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Introduction
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March 2022 - present
January 2012 - February 2015
Publications
Publications (50)
Salinity is one of the main abiotic stresses that limits plant growth. This study addressed how the composition and diversity of root-associated bacterial communities reacts over time to salt-induced stress conditions. To understand its adaptation to soil salinization, the microbiome was studied by total DNA extraction and sequencing, using the Ill...
The understanding of selective forces driving the compartmentalization of microbiota in plants remains limited. In this study, we performed a phenotypic characterization of bacterial endophytes isolated from the medicinal plant Origanum heracleoticum, together with the determination of the antibiotic resistance profiles and the antagonistic interac...
Antibiotic resistance (AR) is recognized by the World Health Organization as a major threat to human health, and recent studies highlight the role of microplastics (MPs) in its spread. MPs in the environment may act as vectors for antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Bacterial communities on the plastisphere,...
Background: Self-organizing maps (SOMs) are a class of neural network algorithms able to visually describe a high-dimensional dataset onto a two-dimensional grid. SOMs were explored to classify soils based on an array of physical, chemical, and biological parameters. Methods: The SOM analysis was performed considering soil physical, chemical, and m...
In the last century, old-growth forests in boreal and sub-boreal zone have decreased, along with their contribution to biological diversity. In order to carry on management strategies aimed at maintaining deadwood diversity in old-growth forests, it is fundamental to identify simply and readily measurable indicators. This study investigated the dea...
Background
Colorectal cancer (CRC) risk is strongly affected by dietary habits with red and processed meat increasing risk, and foods rich in dietary fibres considered protective. Dietary habits also shape gut microbiota, but the role of the combination between diet, the gut microbiota, and the metabolite profile on CRC risk is still missing an une...
Oleuropein (OLE), a phenolic compound particularly abundant in the olive leaves, has been reported to have beneficial activities against colorectal cancer (CRC). In vitro studies suggested that these latter could be due to a modulation of the intestinal microbiota. Aiming to evaluate if OLE could affect the intestinal microbiota and the plasma meta...
Vine growing is one of the most economically important sectors of Mediterranean agriculture , but its cultivation practices are highly detrimental to the environment and the associated biota. The application of both natural products inducing endogenous plant defense mechanisms and natural soil management systems represents a potential solution for...
Understanding how microbial communities survive in extreme environmental pressure is critical for interpreting ecological patterns and microbial diversity. Great Gobi A Strictly Protected Area represents an intriguing model for studying the bacterial community since it is a protected and intact wild area of the Mongolian desert. In this work, the c...
Since its creation in 2016, the FoodOn food ontology has become an interconnected partner in various academic and government projects that span agricultural and public health domains. This paper examines recent data interoperability capabilities arising from food-related ontologies belonging to, or compatible with, the encyclopedic Open Biological...
Pistacialentiscus L. is an excluder metallophyte proposed for the revegetation and phytostabilization of metal-contaminated sites in the Mediterranean area. The present study aims at evaluating the linking between bacterial communities and plants spontaneously growing in ecosystems chronically impacted by mining activities. Environmental properties...
Eating disorders (EDs) are syndromes with a multifactorial etiopathogenesis, involving childhood traumatic experiences, as well as biological factors. Human microbiome has been hypothesised to play a fundamental role, impacting on emotion regulation, as well as with eating behaviours through its metabolites such as short chain fatty acids (SCFAs)....
Essential oils (EOs) from medicinal plants have long been used in traditional medicine for their widely known antimicrobial properties and represent a promising reservoir of bioactive compounds against multidrug-resistant pathogens. Endophytes may contribute to the yield and composition of EOs, representing a useful tool for biotechnological applic...
Medicinal plants play an important role in the discovery of new bioactive compounds with antimicrobial activity, thanks to their pharmacological properties. However, members of their microbiota can also synthesize bioactive molecules. Among these, strains belonging to the genera Arthrobacter are commonly found associated with the plant’s microenvir...
Background:
Azurin, a bacterial cupredoxin firstly isolated from the bacterium Pseudomonas aeruginosa, is considered a potential alternative therapeutic tool against different types of cancer.
Aims:
In this work we have explored the relationship possibly existing between azurin and colorectal cancer (CRC), in light of the evidence that microbial...
New sensors technology presents an opportunity to produce high-resolution soil maps to
support agricultural decisions. Maps and profile characterization were performed within the
EXCALIBUR project for 18 trials in 8 States grouped-by 3 Environmental zones: Atlantic
central (n=3), Continental (n=9), Mediterranean north (n=6), applying gamma-ray...
Endophytes are beneficial microorganisms exerting growth-promoting activities in plants; they are most often located within the plant intercellular spaces and can be found in all plant tissues, including roots, leaves, stems, flowers, and seeds. In this work, we investigated the cultivable bacterial community of the seeds and the two-week sprouts o...
The composition of the intestinal microbiota plays a critical role in shaping the immune system. Modern lifestyle, the inappropriate use of antibiotics, and exposure to pollution have significantly affected the composition of commensal microorganisms. The intestinal microbiota has been shown to sustain inappropriate autoimmune responses at distant...
The composition of the intestinal microbiota plays a critical role in shaping the immune system. Modern lifestyle, the inappropriate use of antibiotics, and exposure to pollution have significantly affected the composition of commensal microorganisms. The intestinal microbiota has been shown to sustain inappropriate autoimmune responses at distant...
The core microbiome, which refers to a set of consistent microbial features across populations, is of major interest in microbiome research and has been addressed by numerous studies. Understanding the core microbiome can help identify elements that lead to dysbiosis, and lead to treatments for microbiome-related health states. However, defining th...
Food ontologies are acquiring a central role in human nutrition, providing a standardized terminology for a proper description of intervention and observational trials. In addition to bioactive molecules, several fermented foods, particularly dairy products, provide the host with live microorganisms, thus carrying potential “genetic/functional” nut...
Faecal (FM) and colon mucosal associated microbiota (MAM) were studied in a model of colorectal cancer (CRC), the Apc -mutated Pirc rats, and in age-paired wt F344 rats. Principal Coordinates Analysis indicated that samples’ distribution was driven by age, with samples of young rats (1 month old; without tumours) separated from older ones (11-month...
![Bacterial community response [α-diversity: (A–C); β-diversity: (D)] to...](publication/356655754/figure/fig3/AS:11431281254206901@1719078965220/Bacterial-community-response-a-diversity-A-C-b-diversity-D-to-alcohol-binge_Q320.jpg)
Introduction
Chronic alcohol consumption is known to cause gut dysbiosis (changes in microbiota composition and/or function, disruptive of the normal host–microbiota interactions). However, little is known about the changes that alcohol binge drinking induces in the gut microbiota. Here, we have tested the hypothesis that a protocol of alcohol bing...
The industrial revolution was the main driver for the “westernization” of human lifestyle,
increasing the intake of highly industrially processed foods, rich in simple sugars and
saturated fats. This new dietary pattern is often referred to as the “western diet”. The issue of using this term is that it lacks a standardized definition. Moreover, the...
Background:
The microbiome is emerging as a crucial player of the immune checkpoint in cancer. Melanoma is a highly immunogenic tumour, and the gut microbiome composition has been correlated to prognosis and evolution of advanced melanoma and proposed as biomarker for immune checkpoint therapy.
Objectives:
We investigated the gut fungal and bact...
Studies so far conducted on irritable bowel syndrome (IBS) have been focused mainly on the role of gut bacterial dysbiosis in modulating the intestinal permeability, inflammation, and motility, with consequences on the quality of life. Limited evidences showed a potential involvement of gut fungal communities. Here, the gut bacterial and fungal mic...
The vaginal microbiota plays a critical role in pregnancy. Bacteria from Lactobacillus spp. are thought to maintain immune homeostasis and modulate the inflammatory responses against pathogens implicated in cervical shortening, one of the risk factors for spontaneous preterm birth. We studied vaginal microbiota in 46 pregnant women of predominantly...
Social insects are successful animal invaders. Their survival and success, and in some cases also their impact on invaded ecosystem functioning, is often mediated by symbiosis with microorganisms. Here, we report a comprehensive comparative characterization of the gut microbial communities of different castes and developmental stages of the invasiv...
Ports and marinas are central nodes in transport network and play a strategic role in coastal development. They receive pollution from land-based sources, marine traffic and port infrastructures on one side and constitute a potential pollution source for the adjacent coastal areas on the other. The aim of the present study was to evaluate the effec...
Despite the deep knowledge of the honey bee (Apis mellifera) gut microbiome, information on the microbial communities of other hive components is still scarce. Propolis originates from a natural resinous mixture that honeybees collect from different plants sources and modify; it is used mainly to ensure the hygiene of the hive. By virtue of its ant...
APC mutation is the first event triggering colon carcinogenesis (CRC). The contribution of APC to colon mucosa DNA damage is not well characterized yet. Similarly, the role of genotoxin-producer gut microorganisms is unclear. DNA strand breaks and oxidative damage were measured in Pirc rats, mutated in Apc, with the COMET assay at 1 (T1) and 11 mon...
Investigation of the fungal communities in animal models of Inflammatory Bowel Diseases (IBD) showed a controversial role of Saccharomyces cerevisiae and Candida spp. In health and disease. These conflicting observations could be ascribed to immunogenic differences among co-specific strains. To assess the relevance of intra-strains differences on y...
Trained immunity is the enhanced response of the innate immune system to a secondary infection after an initial encounter with a microorganism. This non-specific response to reinfection is a primitive form of adaptation that has been shown to be conserved from plants to mammals. Insects lack an acquired immune component and rely solely on an innate...
Pollution affects most of the urban and forest environments at different levels causing well-known effects on human and plant health. The influence that pollutants exert on plant-associated microbiota might direct plant health and, in some cases, also the removal of pollutants by plants. With the advent of nanotechnologies, an increasing amount of...
The present study aimed to evaluate the impact of polycyclic aromatic hydrocarbons (PAHs) produced by multiple emission sources on prokaryotic communities in sediments chronically affected by anthropogenic pressures. In this context, surface sediments were investigated in three Mediterranean touristic ports over three sampling periods and in differ...
Background and aim:
A personalized approach to therapy has great promise to improve disease outcomes. To this end, the identification of different subsets of patients according with the prevalent pathogenic process might guide in the choice of therapeutic strategy. We hypothesize that UC patients might be stratified according to distinctive cytoki...
Fifteen bifidobacterial strains were obtained from faeces of Rousettus aegyptiacus; after grouping them by RAPD PCR only eight were selected and characterized. Analysis of 16S rRNA and of five housekeeping (hsp60, rpoB, clpC, dnaJ, dna G) genes revealed that these eight strains were classified into five clusters: Cluster I (RST 8 and RST 16T), Clus...
Microgravity produces a variety of physical, chemical, and biological cues leading to an intricate and largely unresolved network of mechanosensitive molecules, transduction pathways, oxidative stress-related responses, and adaptations. The bone loss observed in astronauts and animal models after spaceflight is attributable to alterations in the bo...
Background
The multidisciplinary nature of nutrition research is one of its main strengths. At the same time, however, it presents a major obstacle to integrate data analysis, especially for the terminological and semantic interpretations that specific research fields or communities are used to. To date, a proper ontology to structure and formalize...
Given the crucial role of microbiota in host development, health, and environmental interactions, genomic analyses focusing on host-microbiota interactions should certainly be considered in the investigation of the adaptive mechanisms to environmental stress. Recently, several studies suggested that microbiota associated to digestive tract is a key...
In this study, we evaluate the long-lasting effects on soil microbial communities of a change within a single land-use category, specifically the conversion from natural forest to forest plantation. To minimize the effects of impacts other than land-use (i.e., climatic and anthropogenic), we chose three sites within a Natural Park, with homogeneous...
Pollution by petroleum hydrocarbons is one of the major envi-ronmental problems in ports and it is mainly associated with ship/boat traffic and related facilities. Ports are not closed systems and their pollution may impact adjacent coastal areas. Hydrocar-bon degraders and particularly the obligate hydrocarbonoclastic bacteria carry out a fundamen...
Questions
Questions (3)
Hi all,
I am using JSpeciesWS webservice (https://jspecies.ribohost.com/jspeciesws/#home) to perform an ANI analysis. The results are a pairwise matrix of ANI values between all included genomes.
I am noticing sligtlhy different ANI values in the same pair of genomes above and below the diagonal of the matrix. Anibody can help me understanding what this difference is? Which value should i report?
Francesco.
As an informal group of researchers, we are collaboratively developing an ontology. All the development and discussion is being carried out on a GitHub repository, ad we would like to give credit to the entire work-group in the developed resources.
We already asked to ORCID but they deal with single researchers and not groups. They suggested to use RAID (https://www.raid.org.au/), which indeed seems to do the job.
Does anyone know of alternative solutions to give credit to informal "organization" in the development of software or database/ontologies? Does anyone have experience and best practice advice to share on this?
Thanks for the help,
Francesco.
I am currently analysing 16S amplicon data of microbial populations from environmental samples, and trying to apply network analysis to explore OTU-OTU and OTU-environmental properties relationships. At the moment I have successfully created OTU co-occurrance networks using the Cytoscape plugin CoNet, and I am now trying to move forward to the ecological interpretation of the networks. Since I wasn't able to find some good references regarding ecological interpretation of the networks shape, and interpretation and use of network properties, Can anybody suggests some review/articles/books or other resources type covering the use of network analysis in (microbial) population studies?
