Papers by Carlotta De Filippo
UniFrac distance matrix * Fierer et al. 2010 forensic skin (FS) dataset: subject identification (... more UniFrac distance matrix * Fierer et al. 2010 forensic skin (FS) dataset: subject identification (3 classes) * Fierer et al. 2010 forensic skin (FS) dataset: subject/hand identification (6 classes). Classification accuracy in terms of average K-category correlation coefficient (KCCC) using weighted and unweighted PhyloRelief, LEfSe using OTUs and classified taxa, RF and MetaPhyl. In parentheses, the number of selected OTUs (best model). Case study: gut microbiota of Red Colobus monkeys Seven social groups inhabiting two forests in the Udzungwa Mountains of Tanzania (Barelli et al. submitted): Magombera (disturbed) vs. Mwanihana (undisturbed). The most relevant clades selected by PhyloRelief (Kruskal-Wallis test, P<0.01) highlight that, beside more evident differences, there is a general rearrangement of the taxa within the Bacteroidales and Clostridiales order, resulting in a lower diversity of the microbiota of the Magombera individuals.
Frontiers in Endocrinology, Apr 5, 2023
A vast literature strongly suggests that the endocannabinoid (eCB) system and related bioactive l... more A vast literature strongly suggests that the endocannabinoid (eCB) system and related bioactive lipids (the paracannabinoid system) contribute to numerous physiological processes and are involved in pathological conditions such as obesity, type 2 diabetes, and intestinal inflammation. The gut paracannabinoid system exerts a prominent role in gut physiology as it affects motility, permeability, and inflammatory responses. Another important player in the regulation of host metabolism is the intestinal microbiota, as microorganisms are indispensable to protect the intestine against exogenous pathogens and potentially harmful resident microorganisms. In turn, the composition of the microbiota is regulated by intestinal immune responses. The intestinal microbial community plays a fundamental role in the development of the innate immune system and is essential in shaping adaptive immunity. The active interplay between microbiota and paracannabinoids is beginning to appear as potent regulatory system of the gastrointestinal homeostasis. In this context, oleoylethanolamide (OEA), a key component of the physiological systems involved in the regulation of dietary fat consumption, energy homeostasis, intestinal motility, and a key factor in modulating eating behavior, is a less studied lipid mediator. In the small intestine namely duodenum and jejunum, levels of OEA change according to the nutrient status as they decrease during food deprivation and increase upon refeeding. Recently, we and others showed that OEA treatment in rodents protects against inflammatory events and changes the intestinal microbiota composition. In this review, we briefly define the role of OEA and of the gut microbiota in intestinal homeostasis and recapitulate recent findings suggesting an interplay between OEA and the intestinal microorganisms.
Scientific Reports, Mar 8, 2023
he human microbiome refers to the complex microbial ecosystems that colonize different niches in ... more he human microbiome refers to the complex microbial ecosystems that colonize different niches in our bodies and significantly impact homeostasis and overall health. The most studied is certainly the gut microbiome, but knowledge is also increasing on the oral, cutaneous, vaginal communities, etc. Research in the human microbiome field is rapidly evolving and fundamentally altering the way we conceptualize and treat disease. Based on this, we believe this Collection addresses the complex role of the human microbiome and its implications for a multitude of diseases and biological dysfunctions. Despite being confined to the gastrointestinal tract (GI), the impact of the gut microbiome on human physiopathology is proving to be ever more extensive. The gut microbiome itself forms a powerful endocrine organ with a unique metabolome that supplements the host biochemistry beyond what it is designed to provide for itself creating a perfect symbiotic relationship! Microorganisms and their metabolites interact with, and/or cross the protective gut epithelial barrier influencing several physiological systems including the immune system, metabolism, neurological signaling and perhaps most unexpectedly, the brain, giving rise to the gut-brain-axis 1,2. Traditionally, the gut microbiome and its impact on human biology have been studied using surveillant and correlative techniques. The composition of the gut microbiome would be determined in the context of a disease state and related to a selection of biological markers such as cytokines, gene expression or a behavioral output. Causality would be established by using germ-free mice or strong antibiotic treatment where the absence of a gut microbiome would create dysbiosis and behavioral or biochemical changes 3,4. While these seminal studies were absolutely essential to drive our current understanding of the breadth of gut microbiome action through the host physiology, research moving forward must expand and become more sophisticated to address the underlying mechanisms such that the human microbiome can be leveraged upon to develop useful preventive and therapeutic interventions. Despite the undoubted advantages of animal models, translational research from animals to humans poses a barrier to pushing the boundaries of gut microbiome research which requires creativity and innovation to be overcome by the current and next generation of researchers. Studies investigating the causality of the human microbiome need to use current tools but must also evolve to develop new methods to gain insights into possible causal mechanisms linking the gut microbiome and its metabolome to human disease. Especially for studies of probiotic, prebiotic or symbiotic interventions, translation to human utility requires understanding metabolite production and fate and dissecting common molecular pathways. Furthermore, to understand the causality of the gut microbiome in human diseases, there is an increasing need for a mechanistic understanding of how the metabolic environment can shape microbial communities, and how metabolites that are produced by the microbial ecosystem can affect the host. While next-generation sequencing provides information on the taxonomic composition of the microbial communities present in a given district and on their metabolic potential, metabolomic analysis represents a direct reading of the function of the system, in particular the intestinal system 5. Therefore, to elucidate the mechanisms underlying the host-microbe interaction, it is necessary to associate the knowledge of the microbial community with the metabolomic profile, able to represent the phenotype in depth and, therefore, obtain insights into the cellular processes in response to some stimuli or interactions. This Collection discusses the influence of the various microbiome communities on immune inflammatory signals including cytokines, neuroendocrine hormones, bacterial components, neuroactive molecules, and/or microbial metabolites, among others. Given that the GI microbiome is a critical and often overlooked aspect of innate immunity, the overarching goal of this Collection is to gather recent and current research on the microbiome and its far-reaching impacts on a multitude of pathologies, possibly through immune inflammatory mechanisms. Together, this Collection reflects an innovative forum of current knowledge for a wide role of the microbiome in human disease. Wong et al., examined the significance of the role the microbiota-gut-brain axis' bidirectional effects play between the GI and the central nervous system to understand the pathophysiology of psychiatric disorders including autism spectrum disorder (ASD) 6. They show that the gut microbiome of people with ASD
Frontiers in Microbiology, Nov 3, 2016
The geographically isolated region of the Yaghnob Valley, Tajikistan, has allowed its inhabitants... more The geographically isolated region of the Yaghnob Valley, Tajikistan, has allowed its inhabitants to maintain a unique culture and lifestyle. Their fermented goat milk constitutes one of the staple foods for the Yaghnob population, and is produced by backslopping, i.e., using the previous fermentation batch to inoculate the new one. This study addresses the yeast composition of the fermented milk, assessing genotypic, and phenotypic properties. The 52 isolates included in this study revealed small species diversity, belonging to Kluyveromyces marxianus, Pichia fermentans, Saccharomyces cerevisiae, and one Kazachstania unispora. The K. marxianus strains showed two different genotypes, one of which never described previously. The two genetically different groups also differed significantly in several phenotypic characteristics, such as tolerance toward high temperatures, low pH, and presence of acid. Microsatellite analysis of the S. cerevisiae strains from this study, compared to 350 previously described strains, attributed the Yaghnobi S. cerevisiae to two different ancestry origins, both distinct from the wine and beer strains, and similar to strains isolated from human and insects feces, suggesting a peculiar origin of these strains, and the existence of a gut reservoir for S. cerevisiae. Our work constitutes a foundation for strain selection for future applications as starter cultures in food fermentations. This work is the first ever on yeast diversity from fermented milk of the previously unexplored area of the Yaghnob Valley.
Nutrition Metabolism and Cardiovascular Diseases, Oct 1, 2021
Nutrients, Sep 21, 2021
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Springer eBooks, 2001
DNA damage has recently attracted much attention because of its supposed relationship with proces... more DNA damage has recently attracted much attention because of its supposed relationship with processes such as ageing and carcinogenesisl.
Frontiers in Immunology
The composition of the intestinal microbiota plays a critical role in shaping the immune system. ... more 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 sites in animal models of disease, and may also have a role in immune-mediated central nervous system (CNS) diseases such as multiple sclerosis (MS). We studied the composition of the gut mycobiota in fecal samples from 27 persons with MS (pwMS) and in 18 healthy donors (HD), including 5 pairs of homozygous twins discordant for MS. We found a tendency towards higher fungal abundance and richness in the MS group, and we observed that MS twins showed a higher rate of food-associated strains, such as Saccharomyces cerevisiae. We then found that in pwMS, a distinct population of cells with antibacterial and antifungal activity is expanded duri...
Microbiota: a continuum from insects to primates, 2017
Irritable Bowel Syndrome (IBS) is a psychosomatic gastrointestinal disorder which aetiology is no... more Irritable Bowel Syndrome (IBS) is a psychosomatic gastrointestinal disorder which aetiology is not well clear, although several factors indicate the involvement of the gut microbiota, remarking the importance of the microbiota-gut-brain axis in IBS pathophysiology. We therefore characterized the gut microbiota in a cohort of 20 IBS subjects and 21 healthy subjects (HS) focusing also on the characterization of the fungal gut microbiota
For over a century microbiology and immunology have classified microorganisms in pathogenic or no... more For over a century microbiology and immunology have classified microorganisms in pathogenic or non-pathogenic. This definition, clearly relevant at the level of strain and species for most bacteria, has never been probed in fungal species. Understanding the nature of fungal pathogenesis will result in developing more effective therapies for fighting invasive fungal infection. Currently, several studies attempt to address pathogenicity mechanisms using different strains as a model. This study was designed to explore the immune-based diversity of Aspergillus spp strains and Saccharomyces cerevisiae fungal strains comparing different fungal life stages, from conidia to hyphae to spores. Our results show a wide strain-dependent variation of the immune response elicited indicating that different isolates possess diverse virulence and infectivity. Moreover, in contrast to the S. cerevisiae yeast cell-induced Th1 response, dendritic cells stimulated with yeast spores induce cellular responses shifted towards Th17 differentiation. The switch between spores and yeast is crucial for the commensalism of S. cerevisiae and depends on the use of a different receptor repertoire. We demonstrate that the differential recognition of specific mannan structures is one of the master regulator of the discrimination between harmful and harmless fungi. The in-vitro preliminary classification and characterization of fungal biodiversity in inducing immune responses led us to start the investigation on how/if the different cell mediated immunogenicity could result in differences in trained immunity properties of the tested S. cerevisiae strains. Thus, the definition of markers of inflammation or pathogenicity cannot be generalized. Understanding the role of cell wall composition in different strains and variation in the balance between tolerance and inflammation responses might lead to fully understand the boundaries between safety and pathogenicity.
The 14th European Nutrition Conference FENS 2023
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
Crustaceana, 1999
Three species of the stygobitic isopod genus Stenasellus have been described from Italy: Stenasel... more Three species of the stygobitic isopod genus Stenasellus have been described from Italy: Stenasellus racovitzai, S. nuragicus, and S. assorgiai. Recent electrophoretic data suggest the presence of more than one species in the "racovitzai"-group. In order to clarify the degree of genetic variability and the evolutionary trends in the "racovitzai"-group, we have analysed three natural populations currently known from Italy and Corsica, by the Random Ampli ed Polymorphic DNA (RAPD) technique. RAPD has proven to be a rapid and valid method for the detection of intraand interspeci c genetic polymorphism in Crustacea and to be suitable for the analysis of DNA of preserved samples. This technique was carried out to generate RAPD ngerprints from the populations of the ve localities. The molecular data obtained by RAPD markers con rm previously obtained morphological and electrophoretic results.
BMC Gastroenterology, May 2, 2018
Background: Rett syndrome (RTT) is a neurological disorder mainly caused by mutations in MeCP2 ge... more Background: Rett syndrome (RTT) is a neurological disorder mainly caused by mutations in MeCP2 gene. It has been shown that MeCP2 impairments can lead to cytokine dysregulation due to MeCP2 regulatory role in T-helper and T-reg mediated responses, thus contributing to the pro-inflammatory status associated with RTT. Furthermore, RTT subjects suffer from an intestinal dysbiosis characterized by an abnormal expansion of the Candida population, a known factor responsible for the hyper-activation of pro-inflammatory immune responses. Therefore, we asked whether the intestinal fungal population of RTT subjects might contribute the sub-inflammatory status triggered by MeCP2 deficiency. Methods: We evaluated the cultivable gut mycobiota from a cohort of 50 RTT patients and 29 healthy controls characterizing the faecal fungal isolates for their virulence-related traits, antifungal resistance and immune reactivity in order to elucidate the role of fungi in RTT's intestinal dysbiosis and gastrointestinal physiology. Results: Candida parapsilosis, the most abundant yeast species in RTT subjects, showed distinct genotypic profiles if compared to healthy controls' isolates as measured by hierarchical clustering analysis from RAPD genotyping. Their phenotypical analysis revealed that RTT's isolates produced more biofilm and were significantly more resistant to azole antifungals compared to the isolates from the healthy controls. In addition, the high levels of IL-1β and IL-10 produced by peripheral blood mononuclear cells and the mixed Th1/Th17 cells population induced by RTT C. parapsilosis isolates suggest the capacity of these intestinal fungi to persist within the host, being potentially involved in chronic, pro-inflammatory responses. Conclusions: Here we demonstrated that intestinal C. parapsilosis isolates from RTT subjects hold phenotypic traits that might favour the previously observed low-grade intestinal inflammatory status associated with RTT. Therefore, the presence of putative virulent, pro-inflammatory C. parapsilosis strains in RTT could represent an additional factor in RTT's gastrointestinal pathophysiology, whose mechanisms are not yet clearly understood.
British Journal of Dermatology, 2022
Data availability The data that support the findings of this study are openly available from the ... more Data availability The data that support the findings of this study are openly available from the European Nucleotide Archive at https://www.ebi.ac.uk/ena/browser/ view/PRJEB35665. A GitHub repository (https://github.com/FrancescoVit/Supplemen-tary_Vitali_Melanoma) was created to store the data (bacterial and fungal community counts; bacterial and fungal zero-radius operational taxonomic unit taxonomy) and code to reproduce all of the analyses reported in the manuscript.
PLOS Computational Biology, Mar 27, 2015
Metagenomics is revolutionizing our understanding of microbial communities, showing that their st... more Metagenomics is revolutionizing our understanding of microbial communities, showing that their structure and composition have profound effects on the ecosystem and in a variety of health and disease conditions. Despite the flourishing of new analysis methods, current approaches based on statistical comparisons between high-level taxonomic classes often fail to identify the microbial taxa that are differentially distributed between sets of samples, since in many cases the taxonomic schema do not allow an adequate description of the structure of the microbiota. This constitutes a severe limitation to the use of metagenomic data in therapeutic and diagnostic applications. To provide a more robust statistical framework, we introduce a class of feature-weighting algorithms that discriminate the taxa responsible for the classification of metagenomic samples. The method unambiguously groups the relevant taxa into clades without relying on pre-defined taxonomic categories, thus including in the analysis also those sequences for which a taxonomic classification is difficult. The phylogenetic clades are weighted and ranked according to their abundance measuring their contribution to the differentiation of the classes of samples, and a criterion is provided to define a reduced set of most relevant clades. Applying the method to public datasets, we show that the data-driven definition of relevant phylogenetic clades accomplished by our ranking strategy identifies features in the samples that are lost if phylogenetic relationships are not considered, improving our ability to mine metagenomic datasets. Comparison with supervised classification methods currently used in metagenomic data analysis highlights the advantages of using phylogenetic information.
Cellular and Molecular Life Sciences, Feb 6, 2009
In this study, a proteomic approach that combines selective labelling of proteins containing redu... more In this study, a proteomic approach that combines selective labelling of proteins containing reduced cysteine residues with two-dimensional electrophoresis/mass spectrometry was used to evaluate the redox state of protein cysteines during chronological ageing in Saccharomyces cerevisiae. The procedure was developed on the grounds that biotinconjugated iodoacetamide (BIAM) specifically reacts with reduced cysteine residues. BIAM-labelled proteins can then be selectively isolated by streptavidin affinity capture. We compared cells grown on 2 % glucose in the exponential phase and during chronological ageing and we found that many proteins undergo cysteine oxidation. The target proteins include enzymes involved in glucose metabolism. Both caloric restriction and growth on glycerol resulted in a decrease in the oxidative modification. Furthermore, in these conditions a reduced production of ROS and a more negative glutathione half cell redox potential were observed.
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Papers by Carlotta De Filippo