Francesca De Filippis

ORCID: 0000-0002-3474-2884
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About
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Research Areas
  • Gut microbiota and health
  • Probiotics and Fermented Foods
  • Diet and metabolism studies
  • Identification and Quantification in Food
  • Meat and Animal Product Quality
  • Nutritional Studies and Diet
  • Fermentation and Sensory Analysis
  • Genomics and Phylogenetic Studies
  • Food Safety and Hygiene
  • Listeria monocytogenes in Food Safety
  • Mycorrhizal Fungi and Plant Interactions
  • Microbial Community Ecology and Physiology
  • Asthma and respiratory diseases
  • Advanced Chemical Sensor Technologies
  • Protein Hydrolysis and Bioactive Peptides
  • Clostridium difficile and Clostridium perfringens research
  • Food composition and properties
  • Milk Quality and Mastitis in Dairy Cows
  • Polyamine Metabolism and Applications
  • MicroRNA in disease regulation
  • Soil Carbon and Nitrogen Dynamics
  • Insect Utilization and Effects
  • Metabolomics and Mass Spectrometry Studies
  • Oral microbiology and periodontitis research
  • Salivary Gland Disorders and Functions

University of Naples Federico II
2016-2025

Industrial University of Ho Chi Minh City
2025

Sapienza University of Rome
2011-2024

Federico II University Hospital
2017-2024

University of Palermo
2024

Policlinico Umberto I
2023-2024

Université Hassan II Mohammedia
2021

Ospedale Regina Apostolorum
2020

Roma Tre University
2013

University of Bologna
2007

Mozzarella (M), Grana Padano (GP) and Parmigiano Reggiano (PR) are three of the most important traditional Italian cheeses. In cheese manufactures initial fermentation is carried out by adding natural whey cultures (NWCs) according to a back-slopping procedure. this study, NWCs corresponding curds from M, GP PR were analyzed culture-independent pyrosequencing amplified V1-V3 regions 16S rRNA gene, in order provide insights into microbiota involved curd acidification. Moreover,...

10.1371/journal.pone.0089680 article EN cc-by PLoS ONE 2014-02-24

<h3>Objectives</h3> Habitual diet plays a major role in shaping the composition of gut microbiota, and also determines repertoire microbial metabolites that can influence host. The typical Western corresponds to an omnivore; however, Mediterranean (MD), common culture, is date nutritionally recommended dietary pattern includes high-level consumption cereals, fruit, vegetables legumes. To investigate potential benefits MD this cross-sectional survey, we assessed microbiota metabolome cohort...

10.1136/gutjnl-2015-309957 article EN Gut 2015-09-28

Objectives This study aimed to explore the effects of an isocaloric Mediterranean diet (MD) intervention on metabolic health, gut microbiome and systemic metabolome in subjects with lifestyle risk factors for disease. Design Eighty-two healthy overweight obese a habitually low intake fruit vegetables sedentary participated parallel 8-week randomised controlled trial. Forty-three participants consumed MD tailored their habitual energy intakes (MedD), 39 maintained regular diets (ConD)....

10.1136/gutjnl-2019-320438 article EN cc-by-nc Gut 2020-02-19

Prevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. In cross-continent meta-analysis exploiting >6,500 metagenomes, we obtained >1,000 genomes explored the genetic population structure of P. copri. encompasses four distinct clades (>10% inter-clade divergence) propose constitute complex, all were confirmed by isolate sequencing. These are nearly ubiquitous co-present in non-Westernized populations. Genomic analysis showed...

10.1016/j.chom.2019.08.018 article EN cc-by Cell Host & Microbe 2019-10-10
David Danko Daniela Bezdan Evan E. Afshin Sofia Ahsanuddin Chandrima Bhattacharya and 95 more Daniel Butler Kern Rei Chng Daisy Donnellan Jochen Hecht Katelyn Jackson Katerina Kuchin Mikhail Karasikov Abigail Lyons Lauren Mak Dmitry Meleshko Harun Mustafa Beth Mutai Russell Y. Neches Amanda Hui Qi Ng Olga Nikolayeva Tatyana Nikolayeva Eileen Png Krista Ryon Jorge L. Sánchez Heba Shaaban Maria A. Sierra Dominique Thomas Ben Young Omar O. Abudayyeh Josue Alicea Malay Bhattacharyya Ran Blekhman Eduardo Castro‐Nallar A Cañas Aspassia D. Chatziefthimiou Robert W. Crawford Francesca De Filippis Youping Deng Christelle Desnues Emmanuel Dias‐Neto Marius Dybwad Eran Elhaik Danilo Ercolini Alina Frolova Dennis Gankin Jonathan S. Gootenberg Alexandra B. Graf David C. Green Iman Hajirasouliha Jaden J. A. Hastings Mark Hernandez Gregorio Iraola Soojin Jang André Kahles Frank J. Kelly Kaymisha Knights Nikos C. Kyrpides Paweł P. Łabaj Patrick K. H. Lee Marcus H. Y. Leung Per O. Ljungdahl Gabriella Mason-Buck Ken McGrath Cem Meydan Emmanuel F. Mongodin Milton Ozório Moraes Niranjan Nagarajan Marina Nieto‐Caballero Houtan Noushmehr Manuela Oliveira Stephan Ossowski Olayinka Osuolale Orhan Özcan David Páez-Espino Nicolás Rascovan Hugues Richard Gunnar Rätsch Lynn M. Schriml Torsten Semmler Uğur Sezerman Leming Shi Tieliu Shi Rania Siam Le Huu Song Haruo Suzuki Denise Syndercombe Court Scott Tighe Xinzhao Tong Klas I. Udekwu Juan A. Ugalde Brandon Valentine Dimitar Vassilev Elena Vayndorf Thirumalaisamy P. Velavan Jun Wu María Mercedes Zambrano Jifeng Zhu Sibo Zhu Christopher E. Mason Natasha Abdullah

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog urban microbial ecosystem. This provides an annotated, geospatial profile strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, 838,532 CRISPR arrays not found reference databases. identified 4,246 known species microorganisms consistent...

10.1016/j.cell.2021.05.002 article EN cc-by Cell 2021-05-26

The larva of the black soldier fly (Hermetia illucens) has emerged as an efficient system for bioconversion organic waste. Although many research efforts are devoted to optimization rearing conditions increase yield process, microbiological aspects related this insect still neglected. Here, we describe microbiota midgut H. illucens larvae, showing effect different diets and regions in shaping microbial load diversity. bacterial communities residing three parts midgut, characterized by...

10.1128/aem.01864-18 article EN Applied and Environmental Microbiology 2018-11-29

Abstract Traditional cheeses harbour complex microbial consortia that play an important role in shaping typical sensorial properties. However, the metabolism is considered difficult to control. Microbial community succession and related gene expression were analysed during ripening of a traditional Italian cheese, identifying parameters could be modified accelerate ripening. Afterwards, we modulated conditions observed consistent changes structure function. We provide concrete evidence...

10.1038/srep21871 article EN cc-by Scientific Reports 2016-02-25
Kern Rei Chng Chenhao Li Denis Bertrand Amanda Hui Qi Ng Junmei Samantha Kwah and 95 more Hwee Meng Low Chengxuan Tong Maanasa Natrajan Michael Hongjie Zhang Licheng Xu Karrie Kwan Ki Ko Eliza Xin Pei Ho Tamar V. Av‐Shalom Jeanette Teo Chiea Chuen Khor David Danko Daniela Bezdan Ebrahim Afshinnekoo Sofia Ahsanuddin Chandrima Bhattacharya Daniel Butler Kern Rei Chng Francesca De Filippis Jochen Hecht André Kahles Mikhail Karasikov Nikos C. Kyrpides Marcus H. Y. Leung Dmitry Meleshko Harun Mustafa Beth Mutai Russell Y. Neches Amanda Hui Qi Ng Marina Nieto‐Caballero Olga Nikolayeva Tatyana Nikolayeva Eileen Png Jorge L. Sánchez Heba Shaaban Maria A. Sierra Xinzhao Tong Ben Young Josue Alicea Malay Bhattacharyya Ran Blekhman Eduardo Castro‐Nallar A Cañas Aspassia D. Chatziefthimiou Robert W. Crawford Youping Deng Christelle Desnues Emmanuel Dias‐Neto Daisy Donnellan Marius Dybwad Eran Elhaik Danilo Ercolini Alina Frolova Alexandra B. Graf David C. Green Iman Hajirasouliha Mark Hernandez Gregorio Iraola Soojin Jang Angela Jones Frank J. Kelly Kaymisha Knights Paweł P. Łabaj Patrick K. H. Lee Levy Shawn Per O. Ljungdahl Abigail Lyons Gabriella Mason-Buck Ken McGrath Emmanuel F. Mongodin Milton Ozório Moraes Niranjan Nagarajan Houtan Noushmehr Manuela Oliveira Stephan Ossowski Olayinka Osuolale Orhan Özcan David Páez-Espino Nicolás Rascovan Hugues Richard Gunnar Rätsch Lynn M. Schriml Torsten Semmler Uğur Sezerman Leming Shi Le Huu Song Haruo Suzuki Denise Syndercombe Court Dominique Thomas Scott Tighe Klas I. Udekwu Juan A. Ugalde Brandon Valentine Dimitar Vassilev Elena Vayndorf Thirumalaisamy P. Velavan

Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report first extensive genomic characterization microbiomes, pathogens antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up 1.5 years apart) 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches genes characterized by biofilm-forming human-microbiome-influenced...

10.1038/s41591-020-0894-4 article EN cc-by Nature Medicine 2020-06-01

Abstract Gut microbes programme their metabolism to suit intestinal conditions and convert dietary components into a panel of small molecules that ultimately affect host physiology. To unveil what is behind the effects key on microbial functions way they modulate host–microbe interaction, we used for first time multi-omic approach goes mere gut phylogenetic composition provides an overall picture functional repertoire in 27 fecal samples from omnivorous, vegan vegetarian volunteers. Based...

10.1038/s41598-020-61192-y article EN cc-by Scientific Reports 2020-03-06

Abstract Understanding the functional potential of gut microbiome is primary importance for design innovative strategies allergy treatment and prevention. Here we report features 90 children affected by food (FA) or respiratory (RA) allergies 30 age-matched, healthy controls (CT). We identify specific microbial signatures in allergic children, such as higher abundance Ruminococcus gnavus Faecalibacterium prausnitzii , a depletion Bifidobacterium longum Bacteroides dorei B. vulgatu s...

10.1038/s41467-021-26266-z article EN cc-by Nature Communications 2021-10-13

Microbial growth on meat to unacceptable levels contributes significantly change structure, color and flavor cause spoilage. The types of microorganisms initially present in depend several factors multiple sources contamination can be identified. aims this study were evaluate the microbial diversity beefsteaks before after aerobic storage at 4°C investigate by examining microbiota carcasses wherefrom steaks originated processing environment where beef was handled. Carcass, environmental...

10.1371/journal.pone.0070222 article EN cc-by PLoS ONE 2013-07-25

The bacterial ecology during rye and wheat sourdough preparation was described by 16S rRNA gene pyrosequencing. Viable plate counts of presumptive lactic acid bacteria, the ratio between bacteria yeasts, rate acidification, a permutation analysis based on biochemical microbial features, number operational taxonomic units (OTUs), diversity indices all together demonstrated maturity sourdoughs 5 to 7 days propagation. Flours were mainly contaminated metabolically active genera (Acinetobacter,...

10.1128/aem.02955-13 article EN Applied and Environmental Microbiology 2013-10-05

Intermediates of production two batches traditional mozzarella cheese were analyzed by culture-independent pyrosequencing. The quantitative distribution taxa within the samples suggested that thermophilic lactic acid bacteria from natural starter mainly responsible for fermentation, while microorganisms found in raw milk did not develop during fermentation.

10.1128/aem.02218-12 article EN Applied and Environmental Microbiology 2012-09-01

ABSTRACT Microbial contamination in food processing plants can play a fundamental role quality and safety. The aims of this study were to learn more about the possible influence meat environment on initial fresh investigate differences between small-scale retail distribution (SD) large-scale (LD) facilities. Samples collected from butcheries ( n = 20), including LD 10) SD facilities, over two sampling campaigns. included beef pork cuts swab samples knife, chopping board, butcher's hand....

10.1128/aem.00793-16 article EN Applied and Environmental Microbiology 2016-04-30
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