Filippo Biscarini

Filippo Biscarini
Italian National Research Council | CNR · Institute of Agricultural Biology and Biotechnology IBBA

PhD - University of Wageningen

About

190
Publications
40,339
Reads
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1,736
Citations
Introduction
My research activities span from plant and animal breeding & genetics, to bioinformatics and biostatistics applications in plant & animal science and human medicine. I worked for the breeding industry, for universities and research centres in many places: Italy, Ireland, Canada, The Netherlands, Germany, Spain, The United Kingdom, Belgium. I am now Senior Scientist at CNR, where I rejoined my research group after a 2-yr secondment at the Data Analysis Team of the ERC (European Research Council).
Additional affiliations
December 2018 - present
European Research Council
Position
  • Seconded National Expert
Description
  • Seconded National Expert in the Data Analysis and Call Coordination Unit of the ERCEA (ERC Executive Agency). Data Analysis and Tool Development (software) to assist scientific research proposal Call Coordination and Project monitoring.
November 2018 - present
Italian National Research Council
Position
  • Senior Researcher
Description
  • Bioinformatics and biostatistics applied to plant and animal breeding and genetics and to human medicine
April 2017 - March 2018
Cardiff University
Position
  • Researcher
Description
  • Analysis of 'omics data (RNAsequencing, small RNA, proteomics, metabolomics, metagenomics) from patients and healthy controls. Statistical counselling and guidance to staff and students.

Publications

Publications (190)
Article
Full-text available
Background: In this study we carried out a genome-wide association analysis for plant and grain morphology and root architecture in a unique panel of temperate rice accessions adapted to European pedo-climatic conditions. This is the first study to assess the association of selected phenotypic traits to specific genomic regions in the narrow genet...
Article
Full-text available
Background Noise (errors) in scientific data is endemic and may have a detrimental effect on statistical analyses and experimental results. The effects of noisy data have been assessed in genome-wide association studies for case-control experiments in human medicine. Little is known, however, on the impact of noisy data on genomic predictions, a wi...
Article
Full-text available
Background Highly polygenic traits such as fruit weight, sugar content and acidity strongly influence the agroeconomic value of peach varieties. Genomic Selection (GS) can accelerate peach yield and quality gain if predictions show higher levels of accuracy compared to phenotypic selection. The available IPSC 9K SNP array V1 allows standardized and...
Article
Full-text available
Graves' Disease (GD) is an autoimmune condition in which thyroid-stimulating antibodies (TRAB) mimic thyroid-stimulating hormone function causing hyperthyroidism. 5% of GD patients develop inflammatory Graves' orbitopathy (GO) characterized by proptosis and attendant sight problems. A major challenge is to identify which GD patients are most likely...
Article
Full-text available
Direct measurements of methane (CH4) from individual animals are difficult and expensive. Predictions based on proxies for CH4 are a viable alternative. Most prediction models are based on multiple linear regressions (MLR) and predictor variables that are not routinely available in commercial farms, such as dry matter intake (DMI) and diet composit...
Article
Full-text available
Background The oral ecosystem conditions dental health, and is known to be positively modified by oral hygiene which cannot always be performed between meals, especially outside home. It is therefore important to identify the practices to be adopted to influence the oral environment in an anticariogenic direction. Milk and cheese are considered fun...
Article
Natural whey cultures (NWC) are undefined multiple-strain bacterial starter communities that can be affected by even small changes along the entire dairy chain. We applied a multidisciplinary approach to investigate how the addition of 2 mycotoxin-detoxifying agents [sodium smectite and lignocellulose-based material (B1); leonardite and betaine (B2...
Article
Full-text available
Post-weaning diarrhea (PWD) in pigs has mainly an infectious basis and control strategies are centred on antibiotics added to the diet. Given concerns on the spread of multi-resistant bacteria, it is necessary to develop alternative prophylactic approaches to control PWD in piglets. The most promising alternative strategies are based on substances...
Article
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Early feed restriction of lambs may program animals to achieve reduced feed efficiency traits as a consequence of permanent mitochondrial dysfunction. The hypothesis at the background of the present study is that dietary administration of L-Carnitine (a compound that promotes the activation and transportation of fatty acids into the mitochondria) d...
Article
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The present study evaluated the effects of feed supplemented with two dietary sources of n-3 polyunsaturated fatty acids (PUFAs; fish oil and extruded flaxseed) on the gut microbiota, caecal fermentations, gastrointestinal histology, and histochemistry in rabbits. Fifteen male New Zealand White rabbits were divided into three groups (n = 5/group) a...
Article
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Toll-like receptors (TLR) are crucial components in the initiation of innate immune responses to a variety of pathogens, triggering the production of pro-inflammatory cytokines and type I and II interferons, which are responsible for innate antiviral responses. Among the different TLRs, TLR7 recognizes several single-stranded RNA viruses including...
Article
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Goji berries show health benefits, although the possible mechanisms of action, including compositional changes in the gut microbiome, are still not fully understood. The aim of this study was to evaluate the effect of Goji berry supplementation on microbiota composition and metabolites in the digestive tracts of rabbits. Twenty-eight New Zealand Wh...
Article
Full-text available
The combined impact of common and rare exonic variants in COVID-19 host genetics is currently insufficiently understood. Here, common and rare variants from whole-exome sequencing data of about 4000 SARS-CoV-2-positive individuals were used to define an interpretable machine-learning model for predicting COVID-19 severity. First, variants were conv...
Preprint
Full-text available
The extent to which genomic convergence shapes locally adapted phenotypes in different species remains a fundamental question in evolutionary biology. It would help assessing the relative role of historical contingencies versus determinism in evolution. To bring new insights to this debate we set up a framework which aimed to compare the adaptive t...
Article
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Background Human milk is a vehicle for bioactive compounds and beneficial bacteria which promote the establishment of a healthy gut microbiome of newborns, especially of preterm infants. Pasteurized donor human milk (PDHM) is the second-best option when preterm mother’s own milk is unavailable. Since pasteurization affect the microbiological qualit...
Poster
The bovine rumen epithelium has a crucial role in nutrient uptake and maintenance of ruminal health. This study aimed to explore the role of microRNAs (miRNAs) in the epithelial transcriptome during transition from forage to a high-grain diet and potential modulation by supplementation with a phytogenic feed additive (PYT). Rumen biopsies were coll...
Article
Full-text available
The cows receiving antibiotics for intra-mammary infection (IMI) produce milk that cannot be marketed. This is considered waste milk (WM), and a convenient option for farmers is using it as calf food. However, adding to the risk of selecting resistant bacteria, residual antibiotics might interfere with the gut microbiome development and influence g...
Conference Paper
Full-text available
INTRODUCCIÓN Estudios previos de nuestro grupo han demostrado cómo la restricción de alimento en la fase de lactancia de corderos programa a los animales para mostrar una reducción de la eficiencia alimentaria durante el cebo (Santos et al., 2018), fundamentalmente debido a una disfunción mitocondrial y a un aumento del grado de engrasamiento. La a...
Article
Full-text available
Background Graves’ disease (GD) is an autoimmune condition in which autoantibodies to the thyrotropin receptor (TSHR) cause hyperthyroidism. About 50% of GD patients also have Graves’ orbitopathy (GO), an intractable disease in which expansion of the orbital contents causes diplopia, proptosis and even blindness. Murine models of GD/GO, developed i...
Article
Full-text available
On-farm culture (OFC) systems facilitate pathogen-based mastitis management and can facilitate antimicrobial stewardship on dairy farms. Interpretation of the results, however, may present a challenge for those with limited microbiology experience. Here, we compared results of 3 OFC systems interpreted by trained and untrained observers against res...
Article
Full-text available
Within the GEN-COVID Multicenter Study, biospecimens from more than 1000 SARS-CoV-2 positive individuals have thus far been collected in the GEN-COVID Biobank (GCB). Sample types include whole blood, plasma, serum, leukocytes, and DNA. The GCB links samples to detailed clinical data available in the GEN-COVID Patient Registry (GCPR). It includes ho...
Article
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The microbiota is extremely important for the animal’s health, but, to date, knowledge on the intestinal microbiota of the rabbit is very limited. This study aimed to describe bacterial populations that inhabit the different gastrointestinal compartments of the rabbit: stomach, duodenum, jejunum, ileum, caecum, and colon. Samples of the luminal con...
Article
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The microbiome is now seen as an important resource to understand animal health and welfare in many species. However, there are few studies aiming at identifying the association between fecal microbiome composition and husbandry conditions in sheep. A wide range of stressors associated with management and housing of animals increases the hypothalam...
Article
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Semi-feral local livestock populations, like Maremmana cattle, are the object of renewed interest for the conservation of biological diversity and the preservation and exploitation of unique and potentially relevant genetic material. The aim of this study was to estimate genetic diversity parameters in semi-feral Maremmana cattle using both pedigre...
Article
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Lactating cows are routinely treated at dry-off with antibiotic infusions in each quarter for the cure and prevention of pathogenic intramammary infection, which remains the most common disease in dairy herds. This approach is known as blanket dry-cow therapy, usually effective for the prevention and cure of infections, but has been shown to potent...
Preprint
Full-text available
Within the GEN-COVID Multicenter Study, biospecimens from more than 1,000 SARS-CoV-2-positive individuals have thus far been collected in the GEN-COVID Biobank (GCB). Sample types include whole blood, plasma, serum, leukocytes, and DNA. The GCB links samples to detailed clinical data available in the GEN-COVID Patient Registry (GCPR). It includes h...
Article
Full-text available
Simple Summary: In order to assess sources of variation related to Polverara breed plumage color (black vs. white), we carried out genome-wide analyses to identify the genomic regions involved in this trait. The present work has revealed new candidate genes involved in the phenotypic variability in local chicken populations. These results also cont...
Article
Full-text available
Staphylococcus aureus is recognized worldwide as one of the main contagious mastitis agents in cattle and can express a set of antimicrobial resistance genes and virulence-associated genes that explain the wide range of outcomes of intramammary infections. Staphylococcus aureus strains are heterogeneous: their different resistance and virulence pat...
Article
Full-text available
Streptococcus uberis is an important causative agent for clinical and subclinical mastitis in dairy cattle. The aim of this study was to develop 2 multiplex PCR assays (mPCR) for the simultaneous detection of virulence factors and housekeeping genes for use when investigating the genetic variability and distribution of Strep. uberis virulence facto...
Conference Paper
The use of machine learning (ML) algorithms in predictive modelling of CH 4 emission from heterogeneous across-country datasets containing missing or imputed data-points is rarely reported. The objective was to use ML ensemble algorithms to predict CH 4 output and assess the effects of imputation on within and between-herd prediction accuracies. Da...
Conference Paper
Early lactation is a challenging time for dairy cows, which have to simultaneously cope with milk production and body maintenance. The rapid increase in energy requirements is only partially met by feed and cows enter in a state of negative energy balance (NEB), frequently associated with metabolic diseases and reduced fertility. To counterbalance...
Article
Full-text available
A 1000-cow study across four European countries was undertaken to understand to what extent ruminant microbiomes can be controlled by the host animal and to identify characteristics of the host rumen microbiome axis that determine productivity and methane emissions. A core rumen microbiome, phylogenetically linked and with a preserved hierarchical...
Conference Paper
Full-text available
Post-weaning diarrhoea (PWD) represents the most important threat for the pig industry all over the world with a morbidity over 50% among weaned piglets during outbreaks of the disease. Given the public health concerns about the spread of multi-resistant bacteria due to the use of antibiotics in livestock, it is necessary to develop alternative str...
Conference Paper
At 148 DIM, basal plasma glucose (62.2 vs. 51.6 mg/dL ±3.62, p=.011) and insulin (0.34 vs. 0.13 µg/L ± 0.09, p=.036) concentration were significantly higher in ewes than in goats. After glucose infusion, glucose (p=.06) and insulin (p=.07) concentrations were numerically greatest in ewes. The area under the glucose concentration curve, fractional g...
Conference Paper
In dairy cattle, microbiomes are known to affect milk production, well-being and health of the animals. Within the FARM-INN project, the rumen, milk and hindgut microbiomes of dairy cows will be analysed to better understand their contribution to the efficient production of high-quality milk for direct consumption and transformation into cheese and...
Conference Paper
Most lactating cows are routinely treated in each quarter with antibiotic at drying off. This is defined as the ‘blanket’ approach, and it is considered effective in preventing new infections and curing the existing infections. However, this farming practice can potentially interfere with the milk microbiota balance, as well as promote the selectio...
Conference Paper
THE RANDOMISED PROBIOTIC TRIAL OF INDIGO STUDY (INVESTIGATION OF NOVEL BIOMARKERS AND DEFINITION OF ROLE OF THE MICROBIOME IN GRAVES' ORBITOPATHY) 1Mario Salvi, 1Giuseppe Colucci, 2Giulia Masetti, 1Danila Covelli, 1,2Ilaria Muller, 3Hedda Koehling, 4Iveta Garaiova,4Daryn Michael, 2Lei Zhang, 2Marian Ludgate, 2Julian Marchesi, 5Filippo Biscarini,...
Article
Full-text available
Copy number variants (CNVs) are an important source of genetic variation complementary to single nucleotide polymorphisms (SNPs). Only few studies have been conducted in dogs on CNVs derived from high-density SNP array data, and many canine breeds still remain uncharacterized, e.g., the Braque Français, type Pyrénées breed (BRA). Therefore, in an e...
Article
Full-text available
The evaluation of genetic variability is a useful research tool for the correct management of selection and conservation strategies in dog breeds. In addition to pedigree genealogies, genomic data allow a deeper knowledge of the variability and genetic structure of populations. To date, many dog breeds, such as small regional breeds, still remain u...
Data
Kinship matrices for Braque Français, type Pyrénées dogs. Heatmap of kinship matrices in BRA estimated from pedigree data or from molecular marker data. (PDF)
Data
History of BRA and introduction to Italy. A few elements on the history of the Braque Français type Pyrénées canine breed, and the directional selection practiced in Italy. (PDF)
Article
Full-text available
The rumen microbiome is fundamental for the productivity and health of dairy cattle and diet is known to influence the rumen microbiota composition. In this study, grape-pomace, a natural source of polyphenols, and copper sulfate were provided as feed supplementation in 15 Holstein-Friesian calves, including 5 controls. After 75 days of supplementa...
Data
Metataxonomics pipeline command lines. Specific command lines used in the Qiime bioinformatics pipeline to process 16S rRNA-gene sequencing data. (PDF)
Data
Finishing diets. Ingredients and nutrient composition of the finishing diets fed to the three experimental groups (control, grape pomace and copper supplementation). (PDF)
Data
Custom-formulated concentrate. Ingredients and nutrient composition of the custom-formulated concentrate, which was fed to all calves prior to the feed supplementation experiment. (PDF)
Data
Alpha- and beta-diversity indices. Break out of the calculations involved in the estimation of the alpha- and beta-diversity indices used in this study. (PDF)
Data
Sequencing metrics. Number of 16S rRNA gene sequences retained after successive steps of the bioinformatics processing and filtering: comparison between two quality filtering thresholds (Phred>3, default in the Qiime pipeline; Phred>19, threshold used in this study). (PDF)
Article
Full-text available
Experimental models of hyperthyroid Graves’ disease (GD) and Graves’ orbitopathy (GO) are efficiently developed by genetic immunisation by electroporation with human thyrotropin hormone receptor (hTSHR) A-subunit plasmid in female BALB/c (H-2d) mice. We investigated susceptibility in C57BL/6 J (H-2b) animals to allow studies on disease mechanisms i...
Article
Full-text available
Background: Variation in induced models of autoimmunity has been attributed to the housing environment and its effect on the gut microbiota. In Graves’ disease (GD), autoantibodies to the thyrotropin receptor (TSHR) cause autoimmune hyperthyroidism. Many GD patients develop Graves’ orbitopathy or ophthalmopathy (GO) characterized by orbital tissue...