78 results on '"Stefanini I"'
Search Results
2. Strategies to augment non-immune system based defence mechanisms against gastrointestinal diseases in pigs
- Author
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Modesto, M., Stefanini, I., D’Aimmo, M.R., Nissen, L., Tabanelli, D., Mazzoni, M., Bosi, P., Strozzi, G.P., and Biavati, B.
- Published
- 2011
- Full Text
- View/download PDF
3. The tumour microenvironment shapes dendritic cell plasticity in a human organotypic melanoma culture
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Blasio, S. Di, Wigcheren, G.F. van, Becker, A., Duffelen, A. van, Gorris, M.A., Verrijp, K., Stefanini, I., Bakker, G.J., Bloemendal, M., Halilovic, A., Vasaturo, A., Bakdash, G., Hato, S.V., Wilt, J.H.W. de, Schalkwijk, J., Vries, I.J.M. de, Textor, J.C., Bogaard, E.H.J. van den, Tazzari, M., Figdor, C.G., Blasio, S. Di, Wigcheren, G.F. van, Becker, A., Duffelen, A. van, Gorris, M.A., Verrijp, K., Stefanini, I., Bakker, G.J., Bloemendal, M., Halilovic, A., Vasaturo, A., Bakdash, G., Hato, S.V., Wilt, J.H.W. de, Schalkwijk, J., Vries, I.J.M. de, Textor, J.C., Bogaard, E.H.J. van den, Tazzari, M., and Figdor, C.G.
- Abstract
Contains fulltext : 220729.pdf (publisher's version ) (Open Access), The tumour microenvironment (TME) forms a major obstacle in effective cancer treatment and for clinical success of immunotherapy. Conventional co-cultures have shed light onto multiple aspects of cancer immunobiology, but they are limited by the lack of physiological complexity. We develop a human organotypic skin melanoma culture (OMC) that allows real-time study of host-malignant cell interactions within a multicellular tissue architecture. By co-culturing decellularized dermis with keratinocytes, fibroblasts and immune cells in the presence of melanoma cells, we generate a reconstructed TME that closely resembles tumour growth as observed in human lesions and supports cell survival and function. We demonstrate that the OMC is suitable and outperforms conventional 2D co-cultures for the study of TME-imprinting mechanisms. Within the OMC, we observe the tumour-driven conversion of cDC2s into CD14(+) DCs, characterized by an immunosuppressive phenotype. The OMC provides a valuable approach to study how a TME affects the immune system.
- Published
- 2020
4. The tumorigenic role of Low Molecular Weight Phosphotyrosine-Phosphatase (LMW-PTP): SW04.S17–49
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Raugei, G., Cavalieri, D., Marconi, C., Taddei, M. L., Stefanini, I., and Pietrovito, L.
- Published
- 2013
5. Age and gender affect the composition of fungal population of the human gastrointestinal tract
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Strati, F, Di Paola, M, Stefanini, I, Albanese, D, Rizzetto, L, Lionetti, P, Calabro, A, Jousson, O, Donati, C, Cavalieri, D, De Filippo, C, Strati F., Di Paola M., Stefanini I., Albanese D., Rizzetto L., Lionetti P., Calabro A., Jousson O., Donati C., Cavalieri D., De Filippo C., Strati, F, Di Paola, M, Stefanini, I, Albanese, D, Rizzetto, L, Lionetti, P, Calabro, A, Jousson, O, Donati, C, Cavalieri, D, De Filippo, C, Strati F., Di Paola M., Stefanini I., Albanese D., Rizzetto L., Lionetti P., Calabro A., Jousson O., Donati C., Cavalieri D., and De Filippo C.
- Abstract
The fungal component of the human gut microbiota has been neglected for long time due to the low relative abundance of fungi with respect to bacteria, and only recently few reports have explored its composition and dynamics in health or disease. The application of metagenomics methods to the full understanding of fungal communities is currently limited by the under representation of fungal DNA with respect to the bacterial one, as well as by the limited ability to discriminate passengers from colonizers. Here, we investigated the gut mycobiota of a cohort of healthy subjects in order to reduce the gap of knowledge concerning fungal intestinal communities in the healthy status further screening for phenotypical traits that could reflect fungi adaptation to the host. We studied the fecal fungal populations of 111 healthy subjects by means of cultivation on fungal selective media and by amplicon-based ITS1 metagenomics analysis on a subset of 57 individuals. We then characterized the isolated fungi for their tolerance to gastrointestinal (GI) tract-like challenges and their susceptibility to antifungals. A total of 34 different fungal species were isolated showing several phenotypic characteristics associated with intestinal environment such as tolerance to body temperature (37°C), to acidic and oxidative stress, and to bile salts exposure. We found a high frequency of azoles resistance in fungal isolates, with potential and significant clinical impact. Analyses of fungal communities revealed that the human gut mycobiota differs in function of individuals' life stage in a gender-related fashion. The combination of metagenomics and fungal cultivation allowed an in-depth understanding of the fungal intestinal community structure associated to the healthy status and the commensalism-related traits of isolated fungi. We further discussed comparatively the results of sequencing and cultivation to critically evaluate the application of metagenomics-based approaches to fungal
- Published
- 2016
6. Altered gut microbiota in Rett syndrome
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Strati, F, Cavalieri, D, Albanese, D, De Felice, C, Donati, C, Hayek, J, Jousson, O, Leoncini, S, Pindo, M, Renzi, D, Rizzetto, L, Stefanini, I, Calabro, A, De Filippo, C, Strati F, Cavalieri D, Albanese D, De Felice C, Donati C, Hayek J, Jousson O, Leoncini S, Pindo M, Renzi D, Rizzetto L, Stefanini I, Calabro A, De Filippo C, Strati, F, Cavalieri, D, Albanese, D, De Felice, C, Donati, C, Hayek, J, Jousson, O, Leoncini, S, Pindo, M, Renzi, D, Rizzetto, L, Stefanini, I, Calabro, A, De Filippo, C, Strati F, Cavalieri D, Albanese D, De Felice C, Donati C, Hayek J, Jousson O, Leoncini S, Pindo M, Renzi D, Rizzetto L, Stefanini I, Calabro A, and De Filippo C
- Published
- 2016
7. Biodiversity of the human gut mycobiota and its adaptation to the gastrointestinal tract
- Author
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Strati, F, Stefanini, I, Di Paola, M, Rizzetto, L, Cavalieri, D, De Filippo, C, Strati F, Stefanini I, Di Paola M, Rizzetto L, Cavalieri D, De Filippo C., Strati, F, Stefanini, I, Di Paola, M, Rizzetto, L, Cavalieri, D, De Filippo, C, Strati F, Stefanini I, Di Paola M, Rizzetto L, Cavalieri D, and De Filippo C.
- Published
- 2015
8. Survival of metastatic melanoma patients after dendritic cell vaccination correlates with expression of leukocyte phosphatidylethanolamine-binding protein 1/Raf kinase inhibitory protein
- Author
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Buschow, S.I., Ramazzotti, M., Reinieren-Beeren, I.M.J., Heinzerling, L.M., Westdorp, H., Stefanini, I., Beltrame, L., Hato, S.V., Ellebaek, E., Gross, S., Nguyen, V.A., Weinlich, G., Ragoussis, J., Baban, D., Schuler-Thurner, B., Svane, I.M., Romani, N., Austyn, J.M., Vries, I.J.M. de, Schuler, G., Cavalieri, D., Figdor, C.G., Buschow, S.I., Ramazzotti, M., Reinieren-Beeren, I.M.J., Heinzerling, L.M., Westdorp, H., Stefanini, I., Beltrame, L., Hato, S.V., Ellebaek, E., Gross, S., Nguyen, V.A., Weinlich, G., Ragoussis, J., Baban, D., Schuler-Thurner, B., Svane, I.M., Romani, N., Austyn, J.M., Vries, I.J.M. de, Schuler, G., Cavalieri, D., and Figdor, C.G.
- Abstract
Item does not contain fulltext, Immunotherapy for metastatic melanoma offers great promise but, to date, only a subset of patients have responded. There is an urgent need to identify ways of allocating patients to the most beneficial therapy, to increase survival and decrease therapy-associated morbidity and costs. Blood-based biomarkers are of particular interest because of their straightforward implementation in routine clinical care. We sought to identify markers for dendritic cell (DC) vaccine-based immunotherapy against metastatic melanoma through gene expression analysis of peripheral blood mononuclear cells. A large-scale microarray analysis of 74 samples from two treatment centers, taken directly after the first round of DC vaccination, was performed. We found that phosphatidylethanolamine binding protein 1 (PEBP1)/Raf Kinase inhibitory protein (RKIP) expression can be used to identify a significant proportion of patients who performed poorly after DC vaccination. This result was validated by q-PCR analysis on blood samples from a second cohort of 95 patients treated with DC vaccination in four different centers. We conclude that low PEBP1 expression correlates with poor overall survival after DC vaccination. Intriguingly, this was only the case for expression of PEBP1 after, but not prior to, DC vaccination. Moreover, the change in PEBP1 expression upon vaccination correlated well with survival. Further analyses revealed that PEBP1 expression positively correlated with genes involved in T cell responses but inversely correlated with genes associated with myeloid cells and aberrant inflammation including STAT3, NOTCH1, and MAPK1. Concordantly, PEBP1 inversely correlated with the myeloid/lymphoid-ratio and was suppressed in patients suffering from chronic inflammatory disease.
- Published
- 2017
9. Survival of metastatic melanoma patients after dendritic cell vaccination correlates with expression of leukocyte phosphatidylethanolamine-binding protein 1/Raf kinase inhibitory protein
- Author
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Buschow, S.I. (Sonja I.), Ramazzotti, M. (Matteo), Reinieren-Beeren, I. (Inge), Heinzerling, L. (L.), Westdorp, H. (Harm), Stefanini, I. (Irene), Beltrame, L. (Luca), Hato, S.V. (Stanleyson V.), Ellebaek, E. (Eva), Gross, S. (Stefanie), Nguyen, V.A. (Van Anh), Weinlich, G. (Georg), Ragoussis, J. (Jiannis), Baban, D. (Dilair), Schuler-Thurner, B. (Beatrice), Svane, I.M. (Inge M.), Romani, N. (Nikolaus), Austyn, J.M. (Jonathan), Vries, I.J.M. (Jolanda) de, Schuler, G. (Gerhard), Cavalieri, D. (Duccio), Figdor, C.G. (Carl), Buschow, S.I. (Sonja I.), Ramazzotti, M. (Matteo), Reinieren-Beeren, I. (Inge), Heinzerling, L. (L.), Westdorp, H. (Harm), Stefanini, I. (Irene), Beltrame, L. (Luca), Hato, S.V. (Stanleyson V.), Ellebaek, E. (Eva), Gross, S. (Stefanie), Nguyen, V.A. (Van Anh), Weinlich, G. (Georg), Ragoussis, J. (Jiannis), Baban, D. (Dilair), Schuler-Thurner, B. (Beatrice), Svane, I.M. (Inge M.), Romani, N. (Nikolaus), Austyn, J.M. (Jonathan), Vries, I.J.M. (Jolanda) de, Schuler, G. (Gerhard), Cavalieri, D. (Duccio), and Figdor, C.G. (Carl)
- Abstract
Immunotherapy for metastatic melanoma offers great promise but, to date, only a subset of patients have responded. There is an urgent need to identify ways of allocating patients to the most beneficial therapy, to increase survival and decrease therapy-associated morbidity and costs. Blood-based biomarkers are of particular interest because of their straightforward implementation in routine clinical care. We sought to identify markers for dendritic cell (DC) vaccine-based immunotherapy against metastatic melanoma through gene expression analysis of peripheral blood mononuclear cells. A large-scale microarray analysis of 74 samples from two treatment centers, taken directly after the first round of DC vaccination, was performed. We found that phosphatidylethanolamine binding protein 1 (_PEBP1_)/ Raf Kinase inhibitory protein (RKIP) expression can be used to identify a significant proportion of patients who performed poorly after DC vaccination. This result was validated by q-PCR analysis on blood samples from a second cohort of 95 patients treated with DC vaccination in four different centers. We conclude that low _PEBP1_ expression correlates with poor overall survival after DC vaccination. Intriguingly, this was only the case for expression of _PEBP1_ after, but not prior to, DC vaccination. Moreover, the change in _PEBP1_ expression upon vaccination correlated well with survival. Further analyses revealed that _PEBP1_ expression positively correlated with genes involved in T cell responses but inversely correlated with genes associated with myeloid cells and aberrant inflammation including _STAT3, NOTCH1,_ and _MAPK1_. Concordantly, _PEBP1_ inversely correlated with the myeloid/ lymphoid-ratio and was suppressed in patients suffering from chronic inflammatory disease.
- Published
- 2017
- Full Text
- View/download PDF
10. Survival of metastatic melanoma patients after dendritic cell vaccination correlates with expression of leukocyte phosphatidylethanolamine-binding protein 1/Raf kinase inhibitory protein
- Author
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Buschow, Sonja, Ramazzotti, M, Reinieren-Beeren, IMJ, Heinzerling, LM, Westdorp, H, Stefanini, I, Beltrame, L, Hato, S V, Ellebaek, E, Gross, S, Nguyen, VA, Weinlich, G, Ragoussis, J, Baban, D, Schuler-Thurner, B, Svane, IM, Romani, N, Austyn, JM, de Vries, IJM, Schuler, G, Cavalieri, D, Figdor, CG, Buschow, Sonja, Ramazzotti, M, Reinieren-Beeren, IMJ, Heinzerling, LM, Westdorp, H, Stefanini, I, Beltrame, L, Hato, S V, Ellebaek, E, Gross, S, Nguyen, VA, Weinlich, G, Ragoussis, J, Baban, D, Schuler-Thurner, B, Svane, IM, Romani, N, Austyn, JM, de Vries, IJM, Schuler, G, Cavalieri, D, and Figdor, CG
- Published
- 2017
11. FastGC PTR-ToF-MS analysis of yeast VOCs
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Iuliia Khomenko, Stefanini, I., Luca Cappellin, Cappelletti, V., Pietro Franceschi, Märk, T. D., and Franco Biasioli
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Settore CHIM/01 - CHIMICA ANALITICA - Published
- 2016
12. Dynamic changes in microbiota and mycobiota during spontaneous 'Vino Santo Trentino' fermentation
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Stefanini, I, Albanese, D, Cavazza, A, Franciosi, E, De Filippo, C, Donati, C, and Cavalieri, D.
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microbiota, mycobiota, Vino Santo Trentino, fermentation - Published
- 2016
13. Social wasps are mating nests for yeasts
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Stefanini, I., Dapporto, L., Berná, L., Polsinelli, M., Turillazzi, S., and Cavalieri, D.
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Insects ,Ecologia di Saccharomyces cerevisiae ,Incrocio sessuale di lievito ,Mating ,Ecology ,Evolution ,Saccharomyces paradoxus ,Social wasps ,Saccharomyces cerevisiae ecology ,Saccharomyces cerevisiae ,Insetti ,Outbreeding ,Settore BIO/19 - MICROBIOLOGIA GENERALE - Published
- 2015
14. Isolation, identification and characterization of yeasts from fermented goat milk of the yaghnob valley in tajikistan
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Qvirist, L, De Filippo, C, Strati, F, Stefanini, I, Sordo, M, Andlid, T, Felis, G, Mattarelli, P, Cavalieri, D, Qvirist, L. A., De Filippo, C., Strati, Francesco, Stefanini, Irene, Sordo, Maddalena, Andlid, T., Felis, G. E., Mattarelli, P., Cavalieri, D., Qvirist, L, De Filippo, C, Strati, F, Stefanini, I, Sordo, M, Andlid, T, Felis, G, Mattarelli, P, Cavalieri, D, Qvirist, L. A., De Filippo, C., Strati, Francesco, Stefanini, Irene, Sordo, Maddalena, Andlid, T., Felis, G. E., Mattarelli, P., and Cavalieri, D.
- Abstract
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.
- Published
- 2016
15. Characterization of the bacterial and fungal microbiota in Rett syndrome
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Strati, F, Albanese, D, Renzi, D, Rizzetto, L, Stefanini, I, Jousson, O, Hayek, J, De Felice, C, Donati, C, Calabrò, A, Cavalieri, D, De Filippo, C, Strati, Francesco, Albanese, Davide, Renzi, D., Rizzetto, Lisa, Stefanini, Irene, Jousson, O., Hayek, J., De Felice, C., Donati, Claudio, Calabrò, A., Cavalieri, Duccio, De Filippo, Carlotta, Strati, F, Albanese, D, Renzi, D, Rizzetto, L, Stefanini, I, Jousson, O, Hayek, J, De Felice, C, Donati, C, Calabrò, A, Cavalieri, D, De Filippo, C, Strati, Francesco, Albanese, Davide, Renzi, D., Rizzetto, Lisa, Stefanini, Irene, Jousson, O., Hayek, J., De Felice, C., Donati, Claudio, Calabrò, A., Cavalieri, Duccio, and De Filippo, Carlotta
- Abstract
The human gut microbiota directly affect human health. Alterations in the composition of commensal bacteria can lead to chronic inflammation also predisposing individuals to fungal infections. Commensal fungi are important in human health and changes in commensal fungal populations have been shown to deeply affect pathologies not directly related to fungi, such as Inflammatory Bowel Diseases. Rett syndrome (RTT) is a neurodegenerative disorder caused by a mutation in MECP2. High proportion of RTT subjects suffer of gastrointestinal disorders, implying a link between RTT and the gut microbiota. We studied the bacterial and fungal gut microbiota of patients affected by RTT by a multilevel approach to understand whether changes in gut microbiota of RTT patients could be associated with GI abnormalities, inflammatory status and cytokine dysregulation previously observed. Our findings revealed that RTT patients harbor a distinct and less diverse bacterial and fungal microbiota compared to healthy subjects in which Bifidobacterium and Candida are the most abundant genera. The immunological responses exerted by RTT yeast isolates in our in vitro cell model suggest that fungi could contribute to the gastrointestinal abnormalities and intestinal inflammation observed in our RTT study cohort.
- Published
- 2015
16. Diverse strain immune reactivity shapes fungal inflammation or tolerance
- Author
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Rizzetto, L., Di Paola, M., Ifrim, D.C., Stefanini, I., De Filippo, C., Giovannini, G., Lionetti, P., Netea, M.G., Romani, L., and Cavalieri, D.
- Subjects
Fungal strains ,Immune reactivity ,Infection ,Tolerance ,Settore BIO/19 - MICROBIOLOGIA GENERALE - Published
- 2013
17. Characterization of fecal mycobiota reveals yeast-host coevolution in pediatric Crohn’s disease
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De Filippo, C., Di Paola, M., Rizzetto, L., Stefanini, I., Berná, L., Ramazzotti, M., Dapporto, L., Rivero, D., Gut, I.G., Legras, J.L., Massi Benedetti, C., De Luca, A., Romani, L., Lionetti, P., and Cavalieri, D.
- Subjects
Microbiota intestinale ,Inflammatory Bowel Disease ,Saccharomyces cerevisiae ,Gut microbiota ,Malattie infiammatorie croniche intestinali ,Settore MED/07 - MICROBIOLOGIA E MICROBIOLOGIA CLINICA - Published
- 2013
18. Social insect intestines are mating nests for Saccharomyces cerevisiae
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Stefanini, I., Dapporto, L., Bernà, L., Polsinelli, M., Turillazzi, S., and Cavalieri, D.
- Subjects
Ecologia di Saccharomyces cerevisiae ,Incrocio sessuale di lievito ,Settore BIO/18 - GENETICA ,Saccharomyces cerevisiae ecology ,Yeast mating ,Social insects ,Settore BIO/19 - MICROBIOLOGIA GENERALE ,Insetti sociali - Published
- 2013
19. Systems biology approach for the identification of genetic determinants of colony morphology switch in natural S. cerevisiae strain
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Cappelletti, V., Stefanini, I., Bernà, L., Ramazzotti, M., Cestaro, A., Gut, I., Kapushesky, M., Csikász Nagy, A., and Cavalieri, D.
- Subjects
Settore BIO/18 - GENETICA - Published
- 2013
20. The touch of death: killer mediated contact inhibition and Hsp12p secretion determines differential fitness in a community of grape yeast isolates
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Rivero, D., Bernà, L., Baruffini, E., Stefanini, I., and Cavalieri, D.
- Subjects
Settore BIO/18 - GENETICA - Published
- 2013
21. Dietary Nitrate: Effects on the health of weaning pigs and Antimicrobial activity on seven probiotic Bifidobacterium spp. strains
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Biavati, B., Modesto, M., Stefanini, I., D'Aimmo, M. R., Mazzoni, M., Trevisi, P., Tittarelli, C., Bosi, P., Strozzi, G. P., Allesina, S., Deidda, F., Barba, M., and Lorenzini, P.
- Subjects
Feeding and growth ,Health and welfare - Abstract
The potential role of nitrite as an antimicrobial substance in the stomach may be of some importance in the ecology of the gastrointestinal tract and in host physiology. It has been shown that nitrite, under the acidic conditions of the stomach, may kill gut pathogens like Salmonella enteritidis, Escherichia coli, Salmonella typhimurium, and Yersinia enterocolitica, whereas acid alone has only a bacteriostatic effect. An in vivo study was conducted in order to assess the effects of dietary nitrate on microbiota and on the health of the gut (particularly in the stomach and small intestine). 96 weaning pigs were fed a diet containing high nitrate levels (15 mg and 150 mg) and then challenged with Salmonella enterica serovar typhimurium. Differences in composition of the gut microbiota were assessed by analysing samples from the pigs: To date analysis of 48 pigs has been completed.. Preliminary results demonstrated no effect on the population densities of microbial groups either from the challenge or from nitrate intake. However, increasing the time from challenge decreased either the counts of LAB in the stomach and jejunum or of clostridia in the stomach. Bifidobacteria also decreased in the stomach contents as nitrate supplementation increased. Supplementing the feedstuff with high dietary nitrate intake and then challenging with Salmonella did not affect the gastric pH or the degree of ulceration in the pigs. The synergistic bactericidal effects of pH, nitrite and thiocyanate on seven probiotic Bifidobacterium spp. strains were also investigated in an in vitro study. The results of the in vitro study demonstrated that an inhibitory effect exists on the seven probiotic bifidobacteria investigated with an exposure longer than 2 hours and pH values < 5.0. Addition of thiocyanate also increased the susceptibility of the tested strains. In this in vitro study, the most resistant strains at all conditions were B. animalis subsp. lactis Ra 18 and P32 and B. choerinum Su 877, Su 837 and Su 891.
- Published
- 2007
22. Effect of probiotic inocula and/or nutribiotics on the population density of lactic acid bacteria in the intestine of weaning pigs
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D'Aimmo, M. R., Modesto, M., Stefanini, I., Mazzoni, M., Trevisi, P., Tittarelli, C., Bosi, P., and Biavati, B.
- Subjects
fluids and secretions ,food and beverages ,Health and welfare ,digestive system - Abstract
Food safety and health issues increased the need to use alternative procedures to antibiotics to combat pathogens in livestock. We evaluated the potential health-improving effects of both a probiotic and/or prebiotic feed formula in four series of trials. In a first and second experimental series, weaning pigs were fed respectively with different strains of Bifidobacterium spp. as probiotics and different fructo- and galacto-oligosaccharides as prebiotics. The best probiotic strains and prebiotic fiber resulting from these two series were jointly used in a third series. The composition of the cecal microbiota of the weaning pigs was analyzed and in vivo trials were conducted to evaluate the effects of the feed supplements. Bifidobacteria strains with a similar ability to develop in the hindgut had a different effect on the piglet performance depending on the dose in which they were provided. Our data also support that the presence of fructo-oligosaccharides can stimulate the occurrence of bifidobacteria in the cecum. We did however not observe an additional growth stimulus when they were supplemented with an increasing dose of bifidobacteria. In the fourth series of trials the best feed supplementation formula (1011 cfu of a Bifidobacterium animalis subps. lactis twice a day per pig) was challenged by infecting the pigs with a pathogenic strain of Salmonella.
- Published
- 2006
23. DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells.
- Author
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Cavalieri, D., Rivero, D., Beltrame, L., Buschow, S.I., Calura, E., Rizzetto, L., Gessani, S., Gauzzi, M.C., Reith, W., Baur, A., Bonaiuti, R., Brandizi, M., Filippo, C. De, D'Oro, U., Draghici, S., Dunand-Sauthier, I., Gatti, E., Granucci, F., Gundel, M., Kramer, M., Kuka, M., Lanyi, A., Melief, C.J., Montfoort, N. van, Ostuni, R., Pierre, P., Popovici, R., Rajnavolgyi, E., Schierer, S., Schuler, G., Soumelis, V., Splendiani, A., Stefanini, I., Torcia, M.G., Zanoni, I., Zollinger, R., Figdor, C.G., Austyn, J.M., Cavalieri, D., Rivero, D., Beltrame, L., Buschow, S.I., Calura, E., Rizzetto, L., Gessani, S., Gauzzi, M.C., Reith, W., Baur, A., Bonaiuti, R., Brandizi, M., Filippo, C. De, D'Oro, U., Draghici, S., Dunand-Sauthier, I., Gatti, E., Granucci, F., Gundel, M., Kramer, M., Kuka, M., Lanyi, A., Melief, C.J., Montfoort, N. van, Ostuni, R., Pierre, P., Popovici, R., Rajnavolgyi, E., Schierer, S., Schuler, G., Soumelis, V., Splendiani, A., Stefanini, I., Torcia, M.G., Zanoni, I., Zollinger, R., Figdor, C.G., and Austyn, J.M.
- Abstract
Contains fulltext : 88001.pdf (publisher's version ) (Closed access), BACKGROUND: The advent of Systems Biology has been accompanied by the blooming of pathway databases. Currently pathways are defined generically with respect to the organ or cell type where a reaction takes place. The cell type specificity of the reactions is the foundation of immunological research, and capturing this specificity is of paramount importance when using pathway-based analyses to decipher complex immunological datasets. Here, we present DC-ATLAS, a novel and versatile resource for the interpretation of high-throughput data generated perturbing the signaling network of dendritic cells (DCs). RESULTS: Pathways are annotated using a novel data model, the Biological Connection Markup Language (BCML), a SBGN-compliant data format developed to store the large amount of information collected. The application of DC-ATLAS to pathway-based analysis of the transcriptional program of DCs stimulated with agonists of the toll-like receptor family allows an integrated description of the flow of information from the cellular sensors to the functional outcome, capturing the temporal series of activation events by grouping sets of reactions that occur at different time points in well-defined functional modules. CONCLUSIONS: The initiative significantly improves our understanding of DC biology and regulatory networks. Developing a systems biology approach for immune system holds the promise of translating knowledge on the immune system into more successful immunotherapy strategies.
- Published
- 2010
24. DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cell
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Cavalieri, D, Rivero, D, Beltrame, L, Buschow, S, Calura, E, Rizzetto, L, Gessani, S, Gauzzi, M, Reith, W, Baur, A, Bonaiuti, R, Brandizi, M, De Filippo, C, D'Oro, U, Draghici, S, Dunand Sauthier, I, Gatti, E, Granucci, F, Gündel, M, Kramer, M, Kuka, M, Lanyi, A, Melief, C, Van Montfoort, N, Ostuni, R, Pierre, P, Popovici, R, Rajnavolgyi, E, Schierer, S, Schuler, G, Soumelis, V, Splendiani, A, Stefanini, I, Torcia, M, Zanoni, I, Zollinger, R, Figdor, C, Austyn, J, Buschow, SI, Melief, CJ, Torcia, MG, Figdor, CG, Austyn, JM, GRANUCCI, FRANCESCA, ZANONI, IVAN, Cavalieri, D, Rivero, D, Beltrame, L, Buschow, S, Calura, E, Rizzetto, L, Gessani, S, Gauzzi, M, Reith, W, Baur, A, Bonaiuti, R, Brandizi, M, De Filippo, C, D'Oro, U, Draghici, S, Dunand Sauthier, I, Gatti, E, Granucci, F, Gündel, M, Kramer, M, Kuka, M, Lanyi, A, Melief, C, Van Montfoort, N, Ostuni, R, Pierre, P, Popovici, R, Rajnavolgyi, E, Schierer, S, Schuler, G, Soumelis, V, Splendiani, A, Stefanini, I, Torcia, M, Zanoni, I, Zollinger, R, Figdor, C, Austyn, J, Buschow, SI, Melief, CJ, Torcia, MG, Figdor, CG, Austyn, JM, GRANUCCI, FRANCESCA, and ZANONI, IVAN
- Abstract
Background: The advent of Systems Biology has been accompanied by the blooming of pathway databases. Currently pathways are defined generically with respect to the organ or cell type where a reaction takes place. The cell type specificity of the reactions is the foundation of immunological research, and capturing this specificity is of paramount importance when using pathway-based analyses to decipher complex immunological datasets. Here, we present DC-ATLAS, a novel and versatile resource for the interpretation of high-throughput data generated perturbing the signaling network of dendritic cells (DCs). Results: Pathways are annotated using a novel data model, the Biological Connection Markup Language (BCML), a SBGN-compliant data format developed to store the large amount of information collected. The application of DC-ATLAS to pathway-based analysis of the transcriptional program of DCs stimulated with agonists of the toll-like receptor family allows an integrated description of the flow of information from the cellular sensors to the functional outcome, capturing the temporal series of activation events by grouping sets of reactions that occur at different time points in well-defined functional modules. Conclusions: The initiative significantly improves our understanding of DC biology and regulatory networks. Developing a systems biology approach for immune system holds the promise of translating knowledge on the immune system into more successful immunotherapy strategies. © 2010 Cavalieri et al; licensee BioMed Central Ltd.
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- 2010
25. Bifidobacterium lemurum sp. nov., from faeces of the ring-tailed lemur (Lemur catta)
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Paola Mattarelli, Caterina Spiezio, Monica Marianna Modesto, Samanta Michelini, Bruno Biavati, Camillo Sandri, Ilaria Stefanini, Annamaria Pisi, Gianfranco Filippini, Modesto, M., Michelini, S., Stefanini, I., Sandri, C., Spiezio, C., Pisi, A., Filippini, G., Biavati, B., and Mattarelli, P.
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DNA, Bacterial ,Bifidobacterium longum ,Molecular Sequence Data ,Lemur ,Lemur catta ,Microbiology ,ring-tailed lemur ,Feces ,RNA, Ribosomal, 16S ,biology.animal ,Animals ,Bifidobacterium lemurum ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Base Composition ,biology ,Phylogenetic tree ,Strain (chemistry) ,Sequence Analysis, DNA ,General Medicine ,biology.organism_classification ,16S ribosomal RNA ,rpoB ,New species ,Bacterial Typing Techniques ,Bifidobacteriaceae ,Genes, Bacterial ,Bifidobacterium ,Multilocus Sequence Typing - Abstract
Four Gram-positive-staining, microaerophilic, non-spore-forming, fructose-6-phosphate phosphoketolase-positive bacterial strains were isolated from a faecal sample of a 5-year-old ring-tailed lemur (Lemur catta). The strains showed a peculiar morphology, resembling a small coiled snake, a ring shape, or forming a little ‘Y’ shape. The isolated strains appeared identical, and LMC 13T was chosen as a representative strain and characterized further. Strain LMC 13T showed an A3β peptidoglycan type, similar to that found in Bifidobacterium longum . The DNA base composition was 57.2 mol% G+C. Almost-complete 16S rRNA, hsp60, rpoB, dnaJ, dnaG, purF, clpC and rpoC gene sequences were obtained, and phylogenetic relationships were determined. Comparative analysis of 16S rRNA gene sequences showed that strain LMC 13T showed the highest similarity to B. longum subsp. suis ATCC 27533T (96.65 %) and Bifidobacterium saguini DSM 23967T (96.64 %). Strain LMC 13T was located in an actinobacterial cluster and was more closely related to the genus Bifidobacterium than to other genera in the Bifidobacteriaceae . On the basis of these results, strain LMC 13T represents a novel species within the genus Bifidobacterium , for which the name Bifidobacterium lemurum sp. nov. is proposed; the type strain is LMC 13T ( = DSM 28807T = JCM 30168T).
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- 2015
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26. Isolation, identification and characterization of yeasts from fermented goat milk of the yaghnob valley in tajikistan
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Linnea Qvirist, Maddalena Sordo, Duccio Cavalieri, Francesco Strati, Irene Stefanini, Carlotta De Filippo, Thomas Andlid, Giovanna E. Felis, Paola Mattarelli, Qvirist, L, De Filippo, C, Strati, F, Stefanini, I, Sordo, M, Andlid, T, Felis, G, Mattarelli, P, Cavalieri, D, Qvirist, Linnea A., Filippo, Carlotta De, Strati, Francesco, Stefanini, Irene, Sordo, Maddalena, Andlid, Thoma, Felis, Giovanna E., Mattarelli, Paola, and Cavalieri, Duccio
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0301 basic medicine ,Microbiology (medical) ,Genotyping ,Identification ,030106 microbiology ,Saccharomyces cerevisiae ,Population ,lcsh:QR1-502 ,Biology ,Fermented goat milk ,Yaghnob Valley Tajikistan ,Microbiology ,lcsh:Microbiology ,03 medical and health sciences ,fermented goat milk ,genotyping ,identification ,phenotyping ,yeast ,Kluyveromyces marxianus ,Botany ,Food science ,education ,Original Research ,Wine ,education.field_of_study ,Phenotyping ,Yeast ,Strain (biology) ,fermented milk, yaghnobi, Tajikistan, yeast, Kluvyeromyces marxianus ,food and beverages ,biology.organism_classification ,Isolation (microbiology) ,Fermentation ,Settore BIO/19 - MICROBIOLOGIA GENERALE - Abstract
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.
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- 2016
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27. Age and Gender Affect the Composition of Fungal Population of the Human Gastrointestinal Tract
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Francesco Strati, Monica Di Paola, Irene Stefanini, Davide Albanese, Lisa Rizzetto, Paolo Lionetti, Antonio Calabrò, Olivier Jousson, Claudio Donati, Duccio Cavalieri, Carlotta De Filippo, Strati, F, Di Paola, M, Stefanini, I, Albanese, D, Rizzetto, L, Lionetti, P, Calabro, A, Jousson, O, Donati, C, Cavalieri, D, and De Filippo, C
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0301 basic medicine ,Microbiology (medical) ,Mycobiota ,fungi-host interactions ,030106 microbiology ,lcsh:QR1-502 ,human gut mycobiota ,Biology ,Microbiology ,lcsh:Microbiology ,03 medical and health sciences ,medicine ,antifungal resistance ,commensal fungi ,fungal metagenomics ,Commensal fungi ,Feces ,Original Research ,Fungal metagenomics ,2. Zero hunger ,Host (biology) ,Human gut mycobiota ,Human gastrointestinal tract ,Antifungal resistance ,Amplicon ,biology.organism_classification ,030104 developmental biology ,medicine.anatomical_structure ,Fungi-host interaction ,13. Climate action ,Metagenomics ,Fungi-host interactions ,Fungal metagenomic ,Adaptation ,Settore BIO/19 - MICROBIOLOGIA GENERALE ,Bacteria - Abstract
The fungal component of the human gut microbiota has been neglected for long time due to the low relative abundance of fungi with respect to bacteria, and only recently few reports have explored its composition and dynamics in health or disease. The application of metagenomics methods to the full understanding of fungal communities is currently limited by the under representation of fungal DNA with respect to the bacterial one, as well as by the limited ability to discriminate passengers from colonizers. Here, we investigated the gut mycobiota of a cohort of healthy subjects in order to reduce the gap of knowledge concerning fungal intestinal communities in the healthy status further screening for phenotypical traits that could reflect fungi adaptation to the host. We studied the fecal fungal populations of 111 healthy subjects by means of cultivation on fungal selective media and by amplicon-based ITS1 metagenomics analysis on a subset of 57 individuals. We then characterized the isolated fungi for their tolerance to gastrointestinal (GI) tract-like challenges and their susceptibility to antifungals. A total of 34 different fungal species were isolated showing several phenotypic characteristics associated with intestinal environment such as tolerance to body temperature (37°C), to acidic and oxidative stress, and to bile salts exposure. We found a high frequency of azoles resistance in fungal isolates, with potential and significant clinical impact. Analyses of fungal communities revealed that the human gut mycobiota differs in function of individuals' life stage in a gender-related fashion. The combination of metagenomics and fungal cultivation allowed an in-depth understanding of the fungal intestinal community structure associated to the healthy status and the commensalism-related traits of isolated fungi. We further discussed comparatively the results of sequencing and cultivation to critically evaluate the application of metagenomics-based approaches to fungal gut populations.
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- 2016
28. DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells
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Matthijs Kramer, Roberto Bonaiuti, Ivan Zanoni, Gerold Schuler, Walter Reith, Sorin Draghici, Damariz Rivero, Vassili Soumelis, Jonathan M. Austyn, Ugo D'Oro, Cornelis J. M. Melief, Andrea Splendiani, Carl G. Figdor, Maria Torcia, Enrica Calura, Marco Brandizi, Renato Ostuni, Sandra Gessani, Duccio Cavalieri, Francesca Granucci, Sonja I. Buschow, Maria Cristina Gauzzi, Arpad Lanyi, Stephan Schierer, Nadine van Montfoort, Éva Rajnavölgyi, Michaela Gündel, Philippe Pierre, Raphaël Zollinger, Luca Beltrame, Lisa Rizzetto, Andreas Baur, Isabelle Dunand-Sauthier, Carlotta De Filippo, Mirela Kuka, Evelina Gatti, Irene Stefanini, Razvan Popovici, Reith, Walter, Dunand-Sauthier, Isabelle, Pierre, Philippe, Università degli Studi di Firenze [Firenze], Radboud University Medical Center [Nijmegen], Istituto Superiore di Sanità, Rome (ISS), Department of Therapeutic Research and Medicines Evaluation, University of Geneva Medical School, Department of Pathology and Immunology, University of Erlangen, Department of Dermatology, Leaf Bioscience, Novartis Vaccines, Siena, Italy, Novartis Vaccines, Wayne State University [Detroit], Centre d'Immunologie de Marseille - Luminy (CIML), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU), University of Milano-Bicocca (UNIMIB), Department of Biotechnology and Biosciences, University of Debrecen Egyetem [Debrecen], Leiden University Medical Center (LUMC), Miravtech Corporation, Immunité et cancer (U932), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Curie-Université Paris Descartes - Paris 5 (UPD5), University of Oxford [Oxford], Cavalieri, D, Rivero, D, Beltrame, L, Buschow, S, Calura, E, Rizzetto, L, Gessani, S, Gauzzi, M, Reith, W, Baur, A, Bonaiuti, R, Brandizi, M, De Filippo, C, D'Oro, U, Draghici, S, Dunand Sauthier, I, Gatti, E, Granucci, F, Gündel, M, Kramer, M, Kuka, M, Lanyi, A, Melief, C, Van Montfoort, N, Ostuni, R, Pierre, P, Popovici, R, Rajnavolgyi, E, Schierer, S, Schuler, G, Soumelis, V, Splendiani, A, Stefanini, I, Torcia, M, Zanoni, I, Zollinger, R, Figdor, C, Austyn, J, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Dipartimento di Biotecnologie e Bioscienze = Department of Biotechnology and Biosciences [Milano-Bicocca] (BTBS), Università degli Studi di Milano-Bicocca [Milano] (UNIMIB), Université Paris Descartes - Paris 5 (UPD5)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Buschow, Si, Gauzzi, Mc, Kuka, Mirela, Melief, Cj, van Montfoort, N, Torcia, Mg, Figdor, Cg, Austyn, J. M., Istituto Superiore di Sanità, Rome ( ISS ), Centre d'Immunologie de Marseille - Luminy ( CIML ), Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Aix Marseille Université ( AMU ) -Centre National de la Recherche Scientifique ( CNRS ), University of Milano-Bicocca ( UNIMIB ), Immunité et cancer ( U932 ), Université Paris Descartes - Paris 5 ( UPD5 ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Institut Curie, Università degli Studi di Firenze = University of Florence (UniFI), Istituto Superiore di Sanità (ISS), Università degli Studi di Milano-Bicocca = University of Milano-Bicocca (UNIMIB), Universiteit Leiden, and University of Oxford
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Cell type ,Markup language ,Computer science ,Systems biology ,medicine.medical_treatment ,Immunology ,Computational biology ,ddc:616.07 ,computer.software_genre ,03 medical and health sciences ,0302 clinical medicine ,Immune system ,Immune Regulation [NCMLS 2] ,medicine ,[ SDV.IMM ] Life Sciences [q-bio]/Immunology ,Elméleti orvostudományok ,Molecular gastro-enterology and hepatology [IGMD 2] ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,Applied Mathematics ,Research ,Dendritic cells, toll like receptors, pattern recognition receptors, systems biology ,Pattern recognition receptor ,Immunotherapy ,Orvostudományok ,dendritic cells ,toll-like receptors ,TLR ,TLR pathways ,systems biology ,pathway analysis ,Computer Science Applications ,Computational Theory and Mathematics ,DECIPHER ,[SDV.IMM]Life Sciences [q-bio]/Immunology ,Data mining ,Signal transduction ,computer ,030215 immunology - Abstract
Contains fulltext : 88001.pdf (Publisher’s version ) (Closed access) BACKGROUND: The advent of Systems Biology has been accompanied by the blooming of pathway databases. Currently pathways are defined generically with respect to the organ or cell type where a reaction takes place. The cell type specificity of the reactions is the foundation of immunological research, and capturing this specificity is of paramount importance when using pathway-based analyses to decipher complex immunological datasets. Here, we present DC-ATLAS, a novel and versatile resource for the interpretation of high-throughput data generated perturbing the signaling network of dendritic cells (DCs). RESULTS: Pathways are annotated using a novel data model, the Biological Connection Markup Language (BCML), a SBGN-compliant data format developed to store the large amount of information collected. The application of DC-ATLAS to pathway-based analysis of the transcriptional program of DCs stimulated with agonists of the toll-like receptor family allows an integrated description of the flow of information from the cellular sensors to the functional outcome, capturing the temporal series of activation events by grouping sets of reactions that occur at different time points in well-defined functional modules. CONCLUSIONS: The initiative significantly improves our understanding of DC biology and regulatory networks. Developing a systems biology approach for immune system holds the promise of translating knowledge on the immune system into more successful immunotherapy strategies.
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- 2010
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29. Altered gut microbiota in Rett syndrome
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Francesco Strati, Irene Stefanini, Silvia Leoncini, Lisa Rizzetto, Carlotta De Filippo, Claudio De Felice, Olivier Jousson, Daniela Renzi, Duccio Cavalieri, Claudio Donati, Antonino Salvatore Calabrò, Joussef Hayek, Davide Albanese, Massimo Pindo, Strati, F, Cavalieri, D, Albanese, D, De Felice, C, Donati, C, Hayek, J, Jousson, O, Leoncini, S, Pindo, M, Renzi, D, Rizzetto, L, Stefanini, I, Calabro, A, De Filippo, C, and Calabrò, A
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SCFAs ,0301 basic medicine ,Methyl-CpG-Binding Protein 2 ,gut microbiome ,Intestinal dysbiosi ,Gut flora ,0302 clinical medicine ,Rett syndrome ,fluids and secretions ,Anaerostipes ,Mycobiota ,Lactobacillus ,Bifidobacterium ,2. Zero hunger ,biology ,Fatty Acids ,Gastrointestinal Microbiome ,Biodiversity ,3. Good health ,Intestines ,Intestinal dysbiosis ,Settore BIO/19 - MICROBIOLOGIA GENERALE ,Microbiology (medical) ,congenital, hereditary, and neonatal diseases and abnormalities ,food.ingredient ,Metataxonomic ,Gut microbiota ,Microbiology ,digestive system ,03 medical and health sciences ,food ,medicine ,Humans ,Metabolomics ,Inflammation ,Bacteria ,Research ,Metataxonomics ,Fungi ,SCFA ,biology.organism_classification ,medicine.disease ,030104 developmental biology ,Immunology ,Constipation ,Dysbiosis ,Metagenomics ,mycobiota ,030217 neurology & neurosurgery ,Actinomyces - Abstract
Background The human gut microbiota directly affects human health, and its alteration can lead to gastrointestinal abnormalities and inflammation. Rett syndrome (RTT), a progressive neurological disorder mainly caused by mutations in MeCP2 gene, is commonly associated with gastrointestinal dysfunctions and constipation, suggesting a link between RTT’s gastrointestinal abnormalities and the gut microbiota. The aim of this study was to evaluate the bacterial and fungal gut microbiota in a cohort of RTT subjects integrating clinical, metabolomics and metagenomics data to understand if changes in the gut microbiota of RTT subjects could be associated with gastrointestinal abnormalities and inflammatory status. Results Our findings revealed the occurrence of an intestinal sub-inflammatory status in RTT subjects as measured by the elevated values of faecal calprotectin and erythrocyte sedimentation rate. We showed that, overall, RTT subjects harbour bacterial and fungal microbiota altered in terms of relative abundances from those of healthy controls, with a reduced microbial richness and dominated by microbial taxa belonging to Bifidobacterium, several Clostridia (among which Anaerostipes, Clostridium XIVa, Clostridium XIVb) as well as Erysipelotrichaceae, Actinomyces, Lactobacillus, Enterococcus, Eggerthella, Escherichia/Shigella and the fungal genus Candida. We further observed that alterations of the gut microbiota do not depend on the constipation status of RTT subjects and that this dysbiotic microbiota produced altered short chain fatty acids profiles. Conclusions We demonstrated for the first time that RTT is associated with a dysbiosis of both the bacterial and fungal component of the gut microbiota, suggesting that impairments of MeCP2 functioning favour the establishment of a microbial community adapted to the costive gastrointestinal niche of RTT subjects. The altered production of short chain fatty acids associated with this microbiota might reinforce the constipation status of RTT subjects and contribute to RTT gastrointestinal physiopathology. Electronic supplementary material The online version of this article (doi:10.1186/s40168-016-0185-y) contains supplementary material, which is available to authorized users.
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30. Population genomics of Saccharomyces cerevisiae human isolates reveals adaptation to the gastrointestinal tract
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Di Paola, Monica, Filippo, Carlotta, Stefanini, Irene, Lisa Rizzetto, Berna, Luisa, Ramazzotti, Matteo, Dapporto, Leonardo, Rivero, Damariz, Gut, Ivo Glynne, Legras, Jean-Luc, Tocci, Noemi, Lenucci, Marcello S., Romani, Luigina, Lionetti, Paolo, Cavalieri, Duccio, Meyer Children Hosp, Dept Neurosci Psychol Drug Res & Child Hlth, Università degli Studi di Firenze, Research and Innovation Centre, Fondazione Edmund Mach - Edmund Mach Foundation [Italie] (FEM), Molecular Biology / Biología Molecular [Montevideo], Institut Pasteur de Montevideo, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Dept Expt & Clin Biomed Sci, Dept Biol & Med Sci, Oxford Brookes University, Centro Nacional de Analisis Genomico (CNAG), Sciences Pour l'Oenologie (SPO), Université Montpellier 1 (UM1)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Dipartimento Sci & Tecnol Biol & Ambientali, Università del Salento, Polo Unico SantAndrea Fratte, Dept Expt Med & Biochem Sci, Università degli Studi di Perugia (UNIPG), Unidad Biol Mol, Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Di Paola, M, De Filippo, C, Stefanini, I, Rizzetto, L, Berna, L, Ramazzotti, M, Dapporto, L, Rivero, D, Gut, Ig, Legras, Jl, Tocci, N, Lenucci, Marcello Salvatore, Romani, L, Lionetti, P, and Cavalieri, D.
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Population genetics ,Evolution ,[SDV]Life Sciences [q-bio] ,Crohn disease ,saccharomyces cerevisiae ,yeast ,brewer s ,génomique des populations ,Settore BIO/19 - MICROBIOLOGIA GENERALE ,tractus gastrointestinal - Abstract
Présenté au 27. International Conference on Yeast Genetics and Molecular Biology (ICYGMB)Lieu: Edmund Mach Foundation, Levico Terme, ItalieDates: 2015/09/06-12; Population genomics of [i]Saccharomyces cerevisiae[/i] human isolates reveals adaptation to the gastrointestinal tract
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31. Yeasts, arthropods, and environmental matrix: a triad to disentangle the multi-level definition of biodiversity.
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Valentini B, Penna M, Viazzo M, Caprio E, Casacci LP, Barbero F, and Stefanini I
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- Animals, Ecosystem, Farms, Biodiversity, Arthropods microbiology, Yeasts classification, Yeasts isolation & purification, Yeasts genetics
- Abstract
Our understanding of the spread of yeasts in natural ecosystems remains somewhat limited. The recent momentum of yeast ecology research has unveiled novel habitats and vectors that, alongside human activities, impact yeast communities in their natural environments. Yeasts, as non-airborne microorganisms, rely on animal vectors, predominantly insects. However, the overlooked actor in this interplay is the environmental matrix, a player potentially influencing yeast populations and their vectors. This study aims to delve deeper into the intricate, multi-layered connections between yeast populations and ecosystems, focusing on the interactions between the attributes of the environmental matrix, arthropod diversity, and the mycobiota within a renowned yeast-inhabited framework: the vineyard. To investigate these relationships, we sampled both invertebrate and yeast diversity in six organic and conventional vineyards described in terms of management and landscape composition. We identified 80 different invertebrate taxa and isolated 170 yeast strains belonging to 18 species. Notably, new species-specific yeast-insect associations were observed, including the exclusive association between Candida orthopsilosis and Hymenoptera and between Metschnikowia pulcherrima and Coleoptera. These newly identified potential associations provide valuable insights into insect and yeast physiology, hence holding the promise of enhancing our understanding of yeast and arthropod ecology and their collective impact on overall ecosystem health., (© 2024. The Author(s).)
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- 2024
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32. Fungal Identifier (FId): An Updated Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Approach to Ease Ascomycetous Yeast Isolates' Identification in Ecological Studies.
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Abbà S, Valentini B, and Stefanini I
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Culturomics has been temporarily exceeded by the advent of omics approaches such as metabarcoding and metagenomics. However, despite improving our knowledge of microbial population composition, both metabarcoding and metagenomics are not suitable for investigating and experimental testing inferences about microbial ecological roles and evolution. This leads to a recent revival of culturomics approaches, which should be supported by improvements in the available tools for high-throughput microbial identification. This study aimed to update the classical PCR-RFLP approach in light of the currently available knowledge on yeast genomics. We generated and analyzed a database including more than 1400 ascomycetous yeast species, each characterized by PCR-RFLP profiles obtained with 143 different endonucleases. The results allowed for the in silico evaluation of the performance of the tested endonucleases in the yeast species' identification and the generation of FId (Fungal Identifier), an online freely accessible tool for the identification of yeast species according to experimentally obtained PCR-RFLP profiles.
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- 2024
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33. Using wasps as a tool to restore a functioning vine grape mycobiota and preserve the mycobial "terroir".
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Di Paola M, Gori A, Stefanini I, Meriggi N, Renzi S, Nenciarini S, Cerasuolo B, Moriondo M, Romoli R, Pieraccini G, Baracchi D, Turillazzi F, Turillazzi S, and Cavalieri D
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- Animals, Humans, Saccharomyces cerevisiae, Fermentation, Vitis, Wasps, Wine analysis
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In the last one-hundred years, the exponential expansion of wine making has artificialized the agricultural landscape as well as its microbial diversity, spreading human selected Saccharomyces cerevisiae strains. Evidence showed that social wasps can harbor a significant fraction of the yeast phenotypic diversity of a given area of wine production, allowing different strains to overwinter and mate in their gut. The integrity of the wasp-yeast ecological interaction is of paramount importance to maintain the resilience of microbial populations associated to wine aromatic profiles. In a field experiment, we verified whether Polistes dominula wasps, reared in laboratory and fed with a traceable S. cerevisiae strain, could be a useful tool to drive the controlled yeast dispersion directly on grapes. The demonstration of the biotechnological potential of social insects in organic wine farming lays the foundations for multiple applications including maintenance of microbial biodiversity and rewilding vineyards through the introduction of wasp associated microbiomes., (© 2023. Springer Nature Limited.)
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- 2023
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34. A DNA biosensors-based microfluidic platform for attomolar real-time detection of unamplified SARS-CoV-2 virus.
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Robin P, Barnabei L, Marocco S, Pagnoncelli J, Nicolis D, Tarantelli C, Tavilla AC, Robortella R, Cascione L, Mayoraz L, Journot CMA, Mensi M, Bertoni F, Stefanini I, and Gerber-Lemaire S
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The emergence of the coronavirus 2019 (COVID-19) arose the need for rapid, accurate and massive virus detection methods to control the spread of infectious diseases. In this work, a device, deployable in non-medical environments, has been developed for the detection of non-amplified SARS-CoV-2 RNA. A SARS-CoV-2 specific probe was designed and covalently immobilized at the surface of glass slides to fabricate a DNA biosensor. The resulting system was integrated in a microfluidic platform, in which viral RNA was extracted from non-treated human saliva, before hybridizing at the surface of the sensor. The formed DNA/RNA duplex was detected in presence of SYBR Green I using an opto-electronic system, based on a high-power LED and a photo multiplier tube, which convert the emitted fluorescence into an electrical signal that can be processed in less than 10 min. The limit of detection of the resulting microfluidic platform reached six copies of viral RNA per microliter of sample (equal to 10 aM) and satisfied the safety margin. The absence of non-specific adsorption and the selectivity for SARS-CoV-2 RNA were established. In addition, the designed device could be applicable for the detection of a variety of viruses by simple modification of the immobilized probe., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 The Authors.)
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- 2023
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35. Genomic Assembly of Clinical Candida glabrata (Nakaseomyces glabrata) Isolates Reveals within-Species Structural Plasticity and Association with In Vitro Antifungal Susceptibility.
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Stefanini I, Stoakes E, Wu HHT, Xu-McCrae L, Hussain A, Moat J, Dowson CG, David MD, and Constantinidou C
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- Humans, Phylogeny, Genomics, Drug Resistance, Fungal genetics, Microbial Sensitivity Tests, Antifungal Agents pharmacology, Candida glabrata genetics
- Abstract
The opportunistic human pathogen Candida glabrata has become an increasingly important threat to human health, with infections globally characterized by high mortality rates and multidrug resistance. To face this threat, more efficient diagnostic and therapeutic approaches are required, underpinning research to help define the intraspecies epidemiology, genetic variability, and therefore, diagnostic and therapeutic target stability. Previous comparative genetics studies conducted on limited numbers of strains only revealed partial resolution of chromosomal settings. In this study, by combining short- and long-read genome sequencing, phenotypic characterization, and comparative genomics over a large set of strains, we detected strict relationships between large chromosomal rearrangements and phylogenetic clades, genes subjected to different selective pressures, and new sets of genes associated with resistance to antifungals. Overall, these results not only provide a fundamental contribution to our knowledge of C. glabrata evolution and epidemiology but may also lay the foundations for the future development of tailored therapeutic approaches. IMPORTANCE The human pathogen Candida glabrata has become a global threat to human health, with infections characterized by high mortality and multidrug resistance. We have obtained nine fully assembled genomes from clinical isolates through a combination of short- and long-read sequencing approaches. The quality and completeness of such genomes and their subsequent comparison to the broadest set of genomes so far allowed us to pinpoint chromosomal rearrangements in several genomes and detect phylogenetic clades that were not associated with geographic location or isolation source. We identified a new set of genes associated with resistance to antifungals coding for adhesin or adhesin-like proteins, suggesting C. glabrata resists antifungals by forming aggregates or adhering to the host tissue. These results, which provide a fundamental contribution to our knowledge of C. glabrata evolution and epidemiology, may initiate the development of precision medicine interventions for patients with suspected or proven invasive fungal infections.
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- 2022
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36. Forests influence yeast populations vectored by insects into vineyards.
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Valentini B, Barbero F, Casacci LP, Luganini A, and Stefanini I
- Abstract
Introduction: In the vineyard, yeast communities impact the ripening and fermentation of grapes and are influenced by geographical location, climate, and soil characteristics. Despite the great advancement in our knowledge of the vineyard mycobiota, a key step of the process leading to the definition of the vineyard yeast community is still poorly understood: if geography, climate, and soil influence the mycobiota, potentially through selection, where do the yeast originate from, and how can they reach the vineyard? In this perspective, it is currently acknowledged that forests host several yeast species and that insects, particularly social wasps, can vector and maintain the yeasts known to populate the vineyard. Alas, the conveyance, fostered by insects, of yeasts from the forest to the vineyard has not been proven yet. In this study, we aimed to assess the existence of links between a potential natural source of yeasts (woods), the vectors (social wasps), and the composition of the vineyard mycobiota., Methods: For this purpose, the mycobiota of wasps caught in six Italian vineyards were analyzed over 2 years through culturomics approaches., Results: The results clearly indicate that the presence of wooded areas close to vineyards is associated with particular features of the mycobiota vectored by social wasps. Wasps caught in vineyards near wooded areas bear a higher number of yeast cells and higher biodiversity than insects caught in vineyards far from woods. Furthermore, insects caught in vineyards close to woods bear distinctive yeast populations, encompassing species such as Saccharomyces cerevisiae ., Discussion: Overall, our work provides fundamental insights into the ecology of the vineyard mycobiota and highlights the need to maintain a vineyard-woodland mosaic landscape, thus preserving the suitable habitat for yeast species relevant to wine-making., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Valentini, Barbero, Casacci, Luganini and Stefanini.)
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- 2022
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37. Going wild: ecology and genomics are crucial to understand yeast evolution.
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Cavalieri D, Valentini B, and Stefanini I
- Subjects
- Environment, Genome, Genomics, Ecology methods, Saccharomyces cerevisiae genetics
- Abstract
Improved and more accessible genome-sequencing approaches have allowed the analysis of large sets of natural yeast isolates. As a consequence, this unprecedented level of description of yeast-genome characteristics and variations in natural environments has provided crucial insights on yeast ecology and evolution. Here, we review some of the most relevant and intriguing aspects of yeast evolution pointed out, thanks to the combination of yeast ecology and genomics, and critically examine the resulting improvement of our knowledge on this field. Only integrated approaches, taking into consideration not only the characteristics of the microbe but also those of the hosting environment, will significantly move forward the exploration of yeast diversity, ecology, and evolution., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)
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- 2022
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38. Resistance to Arsenite and Arsenate in Saccharomyces cerevisiae Arises through the Subtelomeric Expansion of a Cluster of Yeast Genes.
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Stefanini I, Di Paola M, Liti G, Marranci A, Sebastiani F, Casalone E, and Cavalieri D
- Subjects
- Arsenates toxicity, Comparative Genomic Hybridization, Operon, Saccharomyces cerevisiae genetics, Arsenic toxicity, Arsenites toxicity
- Abstract
Arsenic is one of the most prevalent toxic elements in the environment, and its toxicity affects every organism. Arsenic resistance has mainly been observed in microorganisms, and, in bacteria, it has been associated with the presence of the Ars operon. In Saccharomyces cerevisiae , three genes confer arsenic resistance: ARR1 , ARR2 , and ARR3 . Unlike bacteria, in which the presence of the Ars genes confers per se resistance to arsenic, most of the S. cerevisiae isolates present the three ARR genes, regardless of whether the strain is resistant or sensitive to arsenic. To assess the genetic features that make natural S. cerevisiae strains resistant to arsenic, we used a combination of comparative genomic hybridization, whole-genome sequencing, and transcriptomics profiling with microarray analyses. We observed that both the presence and the genomic location of multiple copies of the whole cluster of ARR genes were central to the escape from subtelomeric silencing and the acquisition of resistance to arsenic. As a result of the repositioning, the ARR genes were expressed even in the absence of arsenic. In addition to their relevance in improving our understanding of the mechanism of arsenic resistance in yeast, these results provide evidence for a new cluster of functionally related genes that are independently duplicated and translocated.
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- 2022
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39. Profile of Bacterial Infections in COVID-19 Patients: Antimicrobial Resistance in the Time of SARS-CoV-2.
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Stefanini I, De Renzi G, Foddai E, Cordani E, and Mognetti B
- Abstract
The global onset of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infections happened suddenly, hence imposing a rapid definition of effective therapeutic approaches. Antibiotics were included among the prophylactic agents because of both the similarity between SARS-CoV-2 and atypical pneumonia symptoms, and the immune-modulating and anti-inflammatory properties of such drugs. Although, this approach could exacerbate the emergence of antimicrobial resistance. To evaluate the impact of the COVID-19 pandemic on the spread and characteristics of bacterial infections, as well as on the frequency of antimicrobial resistance, we investigated and compared clinical bacterial strains isolated in an Italian hospital from COVID-19 patients and non-COVID-19 patients during and before the COVID-19 outbreak. Data clearly indicate the impact of the COVID-19 pandemic on bacterial infections: not only some bacterial species were found in either COVID-19 positive or in COVID-19 negative patients, but isolates from COVID-19 patients also showed higher levels of antimicrobial resistance. Nevertheless, despite some bacterial species were isolated only before or over the pandemic, no differences were observed among the antimicrobial resistance levels. Overall, these results recapitulate the current situation of microbial infections and could also provide an overview of the impact of COVID-19 on bacterial pathogens spread and resistance.
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- 2021
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40. Antimicrobial Resistance, an Update from the Ward: Increased Incidence of New Potential Pathogens and Site of Infection-Specific Antibacterial Resistances.
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Stefanini I, Boni M, Silvaplana P, Lovera P, Pelassa S, De Renzi G, and Mognetti B
- Abstract
In order to monitor the spread of antimicrobial resistance, the European Union requires hospitals to be equipped with infection control centers. With this aim, we analyzed 1583 bacterial strains isolated from samples of different origin from patients with community-onset and nosocomial infections in a public tertiary University Hospital on the outskirts of Turin, Italy. Statistical analyses of the isolates (source, type) and their antimicrobial resistance (AMR) were performed. The survey revealed infections associated with bacterial species considered as not-commensal and not-pathogenic, hence potentially emerging as new threats for human health. Conversely to the general observation of nosocomial strains being more resistant to antibiotics compared to community-acquired strains, nosocomial strains isolated in this study were more resistant only to 1/42 tested antibiotics (tetracycline). By adopting an ecological approach, we observed that blood infections are associated with the broadest range of species compared to infections affecting other areas and we obtained clear indications on the antibiotics that should be preferred in the treatment of infections at specific body sites. Future investigations carried out on a larger geographical scale will clarify whether these indications are limited to the geographical region investigated over this study, or whether the same trends are visible at national or international level.
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- 2020
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41. Saccharomyces cerevisiae - Insects Association: Impacts, Biogeography, and Extent.
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Meriggi N, Di Paola M, Cavalieri D, and Stefanini I
- Abstract
Over the last few years, an increasing number of studies have reported the existence of an association between the budding yeast Saccharomyces cerevisiae and insects. The discovery of this relationship has called into question the hypothesis that S. cerevisiae is unable to survive in nature and that the presence of S. cerevisiae strains in natural specimens is the result of contamination from human-related environments. S. cerevisiae 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 S. cerevisiae 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 S. cerevisiae 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 S. cerevisiae -insect association, disclose its extent in terms of geographical distribution and species involved, and present YeastFinder , a cured online database providing a collection of information on this topic., (Copyright © 2020 Meriggi, Di Paola, Cavalieri and Stefanini.)
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- 2020
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42. Comparative immunophenotyping of Saccharomyces cerevisiae and Candida spp. strains from Crohn's disease patients and their interactions with the gut microbiome.
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Di Paola M, Rizzetto L, Stefanini I, Vitali F, Massi-Benedetti C, Tocci N, Romani L, Ramazzotti M, Lionetti P, De Filippo C, and Cavalieri D
- Abstract
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 yeast immunogenicity and impact on the microbiota, we screened S. cerevisiae and Candida 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 S. cerevisiae 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 in vitro were recapitulated in vivo , 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 Saccharomyces or Candida 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., Competing Interests: The authors declare financial and non-financial competing interests., (© 2020 Published by Elsevier B.V.)
- Published
- 2020
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43. Metagenomic Approaches to Investigate the Contribution of the Vineyard Environment to the Quality of Wine Fermentation: Potentials and Difficulties.
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Stefanini I and Cavalieri D
- Abstract
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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- 2018
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44. Deciphering the mechanism of action of 089, a compound impairing the fungal cell cycle.
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Stefanini I, Rizzetto L, Rivero D, Carbonell S, Gut M, Heath S, Gut IG, Trabocchi A, Guarna A, Ben Ghazzi N, Bowyer P, Kapushesky M, and Cavalieri D
- Subjects
- Animals, Cell Line, Cell Line, Tumor, Humans, K562 Cells, Mammals, Antifungal Agents pharmacology, Cell Cycle drug effects, Fungi drug effects, G2 Phase drug effects, Mycoses drug therapy
- Abstract
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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- 2018
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45. SaccharomycesIDentifier, SID: strain-level analysis of Saccharomyces cerevisiae populations by using microsatellite meta-patterns.
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Stefanini I, Albanese D, Sordo M, Legras JL, De Filippo C, Cavalieri D, and Donati C
- Subjects
- Metagenomics methods, Saccharomyces cerevisiae classification, DNA, Fungal genetics, Genotype, Microsatellite Repeats, Saccharomyces cerevisiae genetics, Software
- Abstract
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.
- Published
- 2017
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46. Survival of metastatic melanoma patients after dendritic cell vaccination correlates with expression of leukocyte phosphatidylethanolamine-binding protein 1/Raf kinase inhibitory protein.
- Author
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Buschow SI, Ramazzotti M, Reinieren-Beeren IMJ, Heinzerling LM, Westdorp H, Stefanini I, Beltrame L, Hato SV, Ellebaek E, Gross S, Nguyen VA, Weinlich G, Ragoussis J, Baban D, Schuler-Thurner B, Svane IM, Romani N, Austyn JM, De Vries IJM, Schuler G, Cavalieri D, and Figdor CG
- Abstract
Immunotherapy for metastatic melanoma offers great promise but, to date, only a subset of patients have responded. There is an urgent need to identify ways of allocating patients to the most beneficial therapy, to increase survival and decrease therapy-associated morbidity and costs. Blood-based biomarkers are of particular interest because of their straightforward implementation in routine clinical care. We sought to identify markers for dendritic cell (DC) vaccine-based immunotherapy against metastatic melanoma through gene expression analysis of peripheral blood mononuclear cells. A large-scale microarray analysis of 74 samples from two treatment centers, taken directly after the first round of DC vaccination, was performed. We found that phosphatidylethanolamine binding protein 1 ( PEBP1) /Raf Kinase inhibitory protein (RKIP) expression can be used to identify a significant proportion of patients who performed poorly after DC vaccination. This result was validated by q-PCR analysis on blood samples from a second cohort of 95 patients treated with DC vaccination in four different centers. We conclude that low PEBP1 expression correlates with poor overall survival after DC vaccination. Intriguingly, this was only the case for expression of PEBP1 after, but not prior to, DC vaccination. Moreover, the change in PEBP1 expression upon vaccination correlated well with survival. Further analyses revealed that PEBP1 expression positively correlated with genes involved in T cell responses but inversely correlated with genes associated with myeloid cells and aberrant inflammation including STAT3, NOTCH1 , and MAPK1 . Concordantly, PEBP1 inversely correlated with the myeloid/lymphoid-ratio and was suppressed in patients suffering from chronic inflammatory disease., Competing Interests: CONFLICTS OF INTEREST The authors declare no conflicts of interest
- Published
- 2017
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47. Relations between Effects and Structure of Small Bicyclic Molecules on the Complex Model System Saccharomyces cerevisiae .
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Brilli M, Trabocchi A, Weil T, Cavalieri D, and Stefanini I
- Abstract
The development of compounds able to modify biological functions largely took advantage of parallel synthesis to generate a broad chemical variance of compounds to be tested for the desired effect(s). The budding yeast Saccharomyces cerevisiae is a model for pharmacological studies since a long time as it represents a relatively simple system to explore the relations among chemical variance and bioactivity. To identify relations between the chemical features of the molecules and their activity, we delved into the effects of a library of small compounds on the viability of a set of S. cerevisiae strains. Thanks to the high degree of chemical diversity of the tested compounds and to the measured effect on the yeast growth rate, we were able to scale-down the chemical library and to gain information on the most effective structures at the substituent level. Our results represent a valuable source for the selection, rational design, and optimization of bioactive compounds.
- Published
- 2017
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48. Core Microbiota and Metabolome of Vitis vinifera L. cv. Corvina Grapes and Musts.
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Stefanini I, Carlin S, Tocci N, Albanese D, Donati C, Franceschi P, Paris M, Zenato A, Tempesta S, Bronzato A, Vrhovsek U, Mattivi F, and Cavalieri D
- Abstract
The composition and changes of the fungal population and of the metabolites present in grapes and in ferments of Vitis vinifera L. cv. Corvina, one of the major components of the Amarone musts, were dissected aiming at the identification of constant characteristics possibly influenced by the productive process. The fungal populations and metabolomic profiles were analyzed in three different vintages. 454-pyrosequencing on the ribosomal ITS1 region has been used to identify the fungal population present in Corvina grapes and fresh must. Samples were also subjected to metabolomics analysis measuring both free volatile compounds and glycosylated aroma precursors through an untargeted approach with comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry. Albeit strongly dependent on the climate, both the mycobiota and metabolome of Corvina grapes and fresh musts show some characteristics recursive in different vintages. Such persistent characteristics are likely determined by the method adopted to produce Amarone or other dry wines made from partially dried grapes. In particular, the harsh conditions imposed by the prolonged withering appear to contribute to the shaping of the fungal populations. The fungal genera and metabolites present in different vintages in V. vinifera L. cv. Corvina grapes and fresh musts represent core components of the peculiar technique of production of Amarone. Their identification allows the in-depth understanding and improved control of the process of production of this economically and culturally relevant wine.
- Published
- 2017
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49. Isolation, Identification and Characterization of Yeasts from Fermented Goat Milk of the Yaghnob Valley in Tajikistan.
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Qvirist LA, De Filippo C, Strati F, Stefanini I, Sordo M, Andlid T, Felis GE, Mattarelli P, and Cavalieri D
- Abstract
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.
- Published
- 2016
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50. Age and Gender Affect the Composition of Fungal Population of the Human Gastrointestinal Tract.
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Strati F, Di Paola M, Stefanini I, Albanese D, Rizzetto L, Lionetti P, Calabrò A, Jousson O, Donati C, Cavalieri D, and De Filippo C
- Abstract
The fungal component of the human gut microbiota has been neglected for long time due to the low relative abundance of fungi with respect to bacteria, and only recently few reports have explored its composition and dynamics in health or disease. The application of metagenomics methods to the full understanding of fungal communities is currently limited by the under representation of fungal DNA with respect to the bacterial one, as well as by the limited ability to discriminate passengers from colonizers. Here, we investigated the gut mycobiota of a cohort of healthy subjects in order to reduce the gap of knowledge concerning fungal intestinal communities in the healthy status further screening for phenotypical traits that could reflect fungi adaptation to the host. We studied the fecal fungal populations of 111 healthy subjects by means of cultivation on fungal selective media and by amplicon-based ITS1 metagenomics analysis on a subset of 57 individuals. We then characterized the isolated fungi for their tolerance to gastrointestinal (GI) tract-like challenges and their susceptibility to antifungals. A total of 34 different fungal species were isolated showing several phenotypic characteristics associated with intestinal environment such as tolerance to body temperature (37°C), to acidic and oxidative stress, and to bile salts exposure. We found a high frequency of azoles resistance in fungal isolates, with potential and significant clinical impact. Analyses of fungal communities revealed that the human gut mycobiota differs in function of individuals' life stage in a gender-related fashion. The combination of metagenomics and fungal cultivation allowed an in-depth understanding of the fungal intestinal community structure associated to the healthy status and the commensalism-related traits of isolated fungi. We further discussed comparatively the results of sequencing and cultivation to critically evaluate the application of metagenomics-based approaches to fungal gut populations.
- Published
- 2016
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