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Mediterranean diet intervention in overweight and obese subjects lowers plasma cholesterol and causes changes in the gut microbiome and metabolome independently of energy intake.

Meslier V, Laiola M, Roager HM, De Filippis F, Roume H, Quinquis B, Giacco R, Mennella I, Ferracane R, Pons N, Pasolli E, Rivellese A, Dragsted LO, Vitaglione P, Ehrlich SD, Ercolini D.

Gut. 2020 Feb 19. pii: gutjnl-2019-320438. doi: 10.1136/gutjnl-2019-320438. [Epub ahead of print]


The fate of cigarette butts in different environments: Decay rate, chemical changes and ecotoxicity revealed by a 5-years decomposition experiment.

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.

Environ Pollut. 2020 Jan 31;261:114108. doi: 10.1016/j.envpol.2020.114108. [Epub ahead of print]


Editorial: interventions in infantile colic - can efficacy be attributed to treatment or to time? Authors' reply.

Nocerino R, De Filippis F, Cecere G, Marino A, Micillo M, Di Scala C, de Caro C, Calignano A, Bruno C, Paparo L, Iannicelli AM, Cosenza L, Maddalena Y, Della Gatta G, Coppola S, Carucci L, Ercolini D, Berni Canani R.

Aliment Pharmacol Ther. 2020 Feb;51(3):398-399. doi: 10.1111/apt.15627. No abstract available.


Attenuated Lactococcus lactis and Surface Bacteria as Tools for Conditioning the Microbiota and Driving the Ripening of Semisoft Caciotta Cheese.

Calasso M, Minervini F, De Filippis F, Ercolini D, De Angelis M, Gobbetti M.

Appl Environ Microbiol. 2020 Feb 18;86(5). pii: e02165-19. doi: 10.1128/AEM.02165-19. Print 2020 Feb 18.


The therapeutic efficacy of Bifidobacterium animalis subsp. lactis BB-12® in infant colic: A randomised, double blind, placebo-controlled trial.

Nocerino R, De Filippis F, Cecere G, Marino A, Micillo M, Di Scala C, de Caro C, Calignano A, Bruno C, Paparo L, Iannicelli AM, Cosenza L, Maddalena Y, Della Gatta G, Coppola S, Carucci L, Ercolini D, Berni Canani R.

Aliment Pharmacol Ther. 2020 Jan;51(1):110-120. doi: 10.1111/apt.15561. Epub 2019 Dec 3.


The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations.

Tett A, Huang KD, 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, Rattei T, Boulund F, Engstrand L, Zink A, Collado MC, Littman DR, Eibach D, Ercolini D, Rota-Stabelli O, Huttenhower C, Maixner F, Segata N.

Cell Host Microbe. 2019 Nov 13;26(5):666-679.e7. doi: 10.1016/j.chom.2019.08.018. Epub 2019 Oct 10.


Metabolic Profiling and Cold-Starvation Stress Response of Oxygen-Tolerant Lactobacillus gasseri Strains Cultured in Batch Bioreactor.

Maresca D, De Filippis F, Robertiello A, Mauriello G.

Microorganisms. 2019 Jul 15;7(7). pii: E200. doi: 10.3390/microorganisms7070200.


Advancing integration of data on food microbiome studies: FoodMicrobionet 3.1, a major upgrade of the FoodMicrobionet database.

Parente E, De Filippis F, Ercolini D, Ricciardi A, Zotta T.

Int J Food Microbiol. 2019 Sep 16;305:108249. doi: 10.1016/j.ijfoodmicro.2019.108249. Epub 2019 Jun 11.


Coffee prevents fatty liver disease induced by a high-fat diet by modulating pathways of the gut-liver axis.

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.

J Nutr Sci. 2019 Apr 22;8:e15. doi: 10.1017/jns.2019.10. eCollection 2019.


Influence of microbial communities on the chemical and sensory features of Falanghina sweet passito wines.

De Filippis F, Aponte M, Piombino P, Lisanti MT, Moio L, Ercolini D, Blaiotta G.

Food Res Int. 2019 Jun;120:740-747. doi: 10.1016/j.foodres.2018.11.033. Epub 2018 Nov 19.


Altered gut microbiota and endocannabinoid system tone in vitamin D deficiency-mediated chronic pain.

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.

Brain Behav Immun. 2019 Apr 3. pii: S0889-1591(18)31247-9. doi: 10.1016/j.bbi.2019.04.006. [Epub ahead of print]


Distinct Genetic and Functional Traits of Human Intestinal Prevotella copri Strains Are Associated with Different Habitual Diets.

De Filippis F, Pasolli E, Tett A, Tarallo S, Naccarati A, De Angelis M, Neviani E, Cocolin L, Gobbetti M, Segata N, Ercolini D.

Cell Host Microbe. 2019 Mar 13;25(3):444-453.e3. doi: 10.1016/j.chom.2019.01.004. Epub 2019 Feb 21.


Large-scale mapping of microbial diversity in artisanal Brazilian cheeses.

Kamimura BA, De Filippis F, Sant'Ana AS, Ercolini D.

Food Microbiol. 2019 Jun;80:40-49. doi: 10.1016/ Epub 2018 Dec 26.


Dynamics of bacterial communities and interaction networks in thawed fish fillets during chilled storage in air.

Zotta T, Parente E, Ianniello RG, De Filippis F, Ricciardi A.

Int J Food Microbiol. 2019 Mar 16;293:102-113. doi: 10.1016/j.ijfoodmicro.2019.01.008. Epub 2019 Jan 16.


Gut microbiota signatures in cystic fibrosis: Loss of host CFTR function drives the microbiota enterophenotype.

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 EV, Dallapiccola B, Lucidi V, Miccheli A, Putignani L.

PLoS One. 2018 Dec 6;13(12):e0208171. doi: 10.1371/journal.pone.0208171. eCollection 2018.


The Intestinal Microbiota of Hermetia illucens Larvae Is Affected by Diet and Shows a Diverse Composition in the Different Midgut Regions.

Bruno D, Bonelli M, De Filippis F, Di Lelio I, Tettamanti G, Casartelli M, Ercolini D, Caccia S.

Appl Environ Microbiol. 2019 Jan 9;85(2). pii: e01864-18. doi: 10.1128/AEM.01864-18. Print 2019 Jan 15.


Strain-Level Diversity Analysis of Pseudomonas fragi after In Situ Pangenome Reconstruction Shows Distinctive Spoilage-Associated Metabolic Traits Clearly Selected by Different Storage Conditions.

De Filippis F, La Storia A, Villani F, Ercolini D.

Appl Environ Microbiol. 2018 Dec 13;85(1). pii: e02212-18. doi: 10.1128/AEM.02212-18. Print 2019 Jan 1.


Gut microbiota composition and butyrate production in children affected by non-IgE-mediated cow's milk allergy.

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 JA, Ercolini D.

Sci Rep. 2018 Aug 21;8(1):12500. doi: 10.1038/s41598-018-30428-3.


Profiling white wine seed vinegar bacterial diversity through viable counting, metagenomic sequencing and PCR-DGGE.

Milanović V, Osimani A, Garofalo C, De Filippis F, Ercolini D, Cardinali F, Taccari M, Aquilanti L, Clementi F.

Int J Food Microbiol. 2018 Dec 2;286:66-74. doi: 10.1016/j.ijfoodmicro.2018.07.022. Epub 2018 Jul 20.


Dietary Interventions to Modulate the Gut Microbiome-How Far Away Are We From Precision Medicine.

De Filippis F, Vitaglione P, Cuomo R, Berni Canani R, Ercolini D.

Inflamm Bowel Dis. 2018 Sep 15;24(10):2142-2154. doi: 10.1093/ibd/izy080. Review.


Revealing the microbiota of marketed edible insects through PCR-DGGE, metagenomic sequencing and real-time PCR.

Osimani A, Milanović V, Garofalo C, Cardinali F, Roncolini A, Sabbatini R, De Filippis F, Ercolini D, Gabucci C, Petruzzelli A, Tonucci F, Clementi F, Aquilanti L.

Int J Food Microbiol. 2018 Jul 2;276:54-62. doi: 10.1016/j.ijfoodmicro.2018.04.013. Epub 2018 Apr 11.


Structure of association networks in food bacterial communities.

Parente E, Zotta T, Faust K, De Filippis F, Ercolini D.

Food Microbiol. 2018 Aug;73:49-60. doi: 10.1016/ Epub 2017 Dec 22.


Different temperatures select distinctive acetic acid bacteria species and promotes organic acids production during Kombucha tea fermentation.

De Filippis F, Troise AD, Vitaglione P, Ercolini D.

Food Microbiol. 2018 Aug;73:11-16. doi: 10.1016/ Epub 2018 Jan 9.


Impact of Lactobacillus curvatus 54M16 on microbiota composition and growth of Listeria monocytogenes in fermented sausages.

Giello M, La Storia A, De Filippis F, Ercolini D, Villani F.

Food Microbiol. 2018 Jun;72:1-15. doi: 10.1016/ Epub 2017 Nov 8.


Recent Past, Present, and Future of the Food Microbiome.

De Filippis F, Parente E, Ercolini D.

Annu Rev Food Sci Technol. 2018 Mar 25;9:589-608. doi: 10.1146/annurev-food-030117-012312. Epub 2018 Jan 18. Review.


Different Lactobacillus populations dominate in "Chorizo de León" manufacturing performed in different production plants.

Quijada NM, De Filippis F, Sanz JJ, García-Fernández MDC, Rodríguez-Lázaro D, Ercolini D, Hernández M.

Food Microbiol. 2018 Apr;70:94-102. doi: 10.1016/ Epub 2017 Sep 14.


A comparison of bioinformatic approaches for 16S rRNA gene profiling of food bacterial microbiota.

De Filippis F, Parente E, Zotta T, Ercolini D.

Int J Food Microbiol. 2018 Jan 16;265:9-17. doi: 10.1016/j.ijfoodmicro.2017.10.028. Epub 2017 Oct 27.


Antibiotic-induced microbiota perturbation causes gut endocannabinoidome changes, hippocampal neuroglial reorganization and depression in mice.

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 FA, Piscitelli F, Ercolini D, de Novellis V, Di Marzo V, Cuomo R, Maione S.

Brain Behav Immun. 2018 Jan;67:230-245. doi: 10.1016/j.bbi.2017.09.001. Epub 2017 Sep 7.


Metabolic gene-targeted monitoring of non-starter lactic acid bacteria during cheese ripening.

Levante A, De Filippis F, La Storia A, Gatti M, Neviani E, Ercolini D, Lazzi C.

Int J Food Microbiol. 2017 Sep 18;257:276-284. doi: 10.1016/j.ijfoodmicro.2017.07.002. Epub 2017 Jul 6.


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.

Berni Canani R, De Filippis F, Nocerino R, Laiola M, Paparo L, Calignano A, De Caro C, Coretti L, Chiariotti L, Gilbert JA, Ercolini D.

Appl Environ Microbiol. 2017 Sep 15;83(19). pii: e01206-17. doi: 10.1128/AEM.01206-17. Print 2017 Oct 1.


Different Amplicon Targets for Sequencing-Based Studies of Fungal Diversity.

De Filippis F, Laiola M, Blaiotta G, Ercolini D.

Appl Environ Microbiol. 2017 Aug 17;83(17). pii: e00905-17. doi: 10.1128/AEM.00905-17. Print 2017 Sep 1.


Draft Genome Sequences of the Aerobic Strains Lactobacillus gasseri AL3 and AL5.

Maresca D, De Filippis F, Tytgat HLP, de Vos WM, Mauriello G.

Genome Announc. 2017 May 4;5(18). pii: e00213-17. doi: 10.1128/genomeA.00213-17.


Monitoring the mycobiota during Greco di Tufo and Aglianico wine fermentation by 18S rRNA gene sequencing.

De Filippis F, La Storia A, Blaiotta G.

Food Microbiol. 2017 May;63:117-122. doi: 10.1016/ Epub 2016 Nov 17.


Unusual sub-genus associations of faecal Prevotella and Bacteroides with specific dietary patterns.

De Filippis F, Pellegrini N, Laghi L, Gobbetti M, Ercolini D.

Microbiome. 2016 Oct 21;4(1):57.


Metagenomics insights into food fermentations.

De Filippis F, Parente E, Ercolini D.

Microb Biotechnol. 2017 Jan;10(1):91-102. doi: 10.1111/1751-7915.12421. Epub 2016 Oct 6. Review.


Polymorphism of the phosphoserine phosphatase gene in Streptococcus thermophilus and its potential use for typing and monitoring of population diversity.

Ricciardi A, De Filippis F, Zotta T, Facchiano A, Ercolini D, Parente E.

Int J Food Microbiol. 2016 Nov 7;236:138-47. doi: 10.1016/j.ijfoodmicro.2016.07.031. Epub 2016 Jul 27.


Overlap of Spoilage-Associated Microbiota between Meat and the Meat Processing Environment in Small-Scale and Large-Scale Retail Distributions.

Stellato G, La Storia A, De Filippis F, Borriello G, Villani F, Ercolini D.

Appl Environ Microbiol. 2016 Jun 13;82(13):4045-54. doi: 10.1128/AEM.00793-16. Print 2016 Jul 1.


Microbiota of an Italian Grana-Like Cheese during Manufacture and Ripening, Unraveled by 16S rRNA-Based Approaches.

Alessandria V, Ferrocino I, De Filippis F, Fontana M, Rantsiou K, Ercolini D, Cocolin L.

Appl Environ Microbiol. 2016 Jun 13;82(13):3988-3995. doi: 10.1128/AEM.00999-16. Print 2016 Jul 1.


Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate.

De Filippis F, Genovese A, Ferranti P, Gilbert JA, Ercolini D.

Sci Rep. 2016 Feb 25;6:21871. doi: 10.1038/srep21871.


FoodMicrobionet: A database for the visualisation and exploration of food bacterial communities based on network analysis.

Parente E, Cocolin L, De Filippis F, Zotta T, Ferrocino I, O'Sullivan O, Neviani E, De Angelis M, Cotter PD, Ercolini D.

Int J Food Microbiol. 2016 Feb 16;219:28-37. doi: 10.1016/j.ijfoodmicro.2015.12.001. Epub 2015 Dec 9.


From an imbalance to a new imbalance: Italian-style gluten-free diet alters the salivary microbiota and metabolome of African celiac children.

Ercolini D, Francavilla R, Vannini L, De Filippis F, Capriati T, Di Cagno R, Iacono G, De Angelis M, Gobbetti M.

Sci Rep. 2015 Dec 18;5:18571. doi: 10.1038/srep18571.


Microbial community dynamics in thermophilic undefined milk starter cultures.

Parente E, Guidone A, Matera A, De Filippis F, Mauriello G, Ricciardi A.

Int J Food Microbiol. 2016 Jan 18;217:59-67. doi: 10.1016/j.ijfoodmicro.2015.10.014. Epub 2015 Oct 24.


High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome.

De Filippis F, Pellegrini N, Vannini L, Jeffery IB, La Storia A, Laghi L, Serrazanetti DI, Di Cagno R, Ferrocino I, Lazzi C, Turroni S, Cocolin L, Brigidi P, Neviani E, Gobbetti M, O'Toole PW, Ercolini D.

Gut. 2016 Nov;65(11):1812-1821. doi: 10.1136/gutjnl-2015-309957. Epub 2015 Sep 28.


The microbiota of high-moisture mozzarella cheese produced with different acidification methods.

Guidone A, Zotta T, Matera A, Ricciardi A, De Filippis F, Ercolini D, Parente E.

Int J Food Microbiol. 2016 Jan 4;216:9-17. doi: 10.1016/j.ijfoodmicro.2015.09.002. Epub 2015 Sep 9.


Coexistence of Lactic Acid Bacteria and Potential Spoilage Microbiota in a Dairy Processing Environment.

Stellato G, De Filippis F, La Storia A, Ercolini D.

Appl Environ Microbiol. 2015 Nov;81(22):7893-904. doi: 10.1128/AEM.02294-15. Epub 2015 Sep 4.


Bacteria and yeast microbiota in milk kefir grains from different Italian regions.

Garofalo C, Osimani A, Milanović V, Aquilanti L, De Filippis F, Stellato G, Di Mauro S, Turchetti B, Buzzini P, Ercolini D, Clementi F.

Food Microbiol. 2015 Aug;49:123-33. doi: 10.1016/ Epub 2015 Feb 7.


Organic cultivation of Triticum turgidum subsp. durum is reflected in the flour-sourdough fermentation-bread axis.

Rizzello CG, Cavoski I, Turk J, Ercolini D, Nionelli L, Pontonio E, De Angelis M, De Filippis F, Gobbetti M, Di Cagno R.

Appl Environ Microbiol. 2015 May 1;81(9):3192-204. doi: 10.1128/AEM.04161-14. Epub 2015 Feb 27.


The same microbiota and a potentially discriminant metabolome in the saliva of omnivore, ovo-lacto-vegetarian and Vegan individuals.

De Filippis F, Vannini L, La Storia A, Laghi L, Piombino P, Stellato G, Serrazanetti DI, Gozzi G, Turroni S, Ferrocino I, Lazzi C, Di Cagno R, Gobbetti M, Ercolini D.

PLoS One. 2014 Nov 5;9(11):e112373. doi: 10.1371/journal.pone.0112373. eCollection 2014.


rRNA-based monitoring of the microbiota involved in Fontina PDO cheese production in relation to different stages of cow lactation.

Dolci P, De Filippis F, La Storia A, Ercolini D, Cocolin L.

Int J Food Microbiol. 2014 Aug 18;185:127-35. doi: 10.1016/j.ijfoodmicro.2014.05.021. Epub 2014 Jun 2.


Salivary microbiota and metabolome associated with celiac disease.

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 DI, De Angelis M, Gobbetti M.

Appl Environ Microbiol. 2014 Jun;80(11):3416-25. doi: 10.1128/AEM.00362-14. Epub 2014 Mar 21.

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