Francesca De Filippis
I'm microbial ecologist and expert in the application of next-generation sequencing (NGS) technologies to the study of microbial communities in complex environments.
Since November 2022, I'm Associate Professor of Microbiology at the Dept. of Agricultural Sciences of the University of Naples Federico II (Italy).
Previously, I was Tenure-Track Assistant Professor (RTDB - Nov. 2019 - Nov. 2022), Junior Lecturer (RTDA - Nov. 2016 - Nov. 2019), Post-Doc (Feb 2015 - Nov. 2016) and PhD student (Jan. 2012 - Jan. 2015) in the same institution.
I also was Visiting Researcher (Jan. 2014 - Dec. 2014) at University College of Cork (Ireland), Department of Microbiology and Visiting Researcher at Argonne National Laboratory, Lemont (USA) (May 2013 - Dec. 2013).
I was included in the list of the World's Top 2% scientists across all fields of year 2019, 2020, 2021 and 2022 by Stanford University (doi:10.1371/journal.pbio.3000918 (2019), 10.17632/btchxktzyw.3 (2020), 10.17632/btchxktzyw.4 (2021) & 10.17632/btchxktzyw.6 (2022)).
I'm member of the Board of Professors of the PhD School in Food Science and of the Managing Board of the Task Force on Microbiome Studies of the University Federico II. Moreover, I'm Associate Editor of the Journal Food Research International (section Microbiome) and Member of the Editorial Board of the journals Foods and Frontiers in Microbiology.
e-mail: francesca.defilippis (at) unina.it
My Research Interests:
Food microbiome
Microbial dynamics during fermented food production or food spoilage. Influence of process parameters on the food microbiome. Influence of the resident microbiome in food processing environment on food quality and safety.
Human microbiome
Influence of external factors (diet, environmental pollution) on human microbiome composition and activity. Human microbiome-health axis. Next Generation Probiotics.
Metagenomics
Application of metagenomics to the study of taxonomic composition and functionality of the microbiome in complex environments (foods, human body, soil, natural environments, etc.). Bioinformatics and data analysis.
Microbial genomics
Comparative genomics of microbial species of biotechnological or epidemiological interest. Strain-tracking of microbial spoilers, pathogens or beneficial microbes.
Short-CV
Present Position
Nov. 2022 – now University of Naples Federico II, Department of Agricultural Sciences. Associate Professor of Microbiology.
March 2018 - now Affiliated Scientist, Italian Experimental Zooprophylactic Institute, Portici, Italy
Past Positions
Nov. 2019 – Nov. 2022 University of Naples Federico II, Department of Agricultural Sciences. Tenure-Track Assistant Professor of Microbiology (RTDB).
Nov. 2016 – Nov. 2019 University of Naples Federico II, Department of Agricultural Sciences. Junior Lecturer of Microbiology (RTDA).
Feb. 2015 – Nov. 2016 University of Naples Federico II, Department of Agricultural Sciences. Post-Doctoral Researcher within the EU granted project DINAMIC: “Diet-induced Arrangement of the gut Microbiome for improvement of Cardiometabolic healt”. Tutor: prof. Danilo Ercolini.
Jan. 2012 - Jan. 2015 University of Naples Federico II, Department of Agricultural Sciences. PhD student in Food Science. Tutor prof. Danilo Ercolini.
Jan. 2014 – Dec. 2014 Department of Microbiology of the University College of Cork (Ireland). Visiting researcher. Research activity: Study of gut microbiome of omnivore, vegetarian and vegan subjects. Supervisor: prof. Paul W. O’Toole
May 2013 – Dec. 2013 Environmental Microbiology and Gilbert Laboratory Divisions of the Center for Environmental Life Sciences at the Argonne National Laboratory, Lemont, IL (USA). Visiting researcher. Research activity: Study of bacterial metatranscriptome during production and ripening of Caciocavallo Silano PDO cheese. Supervisor: prof. Jack A. Gilbert.
Education and Training
July 2016 Erasmus Postgraduate School Molecular Medicine, Rotterdam (The Netherlands). Course “Gene expression data analysis using R: How to make sense out of your RNA-seq/microarray data”.
March 2015 University of Naples Federico II, Department of Agricultural Sciences. PhD in Food Science. Thesis entitled: “The microbiome in dairy products assessed by metagenomics and metatranscriptomics”. Tutor prof. Danilo Ercolini.
Oct. 2011 University of Naples Federico II, Department of Agricultural Sciences. MSc in Food Sciences and Technologies (Final grade: 110/110 cum laude). Thesis entitled: “Production of microbial volatile metabolites in raw beef stored in air and vacuum pack”. Tutor prof. Danilo Ercolini.
Oct. 2009 University of Naples Federico II, Department of Agricultural Sciences. Bachelor in Food Technologies (Final grade: 110/110 cum laude). Thesis entitled: “Contamination by saxitoxin in molluscs”. Tutor prof. Alberto Ritieni.
Teaching Activity
2016 - now University of Naples Federico II, Department of Agricultural Sciences. Course “Biology of Microorganisms” within the BSc in Food Technologies.
2021 - now University of Naples Federico II, Department of Agricultural Sciences. Course “Metagenomics and microbiome studies”, within the MSc in Agro-Food and Environmental Biotechnologies.
2023 University of Naples Federico II. Course: Microbial ecology and 'omics. Course for PhD students recruited within the Marie-Curie Project CRESCENDO.
2022 Industrial University of Ho-Chi-Minh (Vietnam). Course: Metagenomics data analysis.
2022 Universidad de Leon (Spain). Course: Metagenomics in food microbial ecology.
2019 Universidad de Burgos (Spain). Course: Bioinformatic analysis of Whole-Genome Shotgun data.
2016 - 2018 University of Florence. Teaching within the “Summer School on Computational Analysis: from Genomic Diversity to Ecosystem Structure”, organized by the Italian Society of Agro-Food and Environmental Microbiology (SIMTREA). Course: Bioinformatic analysis of high-throughput sequencing data.
2015 - 2021 University of Naples Federico II, Department of Agricultural Sciences. Course “Metagenomics and microbial biotechnologies in food”, within the MSc in Agro-Food and Environmental Biotechnologies.
Scientific Awards and Recognitions
Jan. 2020, 2021, 2022, 2023 - Nominated among the top 2% world's scientists across all fields of year 2019, 2020, 2021 and 2022 in the list published by Stanford University (doi:10.1371/journal.pbio.3000918, 10.17632/btchxktzyw.3, 10.17632/btchxktzyw.4 & 10.17632/btchxktzyw.6)
Sept. 2020 – Nominated among the top 0.1% world experts in Food Microbiology by Expertscape (https://expertscape.com/ex/food+microbiology)
March 2020 Winner of a prize for the best publication on a high-impact journal (IF>8) of the year 2019, granted by the Italian Society of Agro-Food and Environmental Microbiology (SIMTREA) for the publication: De Filippis F. et al. Distinct genetic and functional traits of human intestinal Prevotella copri strains are associated with different habitual diets. Cell Host & Microbe 25:444-53
March 2019 Winner of a prize for the best publication on a high-impact journal (IF>8) of the year 2018, granted by the Italian Society of Agro-Food and Environmental Microbiology (SIMTREA) for the publication: De Filippis F. et al. Recent past, present, and future of the food microbiome. Annu. Rev. Food Sci. Technol. 2018; 9:589-608.
October 2017 Winner of the SfAM Registration Fee Grant, granted by the Society for Applied Microbiology (SfAM) to support the participation to the 4th International Conference on Microbial Diversity 2017 (Bari, Italy).
July 2016 Winner of the FEMS Young Scientist Meeting Grant, granted by the Federation of European Microbiological Societies (FEMS) to support the participation to the FoodMicro2016 conference (Dublin, IR).
March 2016 Winner of a prize for the best publication on the theme of food microbiology of the year 2015, granted by the National Union of the Academies for the Sciences Applied to the Development of Agriculture, to Food Security and to Environmental Protection (UNASA) for the publication: De Filippis F. et al. Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate. Scientific Reports 2016; 6:21871.
June 2015 Winner of the EMBL Advanced Training Centre Corporate Partnership Programme Fellowship, granted by the European Molecular Biology Laboratory (EMBL) to support the participation to the EMBL Conference on the Human Microbiome (Heidelberg, DE).
February 2015 Winner of a prize for the best publication on the theme of food microbiology of the year 2014, granted by the Italian Society of Agro-Food and Environmental Microbiology (SIMTREA) for the publication: De Filippis F. et al. A selected core microbiome drives the early stages of three popular Italian cheese manufactures. PLoS One 2014; 9(2):e89680.
July 2014 Winner of the FEMS Young Scientist Meeting Grant, granted by the Federation of European Microbiological Societies (FEMS) to support the participation to the FoodMicro2014 conference (Nantes, FR).
October 2013 Winner of a prize for the best scientific contribution presented at the 2nd International Conference on Microbial Diversity 2013 (Torino, IT), granted by the International Committee on Food Microbiology and Hygiene (ICFMH) of the International Union of Microbiological Societies (IUMS) for the poster: De Filippis F., et al. Exploring the sources of bacterial spoilers in beefsteaks by culture-independent high-throughput sequencing.
July 2013 Winner of a short mobility grant from the Campania Region within the program ‘‘POR CAMPANIA FSE 2007/2013’’, spent at the Environmental Microbiology and Gilbert Laboratory Divisions of the Center for Environmental Life Sciences at Argonne National Laboratory, Lemont, IL (USA).
March 2012- Winner of a PhD fellowship granted by the Campania Region within the program ‘‘POR CAMPANIA FSE 2007/2013’’ - project CARINA (Safety sustainability and competitiveness of the agro-food production in Campania).
Coordination of Research Projects
2023 - now Principal Investigator of the Project PRIN2022 PNRR HOLOGRAM: Exploiting autochthonous microbial resources from traditional Italian fermented foods for gut-brain axis modulation, granted by the Italian Ministry of research (MUR)
2023 - now Responsible of Research Unit of the Project PRIN2022 MetaOlive: Meta-omic approaches for traditional table olive fermentation, granted by the Italian Ministry of research (MUR)
2023 - now Co-Responsible of Research Unit of the Project DOMINO: Harnessing the microbial potential of fermented foods for healthy and sustainable food systems, granted by EU within the Horizon Europe programme
2022 - now National Biodiversity Future Center (NBFC) granted by the National Recovery and Resilience Plan (NRRP), Mission 4 Component 2 Investment 1.4 and funded by the European Union - NextGenerationEU. Responsible of the activity within the Spoke 6: Microbiome characterization and preservation in traditional fermented foods
2022 - now METROFOOD-IT: Strengthening of the Italian RI for Metrology and Open Access Data in support to the Agrifood, granted by the National Recovery and Resilience Plan (NRRP), Mission 4, Component 2, Investment 1.4 and funded by the European Union - NextGenerationEU. Responsible of the activity: Use of microbiome profiles for food traceability.
2022 - now CRESCENDO: Transdisciplinary Doctoral Program in Microbiome Science at the University of Naples Federico II, co-funded by EU within the call H2020 Marie Sklodowska-Curie COFUND. Role: co-PI and supervisor of one PhD project. (€813,600 to co-finance 10 PhD positions on microbiome-related research)
2021 - now Principal Investigator of the project FOODMICROHERITAGE: Quality and authenticity protection of artisanal fermented foods through the characterization and conservation of their microbial and genetic heritage, granted by the Ministry of Foreign Affairs and International Cooperation within the Executive Programme of Scientific Cooperation between Italy and Vietnam
2020 - now Co-Responsible of Research Unit of the Project H2020-DiTECT: DIgital TEChnologies as an enabler for a conTinuous transformation of food safety system, granted by EU within the call Horizon2020 SFS-2018-2020 - Sustainable Food Security - Resilient and resource-efficient value chains
2019 - 2023 Principal Investigator of the project POLLGUT: Linking environmental pollution and gut microbiota in individuals living in contaminated settlements, granted by the Italian Ministry of Health
Funding from private companies:
2023 - Research Agreement with CAISIAL – Center for Food Industry Innovation. Topic: Study of fresh fish shelf life during distribution.
2023 - Research Agreement with Marino srl. Topic: Characterization of Natural Whey Cultures for PDO Buffalo Mozzarella cheese.
2022 - Research Agreement with Probiotical S.p.A. Topic: Isolation and genomic characterization of probiotic lactobacilli from the vaginal microbiota
2021 - Research Agreement with Marino srl. Topic: Isolation and characterization of lactic acid bacteria to be used as starters in dairy industry
2021 - Research Agreement with University of Milan Topic: Characterization of insect gut metagenome
Participation to Research Projects
2019 – 2023 Project H2020-MASTER: Microbiome Applications for Sustainable food systems through Technologies and EnteRprise, granted by EU within the call Horizon2020 LC-SFS-03-2018 - Microbiome applications for sustainable food systems.
2019 - 2023 Project H2020-SHEALTHY: Non-thermal physical technologies to preServe HEALTHiness of fresh and minimallY processed fruit and vegetables, granted by EU within the call Horizon2020 SFS-16-2018 - Towards healthier and sustainable food.
2019 - 2023 Project PRIN2017-MEDFOOD: Microbiome-tailored food products based on typical Mediterranean diet components, granted by the Italian Ministry of University and Research (MIUR).
2019 – 2022 Project KP-MCB: Exploring strain-level diversity in the gut microbiome across different age, geography, dietary habits and lifestyle, granted by EU within the call HDHL INTIMIC - Knowledge Platform on food, diet, intestinal microbiomics and human health.
2016 – 2019 Project DINAMIC: Diet-induced Arrangement of the gut Microbiome for improvement of Cardiometabolic health, granted by the European Union within the Joint Transnational Call “Intestinal Microbiomics”.
2016 – 2019 Project SPES: Exposure study in sensitive population, within the activity: Evaluation of gut microbiota composition in subjects living in areas with different level of exposure to environmental pollution, granted by Campania Region.
2013 - 2016 Project PRIN 2010/2011 Diet4MicroGut: Study of human microbiome and metabolome as function of omnivore, vegetarian and vegan diet, granted by the Italian Ministry of University and Research (MIUR).
2013 - 2015 Project Biomolecular approaches for the study of microbial diversity and functionality in foods, granted by the European Union.
2012 - 2015 Project CARINA: Safety, Sustainability and Competitiveness of the Agro-Food Production in Campania, granted by the Campania region within the program P.O.R. Campania F.S.E. 2007-2013.
Institutional Responsibilities and Commissions of Trust
2022-now: Member of the COST Action PIMENTO - Promoting Innovation of ferMENTed fOods (CA20128)
2022-now: Associate Editor of the journal Frontiers in Microbiology, for the Section Microorganisms in Vertebrate Digestive Systems (IF 5.640)
2021-now: member of the Board of Professors of the PhD School in Food Science, Univ. of Naples Federico II, Italy
2021-now: member of the Managing Board of the Task Force on Microbiome Studies, Univ. of Naples Federico II, Italy (www.tfm.unina.it)
2021–now: Associate Editor of the journal Foods (IF 4.305)
2020-now: Responsible for the University of Naples Federico II of the International Agreement with the Industrial University of Ho Chi Minh City (Vietnam)
Since 2019: Reviewer of research grants for the Programme PRELUDIUM, National Science Centre, Poland; Swiss National Science Foundation, Switzerland; Israel Science Foundation, Israel; European Research Council, ERC Starting Grant 2023; Katholieke Universiteit Leuven, Belgium; Dutch Research Council (NWO).
Since 2018: Member of PhD final examination committees - 2024: Dr I. Ortega Sanz, University of Burgos (Spain); 2022: Dr. Dr P. Fernandez, University of Leon (Spain); 2022: Dr J. Rodriguez Lopez, University of Jaen (Spain); 2020: Dr A. Zarovska, University of Turin (Italy); 2019: Dr J. Mota Gutierrez, University of Turin (Italy); 2018: Dr N.M. Quijada, University of Burgos (Spain); 2018: Dr G. Bertani, University of Parma (Italy); 2018: Dr L. García Sánchez, University of Burgos (Spain)
2017– now: member of the Theses Committee for the BSc in Food Technologies, Univ. of Naples Federico II, Italy
2017-now: member of the Task Force on Microbiome Studies, Univ. of Naples Federico II, Italy (www.tfm.unina.it)
2017–now: Associate Editor of the journal Food Research International (IF 6.475; Q1 in “Food Science & Technology”) for the section “Microbiome”.
2016–now: member of the International consortium MetaSUB (Metagenomics & Metadesign of Subway & Urban Biomes)
2016–now: member of the Public Engagement Committee, Univ. of Naples Federico II, Italy
2016-now: Faculty member, dept. Agricultural Sciences, Univ. of Naples Federico II, Italy
Membership of Scientific and Organizing Committees
2024-Member of the Scientific Committee of the 28th International ICFMH Conference FoodMicro2024, Burgos, Spain
2023-Member of the Organizing Committee of the 27th Workshop of the Developments in the Italian PhD Research on Food Science, Technology and Biotechnology, Portici, Italy
2020-Member of the Scientific Committee of the 3rd International Symposium on Fruit and Vegetable Processing, Avignon, France
Supervision of Students and post-Docs
Supervision of Post-Doctoral researcher:
2023 Dr Vincenzo Valentino, Post-Doc researcher within the project H2020-DiTECT-"DIgital TEChnologies as an enabler for a conTinuous transformation of food safety system". Activity: Microbiome mapping along food chains.
2022 Dr Rosalia Ferracane, Post-Doc researcher within the project MEDFOOD-“Microbiome-tailored food products based on typical Mediterranean diet components”. Activity: Influence of diet on gut microbiome and metabolome.
Supervision of PhD students:
2024 - on-going Supervisor of the PhD student Martina Parziale, PhD in Food Science, Univ. of Naples Federico II, Naples, Italy. Research project: Development of novel pre- and probiotics for skin microbiome modulation. PhD fellowship granted by Arterra Bioscience SpA.
2023 - on-going Supervisor of the PhD student Asim-ur-Rahman, PhD in Food Science, Univ. of Naples Federico II, Naples, Italy. Research project: Microbiome mapping along meat chain from farm to fork. PhD fellowship granted by EU-H2020 Marie Sklodowska-Curie project CRESCENDO
2023 - on-going Supervisor of the PhD student Raffaele Magliulo, PhD in Food Science, Univ. of Naples Federico II, Naples, Italy. Research project: Fermented foods microbial biodiversity preservation and characterization using multi-omics approaches. PhD fellowship granted by PNRR - CN5: National Biodiversity Future Center
2023 - on-going Supervisor of the PhD student Chiara M. Calvanese, PhD in Food Science, Univ. of Naples Federico II, Naples, Italy. Research project: Genomic characterization of LAB strains for probiotics and postbiotics development. PhD fellowship granted by Probiotical SpA.
2023 - on-going Co-Supervisor of the PhD student Raffaella Ofano, PhD in Food Science, Univ. of Naples Federico II, Naples, Italy. Research project: Multidisciplinary approach for the traceability of geographical origin and the authentication of agri-food products. PhD fellowship granted by PNRR - IR: METROFOOD-IT
2022 - on-going Supervisor of the PhD student Alessia Esposito, PhD in Food Science, Univ. of Naples Federico II, Naples, Italy. Research project: Selection of Next-Generation probiotics from the gut microbiome of subjects with different dietary patterns. PhD fellowship granted by Sacco System.
2021 - 2023 Supervisor of the PhD student Giuseppina Sequino, PhD in Food Science, Univ. of Naples Federico II, Naples, Italy. Research project: Metagenomics and Big Data to improve food safety and quality. PhD fellowship granted by EU-H2020 project DiTECT.
2018-2021 Supervisor of the PhD student Silvia Castellano, PhD in Food Science, Univ. of Naples Federico II, Naples, Italy. Research project: Isolation and genomic characterization of Campylobacter spp. in meat products
Supervision of post-graduate students:
2024 Alessandra De Vivo, research fellowship within the project Meta-Olive-"Meta-omic approaches for traditional table olive fermentation". Activity: Mapping the microbiome of table olive from Mediterranean area.
2022 Chiara M. Calvanese, research fellowship within the project FOODMICROHERITAGE-“Quality of Italian and Vietnamese artisanal fermented foods through the characterization and conservation of their microbial and genetic heritage”. Activity: Isolation and characterization of lactic acid bacteria from traditional fermented foods.
2021 Sara Cavaliere, research fellowship within the project FOODMICROHERITAGE-“Quality of Italian and Vietnamese artisanal fermented foods through the characterization and conservation of their microbial and genetic heritage”. Activity: Analysis of fermented food microbiome.
2021 Alessia Esposito, research fellowship within an industrial project granted by Lactalis Recherche et Développement. Activity: Evaluation of gut microbiome in people with gastrointestinal discomfort upon milk ingestion.
2019-2020 Giuseppina Sequino, research fellowship within the project POLLGUT-“Linking environmental pollution and gut microbiota in individuals living in contaminated settlements”. Activity: Influence of environmental pollution on the human gut microbiome.
Supervision of MSc students:
Since 2016 Supervision of > 30 MSc students in Food Science and Technologies and Agro-Food and Environmental Biotechnologies during the preparation of their experimental theses
Supervision of International visiting students:
Since 2018: N.M. Quijada, Univ. of Burgos, Spain (2018); B. Severino da Silva, Univ. of Campinas, Brazil (2019); I. Botella, Univ. of Valencia, Spain (2021); S. Adell-Valen, Univ. Rovira i Virgili, Spain (2021)
Publications in International Journals
Sequino, G., Cobo Diaz, J.F., Valentino, V., Tassou, C., Volpe, S., Torrieri, E., Nychas, G.-J., Alvarez Ordonez, A., Ercolini, D., De Filippis, F.* 2024. Microbiome mapping in beef processing reveals safety-relevant variations in microbial diversity and genomic features. Food Res. International 186:114318. *corresponding author
Sequino, G., Valentino, V., Esposito, A., Volpe, S., Torrieri, E., De Filippis, F.*, Ercolini, D. 2024. Microbiome dynamics, antibiotic resistance gene patterns and spoilage-associated genomic potential in fresh anchovies stored in different conditions. Food Res. International 175:113788. *corresponding author
De Filippis, F., Bonelli, M., Bruno, D., Sequino, G., Montali, A., Reguzzoni, M., Pasolli, E., Savy, D., Cangemi, S., Cozzolino, V., Tettamanti, G., Ercolini, D., Casartelli, M., Caccia, S. 2023. Plastics shape the black soldier fly larvae gut microbiome and select for biodegrading functions. Microbiome 11:205.
Blanco-Míguez, A., Gálvez, E.J.C., Pasolli, E., De Filippis, F., Amend, L., Huang, K.D., Manghi, P., Lesker, T.R., Riedel, T., Cova, L., Punčochář, M., Thomas, A.M., Valles-Colomer, M., Schober, I., Hitch, T.C.A., Clavel, T., Berry, S.E., Davies, R., Wolf, J., Spector, T.D., Overmann, J., Tett, A., Ercolini, D., Segata, N., Strowig, T. 2023. Extension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions. Cell Host Microbe 31(11):1804-1819.e9.
Valentino, V., De Filippis, F., Sequino, G., Ercolini, D. 2023. Psychrotrophic Bacteria Equipped with Virulence and Colonization Traits Populate the Ice Cream Manufacturing Environment. Appl. Environ. Microbiol. 89(8):e0076523.
Abuqwider, J., Di Porzio, A., Barrella, V., Gatto, C., Sequino, G., De Filippis, F., Crescenzo, R., Spagnuolo, M.S., Cigliano, L., Mauriello, G., Iossa, S., Mazzoli, A. 2023. Limosilactobacillus reuteri DSM 17938 reverses gut metabolic dysfunction induced by Western diet in adult rats. Front. Nutr. 10:1236417.
Di Lorenzo, F., Paparo, L., Pisapia, L., Oglio, F., Pither, M.D., Cirella, R., Nocerino, R., Carucci, L., Silipo, A., De Filippis, F., Ercolini, D., Molinaro, A., Berni Canani, R. 2023. The chemistry of gut microbiome- derived lipopolysaccharides impacts on the occurrence of food allergy in the pediatric age. Front. Mol. Biosci. 10:1266293.
Tagliamonte, S., Barone Lumaga, R., De Filippis, F., Valentino, V., Ferracane, R., Guerville, M., Gandolfi, I., Barbara, G., Ercolini, D., Vitaglione, P. 2023. Milk protein digestion and the gut microbiome influence gastrointestinal discomfort after cow milk consumption in healthy subjects. Food Res. International 170:112953.
Giello, M., Volpe, S., Sequino, G., De Filippis, F., Villani, F., Torrieri, F. 2023. Design of bioactive biopolymer coating based on Latilactobacillus curvatus 54M16 producer of bacteriocins to preserve the safety of minimally processed fennel. Food Packaging and Shelf Life 38:101111.
Pinchera, B., Scotto, R., Zappulo, E., Buonomo, A.R., Maraolo, A.E., Schiano Moriello, N., Viceconte, G., Cattaneo, L., Villari, R., Gison, F., De Filippis, F., Ercolini, D., Gentile, I. 2023. Impact of oral antiviral therapy against HCV on gut microbiota. A prospective study. The new microbiologica 46:196-201.
Rodriguez Lopez, J., GrandeBurgos, M.J., De Filippis, F., Pérez Pulido, R., Ercolini, D., Galvez, A., Lucas, R. 2023. Determination of the effect of the bacteriocin enterocin AS-48 on the microbial loads and bacterial diversity of blueberries. Heliyon 9:e15921.
Coppola, S., Nocerino, R., Paparo, L., Bedogni, G., Calignano, A., Di Scala, C., de Giovanni di Santa Severina, A.F., De Filippis, F., Ercolini, D., Berni Canani, R.B. 2022. Therapeutic Effects of Butyrate on Pediatric Obesity: A Randomized Clinical Trial. JAMA network open 5:e2244912.
Sequino, G., Valentino, V., Torrieri, E., De Filippis, F.* 2022. Specific microbial communities are selected in minimally-processed fruit and vegetables according to the type of product. Foods 11:2164. *corresponding author
Sequino, G., Valentino, V., Villani, F., De Filippis, F.* 2022. Omics-based monitoring of microbial dynamics across the food chain for the improvement of food safety and quality. Food Res. International 157:111242. *corresponding author
Aponte, M., Esposito, F., Sequino, G., Blaiotta, G., De Filippis, F. 2022. Stuck or sluggish fermentations in home-made beers: Beyond the surface. Int. J. Food Microbiol. 383:109956.
Valentino, V., Sequino, G., Cobo-Díaz, J., Álvarez-Ordóñez, A., De Filippis, F., Ercolini, D. 2022. Evidence of virulence and antibiotic resistance genes from the microbiome mapping in minimally processed vegetables producing facilities. Food Res. International 162:112202.
Tarallo, S.*, Ferrero, G.*, De Filippis, F.*, Francavilla, A., Pasolli, E., Panero, V., Cordero, F., Segata, N., Grioni, S., Pensa, R.G., Pardini, B., Ercolini, D., Naccarati, A. 2022. Stool microRNA profiles reflect different dietary and gut microbiome patterns in healthy individuals. Gut 71(7):1302–1314 *co-first authors
Coppola, S., Paparo, L., Chiariotti, L., Ercolini, D., Nocerino, R., de Giovanni Di Santa Severina, A.F., Carucci, L., De Filippis, F., Agangi, A., Napolitano, M., Passariello, A., Messina, F., Berni Canani, R. 2022. Effects of the Mediterranean Diet during pregnancy on the onset of allergy in at risk children: A study protocol of a multi-center, randomized- controlled, parallel groups, prospective trial (the PREMEDI study). Front. Nutr. 9:951223.
De Filippis, F., Esposito, A., Ercolini, D. 2022. Outlook on next‐generation probiotics from the human gut. Cellular and Molecular Life Sciences 79:76.
Valentino, V., De Filippis, F., Menghi, L., Gasperi, F., Ercolini, D. 2022. Food Neophobia and scarce olfactory performances are linked to oral microbiota. Food Res. International 155:111092.
Jaber, M., Altamimi, M., Altamimi, A., Cavaliere, S., De Filippis, F. 2022. Mediterranean diet diminishes the effects of Crohn’s disease and improves its parameters: A systematic review. Nutr. Health 1-16:2601060221102281.
Carucci, L., Nocerino, R., Paparo, L., De Filippis, F., Coppola, S., Giglio, V., Cozzolino, T., Valentino, V., Sequino, G., Bedogni, G., Russo, R., Ercolini, D., Berni Canani, R. 2022. Therapeutic effects elicited by the probiotic Lacticaseibacillus rhamnosus GG in children with atopic dermatitis. The results of the ProPAD trial. Pediatr Allergy Immunol. 33:e13836.
Idbella, M., De Filippis, F., Zotti, M., Sequino, G., Abd-ElGawad, A.M., Fechtali, T., Mazzoleni, S., Bonanomi, G. 2022. Specific microbiome signatures under the canopy of Mediterranean shrubs. Applied Soil Ecology 173:104407.
de Franchis, R., Bozza, L., Canale, P., Chiacchio, M., Cortese, P., D’Avino, A., De Giovanni, M., Dello Iacovo, M., D’Onofrio, A., Federico, A., Gasparini, N., Iaccarino, F., Romano, G., Spadaro, R., Tedesco, M., Vitiello, G., Antignani, A., Auricchio, S., Valentino, V., De Filippis, F., Ercolini, D., Bruzzese, D. 2022. The Effect of Weaning with Adult Food Typical of the Mediterranean Diet on Taste Development and Eating Habits of Children: A Randomized Trial. Nutrients 14, 2486.
Woo, S.L., De Filippis, F., Zotti, M., Vandenberg, A., Hucl, P., Bonanomi, G. 2022. Pea-Wheat Rotation Affects Soil Microbiota Diversity, Community Structure, and Soilborne Pathogens. Microorganisms 10:370.
De Filippis, F., Paparo, L., Nocerino, R., Della Gattta, G., Carucci, L., Russo, R., Pasolli, E., Ercolini, D., Berni Canani, R. 2021. Specific gut microbiome signatures and the associated pro-inflamatory functions are linked to pediatric allergy and acquisition of immune tolerance. Nature Communications 12:5958.
Pinart, M., Nimptsch, K., Forslund, S.K., ...(in alphabetic order) De Filippis, F., .... Pischon, T. 2021. Identification and Characterization of Human Observational Studies in Nutritional Epidemiology on Gut Microbiomics for Joint Data Analysis. Nutrients 3(9):3292.
Danko, D., Bezdan, D., Afshin, E.E., .....(in alphabetic order) De Filippis, F., ..... Mason, C.E. 2021. A global metagenomic map of urban microbiomes and antimicrobial resistance. Cell 184(13): 3376-3393.e17.
De Filippis, F., Valentino, V., Alvarez-Ordonez, A., Cotter, P.D., Ercolini, D. 2021. Environmental microbiome mapping as a strategy to improve quality and safety in the food industry. Curr. Opinion in Food Sci. 38:168-176.
Zotti, M., Bonanomi, G., Mancinelli, G., Barquero, M., De Filippis, F., Giannino, F., Mazzoleni, S., Gonzalez-Andrés, F. 2021. Riding the wave: Response of bacterial and fungal microbiota associated with the spread of the fairy ring fungus Calocybe gambosa. Applied Soil Ecology 163:103963
Idbella, M., Bonanomi, G., De Filippis, F., Amor, G., Chouyia, F.E., Fechtali, T., Mazzoleni, S. 2021. Contrasting effects of Rhizophagus irregularis versus bacterial and fungal seed endophytes on Trifolium repens plant‑soil feedback. Mycorrhiza 30:103-115.
De Filippis, F., Pasolli, E., Ercolini, D. 2020. Newly explored Faecalibacterium diversity is connected to age, lifestyle, geography, and disease. Curr. Biol. 30:1-12.
De Filippis, F., Pasolli, E., Ercolini, D. 2020. The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health. FEMS Microb. Reviews 44:454-489.
Pasolli, E., De Filippis, F., Mauriello, I.E., Cumbo, F., Walsh, A.M., Leech, J., Cotter, P.D., Segata, N., Ercolini, D. 2020. Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome. Nature Communications 11:2610.
Zotti, M., De Filippis, F., Cesarano, G., Ercolini, D., Tesei, G., Allegrezza, M., Giannino, F., Mazzoleni, S., Bonanomi, G. 2020. One ring to rule them all: an ecosystem engineer fungus fosters plant and microbial diversity in a Mediterranean grassland. New Phytologist 227: 884–898.
Laiola, M., De Filippis, F., Vitaglione, P., Ercolini, D. 2020. A Mediterranean Diet Intervention Reduces the Levels of Salivary Periodontopathogenic Bacteria in Overweight and Obese Subjects. Appl. Environ. Microbiol. 86:e00777-20.
Nocerino, R., De Filippis, F., Cecere, G., Marino, A., Micillo, M., Di Scala, C., de Caro, C., Calignano, A., Bruno, C., Paparo, L., Iannicelli, A.M., Cosenza, L., Maddalena, Y., della Gatta, G., Coppola, S., Carucci, L., Ercolini, D., Berni Canani, R. 2020. Editorial: The therapeutic efficacy of Bifidobacterium animalis subsp. lactis BB‐12® in infant colic: A randomised, double blind, placebo‐controlled trial. Author's reply. Alimentary Pharmacology & Therapeutics 51(3):398-399.
Meslier, V., Laiola, M., Roager, H.M., De Filippis, F., Roume, H., Quinquis, B., Giacco, R., Mennella, I., Ferracane, R., Pons, N., Pasolli, E., Rivellese, A., Dragsted, L.O., Vitaglione, P., Ehrlich, S.D., Ercolini, D. 2020. Mediterranean diet intervention in overweight and obese subjects lowers plasma cholesterol and causes changes in the gut microbiome and metabolome independently of energy intake. Gut 69(7):1258-1268.
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.
Idbella, M., Bonanomi, G., De Filippis, F., Amor, G., Chouyia, F.E., Fechtali, T., Mazzoleni, S. 2020. Contrasting effects of Rhizophagus irregularis versus bacterial and fungal seed endophytes on Trifolium repens plant-soil feedback. Mycorrhiza, in press.
Chng, R.K., Li, C., Bertrand, D., .... De Filippis, F., ..... Nagarajan, N. 2020. Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment. Nat. Medicine 26:941-951.
De Angelis, M., Ferrocino, I., Calabrese, F.M., De Filippis, F., Cavallo, N., Siragusa, S., Rampelli, S., Di Cagno, R., Rantsiou, K., Vannini, L., Pellegrini, N., Lazzi, C., Turroni, S., Lorusso, N., Ventura, M., Chieppa, M., Neviani, E., Brigidi, P., O’Toole, P.W., Ercolini, D., Gobbetti, M., Cocolin, L. 2020. Diet influences the functions of the human intestinal microbiome. Scientific Reports 10:4247.4.
Calasso, M., Minervini, F., De Filippis, F., Ercolini, D., De Angelis, M., Gobbetti, M. 2020. Attenuated Lactococcus lactis and Surface Bacteria as Tools for Conditioning the Microbiota and Driving the Ripening of Semisoft Caciotta Cheese. Appl Environ Microbiol 86:e02165-19.5.
Milanovic, V., Aquilanti, L., Tavoletti, S., Garofalo, C., Osimani, A., De Filippis, F., Ferrocino, I., Di Cagno, R., Turroni, S., Lazzi, C., Pellegrini, N., Clementi, F. 2020. Distribution of Antibiotic Resistance Genes in the Saliva of Healthy Omnivores, Ovo-Lacto-Vegetarians, and Vegans. genes in press
Bonanomi, G., De Filippis, F., Zotti, M., Idbella, M., Cesarano, G., Al-Rowaily, S., Abd-ElGawad, A. 2020. Repeated applications of organic amendments promote beneficial Tmicrobiota, improve soil fertility and increase crop yield. Appl Soil Ecol 156:103714.
Bonanomi, G., Maisto, G., De Marco, A., Cesarano, G., Zotti, M., Mazzei, P., Libralato, G., Staropoli, A., Siciliano, A., De Filippis, F., La Storia, A., Piccolo, A., Vinale, F., Crasto, A., Guida, M., Ercolini, D., Incerti, G. 2020. The fate of cigarette butts in different environments: Decay rate, chemical changes and ecotoxicity revealed by a 5-years decomposition experiment. Environmental Pollution 261:114108.6.
Guida, F., Boccella, S., Belardo, C., Iannotta, M., Piscitelli, F., De Filippis, F., Paino, S., Ricciardi, F., Siniscalco, D., Marabese, I., Luongo, L., Ercolini, D., Di Marzo, V., Maione, S. 2020. Altered gut microbiota and endocannabinoid system tone in vitamin D deficiency-mediated chronic pain. Brain Behav. Immun. 85:128-141.
De Filippis, F., Pasolli, E., Tett, A., Tarallo, S., Naccarati, A., De Angelis, M., Neviani, E., Cocolin, L., Gobbetti, M., Segata, N., Ercolini, D. 2019. Distinct genetic and functional traits of human intestinal Prevotella copri strains are associated with different habitual diets. Cell Host & Microbe 25:444-453.
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.
De Filippis, F., Aponte, M., Piombino, P., Lisanti, M.T., 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. 120:740-747.
Kamimura, B.A., De Filippis, F., Sant’Ana, A.S., Ercolini, D. 2019. Large-scale mapping of microbial diversity in artisanal Brazilian cheeses. Food Microbiol. 80:40-49.
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.
Bruno, D., Bonelli, M., De Filippis, F.,Di Lelio, I., Tettamanti, G., Casartelli, M., Ercolini, D., Caccia, S. 2019. The Intestinal Microbiota of Hermetia illucens Larvae Is Affected by Diet and Shows a Diverse Composition in the Different Midgut Regions. Appl. Environ. Microbiol. 85:e01864-18.
Tett, A., Huang, K.D., Asnicar, F., Fehlner-Peach, H., Pasolli, E., Karcher, N., Armanini, F., Manghi, P., Bonham, K., Zolfo, M., De Filippis, F., Magnabosco, C., Bonneau, R., Lusingu, J., Amuasi, J., Reinhard, K.l, Rattei, T., Boulund, F., Engstrand, L., Zink, A., Collado, M.C., Littman, D.R., Eibach, D., Ercolini, D., Rota-Stabelli, O., Huttenhower, C., Maixner, F., Segata, N. 2020. The Prevotella copri complex comprises four distinct clades underrepresented in Westernized populations. Cell Host & Microbe 26:666-679.e7.
Bonanomi, G., De Filippis, F.,Cesarano, G., La Storia, A., Zotti, A., Mazzoleni, S., Incerti, G. 2019. Linking bacterial and eukaryotic microbiota to litter chemistry: Combining next generation sequencing with 13C CPMAS NMR spectroscopy. Soil Biol. Biochem. 129:110-121.
Zotta, T., Parente, E., Iannello, R.G., 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.
Maresca, D., De Filippis, F.,Robertiello, A., Mauriello, G. 2019. Metabolic Profiling and Cold-Starvation Stress Response of Oxygen-Tolerant Lactobacillus gasseriStrains Cultured in Batch Bioreactor. Microorganisms 7:200.
Vitaglione, P., Mazzone, G., Lembo, V., D’Argenio, G., Rossi, A., Guido, M., Savoia, M., Salomone, F., Mennella, I., De Filippis, F., Ercolini, D., Caporaso, N., Morisco, F. 2019. Coffee prevents fatty liver disease induced by a high-fat diet by modulating pathways of the gut–liver axis. J. Nutr. Sci. 8:e15.
Vernocchi, P., Del Chierico, F., Russo, A., Majo, F., Rossitto, M., Valerio, M., Casadei, L., La Storia, A., De Filippis, F.,Rizzo, C., Manetti, C., Paci, P., Ercolini, D., Marini, F., Fiscarelli, E.V., Dallapiccola, B., Lucidi, V., Miccheli, A., Putignani, L. 2018. Gut microbiota signatures in cystic fibrosis: Loss of host CFTR function drives the microbiota enterophenotype. PLoS One 13(12):e0208171.
De Filippis, F., Vitaglione, P., Cuomo, R., Berni Canani, R., Ercolini, D. 2018. Dietary interventions to modulate the gut microbiome – how far away are we from precision medicine. Inflamm. Bowel Dis. Inflamm. Bow. Dis.24(10):2142-2154.
De Filippis, F.*, Troise, A.D., 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. *corresponding author
De Filippis, F., Parente, E., Ercolini, D. 2018. Recent past, present, and future of the food microbiome. Annu. Rev. Food Sci. Technol. 9:589-608.
De Filippis, F., Parente, E., Zotta, T., Ercolini, D. 2018. A comparison of bioinformatic approaches for 16S rRNA gene profiling of food bacterial microbiota.Int. J. Food Microbiol. 265:9-17.
Berni Canani, R.*, De Filippis, F.*, Nocerino, R., Paparo, L., Di Scala, C., Cosenza, L., Della Gatta, G., Calignano, A., De Caro, C., Laiola, M., Gilbert, J.A., Ercolini, D. 2018. Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow’s milk allergy. Sci. Rep.8:12500. *co-first authors
Quijada, N.M., De Filippis, F., Sanz, J.J., Garcia-Fernandez, M.C., Rodriguez-Lazaro, D., Ercolini, D., Hernandez, M. 2018. High-throughput sequencing analysis reveals different Lactobacillus populations that dominate during “Chorizo de León” cured meat making. Food Microbiol. 70:94-102.
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.
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.
Milanovic, V., Osimani, A., Garofalo, C., De Filippis, F., Ercolini, D., Cardinali, F., Taccari, M., Aquilanti, L., Clementi, F. 2018. Profiling white wine seed vinegar bacterial diversity through viable counting, metagenomic sequencing and PCR-DGGE. Int. J. Food Microbiol. 286:66-74.
Osimani, A., Milanovic, V., Garofalo, C., Cardinali, F., Roncolini, A., Sabbatini, R., De Filippis, F., Ercolini, D., Gabucci, C., Petruzzelli, A., Tonucci, F., Clementi, F., Aquilanti, L. 2018. Revealing the microbiota of marketed edible insects through PCR-DGGE, metagenomic sequencing and real-time PCR. Int. J. Food Microbiol. 276:54-62.
Guida, F., Turco, F., Iannotta, M., De Gregorio, D., Palumbo, I., Sarnelli, G., Furiano, A., Napolitano, F., Boccella, S., Luongo, L., Mazzitelli, M., Usiello, A., De Filippis, F., Iannotti, F.A., Piscitelli, F., Ercolini, D., de Novellis, V., Di Marzo, V., Cuomo, R., Maione, S. 2018. Antibiotic-induced microbiota perturbation causes gut endocannabinoidome changes, hippocampal neuroglial reorganization and depression in mice. Brain Behav. Immun. 67:230-245.
Bonanomi, G., Cesarano, G., Antignani, V., Di Maio, C., De Filippis, F., Scala, F. 2018.Conventional farming impairs Rhizoctonia solani disease suppression by disrupting soil food web. Journal of Phytopathology166(9):663-673.
De Filippis, F., Laiola, M., Blaiotta, G., Ercolini, D. 2017. Different amplicon targets for sequencing-based studies of fungal diversity. Appl. Environ. Microbiol. 83(17):e00905-17.
Berni Canani, R.*, De Filippis, F.*, Nocerino R., Laiola, M., Paparo, L., Calignano, A., De Caro, C., Coretti, L., Chiariotti, L., Gilbert, J.A., Ercolini D. 2017. Specific signatures of the gut microbiota and increased levels of butyrate in children treated with fermented cow’s milk containing heat-killed Lactobacillus paracasei CBA L74. Appl. Environ. Microbiol. 83(19):e01206-17.*co-first authors
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.*corresponding author
De Filippis, F., Parente, E., Ercolini, D. 2017. Metagenomics insights into food fermentations. Microbial Biotechnol. 10(1):91-102.
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. *co-corresponding author
Maresca, D., De Filippis, F., Tytgat, H.L.P., de Vos, W.M., Mauriello, G. 2017. Draft genome sequences of the aerobic strains Lactobacillus gasseri AL3 and AL5. Genome Announc. 5:e00213-17.
Cesarano, G., De Filippis, F., La Storia, A., Scala, F., Bonanomi, G. 2017. Organic amendment type and application frequency affect crop yields, soil fertility and microbiome composition. Appl. Soil Ecol. 120:254-264.
De Filippis, F., Pellegrini, N., Laghi, L., Gobbetti, M., Ercolini, D. 2016. Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns. Microbiome 4:57.
Bonanomi, G., De Filippis, F., Cesarano, G., La Storia, A., Ercolini, D., Scala, F. 2016. Organic farming induces changes in soil microbiota that affect agro-ecosystem functions. Soil Biol. Biochem. 103:327-336.
De Filippis, F., Genovese, A., Ferranti, P., Gilbert, J.A., Ercolini, D. 2016. Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate. Sci. Rep.6:21871.
Ricciardi, A., De Filippis, F., Zotta, T., Facchiano, A., Ercolini, D., Parente, E. 2016. Polymorphism of the phosphoserine phosphatase gene in Streptococcus thermnophilusand its potential use for typing and monitoring of population structure. Int. J. Food Microbiol. 236:138-147.
Stellato, G., La Storia, A., De Filippis, F., Borriello, G., Villani, F., Ercolini, D. 2016. Overlap of spoilage-associated microbiota between meat and meat processing environment in small-scale and large-scale retail distribution. Appl. Environ. Microbiol. 82(13):4045-54.
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(13):3988-95.
Parente, E., Cocolin, L., De Filippis, F., Zotta, T., Ferrocino, I., O’Sullivan, O., Neviani, E., De Angelis, M., Cotter, P.D., Ercolini, D. 2016. FoodMicrobionet: A database for the visualization and exploration of food bacterial communities based on network analysis. Int. J. Food. Microbiol. 219:28-37.
Guidone, A., Matera, A., Ricciardi, A., Zotta, T., 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.
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.
De Filippis, F., Pellegrini, N., Vannini, L., Jeffery, I.B., La Storia, A., Laghi, L., Serrazanetti, D.I., Di Cagno, R., Ferrocino, I., Lazzi, C., Turroni, S., Cocolin, L., Brigidi, P., Neviani, E., Gobbetti, M., O’Toole, P.W., Ercolini, D. 2016. High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome. Gut 65:1812–1821.
Ercolini, D., Francavilla, R., Vannini, L., De Filippis, F.,Capriati, T., Di Cagno, R., Iacono, G., De Angelis, M., Gobbetti, M. 2015. From an imbalance to a new imbalance: Italian-style gluten-free diet alters the salivary microbiota and metabolome of African celiac children. Sci. Rep. 5:18571.
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(22):7893-7904.
Rizzello, C.G., Cavoski, I., Turk, J., Ercolini, D., Nionelli, L., Pontonio, E., De Angelis, M., De Filippis, F., Gobbetti, M., Di Cagno, R. 2015. The organic cultivation of Triticum turgidum spp. durum reflects on the axisflour, sourdough fermentation and bread. Appl. Environ. Microbiol.81(9):3192-3204.
Garofalo, C., Osimani, A., Milanović, V., Aquilanti, L., De Filippis, F., Stellato, G., Buzzini, P., Turchetti, B., Di Mauro, S., Ercolini, D., Clementi, F. 2015. Bacteria and yeast microbiota in milk kefir grains from different Italian regions. Food Microbiol. 49:123-133.
De Filippis, F., Vannini, L., La Storia, A., Laghi, L., Piombino, P., Stellato, G., Serrazanetti, D.I., Gozzi, G., Turroni, S., Ferrocino, I., Lazzi, C., Di Cagno, R., Gobbetti, M., Ercolini, D. 2014. The same microbiota and a potentially discriminant metabolome in the saliva of omnivore, ovo-lacto-vegetarian and vegan individuals. PLoS ONE 9(11):e112373.
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(2):e89680.
Francavilla, R., Ercolini, D., Piccolo, M., Vannini, L., Siragusa, S., De Filippis, F., De Pasquale, I., Di Cagno, R., Di Toma, M., Gozzi, G., Serrazanetti, D.I., De Angelis, M., Gobbetti, M. 2014. Salivary microbiota and metabolome associated with celiac disease. Appl. Environ. Microbiol. 80(11):3416-3425.
Casaburi, A., De Filippis, F., Villani, F., Ercolini, D. 2014. Activities of strains of Brochothrix thermosphacta in vitro and in meat. Food Res. Intern. 62:366-374.
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.
Cruciata, M., Sannino, C., Ercolini, D., Scatassa, M.L., 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(7):2050-2061.
De Filippis, F., La Storia, A., Villani, F., Ercolini, D. 2013.Exploring the sources of bacterial spoilers in beefsteaks by culture-independent high-throughput sequencing. PLoS ONE 8(7):e70222.
De Filippis, F., Pennacchia, C., Di Pasqua, R., Fiore, A., Fogliano, V., Villani, F., Ercolini, D. 2013. Decarboxylase gene expression and cadaverine and putrescine production by Serratia proteamaculans in vitro and in beef. Int. J. Food Microbiol.165:332-338.
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(24):7827-7836.
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(7):e69074.
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(22):8142-8145.
Book Chapters
Hill, C.J., De Filippis, F., Jeffery, I.B. 2019. Diet, health, and the gut microbiota. In: Doyle, M.P., DiezGonzalez, F., Hill, C. - Food Microbiology: Fundamentals and Frontiers, 5th Ed. Ed. ASM Press, chapter 31, pp. 815-829. ISBN 9781555819965.
De Filippis, F., Ercolini, D. 2018. Microbiome and diet. In: Haller, D. - The gut microbiome in health and disease. Ed. Springer, chapter 6, pp. 79-88. ISBN 978-3319905457.
Ercolini, D., De Filippis, F. 2017. Nutrizione e salute: ruolo del microbiota intestinale. In: Rivellese, Annuzzi, Capaldo, Vaccaro, Riccardi - Nutrizione Umana. Ed. Idelson-Gnocchi, cap. 18, pp. 315-324. ISBN 978-8879476492.
De Filippis, F., Ercolini, D. 2016. Food microbial ecology in the “omics” era. In: Reference Module in Food Sciences, Elsevier, pp. 1-7, doi: 10.1016/B978-0-08-100596-5.03005-5.
Invited and Selected Talks @ National and International Conferences
2024: Invited Speaker @ the national conference "5th Conference of the Italian Society of the Scientific Societies in Agricultural Sciences - AISSA under40", University of Florence (IT), 26-27 June 2024. Presentation: Microbiome-humans-environment axis: complex interactions that impact our health.
2023: Invited Speaker @ the international Workshop "What do we know about the fermented foods we eat every day?", organized by the Italian Embassy in Vietnam, Hanoi (Vietnam), 14 November 2023. Presentation: Microbiome of Italian fermented foods: role in flavor development and beneficial health effects.
2023: Invited Speaker @ the international conference "Trends in Microbiome and Digital One Health", KAUST University, Jeddah (Saudi Arabia), 30 October - 1 November 2023. Presentation: Mapping the microbiome in food industries to improve food safety and quality
2023: Selected oral presentation @ the international conference "4th International World of Microbiome - WOM2023", Sofia (Bulgaria), 26-28 October 2023. Presentation: Environmental pollution shapes the gut microbiome and drives the enrichment In xenobiotics-degrading activities
2023: Selected oral presentation @ the international conference "7th International Conference on Microbial Diversity - MD2023", Parma (IT), 26-28 September 2023. Presentation: Environmental pollution drives adaptation in gut microbiome functions of highly exposed individuals
2023: Selected oral presentation @ the international conference "13th International Gut Microbiology Symposium 2023", Aberdeen (UK), 12-15 June 2023. Presentation: Linking environmental pollution and gut microbiome in individuals living in highly contaminated settlements
2022: Keynote Speaker @ the Metagenomics and Fermented Foods Symposium organized within the "International Conference "Food & Agriculture Advanced Technology for Sustainable Development 2022 - FAATSD2022", Ho-Chi-Minh City (Vietnam), 24 November 2022. Presentation: Exploiting the microbiome of traditional fermented foods to improve food quality and human health
2022: Keynote Speaker @ the "2nd International Conference on Advanced Technology and Sustainable Development 2022 - ICATSD 2022", Ho-Chi-Minh City (Vietnam), 25 November 2022. Presentation: Sustainable diets and gut microbiome interactions for a healthy living
2022: Selected oral presentation @ the international conference “27th International ICFMH Symposium - FoodMicro2022”, Athens (Greece), 28-31 August 2022. Presentation: Metagenomics unravel the microbial heritage of Italian typical fermented foods
2022: Selected oral presentation @ the international conference “International Union of Microbiological Societies (IUMS) Congress 2022”, Rotterdam (The Netherlands), 20-22 July 2022. Presentation: Metagenomics highlights strain-level selection occurring in Italian typical fermented foods
2022: Keynote Speaker @ the international conference “5th Austrian Microbiome Initiative (AMICI) Symposium”, Wien (Austria), 13 June 2022. Presentation: Exploiting the microbiome of traditional fermented foods to improve food quality and human health
2022: Invited Speaker @ the international conference “56th European Society for Clinical Investigation (ESCI) Scientific Meeting”, Bari (Italy), 8-10 June 2022. Presentation: Gut microbiome-diet interconnections for a healthy living
2022: Invited Speaker @ the international conference “Microbial Foods 2022”, Hillerød (Denmark), 8-12 May 2022. Presentation: Metagenomics unravel the microbial heritage of Italian typical fermented foods
2022: Invited Speaker @ the National conference “DMed - Salone della Dieta Mediterranea”, Paestum (Italy), 26 May 2022. Presentation: Microbiome and Mediterranean diet
2021: Selected oral presentation @ the "6th International Conference on Microbial Diversity 2021”, on-line due to COVID-19, 14-15 December 2021. Presentation: Gut microbiome and allergy development in early life.
2021: Invited Speaker @ the National Conference "Dieta Mediterranea: la cultura della salute dalla tradizione al futuro", Portici (NA), Italy, 4 November 2021. Presentation: The gut microbiome and the Mediterranean diet.
2021: Selected oral presentation @ the "Microbiome Virtual International Forum", on-line due to COVID-19, 14 September 2021. Presentation: Newly Explored Faecalibacterium Diversity Is Connected to Age, Lifestyle, Geography, and Disease.
2021: Invited Speaker @ the "XXVIII National Congress of Phytotherapy", on-line due to COVID-19, 21-23 May 2021. Presentation: Modulation of the gut microbiome by a diet rich in vegetable products.
2020: Keynote Speaker @ the International Conference "Third Symposium on Fruit and Vegetable Processing", on-line due to COVID-19, 24-25 November 2020. Presentation: Metagenomics approaches to explore the microbial community of Fruit & Vegetables;
2019: Invited Speaker @ the International Conference "MIBIOC – The way of the microbiota in cancer”, Milan (Italy), 21-22 Nov. 2019. Presentation: Gut microbiome and diet inter-connections for a healthy living;
2019: Invited Speaker @ the International Course organized by Campden BRI "Advances in food safety and integrity: do those genes suit you?", Chipping Campden (UK), 12 Nov. 2019. Presentation: Metagenomics: future trends;
2019: Selected oral presentation @ the International Conference "5th International Conference on Microbial Diversity 2019”, Catania (Italy), 25-27 Sept. 2019. Presentation: Mediterranean-style dietary intervention promotes the production of beneficial metabolites and modulates gut microbiome in healthy obese subjects;
2019: Invited Speaker @ the International Conference “IAFP’s (International Association for Food Protection) European Symposium on Food Safety”, Nantes (France), 24-26 Apr. 2019. Presentation: Current Research in Food Microbiomes and How Industry Can Benefit;
2018: Selected oral presentation @ the XXXIX Congresso Nazionale della Società Italiana di Nutrizione Umana (SINU2018), Napoli (Italy), 19-21 Nov. 2018. Presentation: Modulation of gut microbiota through a Mediterranean diet intervention in obese subjects;
2018: Invited Speaker @ the International Conference “BioKorea2018”, within the “Korea-Italy Bilateral Workshop on Human Microbiome”, organized by the Italian Embassy in South-Korea, Seoul, 10 May 2018. Presentation: Modulation of the gut microbiome through diet for a healthy living;
2018: Invited Speaker @ the National Conference “Top-Ten in Gastroenterologia”, Bergamo (Italy), 2-3 March 2018. Presentation: Microbiota and nutrition;
2017: Invited Speaker @ the International Conference “4th International Conference of JPI HDHL 2017”, Brussels (Belgium), 1 Dec. 2017. Presentation: The DINAMIC project;
2017: Selected oral presentation @ the International Conference “4th International Conference on Microbial Diversity 2017”, Bari (Italy), 24-26 Oct. 2017. Presentation: Dissection of gut metagenomes highlights a diet-induced selection of specific Prevotella copri strains;
2017: Invited Speaker @ the International Conference “IAFP’s (International Association for Food Protection) European Symposium on Food Safety”, Brussels (Belgium), 29-31 March 2017. Presentation: High-resolution exploration of microbial consortia in food processing environments.
2014: Selected oral presentation @ the International Conference “XXIV Int. ICFMH Symposium FoodMicro2014”, Nantes (France) 1-4 Sept. 2014. Presentation: RNA-based study of the microbiome of an Italian pasta-filata cheese during manufacturing and ripening;
2012: Selected oral presentation @ the National Conference “ALTrIformaggi – Autenticità, Legislazione, Tradizione, innovazione per la valorizzazione delle produzioni casearie”, Avellino (Italy), 29-30 Nov. 2012. Presentation: Microbiota in Water-Buffalo Mozzarella-cheese production.