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Publications: Food Microbiome

Microbial ecology of food fermentations

  • Alessandria V, Ferrocino I, De Filippis F, Fontana M, Rantsiou K, Ercolini D, Cocolin L. (2016) Microbiota of an Italian Grana-like cheese during manufacture and ripening, unraveled by 16S rRNA-based approaches. Appl Environ Microbiol 82:3988-3995.
  • Blaiotta G, Murru N, Di Cerbo A, Succi M, Coppola R, Aponte M. (2017) Commercially standardized process for probiotic “Italico” cheese production. LWT Food Science and Technology 79:601-608.
  • Cocolin L, Alessandria V, Botta C, Gorra R, De Filippis F, Ercolini D, Rantsiou K. (2013) NaOH-debittering induces changes in bacterial ecology during table olives fermentation. PLoS ONE 8:e69074.
  • Cruciata M, Sannino C, Ercolini D, Scatassa ML, De Filippis F, Mancuso I, La Storia A, Moschetti G, Settanni L. (2014) Animal rennets as sources of dairy lactic acid bacteria. Appl Environ Microbiol 80:2050-2061.
  • De Filippis F, Aponte M, Piombino P, Lisanti MT, Moio L, Ercolini D, Blaiotta G. (2019) Influence of microbial communities on the chemical and sensory features of Falanghina sweet passito wines. Food Res Intern in press. doi:10.1016/j.foodres.2018.11.033.
  •  De Filippis F, Genovese A, Ferranti P, Gilbert JA, Ercolini D. (2016) Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate. Sci Rep 6:21871.
  • De Filippis F, La Storia A, Blaiotta G. (2017) Monitoring the mycobiota during Greco di Tufo and Aglianico wine fermentation by 18S rRNA gene sequencing. Food Microbiol 63:117-122.
  • De Filippis F, La Storia A, Stellato G, Gatti M, Ercolini D. (2014) A selected core microbiome drives the early stages of three popular Italian cheese manufactures. PLoS ONE 9: e89680.
  • De Filippis F, Parente E, Ercolini D. (2017) Metagenomics insights into food fermentations. Microbial Biotechnol 10:91-102.
  • De Filippis F, Troise AD, Vitaglione P, Ercolini D. (2018) Different temperatures select distinctive acetic acid bacteria species and promotes organic acids production during Kombucha tea fermentation. Food Microbiol 73:11-16.
  • De Pasquale I, Calasso M, Mancini L, Ercolini D, La Storia A, De Angelis M, Di Cagno R, Gobbetti M. (2014) Causal Relationship between Microbial Ecology Dynamics and Proteolysis during Manufacture and Ripening of Protected Designation of Origin (PDO) Cheese Canestrato Pugliese. Appl Environ Microbiol 80:4085-4094.
  • Dolci P, De Filippis F, La Storia A, Ercolini D, Cocolin L. (2014) rRNA-based monitoring of the microbiota involved in Fontina PDO cheese production in relation to different stages of cow lactation. Int J Food Microbiol 185:127-135.
  • Ercolini D, Pontonio E, De Filippis F, Minervini F, La Storia A, Gobbetti M, Di Cagno R. (2013) Microbial ecology dynamics during rye and wheat sourdough preparation. Appl Environ Microbiol 79:7827-7836.
  • Garofalo D, Osimani A, Milanovic V, Aquilanti L, De Filippis F, Stellato G, Di Mauro S, Turchetti B, Buzzini P, Ercolini D, Clementi F. (2015) Bacteria and yeast microbiota in milk kefir grains from different Italian regions. Food Microbiol 49:123-133.
  • Giello M, La Storia A, Masucci F, Di Francia A, Ercolini D, Villani F. (2017) Dynamics of bacterial communities during manufacture and ripening of traditional Caciocavallo of Castelfranco cheese in relation to cows' feeding. Food Microbiol 63:170-177.
  • Greppi A, Ferrocino I, La Storia A, Rantsiou K, Ercolini D, Cocolin L. (2015) Monitoring of the microbiota of fermented sausages by culture independent rRNA-based approaches. Int J Food Microbiol 212:67-75.
  • Guidone A, Zotta T, Matera A, Ricciardi A, De Filippis F, Ercolini D, Parente E. (2016) The microbiota of high-mosture mozzarella cheese produced with different acidification methods. Int J Food Microbiol 216:9-17.
  • Kamimura BA, De Filippis F, Sant’Ana AS, Ercolini D. (2019) Large-scale mapping of microbial diversity in artisanal Brazilian cheeses. Food Microbiol 80:40-49.
  • Levante A, De Filippis F, La Storia A, Gatti M, Neviani E, Ercolini D, Lazzi C. (2017) Metabolic gene-targeted monitoring of non-starter lactic acid bacteria during cheese ripening. Int J Food Microbiol 257:276-284.
  • Mormile A, Barile M, Mercogliano R, Johansson P, Björkroth KJ, Aponte M, Murru N (2016) Dynamics of lactic acid bacteria in “Pecorino di Tramonti”—a ewe’s milk cheese—with particular emphasis on enterococci: a preliminary study. Annals of Microbiology 66:179-185.
  • Quijada NA, De Filippis F, Sanz JJ, Garcia-Fernandez MC, Rodriguez-Lazaro D, Ercolini, D, Hernandez M. (2018) Different Lactobacillus populations dominate in “Chorizo de León” manufacturing performed in different production plants. Food Microbiol 70:94-102.
  • Ricciardi A, De Filippis F, Zotta T, Facchiano A, Ercolini D, Parente E. (2016) Polymorphism of the phosphoserine phosphatase gene in Streptococcus thermophilus and its potential use for typing and monitoring of population diversity. Int J Food Microbiol 236: 138-147.
  • Ricciardi A, De Filippis F, Zotta T, Facchiano A, Ercolini D, Parente E. (2016) Polymorphism of the phosphoserine phosphatase gene in Streptococcus thermophilus and its potential use for typing and monitoring of population structure. Int J Food Microbiol 236:138-147.
  • Rizzello CG, Cavoski I, Turk J, Ercolini D, Nionelli L, Pontonio E, De Angelis M, De Filippis F, Gobbetti M, Di Cagno R. (2015) Organic cultivation of Triticum turgidum subsp. durum is reflected in the flour-sourdough fermentation-bread axis. Appl Environ Microbiol 81:3192-3204.

 

Microbial ecology of food spoilage

  • De Filippis F, La Storia A, Villani F, Ercolini D. (2013) Exploring the sources of beefsteaks contamination by culture-independent high-throughput sequencing. PLoS ONE 8:e70222.
  • De Filippis F, La Storia A, Villani F, Ercolini D. (2019) Strain-level diversity analysis of Pseudomonas fragi after in situ pangenome reconstruction shows distinctive spoilage-associated metabolic traits clearly selected by different storage conditions. Appl Environ Microbiol 85:e02212-18.
  • Ferrocino I, Greppi A, La Storia A, Rantsiou K, Ercolini D, Cocolin L. (2015) Impact of nisin-activated packaging on microbiota of beef burgers during storage. Appl Environ Microbiol 82:549-559.
  • Giello M, La Storia A, De Filippis F, Ercolini D, Villani F. (2018) Impact of Lactobacillus curvatus 54M16 on microbiota composition and growth of Listeria monocytogenes in fermented sausages. Food Microbiol 72:1-15.
  • Zotta T, Parente E, Iannello RG, De Filippis F, Ricciardi A. (2019) Dynamics of bacterial communities and interaction networks in thawed fish fillets during chilled storage in air. Int J Food Microbiol 293:102-113.

 

Food-processing microbiome

  • Stellato G, La Storia A, Cirillo T, Ercolini D. (2015) Bacterial biogeographical patterns in a cooking center for a hospital foodservice. Int J Food Microbiol 193:99-108.
  • Pothakos V, Stellato G, Ercolini D, Devlieghere F. (2015) Processing environment and ingredients are both sources of Leuconostoc gelidum, which emerges as a major spoiler in ready-to-eat meals. Appl Environ Microbiology 81:3529-3541.
  • Stellato G, De Filippis F, La Storia, A, Ercolini D. (2015) Coexsistence of lactic acid bacteria and potential spoilage microbiota in a dairy processing environment. Appl Environl Microbiol 81:3529-3541.
  • Calasso M, Ercolini D, Mancini L, Stellato G, Minervini F, Di Cagno R, De Angelis M, Gobbetti M. (2016) Relationships among house, rind and core microbiotas during manufacture of traditional Italian cheeses at the same dairy plant. Food Microbiol 54:115-126.
  • Stellato G, La Storia A, De Filippis F, Borriello G, Villani F, Ercolini D. (2016) Overlap of Spoilage-Associated Microbiota between Meat and the Meat Processing Environment in Small-Scale and Large-Scale Retail Distributions. Appl Environ Microbiol 82:4045-54.
  • Stellato G, Utter DR, Voorhis A, De Angelis M, Murat EA, Ercolini D. (2017) A few Pseudomonas oligotypes dominate in the meat and dairy processing environment. Frontiers in Microbiology 8:264.

 

Food safety

  • Giello M, La Storia A, De Filippis F, Ercolini D, Villani F. (2018) Impact of Lactobacillus curvatus 54M16 on microbiota composition and growth of Listeria monocytogenes in fermented sausages. Food Microbiol 72:1-15.

  • Nizza S, Rando F, Fiorito F, Pagnini U, Iovane G, De Martino L (2014) Fecal microbiota and antibiotic resistance in ferrets (Mustela putorius furo) from two captive breeding facilities in Italy. Research in Veterinary Science 96:426–428.

  • Peruzy MF, Murru N, Perugini AG, Capuano F, Delibato E, Mercogliano R, Korkeala H, Proroga YTR. (2017) Evaluation of virulence genes in Yersinia enterocolitica strains using SYBR Green real-time PCR. Food Microbiol 65:231-235.