007;18:558–65.
Article
CAS
Google Scholar
Bravo D, de Alba M, Medina M. Combined treatments of high-pressure with the lactoperoxidase system or lactoferrin on the inactivation of Listeria monocytogenes, Salmonella Enteritidis and Escherichia coli O157:H7 in beef carpaccio. Food Microbiol. 2014;41:27–32.
Article
CAS
PubMed
Google Scholar
Montiel R, Bravo D, de Alba M, Gaya P, Medina M. Combined effect of high pressure treatments and the lactoperoxidase system on the inactivation of Listeria monocytogenes in cold-smoked salmon. Innov Food Sci Emerg Technol. 2012;16:26–32.
Article
CAS
Google Scholar
Liu Y, Ream A, Joerger RD, Liu J, Wang Y. Gene expression profiling of a pressure-tolerant Listeria monocytogenes Scott a ctsR deletion mutant. J Ind Microbiol Biotechnol. 2011;38:1523–33.
Article
CAS
PubMed
Google Scholar
Bowman JP, Bittencourt CR, Ross T. Differential gene expression of Listeria monocytogenes during high hydrostatic pressure processing. Microbiology (Reading). 2008;154(Pt 2):462–75.
Article
CAS
Google Scholar
Pérez-Baltar A, Alía A, Rodríguez A, Córdoba JJ, Medina M, Montiel R. Impact of water activity on the inactivation and gene expression of Listeria monocytogenes during refrigerated storage of pressurized dry-cured ham. Foods. 2020;9.
Rosvall M, Axelsson D, Bergstrom CT. The map equation. Eur Phys J Spec Top. 2009;178:13–23.
Article
Google Scholar
Münch R, Hiller K, Barg H, Heldt D, Linz S, Wingender E, et al. PRODORIC: prokaryotic database of gene regulation. Nucleic Acids Res. 2003;31:266–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bull MK, Hayman MM, Stewart CM, Szabo EA, Knabel SJ. Effect of prior growth temperature, type of enrichment medium, and temperature and time of storage on recovery of Listeria monocytogenes following high pressure processing of milk. Int J Food Microbiol. 2005;101:53–61.
Article
PubMed
Google Scholar
Ciolacu L, Nicolau AI, Wagner M, Rychli K. Listeria monocytogenes isolated from food samples from a Romanian black market shows distinct virulence profiles. Int J Food Microbiol. 2015;209:44–51.
Article
CAS
PubMed
Google Scholar
Wagner E, Zaiser A, Leitner R, Quijada NM, Pracser N, Pietzka A, et al. Virulence characterization and comparative genomics of Listeria monocytogenes sequence type 155 strains. BMC Genomics. 2020;21:847.
Article
CAS
PubMed
PubMed Central
Google Scholar
Luo F, Yang Y, Zhong J, Gao H, Khan L, Thompson DK, et al. Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory. BMC Bioinformatics. 2007;8:299.
Article
PubMed
PubMed Central
CAS
Google Scholar
van Dam S, Võsa U, van der Graaf A, Franke L, de Magalhães JP. Gene co-expression analysis for functional classification and gene-disease predictions. Brief Bioinformatics. 2018;19:575–92.
PubMed
Google Scholar
Schlitt T, Palin K, Rung J, Dietmann S, Lappe M, Ukkonen E, et al. From gene networks to gene function. Genome Res. 2003;13:2568–76.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liu Y, Orsi RH, Gaballa A, Wiedmann M, Boor KJ, Guariglia-Oropeza V. Systematic review of the Listeria monocytogenes σB regulon supports a role in stress response, virulence and metabolism. Future Microbiol. 2019;14:801–28.
Article
CAS
PubMed
Google Scholar
Bonilla CY. Generally stressed out Bacteria: environmental stress response mechanisms in gram-positive Bacteria. Integr Comp Biol. 2020;60:126–33.
Article
CAS
PubMed
Google Scholar
Anast JM, Schmitz-Esser S. The transcriptome of Listeria monocytogenes during co-cultivation with cheese rind bacteria suggests adaptation by induction of ethanolamine and 1,2-propanediol catabolism pathway genes. PLoS One. 2020;15. https://doi.org/10.1371/journal.pone.0233945.
Cortes BW, Naditz AL, Anast JM, Schmitz-Esser S. Transcriptome sequencing of Listeria monocytogenes reveals major gene expression changes in response to lactic acid stress exposure but a less pronounced response to oxidative stress. Front Microbiol. 2020;10. https://doi.org/10.3389/fmicb.2019.03110.
Mujahid S, Bergholz TM, Oliver HF, Boor KJ, Wiedmann M. Exploration of the role of the non-coding RNA SbrE in L. monocytogenes stress response. Int J Mol Sci. 2012;14:378–93.
Article
PubMed
PubMed Central
CAS
Google Scholar
Marinho CM, Dos Santos PT, Kallipolitis BH, Johansson J, Ignatov D, Guerreiro DN, et al. The σB-dependent regulatory sRNA Rli47 represses isoleucine biosynthesis in Listeria monocytogenes through a direct interaction with the ilvA transcript. RNA Biol. 2019;16:1424–37.
Article
PubMed
PubMed Central
Google Scholar
Dar D, Shamir M, Mellin JR, Koutero M, Stern-Ginossar N, Cossart P, et al. Term-seq reveals abundant ribo-regulation of antibiotics resistance in bacteria. Science. 2016;352:aad9822.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ferrer A, Rivera J, Zapata C, Norambuena J, Sandoval Á, Chávez R, et al. Cobalamin protection against oxidative stress in the acidophilic iron-oxidizing bacterium Leptospirillum group II CF-1. Front Microbiol. 2016;7. https://doi.org/10.3389/fmicb.2016.00748.
Mellin JR, Tiensuu T, Bécavin C, Gouin E, Johansson J, Cossart P. A riboswitch-regulated antisense RNA in Listeria monocytogenes. Proc Natl Acad Sci U S A. 2013;110:13132–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Casey A, Fox EM, Schmitz-Esser S, Coffey A, McAuliffe O, Jordan K. Transcriptome analysis of Listeria monocytogenes exposed to biocide stress reveals a multi-system response involving cell wall synthesis, sugar uptake, and motility. Front Microbiol. 2014;5. https://doi.org/10.3389/fmicb.2014.00068.
Tang S, Orsi RH, den Bakker HC, Wiedmann M, Boor KJ, Bergholz TM. Transcriptomic analysis of the adaptation of Listeria monocytogenes to growth on vacuum-packed cold smoked Salmon. Appl Environ Microbiol. 2015;81:6812–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Anast JM, Bobik TA, Schmitz-Esser S. The Cobalamin-dependent gene cluster of Listeria monocytogenes: implications for virulence, stress response, and food safety. Front Microbiol. 2020;11:601816.
Article
PubMed
PubMed Central
Google Scholar
Ivy RA, Wiedmann M, Boor KJ. Listeria monocytogenes grown at 7°C shows reduced acid survival and an altered transcriptional response to acid shock compared to L. monocytogenes grown at 37°C. Appl Environ Microbiol. 2012;78:3824–36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Argov T, Sapir SR, Pasechnek A, Azulay G, Stadnyuk O, Rabinovich L, et al. Coordination of cohabiting phage elements supports bacteria-phage cooperation. Nat Commun. 2019;10:5288.
Article
PubMed
PubMed Central
CAS
Google Scholar
Rollie C, Chevallereau A, Watson BNJ, Chyou T-Y, Fradet O, McLeod I, et al. Targeting of temperate phages drives loss of type I CRISPR-Cas systems. Nature. 2020;578:149–53.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nobrega FL, Walinga H, Dutilh BE, Brouns SJJ. Prophages are associated with extensive CRISPR-Cas auto-immunity. Nucleic Acids Res. 2020;48:12074–84.
Article
PubMed
PubMed Central
Google Scholar
Popowska M, Osińska M, Rzeczkowska M. N-acetylglucosamine-6-phosphate deacetylase (NagA) of Listeria monocytogenes EGD, an essential enzyme for the metabolism and recycling of amino sugars. Arch Microbiol. 2012;194:255–68.
Article
CAS
PubMed
Google Scholar
Vogler AP, Lengeler JW. Analysis of the nag regulon from Escherichia coli K12 and Klebsiella pneumoniae and of its regulation. Mol Gen Genet. 1989;219:97–105.
Article
CAS
PubMed
Google Scholar
Karatzas KAG, Wouters JA, Gahan CGM, Hill C, Abee T, Bennik MHJ. The CtsR regulator of Listeria monocytogenes contains a variant glycine repeat region that affects piezotolerance, stress resistance, motility and virulence. Mol Microbiol. 2003;49:1227–38.
Article
CAS
PubMed
Google Scholar
Karatzas KAG, Bennik MHJ. Characterization of a Listeria monocytogenes Scott a isolate with high tolerance towards high hydrostatic pressure. Appl Environ Microbiol. 2002;68:3183–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Karatzas KAG, Valdramidis VP, Wells-Bennik MHJ. Contingency locus in ctsR of Listeria monocytogenes Scott a: a strategy for occurrence of abundant Piezotolerant isolates within clonal populations. Appl Environ Microbiol. 2005;71:8390–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Joerger RD, Chen H, Kniel KE. Characterization of a spontaneous, pressure-tolerant Listeria monocytogenes Scott a ctsR deletion mutant. Foodborne Pathog Dis. 2006;3:196–202.
Article
CAS
PubMed
Google Scholar
Van Boeijen IKH, Chavaroche AAE, Valderrama WB, Moezelaar R, Zwietering MH, Abee T. Population diversity of Listeria monocytogenes LO28: phenotypic and genotypic characterization of variants resistant to high hydrostatic pressure. Appl Environ Microbiol. 2010;76:2225–33.
Article
PubMed
PubMed Central
CAS
Google Scholar
Aertsen A, Vanoirbeek K, De Spiegeleer P, Sermon J, Hauben K, Farewell A, et al. Heat shock protein-mediated resistance to high hydrostatic pressure in Escherichia coli. Appl Environ Microbiol. 2004;70:2660–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Niven GW, Miles CA, Mackey BM. The effects of hydrostatic pressure on ribosome conformation in Escherichia coli: and in vivo study using differential scanning calorimetry. Microbiology (Reading). 1999;145(Pt 2):419–25.
Article
CAS
PubMed
Google Scholar
Kline BC, McKay SL, Tang WW, Portnoy DA. The Listeria monocytogenes hibernation-promoting factor is required for the formation of 100S ribosomes, optimal fitness, and pathogenesis. J Bacteriol. 2015;197:581–91.
Article
PubMed
PubMed Central
CAS
Google Scholar
Guinane CM, Cotter PD, Ross RP, Hill C. Contribution of penicillin-binding protein homologs to antibiotic resistance, cell morphology, and virulence of Listeria monocytogenes EGDe. Antimicrob Agents Chemother. 2006;50:2824–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vollmer W, Blanot D, de Pedro MA. Peptidoglycan structure and architecture. FEMS Microbiol Rev. 2008;32:149–67.
Article
CAS
PubMed
Google Scholar
Park JT, Uehara T. How bacteria consume their own exoskeletons (turnover and recycling of cell wall peptidoglycan). Microbiol Mol Biol Rev. 2008;72:211–27 table of contents.
Article
CAS
PubMed
PubMed Central
Google Scholar
Alvarez-Añorve LI, Calcagno ML, Plumbridge J. Why does Escherichia coli grow more slowly on glucosamine than on N-acetylglucosamine? Effects of enzyme levels and allosteric activation of GlcN6P deaminase (NagB) on growth rates. J Bacteriol. 2005;187:2974–82.
Article
PubMed
PubMed Central
CAS
Google Scholar
Booth IR, Edwards MD, Black S, Schumann U, Miller S. Mechanosensitive channels in bacteria: signs of closure? Nat Rev Microbiol. 2007;5:431–40.
Article
CAS
PubMed
Google Scholar
Tymoszewska A, Diep DB, Wirtek P, Aleksandrzak-Piekarczyk T. The non-Lantibiotic Bacteriocin Garvicin Q targets man-PTS in a broad Spectrum of sensitive bacterial genera. Sci Rep. 2017;7:8359.
Article
PubMed
PubMed Central
CAS
Google Scholar
Diep DB, Skaugen M, Salehian Z, Holo H, Nes IF. Common mechanisms of target cell recognition and immunity for class II bacteriocins. Proc Natl Acad Sci U S A. 2007;104:2384–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ríos Colombo NS, Chalón MC, Navarro SA, Bellomio A. Pediocin-like bacteriocins: new perspectives on mechanism of action and immunity. Curr Genet. 2018;64:345–51.
Article
PubMed
CAS
Google Scholar
Abachin E, Poyart C, Pellegrini E, Milohanic E, Fiedler F, Berche P, et al. Formation of D-alanyl-lipoteichoic acid is required for adhesion and virulence of Listeria monocytogenes. Mol Microbiol. 2002;43:1–14.
Article
CAS
PubMed
Google Scholar
Somervuo P, Koskinen P, Mei P, Holm L, Auvinen P, Paulin L. BARCOSEL: a tool for selecting an optimal barcode set for high-throughput sequencing. BMC Bioinformatics. 2018;19:257.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kopylova E, Noé L, Touzet H. SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Bioinformatics. 2012;28:3211–7.
Article
CAS
PubMed
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9:357–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Anders S, Pyl PT, Huber W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics. 2015;31:166–9.
Article
CAS
PubMed
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
Article
PubMed
PubMed Central
CAS
Google Scholar
Schiffthaler B, Serrano A, Street N, Delhomme N. Seidr: a gene meta-network calculation toolkit. bioRxiv. 2019;:250696.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498–504.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009;37 Web Server issue: W202–208.
Kiliç S, White ER, Sagitova DM, Cornish JP, Erill I. CollecTF: a database of experimentally validated transcription factor-binding sites in Bacteria. Nucleic Acids Res. 2014;42(Database issue):D156–60.
Article
PubMed
CAS
Google Scholar
Cipriano MJ, Novichkov PN, Kazakov AE, Rodionov DA, Arkin AP, Gelfand MS, et al. RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes. BMC Genomics. 2013;14:213.
Article
CAS
PubMed
PubMed Central
Google Scholar
Novichkov PS, Kazakov AE, Ravcheev DA, Leyn SA, Kovaleva GY, Sutormin RA, et al. RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria. BMC Genomics. 2013;14:745.
Article
CAS
PubMed
PubMed Central
Google Scholar
Robison K, McGuire AM, Church GM. A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J Mol Biol. 1998;284:241–54.
Article
CAS
PubMed
Google Scholar
Pachkov M, Balwierz PJ, Arnold P, Ozonov E, van Nimwegen E. SwissRegulon, a database of genome-wide annotations of regulatory sites: recent updates. Nucleic Acids Res. 2013;41(Database issue):D214–20.
CAS
PubMed
Google Scholar
Gupta S, Stamatoyannopoulos JA, Bailey TL, Noble WS. Quantifying similarity between motifs. Genome Biol. 2007;8:R24.
Article
PubMed
PubMed Central
CAS
Google Scholar
Törönen P, Medlar A, Holm L. PANNZER2: a rapid functional annotation web server. Nucleic Acids Res. 2018;46:W84–8.
Article
PubMed
PubMed Central
CAS
Google Scholar
Alexa A, Rahnenfuhrer J. topGO: topGO: Enrichment analysis for Gene Ontology. Available at: https://bioconductor.org/packages/release/bioc/html/topGO.html
Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 2007;35 Web Server issue: W182–185.
Untergasser A, Nijveen H, Rao X, Bisseling T, Geurts R, Leunissen JAM. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res. 2007;35 Web Server issue: W71–74.
Andreevskaya M, Jääskeläinen E, Johansson P, Ylinen A, Paulin L, Björkroth J, et al. Food spoilage-associated Leuconostoc, Lactococcus, and Lactobacillus species display different survival strategies in response to competition. Appl Environ Microbiol. 2018;84.
Leenhouts K, Buist G, Bolhuis A, ten Berge A, Kiel J, Mierau I, et al. A general system for generating unlabelled gene replacements in bacterial chromosomes. Mol Gen Genet. 1996;253:217–24.
Article
CAS
PubMed
Google Scholar
Maguin E, Duwat P, Hege T, Ehrlich D, Gruss A. New thermosensitive plasmid for gram-positive bacteria. J Bacteriol. 1992;174:5633–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Monk IR, Gahan CGM, Hill C. Tools for functional Postgenomic analysis of Listeria monocytogenes. Appl Environ Microbiol. 2008;74:3921–34.
Article
CAS
PubMed
PubMed Central
Google Scholar
Glaser P, Frangeul L, Buchrieser C, Rusniok C, Amend A, Baquero F, et al. Comparative genomics of Listeria species. Science. 2001;294:849–52.
Article
CAS
PubMed
Google Scholar
Chang AY, Chau VWY, Landas JA, Pang Y. Preparation of calcium competent Escherichia coli and heat-shock transformation. The Undergraduate Journal of Experimental Microbiology and Immunology. 2017;1:22–5.
Google Scholar
Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29:24–6.
Article
CAS
PubMed
PubMed Central
Google Scholar