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Bibliography PRIN2020 proposal 2020BBF4CE

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  1. Parente E, Ricciardi A, Zotta T. 2020. The microbiota of dairy milk: a review. Int Dairy J 10:104714.
  2. Afshari R, Pillidge CJ, Dias DA, Osborn AM, Gill H. 2018. Cheesomics: the future pathway to understanding cheese flavour and quality. Crit Rev Food Sci 60:1–15.
  3. Walsh AM, Macori G, Kilcawley KN, Cotter PD. 2020. Meta-analysis of cheese microbiomes highlights contributions to multiple aspects of quality. Nat Food 1:500–510.
  4. 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 Microb 236:138–147.
  5. 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.
  6. Proctor LM, Creasy HH, Fettweis JM, Lloyd-Price J, Mahurkar A, Zhou W, Buck GA, Snyder MP, Strauss JF, Weinstock GM, White O, Huttenhower C. 2019. The Integrative Human Microbiome Project. Nature 569:641–648.
  7. Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, Gonzalez A, Morton JT, Mirarab S, Xu ZZ, Jiang L, Haroon MF, Kanbar J, Zhu Q, Song SJ, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R, Consortium EMP. 2017. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551:457–463.
  8. De Filippis F, Parente E, Ercolini D. 2018. Recent Past, Present, and Future of the Food Microbiome. Annu Rev Food Sci T 9:589–608.
  9. Pollock J, Glendinning L, Wisedchanwet T, Watson M. 2018. The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies. Appl Environ Microbiol 84:3225.
  10. Gonzalez A, Navas-Molina JA, Kosciolek T, McDonald D, Vázquez-Baeza Y, Ackermann G, DeReus J, Janssen S, Swafford AD, Orchanian SB, Sanders JG, Shorenstein J, Holste H, Petrus S, Robbins-Pianka A, Brislawn CJ, Wang M, Rideout JR, Bolyen E, Dillon M, Caporaso JG, Dorrestein PC, Knight R. 2018. Qiita: rapid, web-enabled microbiome meta-analysis. Nature meth 15:1–6.
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  12. Parente E, De Filippis F, Ercolini D, Ricciardi A, Zotta T. 2019. Advancing integration of data on food microbiome studies: FoodMicrobionet 3.1, a major upgrade of the FoodMicrobionet database. Int J Food Microbiol 305:108249.
  13. Jonnala BRY, McSweeney PLH, Sheehan JJ, Cotter PD. 2018. Sequencing of the Cheese Microbiome and Its Relevance to Industry. Front Microbiol 9:1890–12.
  14. Montel M-C, Buchin S, Mallet A, Delbès-Paus C, Vuitton DA, Desmasures N, Berthier F. 2014. Traditional cheeses: Rich and diverse microbiota with associated benefits. Int J Food Microbiol 177:136–154.
  15. Bokulich NA, Lewis ZT, Boundy-Mills K, Mills DA. 2016. A new perspective on microbial landscapes within food production. Curr Op Biotechnol 37:182–189.
  16. Kamilari E, Tomazou M, Antoniades A, Tsaltas D. 2019. High Throughput Sequencing Technologies as a New Toolbox for Deep Analysis, Characterization and Potentially Authentication of Protection Designation of Origin Cheeses? Int J Food Sci 2019:5837301.
  17. Ercolini D, De Filippis F, La Storia A, Iacono M. 2012. “Remake” by high-throughput sequencing of the microbiota involved in the production of water buffalo mozzarella cheese. Appl Environ Microbiol 78:8142–8145.
  18. Stellato G, De Filippis F, La Storia A, Ercolini D. 2015. Coexistence of Lactic Acid Bacteria and Potential Spoilage Microbiota in a Dairy Processing Environment. Appl Environ Microbiol 81:7893–7904.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. Bottari B, Levante A, Bancalari E, Sforza S, Bottesini C, Prandi B, De Filippis F, Ercolini D, Nocetti M, Gatti M. 2020. The Interrelationship Between Microbiota and Peptides During Ripening as a Driver for Parmigiano Reggiano Cheese Quality. Front Microbiol 11:581658.
  24. Guidone A, Zotta T, Matera A, Ricciardi A, De Filippis F, Ercolini D, Parente E. 2016. The microbiota of high-moisture mozzarella cheese produced with different acidification methods.  Int J Food Microbiol 216:9–17.
  25. Biolcati F, Ferrocino I, Bottero MT, Dalmasso A. 2020. Short communication: High-throughput sequencing approach to investigate Italian artisanal cheese production. J Dairy Sci 103:10015–10021.
  26. Dolci P, Ferrocino I, Giordano M, Pramotton R, Vernetti-Prot L, Zenato S, Barmaz A. 2020. Impact of Lactococcus lactis as starter culture on microbiota and metabolome profile of an Italian raw milk cheese. Int Dairy J 110:104804.
  27. Bertani G, Levante A, Lazzi C, Bottari B, Gatti M, Neviani E. 2019. Dynamics of a natural bacterial community under technological and environmental pressures: the case of natural whey starter for Parmigiano Reggiano cheese. Food Res Int 129:108860.
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  29. 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 Canestrato Pugliese PDO cheese. Appl Environ Microbiol 80:4085–4094.
  30. De Pasquale I, Di Cagno R, Buchin S, De Angelis M, Gobbetti M. 2014. Microbial ecology dynamics reveal a succession in the core microbiota involved in the ripening of pasta filata caciocavallo pugliese cheese. Appl Environ Microbiol 80:6243–6255.
  31. 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.
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  36. Erkus O, Jager VCL de, Geene RTCM, Alen-Boerrigter I van, Hazelwood L, Hijum SAFT van, Kleerebezem M, Smid EJ. 2016. Use of propidium monoazide for selective profiling of viable microbial cells during Gouda cheese ripening. Int J Food Microbiol 228:1–9.
  37. Parente E, Guidone A, Matera A, De Filippis F, Mauriello G, Ricciardi A. 2016. Microbial community dynamics in thermophilic undefined milk starter cultures. Int J Food Microbiol 217:59–67.
  38. Morandi S, Battelli G, Silvetti T, Goss A, Cologna N, Brasca M. 2019. How the biodiversity loss in natural whey culture is affecting ripened cheese quality? The case of Trentingrana cheese.  LWT-Food Sci Technol 115:108480.
  39. Niccum BA, Kastman EK, Kfoury N, Robbat A, Wolfe BE. 2020. Strain-Level Diversity Impacts Cheese Rind Microbiome Assembly and Function. mSystems 5:e00149-20.
  40. Parente E, Cogan TM, Powell IB. 2017. Cheese (Fourth Edition), p. 201–226. In McSweeney, PLH, Fox, PF, Cotter, PD, Everett, DW (eds.), Fourth edition. Elsevier, London, UK.
  41. Tanigawa K, Watanabe K. 2011. Multilocus sequence typing reveals a novel subspeciation of Lactobacillus delbrueckii. Microbiology 157:727–738.
  42. Pasolli E, Asnicar F, Manara S, Zolfo M, Karcher N, Armanini F, Beghini F, Manghi P, Tett A, Ghensi P, Collado MC, Rice BL, DuLong C, Morgan XC, Golden CD, Quince C, Huttenhower C, Segata N. 2019. Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. Cell 176:649-662.e20.
  43. De Filippis F, Pasolli E, Ercolini D. 2020. Newly Explored Faecalibacterium Diversity Is Connected to Age, Lifestyle, Geography, and Disease. Curr Biol 30:4932-4943.e4.
  44. Salzano A, Manganiello G, Neglia G, Vinale F, Nicola DD, D’Occhio M, Campanile G. 2020. A Preliminary Study on Metabolome Profiles of Buffalo Milk and Corresponding Mozzarella Cheese: Safeguarding the Authenticity and Traceability of Protected Status Buffalo Dairy Products. Molecules 25:304.
  45. Minervini F, Celano G, Lattanzi A, Tedone L, Mastro GD, Gobbetti M, De Angelis M. 2015. Lactic Acid Bacteria in Durum Wheat Flour Are Endophytic Components of the Plant during Its Entire Life Cycle. Appl Environ Microbiol 81:6736–6748.
  46. Zhang D, Palmer J, Teh KH, Biggs P, Flint S. 2019. 16S rDNA high-throughput sequencing and MALDI-TOF MS are complementary when studying psychrotrophic bacterial diversity of raw cows’ milk. Int Dairy J 97:86–91.
  47. Szymańska E. 2018. Modern data science for analytical chemical data – A comprehensive review. Anal Chim Acta 1028:1–10.
  48. 4Callao MP, Ruisánchez I. 2018. An overview of multivariate qualitative methods for food fraud detection. Food Control 86:283–293.
  49. Borràs E, Ferré J, Boqué R, Mestres M, Aceña L, Busto O. 2015. Data fusion methodologies for food and beverage authentication and quality assessment – A review. Anal Chim Acta 891:1–14.
  50. Hervás D, Prats-Montalbán JM, Lahoz A, Ferrer A. 2018. Sparse N-way partial least squares with R package sNPLS. Chemometr Intell Lab 179:54–63.
  51. Liu J, Li J, Wang H, Yan J. 2020. Application of deep learning in genomics. Sci China Life Sci 63:1860–1878.
  52. Acin-Albiac M, Filannino P, Gobbetti M, Di Cagno R. 2020. Microbial high throughput phenomics: The potential of an irreplaceable omics. Comput Struct Biotechnology J 18:2290–2299.
  53. Smid EJ, Erkus O, Spus M, Wolkers-Rooijackers JC, Alexeeva S, Kleerebezem M. 2014. Functional implications of the microbial community structure of undefined mesophilic starter cultures. Microb Cell Fact 13:S2.
  54. Gobbetti M, Di Cagno R, Calasso M, Neviani E, Fox PF, De Angelis M. 2018. Drivers that establish and assembly the lactic acid bacteria biota in cheeses. Trends Food Sci Technol 78:244–254.
  55. Cosetta CM, Kfoury N, Robbat A, Wolfe BE. 2020. Fungal volatiles mediate cheese rind microbiome assembly. Environ Microbiol 22:4745–4760.
  56. Irlinger F, Mounier J. 2009. Microbial interactions in cheese: implications for cheese quality and safety. Curr Op Biotechnol 20:142–148.
  57. Parente E, Zotta T, Faust K, De Filippis F, Ercolini D. 2018. Structure of association networks in food bacterial communities. Food Microbiol 73:49–60.
  58. Peschel S, Müller CL, Mutius E von, Boulesteix A-L, Depner M. 2020. NetCoMi: network construction and comparison for microbiome data in R. Brief Bioinform https://doi.org/10.1093/bib/bbaa290.

References, FISR 2019 project Omics4Cheese

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  12. De Filippis, F., Parente, E., Danilo Ercolini. 2018a. Ann. Rev. Food Sci. Technol. 9. https://dx.doi.org/10.1146/annurev-food-030117-012312.
  13. De Filippis, F., Parente, E., Zotta, T., Ercolini, D. 2018b. Int. J. Food Microbiol. 265: 9–17. https://dx.doi.org/10.1016/j.ijfoodmicro.2017.10.028.
  14. Douglas, G. M., Maffei, V. J., Zaneveld, J. et al. 2019. bioRxiv 8 (June). https://dx.doi.org/10.1101/672295.
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  16. Fouhy, F., Clooney, A. G., Stanton, C., Claesson, M.J., Cotter, P. D. 2016. BMC Microbiol. 16: 123. https://dx.doi.org/10.1186/s12866-016-0738-z.
  17. Garofalo, C., Osimani, A., Milanovic, V., Aquilanti, L., et al. 2015. Food Microbiol. 49: 123-133. https://dx.doi.org/10.1016/j.fm.2015.01.017
  18. Gasperi, F., Gallerani, G., Boschetti, A., et al. 2001. J. Sci. Food Agric. 81: 357–363. https://doi.org/10.1002/1097-0010(200102)81:3<357::AID-JSFA818>3.0.CO;2-O.
  19. Gobbetti, M., Di Cagno, R., Calasso, M., et al. 2018. Trends Food Sci. Technol. 78: 244–254. https://dx.doi.org/10.1016/j.tifs.2018.06.010.
  20. Guidone, A., Zotta, T., Matera, A., et al. 2016. Int. J. Food Microbiol. 216: 9–17. https://dx.doi.org/10.1016/j.ijfoodmicro.2015.09.002.
  21. Kuuliala, L., Al Hage, Y., Ioannidis, A.-G., Sader, M., Kerckhof, F.-M., Vanderroost, M., Boon, N. et al. 2018. Food Microbiol. 70: 232–44. https://dx.doi.org/10.1016/j.fm.2017.10.011.
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  30. Pisano, M. B., Scano, P., Murgia, A. et al. 2016. Food Chem. 192: 618–624. https://dx.doi.org/10.1016/j.foodchem.2015.07.061.
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Lezioni a tutta birra: “Una lezione di m….”

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Quando eravamo piccoli, ma piccoli piccoli, molta della nostra vita e quella dei nostri genitori girava intorno a come stava il nostro pancino. Nè noi (che avevamo allora desideri semplici) né i nostri genitori immaginavamo quanto fosse densamente abitato il pancino né quanto fosse complessa la relazione fra i sui numerosi abitanti e la nostra salute. Beh, magari adesso ce ne curiamo di meno, ma quello che si agita dentro di noi (un mondo di microrganismi, il microbioma) condiziona fortemente la nostra salute e il nostro benessere. Ne parleremo, senza troppi tabù e con la consueta leggerezza nella prossima lezione a tutta birra. Intervenite numerosi e, visto che è San Valentino, portate i vostri fidanzati/e/sposi/e…

Interverranno:

  • io vi dirò, in parole semplici, cos’è il microbioma umano, come si studia, perché è importante per la nostra salute e come possiamo “mantenerlo in forma” o intervenire quando perde il suo equilibrio
  • il Dott Orazio Ignomirelli, unità operativa di Endoscopia dell’IRCCS CROB di Rionero in Vulture ci dirà come siamo fatti, visti da dentro, e quali sono le relazioni fra alimentazione e tumori al colon retto

Informazioni pratiche (in corso di definizione):

  • Quando: il giorno 14/02/2018, presumibilmente si inizia verso le 19.30
  • Dove: a Potenza, presso Beer Bros, Via Mantova, 175, tel. 329 349 0239
  • Altro: come di consueto dovete provvedere personalmente alla prenotazione (preferibilmente per telefono) specificando che prenotate per partecipare alla “Lezione e tutta birra”

Literature cited, project 2017J2RMTN

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  1. Berni Canani, , De Filippis, F., et al. 2017. Appl. Environ. Microbiol. 83: e01206-17.  https://dx.doi.org/10.1128/AEM.01206-17.
  2. Bokulich, N. A., Mills, D.A. 2013. Appl. Environmen. Microbiol. 79: 2519–226.  https://dx.doi.org/10.1128/AEM.03870-12.
  3. Callahan, B. J., McMurdie, P. J., Holmes, S. P.. 2017. ISME J. 11: 2639–4263. https://dx.doi.org/10.1038/ismej.2017.119.
  4. Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A.J.A., Holmes, S. P. 2016. Nature Meth. 13: 581–583. https://dx.doi.org/10.1038/nmeth.3869.
  5. De Filippis, F., Parente, E., Ercolini, D. 2017a. Microbial Biotechnol. 10: 91–102. https://dx.doi.org/10.1111/1751-7915.12421.
  6. De Filippis, F., Laiola, M., Blaiotta, G., Ercolini, D.. 2017b. Appl. Environ. Microbiol., 83: e00905–17. https://dx.doi.org/10.1128/AEM.00905-17.
  7. De Filippis, F., Parente, E., Danilo Ercolini. Ann. Rev. Food Sci. Technol. 9. https://dx.doi.org/10.1146/annurev-food-030117-012312.
  8. De Filippis, F., Parente, E., Zotta, T., Ercolini, D. 2018b. J. Food Microbiol. 265: 9–17. https://dx.doi.org/10.1016/j.ijfoodmicro.2017.10.028.
  9. EFSA (2015). The food classification and description system FoodEx 2 (revision 2). Supporting publication 2015:EN-804. http://www.efsa.europa.eu/en/supporting/pub/215e.htm
  10. Emerson, J. B., Adams, R. I., Betancourt Román C. M., Brooks, B., Coil, D. A., Dahlhausen, Holly H. Ganz, K., et al. 2017. Microbiome 5: 86. https://dx.doi.org/10.1186/s40168-017-0285-3.
  11. Erkus, O., de Jager, V.C.L., Geene, R. T. C. M., van Alen-Boerrigter, I., Hazelwood, L., van Hijum, S. A .F. T., Kleerebezem, M., Smid, E. J. 2016. Int. J. Food Microbiol. 228: 1–9. https://dx.doi.org/10.1016/j.ijfoodmicro.2016.03.027.
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Sicurezza e conservazione degli alimenti

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Le lezioni del corso di Sicurezza e conservazione degli alimenti 9 CFU (LM Scienze e Tecnologie Alimentari) inizieranno il giorno 3/10/2017 alle ore 11.30 presso l’aula A9 e proseguiranno con il seguente orario:

Martedì 11:30-13:30 A9

Mercoledì 15:00-17:00 A9

Giovedì 09:30-11:30 A9

Le esercitazioni si svolgeranno nel laboratorio informatico della Scuola SAFE in orari da concordare.

Novità sulla didattica

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A partire dall’AA 2016-2017 l’insegnamento di Microbiologia degli alimenti fermentati per il corso di Laurea Magistrale in Scienze e Tecnologie Alimentari è soppresso. Al suo posto insegnerò Sicurezza e conservazione degli alimenti (9 cfu, la pagina web è qui). Le ragioni di questa scelta sono in parte legate alla necessità di adeguare il percorso formativo del corso di studi. Per gli studenti delle coorti precedenti a quella 2016-2017 (in pratica per tutti quelli immatricolati l’anno scorso o negli anni precedenti) sarà comunque possibile sostenere l’esame (orale) nelle sessioni di esame  ordinarie e straordinarie.

Inoltre, a partire da quest’anno non  coprirò l’insegnamento di Gestione del rischio microbiologico 6 cfu. Presiederò comunque la commissione si esami fino ad aprile 2017.

MIND@FoodMicro2016

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We will be in Dublin for FoodMicro 2016. Here you can download .pdf versions of our posters. You can find more in the FoodMicrobionet website.

  • PO1-FB-075 DIVERSITY OF STREPTOCOCCUS THERMOPHILUS POPULATIONS BY PHOSPHOSERINE PHOSPHATASE (SER-B) POLYMORPHISMS Teresa Zotta*, Annamaria Ricciardi, Francesca De Filippis, Danilo Ercolini, Eugenio Parente
  • PO1-FB-074 PURIFICATION AND FUNCTIONAL CHARACTERIZATION OF HEME-DEPENDENT CATALASE IN RESPIRATIVE STRAIN LACTOBACILLUS CASEI N87 Teresa Zotta, Antonio Varriale, Rocco G. Ianniello, Eugenio Parente, Maria C. Staiano, Annamaria Ricciardi
  • PO1-FB-073 EFFECT OF RESPIRATIVE AND CATALASE-POSITIVE CULTURES OF LACTOBACILLUS CASEI ON THE PRODUCTION OF CHEDDAR CHEESE Annamaria Ricciardi, Anna Reale, Rocco G. Ianniello, Felicia Ciocia, Tiziana Di Renzo, Teresa Zotta, Floriana Boscaino, Raffaele Coppola, Eugenio Parente, Paul L. H. McSweeney