Publications by authors named "Duccio Cavalieri"

121 Publications

Gut microbiota profiles and characterization of cultivable fungal isolates in IBS patients.

Appl Microbiol Biotechnol 2021 Apr 10;105(8):3277-3288. Epub 2021 Apr 10.

Department of Agriculture and Food Sciences, University of Bologna, Viale Fanin 44, 40127, Bologna, Italy.

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 microbiota of a cohort of IBS patients have been characterized and compared with that of healthy subjects (HS). The IBS microbial community structure differed significantly compared to HS. In particular, we observed an enrichment of bacterial taxa involved in gut inflammation, such as Enterobacteriaceae, Streptococcus, Fusobacteria, Gemella, and Rothia, as well as depletion of health-promoting bacterial genera, such as Roseburia and Faecalibacterium. Gut microbial profiles in IBS patients differed also in accordance with constipation. Sequence analysis of the gut mycobiota showed enrichment of Saccharomycetes in IBS. Culturomics analysis of fungal isolates from feces showed enrichment of Candida spp. displaying from IBS a clonal expansion and a distinct genotypic profiles and different phenotypical features when compared to HS of Candida albicans isolates. Alongside the well-characterized gut bacterial dysbiosis in IBS, this study shed light on a yet poorly explored fungal component of the intestinal ecosystem, the gut mycobiota. Our results showed a differential fungal community in IBS compared to HS, suggesting potential for new insights on the involvement of the gut mycobiota in IBS. KEY POINTS: • Comparison of gut microbiota and mycobiota between IBS and healthy subjects • Investigation of cultivable fungi in IBS and healthy subjects • Candida albicans isolates result more virulent in IBS subjects compared to healthy subjects.
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http://dx.doi.org/10.1007/s00253-021-11264-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8053167PMC
April 2021

MinION technology for microbiome sequencing applications for the conservation of cultural heritage.

Microbiol Res 2021 Jun 18;247:126727. Epub 2021 Feb 18.

Department of Biology, University of Florence, Florence, Italy. Electronic address:

The MinION single-molecule sequencing system has been attracting the attention of the community of microbiologists involved in the conservation of cultural heritage. The use of MinION for the conservation of cultural heritage is extremely recent, but surprisingly the only few applications available have been exploring many different substrates: stone, textiles, paintings and wax. The use of MinION sequencing is mainly used to address the metataxonomy (with special emphasis on non-cultivable microorganisms) with the effort to identify species involved in the degradation of the substrates. In this review, we show the current applications available on different artworks, showing how this technology can be a useful tool for microbiologists and conservators also in light of its low cost and the easy chemistry.
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http://dx.doi.org/10.1016/j.micres.2021.126727DOI Listing
June 2021

Antifungals, arthropods and antifungal resistance prevention: lessons from ecological interactions.

Proc Biol Sci 2021 02 3;288(1944):20202716. Epub 2021 Feb 3.

Department of Biology, University of Florence, Sesto Fiorentino, Florence, Italy.

Arthropods can produce a wide range of antifungal compounds, including specialist proteins, cuticular products, venoms and haemolymphs. In spite of this, many arthropod taxa, particularly eusocial insects, make use of additional antifungal compounds derived from their mutualistic association with microbes. Because multiple taxa have evolved such mutualisms, it must be assumed that, under certain ecological circumstances, natural selection has favoured them over those relying upon endogenous antifungal compound production. Further, such associations have been shown to persist versus specific pathogenic fungal antagonists for more than 50 million years, suggesting that compounds employed have retained efficacy in spite of the pathogens' capacity to develop resistance. We provide a brief overview of antifungal compounds in the arthropods' armoury, proposing a conceptual model to suggest why their use remains so successful. Fundamental concepts embedded within such a model may suggest strategies by which to reduce the rise of antifungal resistance within the clinical milieu.
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http://dx.doi.org/10.1098/rspb.2020.2716DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7893227PMC
February 2021

Altered feeding behavior and immune competence in paper wasps: A case of parasite manipulation?

PLoS One 2020 16;15(12):e0242486. Epub 2020 Dec 16.

Dipartimento di Biologia, Università di Firenze, Firenze, Italia.

Paper wasps (Polistes dominula), parasitized by the strepsipteran Xenos vesparum, are castrated and desert the colony to gather on plants where the parasite mates and releases primary larvae, thus completing its lifecycle. One of these plants is the trumpet creeper Campsis radicans: in a previous study the majority of all wasps collected from this plant were parasitized and focused their foraging activity on C. radicans buds. The unexpected prevalence and unusual feeding strategy prompted us to investigate the influence of this plant on wasp behavior and physiology through a multidisciplinary approach. First, in a series of laboratory bioassays, we observed that parasitized wasps spent more time than non-parasitized ones on fresh C. radicans buds, rich of extra-floral nectaries (EFNs), while the same wasps ignored treated buds that lacked nectar drops. Then, we described the structure and ultra-structure of EFNs secreting cells, compatible with the synthesis of phenolic compounds. Subsequently, we analysed extracts from different bud tissues by HPLC-DAD-MS and found that verbascoside was the most abundant bioactive molecule in those tissues rich in EFNs. Finally, we tested the immune-stimulant properties of verbascoside, as the biochemical nature of this compound indicates it might function as an antibacterial and antioxidant. We measured bacterial clearance in wasps, as a proxy for overall immune competence, and observed that it was enhanced after administration of verbascoside-even more so if the wasp was parasitized. We hypothesize that the parasite manipulates wasp behavior to preferentially feed on C. radicans EFNs, since the bioactive properties of verbascoside likely increase host survival and thus the parasite own fitness.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0242486PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7743958PMC
January 2021

Active microbial ecosystem in Iron-Age tombs of the Etruscan civilization.

Environ Microbiol 2020 Nov 16. Epub 2020 Nov 16.

Department of Biology and Biotechnology, Sapienza University of Rome, Rome, Italy.

Earth's microbial biosphere extends down through the crust and much of the subsurface, including those microbial ecosystems located within cave systems. Here, we elucidate the microbial ecosystems within anthropogenic 'caves'; the Iron-Age, subterranean tombs of central Italy. The interior walls of the rock (calcium-rich macco) were painted ~2500 years ago and are covered with CaCO needles (known as moonmilk). The aims of the current study were to: identify biological/geochemical/biophysical determinants of and characterize bacterial communities involved in CaCO precipitation; challenge the maxim that biogenic activity necessarily degrades surfaces; locate the bacterial cells that are the source of the CaCO precipitate; and gain insight into the kinetics of moonmilk formation. We reveal that this environment hosts communities that consist primarily of bacteria that are mesophilic for temperature and xerotolerance (including Actinobacteria, Bacteroidetes and Proteobacteria); is populated by photosynthetic Cyanobacteria exhibiting heterotrophic nutrition (Calothrix and Chroococcidiopsis); and has CaCO precipitating on the rock surfaces (confirmation that this process is biogenic) that acts to preserve rather than damage the painted surface. We also identified that some community members are psychrotolerant (Polaromonas), acidotolerant or acidophilic (members of the Acidobacteria), or resistant to ionizing radiation (Brevundimonas and Truepera); elucidate the ways in which microbiology impacts mineralogy and vice versa; and reveal that biogenic formation of moonmilk can occur rapidly, that is, over a period of 10 to 56 years. We discuss the paradox that these ecosystems, that are for the most part in the dark and lack primary production, are apparently highly active, biodiverse and biomass-rich.
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http://dx.doi.org/10.1111/1462-2920.15327DOI Listing
November 2020

Applications of Wild Isolates of Yeast for Industrial Fermentation: The Gut of Social Insects as Niche for Yeast Hybrids' Production.

Front Microbiol 2020 29;11:578425. Epub 2020 Oct 29.

Department of Biology, University of Florence, Florence, Italy.

In the industry of fermented food and beverages, yeast cultures are often selected and standardized in order to ensure a better control of fermentation and a more stable product over time. Several studies have shown that the organoleptic characteristics of fermented products reflect geographic variations of the microbial community composition. Despite investigations of the worldwide distribution and genetic diversity of , it is still unclear how and to what extent human intervention has shaped the brewer's yeast population structure. The genotypic and phenotypic characterization of environmental yeast populations and their potential application in the fermentative processes can significantly enrich the industrial fermentation products. Social insects have proven to be closely associated to the yeasts ecology. The relationships between yeasts and insects represent a fundamental aspect for understanding the ecological and evolutionary forces shaping their adaptation to different niches. Studies on phylogenetic relationships of populations showed genetic differences among strains isolated from gut and non-gut environments (i.e., natural sources and fermentation). Recent evidences showed that insect's gut is a reservoir and an evolutionary niche for , contributing to its survival and evolution, favoring its dispersion, mating and improving the inter-specific hybrids production during hibernation. Here, we discuss the potential use of social insects for production of a wide range of hybrid yeasts from environmental isolates suitable for industrial and biotechnological applications.
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http://dx.doi.org/10.3389/fmicb.2020.578425DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7661385PMC
October 2020

To the Land and Beyond: Crab Microbiomes as a Paradigm for the Evolution of Terrestrialization.

Front Microbiol 2020 7;11:575372. Epub 2020 Oct 7.

Department of Biology, University of Florence, Florence, Italy.

The transition to terrestrial environments by formerly aquatic species has occurred repeatedly in many animal phyla and lead to the vast diversity of extant terrestrial species. The differences between aquatic and terrestrial habitats are enormous and involved remarkable morphological and physiological changes. Convergent evolution of various traits is evident among phylogenetically distant taxa, but almost no information is available about the role of symbiotic microbiota in such transition. Here, we suggest that intertidal and terrestrial brachyuran crabs are a perfect model to study the evolutionary pathways and the ecological role of animal-microbiome symbioses, since their transition to land is happening right now, through a number of independent lineages. The microorganisms colonizing the gut of intertidal and terrestrial crabs are expected to play a major role to conquer the land, by reducing water losses and permitting the utilization of novel food sources. Indeed, it has been shown that the microbiomes hosted in the digestive system of terrestrial isopods has been critical to digest plant items, but nothing is known about the microbiomes present in the gut of truly terrestrial crabs. Other important physiological regulations that could be facilitated by microbiomes are nitrogen excretion and osmoregulation in the new environment. We also advocate for advances in comparative and functional genomics to uncover physiological aspects of these ongoing evolutionary processes. We think that the multidisciplinary study of microorganisms associated with terrestrial crabs will shed a completely new light on the biological and physiological processes involved in the sea-land transition.
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http://dx.doi.org/10.3389/fmicb.2020.575372DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7575764PMC
October 2020

- Insects Association: Impacts, Biogeography, and Extent.

Front Microbiol 2020 14;11:1629. Epub 2020 Jul 14.

Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.

Over the last few years, an increasing number of studies have reported the existence of an association between the budding yeast and insects. The discovery of this relationship has called into question the hypothesis that is unable to survive in nature and that the presence of strains in natural specimens is the result of contamination from human-related environments. cells benefit from this association as they find in the insect intestine a shelter, but also a place where they can reproduce themselves through mating, the latter being an event otherwise rarely observed in natural environments. On the other hand, insects also take advantage in hosting as they rely on yeasts as nutriment to properly develop, to localize suitable food, and to enhance their immune system. Despite the relevance of this relationship on both yeast and insect ecology, we are still far from completely appreciating its extent and effects. It has been shown that other yeasts are able to colonize only one or a few insect species. Is it the same for cells or is this yeast able to associate with any insect? Similarly, is this association geographically or topographically limited in areas characterized by specific physical features? With this review, we recapitulate the nature of the -insect association, disclose its extent in terms of geographical distribution and species involved, and present , a cured online database providing a collection of information on this topic.
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http://dx.doi.org/10.3389/fmicb.2020.01629DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7372139PMC
July 2020

Gut microbial composition in different castes and developmental stages of the invasive hornet Vespa velutina nigrithorax.

Sci Total Environ 2020 Nov 15;745:140873. Epub 2020 Jul 15.

Department of Biology, University of Florence, Via Madonna del Piano, 50019 Firenze, Italy.

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 invasive hornet Vespa velutina nigrithorax. The species recently colonized Europe, becoming a high ecological and economic concern, as it threatens pollinator survival and competes with native hornet species. We used targeted meta-genomics to describe the yeasts and bacteria gut communities of individuals of different reproductive phenotypes (workers and future queens), life stages (larvae, newly emerged individuals and adults) and colony non-living samples (nest paper and larval faeces). Bacilli, Gammaproteobacteria, Actinobacteria, Alphaproteobacteria were the most abundant classes of bacteria, and Saccharomycetes, Dothideomycetes, Tremellomycetes and Eurotiomycetes were the most represented yeast classes. We found that the microbial compositions significantly differ across developmental stages and castes, with yeast and bacterial communities switching in frequency and abundance during ontogeny and according to reproductive phenotype. Moreover, the gut microbial communities poorly mirror those found in the nest, suggesting that hornets possess a specific microbial signature. Our results provide the first metagenomic resource of the microbiome of V. velutina in Europe and suggest the importance of considering life stages, reproductive phenotypes and nest influence in order to obtain a comprehensive picture of social insect microbial communities.
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http://dx.doi.org/10.1016/j.scitotenv.2020.140873DOI Listing
November 2020

Comparative immunophenotyping of and spp. strains from Crohn's disease patients and their interactions with the gut microbiome.

J Transl Autoimmun 2020 26;3:100036. Epub 2020 Jan 26.

Department of Biology, University of Florence, Via Madonna Del Piano 6, 50019 Sesto Fiorentino, Florence, Italy.

Investigation of the fungal communities in animal models of Inflammatory Bowel Diseases (IBD) showed a controversial role of and 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 yeast immunogenicity and impact on the microbiota, we screened and spp. Strains isolated from fecal samples of IBD patients. We compared the cytokine profiles, obtained upon stimulation of Peripheral Blood Mononuclear Cells (PBMCs) and Dendritic Cells with different yeast strains, and evaluated the relationship between strain's cell wall sugar amount and immune response. Moreover, the gut microbiota composition was explored in relation to fungal isolation from fecal samples by metabarcoding analysis. The comparison of cytokine profiles showed strain dependent rather than species-dependent differences in immune responses. Differences in immunogenicity correlated with the cell wall composition of intestinal strains. Stimulation of human healthy PBMCs with different strains showed a pro-inflammatory IL-6 response counterbalanced by IL-10 production. Interestingly, Crohn's (CD) patients responded differently to "self" and "non-self" strains, eliciting pure Th1 or Th17 cytokine patterns. The differences observed were recapitulated , where different strains contributed in dramatically different ways to local epithelial activity and to the inflammation of wild type and Interleukin-deficient mice. Furthermore, we observed that the gut microbiota profiles significantly differentiated according to the presence of or spp. or the absence of fungal isolates in fecal samples. Our results show the importance to deepen metagenomics and immunophenotyping analyses to the strain level, to elucidate the role of fungal and bacterial communities in health and disease.
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http://dx.doi.org/10.1016/j.jtauto.2020.100036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7388382PMC
January 2020

ERNICA guidelines for the management of rectosigmoid Hirschsprung's disease.

Orphanet J Rare Dis 2020 06 25;15(1):164. Epub 2020 Jun 25.

Department of Pediatric Surgery, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.

Background: Hirschsprung's disease (HSCR) is a serious congenital bowel disorder with a prevalence of 1/5000. Currently, there is a lack of systematically developed guidelines to assist clinical decision-making regarding diagnostics and management.

Aims: This guideline aims to cover the diagnostics and management of rectosigmoid HSCR up to adulthood. It aims to describe the preferred approach of ERNICA, the European Reference Network for rare inherited and congenital digestive disorders.

Methods: Recommendations within key topics covering the care pathway for rectosigmoid HSCR were developed by an international workgroup of experts from 8 European countries within ERNICA European Reference Network from the disciplines of surgery, medicine, histopathology, microbiology, genetics, and patient organization representatives. Recommendation statements were based on a comprehensive review of the available literature and expert consensus. AGREE II and GRADE approaches were used during development. Evidence levels and levels of agreement are noted.

Results: Thirty-three statements within 9 key areas were generated. Most recommendations were based on expert opinion.

Conclusion: In rare or low-prevalence diseases such as HSCR, there remains limited availability of high-quality clinical evidence. Consensus-based guidelines for care are presented.
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http://dx.doi.org/10.1186/s13023-020-01362-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7318734PMC
June 2020

Propolis hosts a diversemicrobial community.

World J Microbiol Biotechnol 2020 Mar 10;36(3):50. Epub 2020 Mar 10.

Department of Biology, University of Florence, Via Madonna del Piano, 6, 50019, Sesto Fiorentino, Florence, Italy.

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 antimicrobial properties, propolis has been considered relatively aseptic, yet its ability to harbor microorganisms has not been previously investigated. In this study we report the first description of the diversity of the microbial community of propolis by both targeted-metagenomics analysis and cultivation. We demonstrated that propolis hosts a variety of microbial strains belonging to taxa already described in other hive components. Some of them are cultivable in standard laboratory conditions, and show metabolic characteristics compatible with their persistence in different physiological states inside propolis. Isolated bacteria produce antimicrobials against Gram-negative and Gram-positive bacteria, and entomopathogenic fungi, with different spectra of inhibition. Metagenomics analysis shows the presence of bacteria and fungi with great potential to outcompete potentially harmful microorganisms. These findings suggest that the characterized microbiota could contribute to the overall antimicrobial properties of propolis and to its ecological role as "disinfectant" within the hive.
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http://dx.doi.org/10.1007/s11274-020-02827-0DOI Listing
March 2020

Induces Immune Enhancing and Shapes Gut Microbiota in Social Wasps.

Front Microbiol 2019 15;10:2320. Epub 2019 Oct 15.

Dipartimento di Biologia, Università degli Studi di Firenze, Firenze, Italy.

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 one, and they have expanded it upon traits of plasticity and adaptation against pathogens in the form of immune priming. The recent discoveries of the role of in the insect's ecology and the ability of this yeast to induce trained immunity in different organisms suggest that insects could have developed mechanisms of adaptation and immune enhancing. Here, we report that two yeast strains of , previously shown to induce trained immunity in mammals, enhance resistance to infection in the paper wasp . The reduction of injected load by strains was statistically significant in future foundresses but not in workers, and this occurs before and after hibernation. We thus investigated if the effect on was mirrored by variation in the gut microbiota composition. Foundresses, showing immune enhancing, had statistically significant changes in composition and diversity of gut bacterial communities but not in the fungal communities. Our results demonstrate that can prime insect responses against bacterial infections, providing an advantage to future foundress wasps to carry these microorganisms. Understanding the mechanisms involved in the generation of specific and long-lasting immune response against pathogenic infections in insects and the influence of the induction of trained immunity on the commensal gut microbiota could have a major impact on modern immunology.
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http://dx.doi.org/10.3389/fmicb.2019.02320DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6803456PMC
October 2019

Gut Microbiota Profiles Differ among Individuals Depending on Their Region of Origin: An Italian Pilot Study.

Int J Environ Res Public Health 2019 10 23;16(21). Epub 2019 Oct 23.

Division of Gastroenterology, Fondazione IRCCS Casa Sollievo della Sofferenza, 71013 San Giovanni Rotondo, Italy.

Background And Aims: Microbiota heterogeneity among humans is mainly due to genetic background, age, dietary habits, lifestyle and local environments. In this study we investigated whether the gut microbiota profile of Italian healthy volunteers could differ based on their geographical origin.

Materials And Methods: 16S rRNA gene sequencing was employed to analyze the gut microbiota of 31 healthy volunteers from three different Italian regions: Apulia (South), Lazio (Center) and Lombardy (North).

Results: Differences in microbiota composition were detected when the study participants were grouped by their region of origin and when they were classified based on age classes (-values < 0.05). Also species richness was significantly different both according to Italian Regions (median richness: 177.8 vs. 140.7 vs. 168.0 in Apulia, Lazio and Lombardy; < 0.001) and according to age classes (median richness: 140.1 vs. 177.8 vs. 160.0 in subjects < 32, 32-41 and > 41 years; < 0.001), whereas the Shannon index and beta diversity did not change.

Conclusions: This study identified differences in the gut microbiota composition and richness among individuals with the same ethnicity coming from three different Italian regions. Our results underline the importance of studies on population-specific variations in human microbiota composition leading to geographically tailored approaches to microbiota engineering.
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http://dx.doi.org/10.3390/ijerph16214065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6862301PMC
October 2019

Characterization of Bifidobacterium species in feaces of the Egyptian fruit bat: Description of B. vespertilionis sp. nov. and B. rousetti sp. nov.

Syst Appl Microbiol 2019 Nov 23;42(6):126017. Epub 2019 Sep 23.

Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy. Electronic address:

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 16), Cluster II (RST 9 and RST 27), Cluster III (RST 7 and RST 11), Cluster IV (RST 19), Cluster V (RST 17) were closest to Bifidobacterium avesanii DSM 100685 (96.3%), Bifidobacterium callitrichos DSM 23973 (99.2% and 99.7%), Bifidobacterium tissieri DSM 100201 (99.7 and 99.2%), Bifidobacterium reuteri DSM 23975 (98.9%) and Bifidobacterium myosotis DSM 100196 (99.3%), respectively. Strains in Cluster I and strain RST 9 in Cluster II could not be placed within any recognized species while the other ones were identified as known species. The average nucleotide identity values between two novel strains, RST 16 and RST 9 and their closest relatives were lower than 79% and 89%, respectively. In silico DNA-DNA hybridization values for those closest relatives were 32.5 and 42.1%, respectively. Phenotypic and genotypic tests demonstrated that strains in Cluster I and RST 9 in Cluster II represent two novel species for which the names Bifidobacterium vespertilionis sp. nov. (RST 16=BCRC 81138=NBRC 113380=DSM 106025 ; RST 8=BCRC 81135=NBRC 113377) and Bifidobacterium rousetti sp. nov. (RST 9=BCRC 81136=NBRC 113378=DSM 106027) are proposed.
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http://dx.doi.org/10.1016/j.syapm.2019.126017DOI Listing
November 2019

IL-13 mRNA Tissue Content Identifies Two Subsets of Adult Ulcerative Colitis Patients With Different Clinical and Mucosa-Associated Microbiota Profiles.

J Crohns Colitis 2020 Mar;14(3):369-380

Istituto Superiore di Sanità, National Center for Drug Research and Evaluation, Rome, Italy.

Background And Aims: A personalized approach to therapy hold great promise to improve disease outcomes. To this end, the identification of different subsets of patients according to the prevalent pathogenic process might guide the choice of therapeutic strategy. We hypothesize that ulcerative colitis [UC] patients might be stratified according to distinctive cytokine profiles and/or to a specific mucosa-associated microbiota.

Methods: In a cohort of clinically and endoscopic active UC patients and controls, we used quantitative PCR to analyse the mucosal cytokine mRNA content and 16S rRNA gene sequencing to assess the mucosa-associated microbiota composition.

Results: We demonstrate, by means of data-driven approach, the existence of a specific UC patient subgroup characterized by elevated IL-13 mRNA tissue content separate from patients with low IL-13 mRNA tissue content. The two subsets differ in clinical-pathological characteristics. High IL-13 mRNA patients are younger at diagnosis and have a higher prevalence of extensive colitis than low IL-13 mRNA patients. They also show more frequent use of steroid/immunosuppressant/anti-tumour necrosis factor α therapy during 1 year of follow-up. The two subgroups show differential enrichment of mucosa-associated microbiota genera with a prevalence of Prevotella in patients with high IL-13 mRNA tissue content and Sutterella and Acidaminococcus in patients with low IL-13 mRNA tissue content.

Conclusion: Assessment of mucosal IL-13 mRNA might help in the identification of a patient subgroup that might benefit from a therapeutic approach modulating IL-13.

Podcast: This article has an associated podcast which can be accessed at https://academic.oup.com/ecco-jcc/pages/podcast.
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http://dx.doi.org/10.1093/ecco-jcc/jjz154DOI Listing
March 2020

A Metagenomics Study on Hirschsprung's Disease Associated Enterocolitis: Biodiversity and Gut Microbial Homeostasis Depend on Resection Length and Patient's Clinical History.

Front Pediatr 2019 9;7:326. Epub 2019 Aug 9.

Department, of Biology, University of Florence, Firenze, Italy.

Since 2010, several researches demonstrated that microbiota dynamics correlate and can even predispose to Hirschsprung (HSCR) associated enterocolitis (HAEC). This study aims at assessing the structure of the microbiota of HSCR patients in relation to extent of aganglionosis and HAEC status. All consecutive HSCR patients admitted to Gaslini Institute (Genova, Italy) between May 2012 and November 2014 were enrolled. Institutional review board (IRB) approval was obtained. Stools were sampled and 16S rDNA V3-V4 regions were sequenced using the Illumina-MiSeq. Taxonomy assignments were performed using QIIME RDP. Alpha diversity indexes were analyzed by Shannon and Simpson Indexes, and Phylogenetic Diversity. We enrolled 20 patients. Male to female ratio was 4:1. Six patients suffered from Total Colonic Aganglionosis (TCSA). Considering sample site (i.e., extent of aganglionosis), we confirmed the known relationship between sample site and both biodiversity and composition of intestinal microbiota. Patients with TCSA showed lower biodiversity and increased Proteobacteria/Bacteroidetes relative abundance ratio. When addressing biodiversity, composition and dynamics of TCSA patients we could not find any significant relationship with regard to HAEC occurrences. The composition of HAEC predisposing microbiota is specific to each patient. We could confirm that total colon resections can change the composition of intestinal microbiota and to dramatically reduce microbial diversity. The subsequent reduction of system robustness could expose TCSA patients to environmental microbes that might not be part of the normal microbiota. Future long-term studies should investigate both patients and their family environment, as well as their disease history.
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http://dx.doi.org/10.3389/fped.2019.00326DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6696876PMC
August 2019

Environmental pollution effects on plant microbiota: the case study of poplar bacterial-fungal response to silver nanoparticles.

Appl Microbiol Biotechnol 2019 Oct 11;103(19):8215-8227. Epub 2019 Aug 11.

Department of Agriculture, Food, Environment and Forestry, University of Florence, 50145, Florence, Italy.

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 engineered nanoparticles are being introduced into the environment, and consequently, their impact on plant-associated microorganisms needs to be investigated. In this context, silver nanoparticles (Ag-NPs) were experimentally supplied at leaf and root level of poplar plants to assess Ag-NPs effects on plant microbiota. Leaf Ag-NP treatment increased bacteria and fungi evenness and determined a significant reduction in both microbial groups, while root Ag-NP treatment reduced the bacterial and fungal biodiversity. Bioinformatics functional analysis showed that Ag-NP treatment reduced the aerobic and stimulated facultative anaerobic and oxidative stress-tolerant bacteria. Our study offers new insights into the effects of Ag-NPs on both phyllosphere and rhizosphere poplar-associated microbiota and may represent a first attempt to understand the behavior of microbial communities of a tree species growing in a polluted environment.
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http://dx.doi.org/10.1007/s00253-019-10071-2DOI Listing
October 2019

Longitudinal Survey of Fungi in the Human Gut: ITS Profiling, Phenotyping, and Colonization.

Front Microbiol 2019 10;10:1575. Epub 2019 Jul 10.

Department of Surgery, Medicine, Dentistry and Morphological Sciences with Interest in Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy.

The fungal component of the intestinal microbiota of eight healthy subjects was studied over 12 months using metagenome survey and culture-based approaches. , , , , , , and were the most recurrent and/or dominant fungal genera, according to metagenomic analysis. The biodiversity of fungal communities was lower and characterized by greater unevenness, when compared to bacterial microbiome. The dissimilarities both among subjects and over the time within the same subject suggested that most of the fungi passed through the gastro-intestinal tract (GIT) without becoming stable colonizers. Certain genera, such as and , were isolated in a minority of cases, although they recurred abundantly and frequently in the metagenomics survey, likely being environmental or food-borne fungi that do not inhabit the GIT. genus was recurrently detected. isolates dominated among the cultivable mycobiota and longitudinally persisted, likely as commensals inhabiting the intestine or regularly reaching it from -colonized districts, such as the oral cavity. Other putative colonizers belonged to , , and , with persisting biotypes being identified. Phenotyping of fungal isolates indicated that adhered to human epithelial cells more efficiently and produced greater amounts of biofilm than non- (NAC) and non- fungi (NCF). The isolates also induced the highest release of HBD-2 by human epithelial cells, further differing from NAC and NCF. Nine representative isolates were administered to mice to evaluate the ability to colonize the intestine. Only two out of three strains persisted in stools of animals 2 weeks after the end of the oral administration, whereas NAC and NCF did not. These results confirm the allochthonous nature of most the intestinal fungi, while appears to be commonly involved in stable colonization. A combination of specific genetic features in the microbe and in the host likely allow colonization from fungi normally present solely as passengers. It remains to be established if other species identified as potential colonizers, in addition to , are true inhabitants of the GIT or rather reach the intestine spreading from other body districts.
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http://dx.doi.org/10.3389/fmicb.2019.01575DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6636193PMC
July 2019

Population genomics reveals evolution and variation of Saccharomyces cerevisiae in the human and insects gut.

Environ Microbiol 2019 01 21;21(1):50-71. Epub 2018 Nov 21.

Department of Biology, University of Florence, Florence, Italy.

The quest to discover the variety of ecological niches inhabited by Saccharomyces cerevisiae has led to research in areas as diverse as wineries, oak trees and insect guts. The discovery of fungal communities in the human gastrointestinal tract suggested the host's gut as a potential reservoir for yeast adaptation. Here, we report the existence of yeast populations associated with the human gut (HG) that differ from those isolated from other human body sites. Phylogenetic analysis on 12 microsatellite loci and 1715 combined CDSs from whole-genome sequencing revealed three subclusters of HG strains with further evidence of clonal colonization within the host's gut. The presence of such subclusters was supported by other genomic features, such as copy number variation, absence/introgressions of CDSs and relative polymorphism frequency. Functional analysis of CDSs specific of the different subclusters suggested possible alterations in cell wall composition and sporulation features. The phenotypic analysis combined with immunological profiling of these strains further showed that sporulation was related with strain-specific genomic characteristics in the immune recognition pattern. We conclude that both genetic and environmental factors involved in cell wall remodelling and sporulation are the main drivers of adaptation in S. cerevisiae populations in the human gut.
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http://dx.doi.org/10.1111/1462-2920.14422DOI Listing
January 2019

Metagenomic Approaches to Investigate the Contribution of the Vineyard Environment to the Quality of Wine Fermentation: Potentials and Difficulties.

Front Microbiol 2018 16;9:991. Epub 2018 May 16.

Department of Biology, University of Florence, Florence, Italy.

The winemaking is a complex process that begins in the vineyard and ends at consumption moment. Recent reports have shown the relevance of microbial populations in the definition of the regional organoleptic and sensory characteristics of a wine. Metagenomic approaches, allowing the exhaustive identification of microorganisms present in complex samples, have recently played a fundamental role in the dissection of the contribution of the vineyard environment to wine fermentation. Systematic approaches have explored the impact of agronomical techniques, vineyard topologies, and climatic changes on bacterial and fungal populations found in the vineyard and in fermentations, also trying to predict or extrapolate the effects on the sensorial characteristics of the resulting wine. This review is aimed at highlighting the major technical and experimental challenges in dissecting the contribution of the vineyard and native environments microbiota to the wine fermentation process, and how metagenomic approaches can help in understanding microbial fluxes and selections across the environments and specimens related to wine fermentation.
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http://dx.doi.org/10.3389/fmicb.2018.00991DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5964215PMC
May 2018

ONS: an ontology for a standardized description of interventions and observational studies in nutrition.

Genes Nutr 2018 30;13:12. Epub 2018 Apr 30.

1Institute of Biometeorology (IBIMET), National Research Council (CNR), Via Giovanni Caproni, 8, 50145 Florence, FI Italy.

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 the concepts used for the description of nutritional studies is still lacking.

Results: We have developed the Ontology for Nutritional Studies (ONS) by harmonizing selected pre-existing de facto ontologies with novel health and nutritional terminology classifications. The ONS is the result of a scholarly consensus of 51 research centers in nine European countries. The ontology classes and relations are commonly encountered while conducting, storing, harmonizing, integrating, describing, and searching nutritional studies. The ONS facilitates the description and specification of complex nutritional studies as demonstrated with two application scenarios.

Conclusions: The ONS is the first systematic effort to provide a solid and extensible formal ontology framework for nutritional studies. Integration of new information can be easily achieved by the addition of extra modules (i.e., nutrigenomics, metabolomics, nutrikinetics, and quality appraisal). The ONS provides a unified and standardized terminology for nutritional studies as a resource for nutrition researchers who might not necessarily be familiar with ontologies and standardization concepts.
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http://dx.doi.org/10.1186/s12263-018-0601-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5928560PMC
April 2018

Intestinal Candida parapsilosis isolates from Rett syndrome subjects bear potential virulent traits and capacity to persist within the host.

BMC Gastroenterol 2018 May 2;18(1):57. Epub 2018 May 2.

Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, Florence, Italy.

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.
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http://dx.doi.org/10.1186/s12876-018-0785-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5930502PMC
May 2018

Deciphering the mechanism of action of 089, a compound impairing the fungal cell cycle.

Sci Rep 2018 04 13;8(1):5964. Epub 2018 Apr 13.

CRI Centre for Research and Innovation, Fondazione Edmund Mach, San Michele all'Adige, Trento, Italy.

Fungal infections represent an increasingly relevant clinical problem, primarily because of the increased survival of severely immune-compromised patients. Despite the availability of active and selective drugs and of well-established prophylaxis, classical antifungals are often ineffective as resistance is frequently observed. The quest for anti-fungal drugs with novel mechanisms of action is thus important. Here we show that a new compound, 089, acts by arresting fungal cells in the G2 phase of the cell cycle through targeting of SWE1, a mechanism of action unexploited by current anti-fungal drugs. The cell cycle impairment also induces a modification of fungal cell morphology which makes fungal cells recognizable by immune cells. This new class of molecules holds promise to be a valuable source of novel antifungals, allowing the clearance of pathogenic fungi by both direct killing of the fungus and enhancing the recognition of the pathogen by the host immune system.
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http://dx.doi.org/10.1038/s41598-018-24341-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5899093PMC
April 2018

Genomic and Phenotypic Variation in Morphogenetic Networks of Two Isolates Subtends Their Different Pathogenic Potential.

Front Immunol 2017 19;8:1997. Epub 2018 Jan 19.

Dipartimento di Medicina Diagnostica, Clinica e di Sanità Pubblica, Università di Modena e Reggio Emilia, Modena, Italy.

The transition from commensalism to pathogenicity of reflects both the host inability to mount specific immune responses and the microorganism's dimorphic switch efficiency. In this study, we used whole genome sequencing and microarray analysis to investigate the genomic determinants of the phenotypic changes observed in two clinical isolates (YL1 and YQ2). experiments employing epithelial, microglial, and peripheral blood mononuclear cells were thus used to evaluate isolates interaction with first line host defenses, measuring adhesion, susceptibility to phagocytosis, and induction of secretory responses. Moreover, a murine model of peritoneal infection was used to compare the pathogenic potential of the two isolates. Genome sequence and gene expression analysis of YL1 and YQ2 showed significant changes in cellular pathways involved in environmental stress response, adhesion, filamentous growth, invasiveness, and dimorphic transition. This was in accordance with the observed marked phenotypic differences in biofilm production, dimorphic switch efficiency, cell adhesion, invasion, and survival to phagocyte-mediated host defenses. The mutations in key regulators of the hyphal growth pathway in the more virulent strain corresponded to an overall greater number of budding yeast cells released. Compared to YQ2, YL1 consistently showed enhanced pathogenic potential, since , it was less susceptible to ingestion by phagocytic cells and more efficient in invading epithelial cells, while YL1 was more effective than YQ2 in recruiting inflammatory cells, eliciting IL-1β response and eluding phagocytic cells. Overall, these results indicate an unexpected isolate-specific variation in pathways important for host invasion and colonization, showing how the genetic background of may greatly affect its behavior both and . Based on this approach, we propose that the co-occurrence of changes in sequence and expression in genes and pathways driving dimorphic transition and pathogenicity reflects a selective balance between traits favoring dissemination of the pathogen and traits involved in host defense evasion. This study highlights the importance of investigating strain-level, rather than species level, differences, when determining fungal-host interactions and defining commensal or pathogen behavior.
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http://dx.doi.org/10.3389/fimmu.2017.01997DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5780349PMC
January 2018

Guidelines and recommendations on yeast cell death nomenclature.

Microb Cell 2018 Jan 1;5(1):4-31. Epub 2018 Jan 1.

Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Bari, Italy.

Elucidating the biology of yeast in its full complexity has major implications for science, medicine and industry. One of the most critical processes determining yeast life and physiology is cel-lular demise. However, the investigation of yeast cell death is a relatively young field, and a widely accepted set of concepts and terms is still missing. Here, we propose unified criteria for the defi-nition of accidental, regulated, and programmed forms of cell death in yeast based on a series of morphological and biochemical criteria. Specifically, we provide consensus guidelines on the differ-ential definition of terms including apoptosis, regulated necrosis, and autophagic cell death, as we refer to additional cell death rou-tines that are relevant for the biology of (at least some species of) yeast. As this area of investigation advances rapidly, changes and extensions to this set of recommendations will be implemented in the years to come. Nonetheless, we strongly encourage the au-thors, reviewers and editors of scientific articles to adopt these collective standards in order to establish an accurate framework for yeast cell death research and, ultimately, to accelerate the pro-gress of this vibrant field of research.
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http://dx.doi.org/10.15698/mic2018.01.607DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5772036PMC
January 2018

SaccharomycesIDentifier, SID: strain-level analysis of Saccharomyces cerevisiae populations by using microsatellite meta-patterns.

Sci Rep 2017 11 10;7(1):15343. Epub 2017 Nov 10.

Computational Biology Unit, Fondazione Edmund Mach, via E. Mach 1, 38010 San Michele all'Adige, Trento, Italy.

Saccharomyces cerevisiae is a common yeast with several applications, among which the most ancient is winemaking. Because individuals belonging to this species show a wide genetic and phenotypic variability, the possibility to identify the strains driving fermentation is pivotal when aiming at stable and palatable products. Metagenomic sequencing is increasingly used to decipher the fungal populations present in complex samples such as musts. However, it does not provide information at the strain level. Microsatellites are commonly used to describe the genotype of single strains. Here we developed a population-level microsatellite profiling approach, SID (Saccharomyces cerevisiae IDentifier), to identify the strains present in complex environmental samples. We optimized and assessed the performances of the analytical procedure on patterns generated in silico by computationally pooling Saccharomyces cerevisiae microsatellite profiles, and on samples obtained by pooling DNA of different strains, proving its ability to characterize real samples of grape wine fermentations. SID showed clear differences among S. cerevisiae populations in grape fermentation samples, identifying strains that are likely composing the populations and highlighting the impact of the inoculation of selected exogenous strains on natural strains. This tool can be successfully exploited to identify S. cerevisiae strains in any kind of complex samples.
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http://dx.doi.org/10.1038/s41598-017-15729-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5681646PMC
November 2017

Bifidobacterium callitrichidarum sp. nov. from the faeces of the emperor tamarin (Saguinus imperator).

Int J Syst Evol Microbiol 2018 Jan 8;68(1):141-148. Epub 2017 Nov 8.

Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.

Three Gram-stain-positive, non-spore-forming, microaerophilic and fructose-6-phosphate phosphoketolase positive strains were isolated from a faecal sample of an adult subject of the emperor tamarin (Saguinus imperator). Given that the isolates revealed identical BOX PCR profiles, strain TRI 5 was selected as a representative and characterized further. Comparative analysis of 16S rRNA gene sequence similarity revealed that strain TRI 5 was closely related to Bifidobacterium saguini DSM 23967 (96.4 %) and to Bifidobacterium longum subsp. longum ATCC 15708 (96.2 %). Multilocus sequence analyses of five housekeeping genes showed the close phylogenetic relatedness of this strain to Bifidobacterium breve DSM 20213 (hsp60 94.1 %), Bifidobacterium saguini DSM 23967 (clpC 91 %), Bifidobacterium avesanii DSM 100685 (dnaG 80.3 %), Bifidobacterium longumsubsp. infantis ATCC 15697 (dnaJ 85.3 %) and Bifidobacterium longumsubsp. longum ATCC 15708 (rpoB 93 %), respectively. The peptidoglycan type was A3β, with an interpeptide bridge comprising l-Orn (Lys) - l-Ser - l-Ala - l-Thr - l-Ala. The DNA G+C content of strain TRI 5 was 60.9 mol%. Based on the data provided, strain TRI 5 represents a novel species of the genus Bifidobacterium for which the name Bifidobacteriumcallitrichidarum sp. nov. is proposed. The type strain is TRI 5 (=DSM 103152=JCM 31790).
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http://dx.doi.org/10.1099/ijsem.0.002472DOI Listing
January 2018
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