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Marsiglia R, Marangelo C, Vernocchi P, Scanu M, Pane S, Russo A, Guanziroli E, Del Chierico F, Valeriani M, Molteni F, Putignani L. Gut Microbiota Ecological and Functional Modulation in Post-Stroke Recovery Patients: An Italian Study. Microorganisms 2023; 12:37. [PMID: 38257864 PMCID: PMC10819831 DOI: 10.3390/microorganisms12010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
Ischemic stroke (IS) can be caused by perturbations of the gut-brain axis. An imbalance in the gut microbiota (GM), or dysbiosis, may be linked to several IS risk factors and can influence the brain through the production of different metabolites, such as short-chain fatty acids (SCFAs), indole and derivatives. This study examines ecological changes in the GM and its metabolic activities after stroke. Fecal samples of 10 IS patients were compared to 21 healthy controls (CTRLs). GM ecological profiles were generated via 16S rRNA taxonomy as functional profiles using metabolomics analysis performed with a gas chromatograph coupled to a mass spectrometer (GC-MS). Additionally fecal zonulin, a marker of gut permeability, was measured using an enzyme-linked immuno assay (ELISA). Data were analyzed using univariate and multivariate statistical analyses and correlated with clinical features and biochemical variables using correlation and nonparametric tests. Metabolomic analyses, carried out on a subject subgroup, revealed a high concentration of fecal metabolites, such as SCFAs, in the GM of IS patients, which was corroborated by the enrichment of SCFA-producing bacterial genera such as Bacteroides, Christensellaceae, Alistipes and Akkermansia. Conversely, indole and 3-methyl indole (skatole) decreased compared to a subset of six CTRLs. This study illustrates how IS might affect the gut microbial milieu and may suggest potential microbial and metabolic biomarkers of IS. Expanded populations of Akkermansia and enrichment of acetic acid could be considered potential disease phenotype signatures.
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Affiliation(s)
- Riccardo Marsiglia
- Immunology, Rheumatology and Infectious Diseases Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy; (R.M.); (C.M.); (P.V.); (M.S.); (F.D.C.)
| | - Chiara Marangelo
- Immunology, Rheumatology and Infectious Diseases Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy; (R.M.); (C.M.); (P.V.); (M.S.); (F.D.C.)
| | - Pamela Vernocchi
- Immunology, Rheumatology and Infectious Diseases Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy; (R.M.); (C.M.); (P.V.); (M.S.); (F.D.C.)
| | - Matteo Scanu
- Immunology, Rheumatology and Infectious Diseases Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy; (R.M.); (C.M.); (P.V.); (M.S.); (F.D.C.)
| | - Stefania Pane
- Unit of Microbiomics, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy; (S.P.); (A.R.)
| | - Alessandra Russo
- Unit of Microbiomics, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy; (S.P.); (A.R.)
| | - Eleonora Guanziroli
- Villa Beretta Rehabilitation Center, Valduce Hospital Como, 23845 Costa Masnaga, Italy; (E.G.); (F.M.)
| | - Federica Del Chierico
- Immunology, Rheumatology and Infectious Diseases Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy; (R.M.); (C.M.); (P.V.); (M.S.); (F.D.C.)
| | - Massimiliano Valeriani
- Developmental Neurology, Bambino Gesù Children Hospital, IRCCS, 00165 Rome, Italy;
- Center for Sensory Motor Interaction, Aalborg University, 9220 Aalborg, Denmark
| | - Franco Molteni
- Villa Beretta Rehabilitation Center, Valduce Hospital Como, 23845 Costa Masnaga, Italy; (E.G.); (F.M.)
| | - Lorenza Putignani
- Unit of Microbiomics and Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy
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Marzano V, Mortera SL, Marangelo C, Piazzesi A, Rapisarda F, Pane S, Del Chierico F, Vernocchi P, Romani L, Campana A, Palma P, Putignani L. The metaproteome of the gut microbiota in pediatric patients affected by COVID-19. Front Cell Infect Microbiol 2023; 13:1327889. [PMID: 38188629 PMCID: PMC10766818 DOI: 10.3389/fcimb.2023.1327889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction The gut microbiota (GM) play a significant role in the infectivity and severity of COVID-19 infection. However, the available literature primarily focuses on adult patients and it is known that the microbiota undergoes changes throughout the lifespan, with significant alterations occurring during infancy and subsequently stabilizing during adulthood. Moreover, children have exhibited milder symptoms of COVID-19 disease, which has been associated with the abundance of certain protective bacteria. Here, we examine the metaproteome of pediatric patients to uncover the biological mechanisms that underlie this protective effect of the GM. Methods We performed nanoliquid chromatography coupled with tandem mass spectrometry on a high resolution analytical platform, resulting in label free quantification of bacterial protein groups (PGs), along with functional annotations via COG and KEGG databases by MetaLab-MAG. Additionally, taxonomic assignment was possible through the use of the lowest common ancestor algorithm provided by Unipept software. Results A COVID-19 GM functional dissimilarity respect to healthy subjects was identified by univariate analysis. The alteration in COVID-19 GM function is primarily based on bacterial pathways that predominantly involve metabolic processes, such as those related to tryptophan, butanoate, fatty acid, and bile acid biosynthesis, as well as antibiotic resistance and virulence. Discussion These findings highlight the mechanisms by which the pediatric GM could contribute to protection against the more severe manifestations of the disease in children. Uncovering these mechanisms can, therefore, have important implications in the discovery of novel adjuvant therapies for severe COVID-19.
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Affiliation(s)
- Valeria Marzano
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Stefano Levi Mortera
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Chiara Marangelo
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Antonia Piazzesi
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Federica Rapisarda
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Stefania Pane
- Unit of Microbiomics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Federica Del Chierico
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Pamela Vernocchi
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Lorenza Romani
- Unit of Infectious Disease, Bambino Gesu’ Children’s Hospital, IRCCS, Rome, Italy
| | - Andrea Campana
- Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Paolo Palma
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Lorenza Putignani
- Unit of Microbiomics and Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
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Vernocchi P, Marangelo C, Guerrera S, Del Chierico F, Guarrasi V, Gardini S, Conte F, Paci P, Ianiro G, Gasbarrini A, Vicari S, Putignani L. Gut microbiota functional profiling in autism spectrum disorders: bacterial VOCs and related metabolic pathways acting as disease biomarkers and predictors. Front Microbiol 2023; 14:1287350. [PMID: 38192296 PMCID: PMC10773764 DOI: 10.3389/fmicb.2023.1287350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/14/2023] [Indexed: 01/10/2024] Open
Abstract
Background Autism spectrum disorder (ASD) is a multifactorial neurodevelopmental disorder. Major interplays between the gastrointestinal (GI) tract and the central nervous system (CNS) seem to be driven by gut microbiota (GM). Herein, we provide a GM functional characterization, based on GM metabolomics, mapping of bacterial biochemical pathways, and anamnestic, clinical, and nutritional patient metadata. Methods Fecal samples collected from children with ASD and neurotypical children were analyzed by gas-chromatography mass spectrometry coupled with solid phase microextraction (GC-MS/SPME) to determine volatile organic compounds (VOCs) associated with the metataxonomic approach by 16S rRNA gene sequencing. Multivariate and univariate statistical analyses assessed differential VOC profiles and relationships with ASD anamnestic and clinical features for biomarker discovery. Multiple web-based and machine learning (ML) models identified metabolic predictors of disease and network analyses correlated GM ecological and metabolic patterns. Results The GM core volatilome for all ASD patients was characterized by a high concentration of 1-pentanol, 1-butanol, phenyl ethyl alcohol; benzeneacetaldehyde, octadecanal, tetradecanal; methyl isobutyl ketone, 2-hexanone, acetone; acetic, propanoic, 3-methyl-butanoic and 2-methyl-propanoic acids; indole and skatole; and o-cymene. Patients were stratified based on age, GI symptoms, and ASD severity symptoms. Disease risk prediction allowed us to associate butanoic acid with subjects older than 5 years, indole with the absence of GI symptoms and low disease severity, propanoic acid with the ASD risk group, and p-cymene with ASD symptoms, all based on the predictive CBCL-EXT scale. The HistGradientBoostingClassifier model classified ASD patients vs. CTRLs by an accuracy of 89%, based on methyl isobutyl ketone, benzeneacetaldehyde, phenyl ethyl alcohol, ethanol, butanoic acid, octadecane, acetic acid, skatole, and tetradecanal features. LogisticRegression models corroborated methyl isobutyl ketone, benzeneacetaldehyde, phenyl ethyl alcohol, skatole, and acetic acid as ASD predictors. Conclusion Our results will aid the development of advanced clinical decision support systems (CDSSs), assisted by ML models, for advanced ASD-personalized medicine, based on omics data integrated into electronic health/medical records. Furthermore, new ASD screening strategies based on GM-related predictors could be used to improve ASD risk assessment by uncovering novel ASD onset and risk predictors.
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Affiliation(s)
- Pamela Vernocchi
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Chiara Marangelo
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Silvia Guerrera
- Child and Adolescent Neuropsychiatry Unit, Department of Neuroscience, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Federica Del Chierico
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | | | | | - Federica Conte
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, Rome, Italy
| | - Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Gianluca Ianiro
- CEMAD Digestive Disease Center, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Antonio Gasbarrini
- CEMAD Digestive Disease Center, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Stefano Vicari
- Child and Adolescent Neuropsychiatry Unit, Department of Neuroscience, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Life Sciences and Public Health Department, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Lorenza Putignani
- Unit of Microbiomics and Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
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Marzano V, Levi Mortera S, Vernocchi P, Del Chierico F, Marangelo C, Guarrasi V, Gardini S, Dentici ML, Capolino R, Digilio MC, Di Donato M, Spasari I, Abreu MT, Dallapiccola B, Putignani L. Williams-Beuren syndrome shapes the gut microbiota metaproteome. Sci Rep 2023; 13:18963. [PMID: 37923896 PMCID: PMC10624682 DOI: 10.1038/s41598-023-46052-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/27/2023] [Indexed: 11/06/2023] Open
Abstract
Williams-Beuren syndrome (WBS) is a rare genetic neurodevelopmental disorder with multi-systemic manifestations. The evidence that most subjects with WBS face gastrointestinal (GI) comorbidities, have prompted us to carry out a metaproteomic investigation of their gut microbiota (GM) profile compared to age-matched healthy subjects (CTRLs). Metaproteomic analysis was carried out on fecal samples collected from 41 individuals with WBS, and compared with samples from 45 CTRLs. Stool were extracted for high yield in bacterial protein group (PG) content, trypsin-digested and analysed by nanoLiquid Chromatography-Mass Spectrometry. Label free quantification, taxonomic assignment by the lowest common ancestor (LCA) algorithm and functional annotations by COG and KEGG databases were performed. Data were statistically interpreted by multivariate and univariate analyses. A WBS GM functional dissimilarity respect to CTRLs, regardless age distribution, was reported. The alterations in function of WBSs GM was primarily based on bacterial pathways linked to carbohydrate transport and metabolism and energy production. Influence of diet, obesity, and GI symptoms was assessed, highlighting changes in GM biochemical patterns, according to WBS subsets' stratification. The LCA-derived ecology unveiled WBS-related functionally active bacterial signatures: Bacteroidetes related to over-expressed PGs, and Firmicutes, specifically the specie Faecalibacterium prausnitzii, linked to under-expressed PGs, suggesting a depletion of beneficial bacteria. These new evidences on WBS gut dysbiosis may offer novel targets for tailored interventions.
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Affiliation(s)
- Valeria Marzano
- Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Stefano Levi Mortera
- Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Pamela Vernocchi
- Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Federica Del Chierico
- Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Chiara Marangelo
- Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Valerio Guarrasi
- GenomeUp s.r.l., Rome, Italy
- Unit of Computer Systems and Bioinformatics, Department of Engineering, University Campus Bio-Medico of Rome, Rome, Italy
| | | | - Maria Lisa Dentici
- Genetics and Rare Diseases Research Division, Medical Genetics Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rossella Capolino
- Genetics and Rare Diseases Research Division, Medical Genetics Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Cristina Digilio
- Genetics and Rare Diseases Research Division, Medical Genetics Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maddalena Di Donato
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Iolanda Spasari
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Teresa Abreu
- Division of Digestive Health and Liver Diseases, Department of Medicine, Crohn's and Colitis Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Bruno Dallapiccola
- Scientific Directorate, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Lorenza Putignani
- Unit of Microbiomics and Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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Policastro V, Righelli D, Ravà L, Vernocchi P, Bianchi M, Vallone C, Signore F, Manco M. Dietary Fatty Acids Contribute to Maintaining the Balance between Pro-Inflammatory and Anti-Inflammatory Responses during Pregnancy. Nutrients 2023; 15:nu15112432. [PMID: 37299395 DOI: 10.3390/nu15112432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND During pregnancy, the balance between pro-inflammatory and anti-inflammatory responses is essential for ensuring healthy outcomes. Dietary Fatty acids may modulate inflammation. METHODS We investigated the association between dietary fatty acids as profiled on red blood cells membranes and a few pro- and anti-inflammatory cytokines, including the adipokines leptin and adiponectin at ~38 weeks in 250 healthy women. RESULTS We found a number of associations, including, but not limited to those of adiponectin with C22:3/C22:4 (coeff -1.44; p = 0.008), C18:1 c13/c14 (coeff 1.4; p = 0.02); endotoxin with C20:1 (coeff -0.9; p = 0.03), C22:0 (coeff -0.4; p = 0.05); MCP-1 with C16:0 (coeff 0.8; p = 0.04); and ICAM-1 with C14:0 (coeff -86.8; p = 0.045). Several cytokines including leptin were associated with maternal body weight (coeff 0.9; p = 2.31 × 10-5), smoking habits (i.e., ICAM-1 coeff 133.3; p = 0.09), or gestational diabetes (i.e., ICAM-1 coeff 688; p = 0.06). CONCLUSIONS In a general cohort of pregnant women, the intake of fatty acids influenced the balance between pro- and anti-inflammatory molecules together with weight gain, smoking habits, and gestational diabetes.
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Affiliation(s)
- Valeria Policastro
- Department of Political Sciences, University of Naples Federico II, 80138 Naples, Italy
- Istituto per le Applicazioni del Calcolo "Mauro Picone", National Research Council, 80131 Naples, Italy
| | - Dario Righelli
- Istituto per le Applicazioni del Calcolo "Mauro Picone", National Research Council, 80131 Naples, Italy
- Department of Statistical Sciences, University of Padova, 35121 Padua, Italy
| | - Lucilla Ravà
- Clinical Epidemiology, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Pamela Vernocchi
- Unit of Human Microbiome, Multimodal Laboratory Medicine Research Area, Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy
| | - Marzia Bianchi
- Research Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Cristina Vallone
- Obstetrics and Gynecology Department, USL Roma1, San Filippo Neri Hospital, 00135 Rome, Italy
| | - Fabrizio Signore
- Obstetrics and Gynecology Department, USL Roma2, Sant 'Eugenio Hospital, 00144 Rome, Italy
| | - Melania Manco
- Research Area for Fetal, Neonatal and Cardiological Sciences, Bambino Gesù Children's Hospital, IRCCS, 00165 Roma, Italy
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Pepe J, Rossi M, Battafarano G, Vernocchi P, Conte F, Marzano V, Mariani E, Mortera SL, Cipriani C, Rana I, Buonuomo PS, Bartuli A, De Martino V, Pelle S, Pascucci L, Toniolo RM, Putignani L, Minisola S, Del Fattore A. Characterization of Extracellular Vesicles in Osteoporotic Patients Compared to Osteopenic and Healthy Controls. J Bone Miner Res 2022; 37:2186-2200. [PMID: 36053959 PMCID: PMC10086946 DOI: 10.1002/jbmr.4688] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 08/16/2022] [Accepted: 08/24/2022] [Indexed: 11/06/2022]
Abstract
Extracellular vesicles (EVs) are mediators of a range of pathological conditions. However, their role in bone loss disease has not been well understood. In this study we characterized plasma EVs of 54 osteoporotic (OP) postmenopausal women compared to 48 osteopenic (OPN) and 44 healthy controls (CN), and we investigated their effects on osteoclasts and osteoblasts. We found no differences between the three groups in terms of anthropometric measurements and biochemical evaluation of serum calcium, phosphate, creatinine, PTH, 25-hydroxy vitamin D and bone biomarkers, except for an increase of CTX level in OP group. FACS analysis revealed that OP patients presented a significantly increased number of EVs and RANKL+ EVs compared with both CN and OPN subjects. Total EVs are negatively associated with the lumbar spine T-score and femoral neck T-score. Only in the OPN patients we observed a positive association between the total number of EVs and RANKL+ EVs with the serum RANKL. In vitro studies revealed that OP EVs supported osteoclastogenesis of healthy donor peripheral blood mononuclear cells at the same level observed following RANKL and M-CSF treatment, reduced the ability of mesenchymal stem cells to differentiate into osteoblasts, while inducing an increase of OSTERIX and RANKL expression in mature osteoblasts. The analysis of miRNome revealed that miR-1246 and miR-1224-5p were the most upregulated and downregulated in OP EVs; the modulated EV-miRNAs in OP and OPN compared to CN are related to osteoclast differentiation, interleukin-13 production and regulation of canonical WNT pathway. A proteomic comparison between OPN and CN EVs evidenced a decrease in fibrinogen, vitronectin, and clusterin and an increase in coagulation factors and apolipoprotein, which was also upregulated in OP EVs. Interestingly, an increase in RANKL+ EVs and exosomal miR-1246 was also observed in samples from patients affected by Gorham-Stout disease, suggesting that EVs could be good candidate as bone loss disease biomarkers. © 2022 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Jessica Pepe
- Department of Clinical, Internal, Anesthesiological and Cardiovascular Sciences, Sapienza University, Rome, Italy
| | - Michela Rossi
- Bone Physiopathology Research Unit, Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giulia Battafarano
- Bone Physiopathology Research Unit, Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Pamela Vernocchi
- Unit of Human Microbiome, Multimodal Laboratory Medicine Research Area, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Federica Conte
- Institute for System Analysis and Computer Science "A.Ruberti", National Research Council (CNR), Rome, Italy
| | - Valeria Marzano
- Unit of Human Microbiome, Multimodal Laboratory Medicine Research Area, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Eda Mariani
- Research Laboratory, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Stefano Levi Mortera
- Unit of Human Microbiome, Multimodal Laboratory Medicine Research Area, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Cristiana Cipriani
- Department of Clinical, Internal, Anesthesiological and Cardiovascular Sciences, Sapienza University, Rome, Italy
| | - Ippolita Rana
- Rare Diseases and Medical Genetic Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Paola Sabrina Buonuomo
- Rare Diseases and Medical Genetic Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Bartuli
- Rare Diseases and Medical Genetic Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Viviana De Martino
- Department of Clinical, Internal, Anesthesiological and Cardiovascular Sciences, Sapienza University, Rome, Italy
| | - Simone Pelle
- "Polo Sanitario San Feliciano - Villa Aurora" Clinic, Rome, Italy
| | - Luisa Pascucci
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
| | - Renato Maria Toniolo
- Department of Orthopaedics and Traumatology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Lorenza Putignani
- Department of Diagnostics and Laboratory Medicine, Unit of Microbiology and Diagnostic Immunology, Unit of Microbiomics, and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Salvatore Minisola
- Department of Clinical, Internal, Anesthesiological and Cardiovascular Sciences, Sapienza University, Rome, Italy
| | - Andrea Del Fattore
- Bone Physiopathology Research Unit, Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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Vernocchi P, Ristori MV, Guerrera S, Guarrasi V, Conte F, Russo A, Lupi E, Albitar-Nehme S, Gardini S, Paci P, Ianiro G, Vicari S, Gasbarrini A, Putignani L. Gut Microbiota Ecology and Inferred Functions in Children With ASD Compared to Neurotypical Subjects. Front Microbiol 2022; 13:871086. [PMID: 35756062 PMCID: PMC9218677 DOI: 10.3389/fmicb.2022.871086] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/19/2022] [Indexed: 12/28/2022] Open
Abstract
Autism spectrum disorders (ASDs) is a multifactorial neurodevelopmental disorder. The communication between the gastrointestinal (GI) tract and the central nervous system seems driven by gut microbiota (GM). Herein, we provide GM profiling, considering GI functional symptoms, neurological impairment, and dietary habits. Forty-one and 35 fecal samples collected from ASD and neurotypical children (CTRLs), respectively, (age range, 3–15 years) were analyzed by 16S targeted-metagenomics (the V3–V4 region) and inflammation and permeability markers (i.e., sIgA, zonulin lysozyme), and then correlated with subjects’ metadata. Our ASD cohort was characterized as follows: 30/41 (73%) with GI functional symptoms; 24/41 (58%) picky eaters (PEs), with one or more dietary needs, including 10/41 (24%) with food selectivity (FS); 36/41 (88%) presenting high and medium autism severity symptoms (HMASSs). Among the cohort with GI symptoms, 28/30 (93%) showed HMASSs, 17/30 (57%) were picky eaters and only 8/30 (27%) with food selectivity. The remaining 11/41 (27%) ASDs without GI symptoms that were characterized by HMASS for 8/11 (72%) and 7/11 (63%) were picky eaters. GM ecology was investigated for the overall ASD cohort versus CTRLs; ASDs with GI and without GI, respectively, versus CTRLs; ASD with GI versus ASD without GI; ASDs with HMASS versus low ASSs; PEs versus no-PEs; and FS versus absence of FS. In particular, the GM of ASDs, compared to CTRLs, was characterized by the increase of Proteobacteria, Bacteroidetes, Rikenellaceae, Pasteurellaceae, Klebsiella, Bacteroides, Roseburia, Lactobacillus, Prevotella, Sutterella, Staphylococcus, and Haemophilus. Moreover, Sutterella, Roseburia and Fusobacterium were associated to ASD with GI symptoms compared to CTRLs. Interestingly, ASD with GI symptoms showed higher value of zonulin and lower levels of lysozyme, which were also characterized by differentially expressed predicted functional pathways. Multiple machine learning models classified correctly 80% overall ASDs, compared with CTRLs, based on Bacteroides, Lactobacillus, Prevotella, Staphylococcus, Sutterella, and Haemophilus features. In conclusion, in our patient cohort, regardless of the evaluation of many factors potentially modulating the GM profile, the major phenotypic determinant affecting the GM was represented by GI hallmarks and patients’ age.
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Affiliation(s)
- Pamela Vernocchi
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare, Rome, Italy
| | - Maria Vittoria Ristori
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare, Rome, Italy
| | - Silvia Guerrera
- Child and Adolescent Neuropsychiatry Unit, Department of Neuroscience, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare, Rome, Italy
| | | | - Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti," National Research Council, Rome, Italy
| | - Alessandra Russo
- Department of Diagnostics and Laboratory Medicine, Unit of Microbiology and Diagnostic Immunology, Unit of Microbiomics, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare, Rome, Italy
| | - Elisabetta Lupi
- Child and Adolescent Neuropsychiatry Unit, Department of Neuroscience, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare, Rome, Italy
| | - Sami Albitar-Nehme
- Department of Diagnostic and Laboratory Medicine, Unit of Microbiology and Diagnostic Immunology, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare, Rome, Italy
| | | | - Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Gianluca Ianiro
- CEMAD Digestive Disease Center, Fondazione Policlinico Universitario "A. Gemelli" Scientific Institute for Research, Hospitalization and Healthcare, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Stefano Vicari
- Child and Adolescent Neuropsychiatry Unit, Department of Neuroscience, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare, Rome, Italy
| | - Antonio Gasbarrini
- CEMAD Digestive Disease Center, Fondazione Policlinico Universitario "A. Gemelli" Scientific Institute for Research, Hospitalization and Healthcare, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Lorenza Putignani
- Department of Diagnostics and Laboratory Medicine, Unit of Microbiology and Diagnostic Immunology, Unit of Microbiomics, and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, Scientific Institute for Research, Hospitalization and Healthcare, Rome, Italy
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8
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Levi Mortera S, Vernocchi P, Basadonne I, Zandonà A, Chierici M, Durighello M, Marzano V, Gardini S, Gasbarrini A, Urbani A, Vicari S, Roncada P, Furlanello C, Venuti P, Putignani L. A metaproteomic-based gut microbiota profiling in children affected by autism spectrum disorders. J Proteomics 2022; 251:104407. [PMID: 34763095 DOI: 10.1016/j.jprot.2021.104407] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 09/02/2021] [Accepted: 10/13/2021] [Indexed: 12/15/2022]
Abstract
During the last decade, the evidences on the relationship between neurodevelopmental disorders and the microbial communities of the intestinal tract have considerably grown. Particularly, the role of gut microbiota (GM) ecology and predicted functions in Autism Spectrum Disorders (ASD) has been especially investigated by 16S rRNA targeted and shotgun metagenomics, trying to assess disease signature and their correlation with cognitive impairment or gastrointestinal (GI) manifestations of the disease. Herein we present a metaproteomic approach to point out the microbial gene expression profiles, their functional annotations, and the taxonomic distribution of gut microbial communities in ASD children. We pursued a LC-MS/MS based investigation, to compare the GM profiles of patients with those of their respective relatives and aged-matched controls, providing a quantitative evaluation of bacterial metaproteins by SWATH analysis. All data were managed by a multiple step bioinformatic pipeline, including network analysis. In particular, comparing ASD subjects with CTRLs, up-regulation was found for some metaproteins associated with Clostridia and with carbohydrate metabolism (glyceraldehyde-3-phosphate and glutamate dehydrogenases), while down-regulation was observed for others associated with Bacteroidia (SusC and SusD family together with the TonB dependent receptor). Moreover, network analysis highlighted specific microbial correlations among ASD subgroups characterized by different functioning levels and GI symptoms. SIGNIFICANCE: To the best of our knowledge, this study represents the first metaproteomic investigation on the gut microbiota of ASD children compared with relatives and age-matched CTRLs. Remarkably, the applied SWATH methodology allowed the attribution of differentially regulated functions to specific microbial taxa, offering a novel and complementary point of view with respect to previous studies.
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Affiliation(s)
- Stefano Levi Mortera
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Pamela Vernocchi
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Ilaria Basadonne
- Department of Psychology and Cognitive Sciences, University of Trento, Rovereto, Italy
| | | | | | - Martina Durighello
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Valeria Marzano
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Antonio Gasbarrini
- Istituto di Patologia Speciale Medica, Università Cattolica del Sacro Cuore, Rome, Italy; UOC Medicina Interna e Gastroenterologia, Area Gastroenterologia ed Oncologia Medica, Dipartimento di Scienze Gastroenterologiche, Endocrino-Metaboliche e Nefro-Urologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Andrea Urbani
- Clinical Chemistry, Biochemistry and Molecular Biology Operations (UOC), Agostino Gemelli Foundation University Hospital IRCCS, Rome, Italy; Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Catholic University of Sacred Heart, Rome, Italy
| | - Stefano Vicari
- Department of Neuroscience, Unit of Head Child & Adolescent Psychiatry, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Department of Life Sciences and Public Health, Catholic University of Sacred Heart, Rome, Italy
| | - Paola Roncada
- Department of Health Sciences, University 'Magna Græcia' of Catanzaro, Catanzaro, Italy
| | | | - Paola Venuti
- Department of Psychology and Cognitive Sciences, University of Trento, Rovereto, Italy
| | - Lorenza Putignani
- Department of Diagnostics and Laboratory Medicine, Unit of Microbiology and Diagnostic Immunology, Unit of Microbiomics and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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9
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Ponziani FR, Picca A, Marzetti E, Calvani R, Conta G, Del Chierico F, Capuani G, Faccia M, Fianchi F, Funaro B, Josè Coelho-Junior H, Petito V, Rinninella E, Paroni Sterbini F, Reddel S, Vernocchi P, Cristina Mele M, Miccheli A, Putignani L, Sanguinetti M, Pompili M, Gasbarrini A. Characterization of the gut-liver-muscle axis in cirrhotic patients with sarcopenia. Liver Int 2021; 41:1320-1334. [PMID: 33713524 DOI: 10.1111/liv.14876] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/25/2021] [Accepted: 03/06/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIM Sarcopenia is frequent in cirrhosis and is associated with unfavourable outcomes. The role of the gut-liver-muscle axis in this setting has been poorly investigated. The aim of this study was to identify gut microbiota, metabolic and inflammatory signatures associated with sarcopenia in cirrhotic patients. METHODS Fifty cirrhotic patients assessed for the presence of sarcopenia by the quantification of muscle mass and strength were compared with age- and sex-matched controls. A multiomic analysis, including gut microbiota composition and metabolomics, serum myokines and systemic and intestinal inflammatory mediators, was performed. RESULTS The gut microbiota of sarcopenic cirrhotic patients was poor in bacteria associated with physical function (Methanobrevibacter, Prevotella and Akkermansia), and was enriched in Eggerthella, a gut microbial marker of frailty. The abundance of potentially pathogenic bacteria, such as Klebsiella, was also increased, to the detriment of autochthonous ones. Sarcopenia was associated with elevated serum levels of pro-inflammatory mediators and of fibroblast growth factor 21 (FGF21) in cirrhotic patients. Gut microbiota metabolic pathways involved in amino acid, protein and branched-chain amino acid metabolism were up-regulated, in addition to ethanol, trimethylamine and dimethylamine production. Correlation networks and clusters of variables associated with sarcopenia were identified, including one centred on Klebsiella/ethanol/FGF21/Eggerthella/Prevotella. CONCLUSIONS Alterations in the gut-liver-muscle axis are associated with sarcopenia in patients with cirrhosis. Detrimental but also compensatory functions are involved in this complex network.
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Affiliation(s)
- Francesca Romana Ponziani
- Internal Medicine and Gastroenterology - Liver Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Anna Picca
- Department of Geriatrics, Neuroscience and Orthopedics, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy.,Aging Research Center, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet and Stockholm University, Stockholm, Sweden
| | - Emanuele Marzetti
- Department of Geriatrics, Neuroscience and Orthopedics, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Riccardo Calvani
- Department of Geriatrics, Neuroscience and Orthopedics, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy.,Aging Research Center, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet and Stockholm University, Stockholm, Sweden
| | - Giorgia Conta
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | - Federica Del Chierico
- Area of Genetics and Rare Diseases, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Giorgio Capuani
- Department of Chemistry, Sapienza University of Rome, Rome, Italy.,Area of Genetics and Rare Diseases, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.,NMR-based Metabolomics Laboratory, Sapienza University of Rome, Rome, Italy
| | - Mariella Faccia
- Internal Medicine and Gastroenterology - Liver Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Francesca Fianchi
- Internal Medicine and Gastroenterology - Liver Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Barbara Funaro
- Internal Medicine and Gastroenterology - Liver Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Helio Josè Coelho-Junior
- Department of Geriatrics, Neuroscience and Orthopedics, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Valentina Petito
- Internal Medicine and Gastroenterology - Liver Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Emanuele Rinninella
- Clinical Nutrition, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | | | - Sofia Reddel
- Area of Genetics and Rare Diseases, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Pamela Vernocchi
- Area of Genetics and Rare Diseases, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Cristina Mele
- Advanced Nutrition in Oncology, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Alfredo Miccheli
- NMR-based Metabolomics Laboratory, Sapienza University of Rome, Rome, Italy.,Clinical Nutrition, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy.,Microbiology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy.,Advanced Nutrition in Oncology, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy.,Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Lorenza Putignani
- Department of Laboratories, Unit of Parasitology and Area of Genetics and Rare Diseases, Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maurizio Sanguinetti
- Microbiology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Maurizio Pompili
- Internal Medicine and Gastroenterology - Liver Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Antonio Gasbarrini
- Internal Medicine and Gastroenterology - Liver Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
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10
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Adorisio R, Cantarutti N, Mortera SL, Sidorina A, Vernocchi P, Baban A, Drago F, Putignani L, Amodeo A. Proteomic Profile in Children and Young Adult Patients with Pulmonary Hypertension Due to Complex Congenital Heart Disease: An Observational Cohort Study. J Heart Lung Transplant 2021. [DOI: 10.1016/j.healun.2021.01.1285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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11
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Mennini M, Reddel S, Del Chierico F, Gardini S, Quagliariello A, Vernocchi P, Valluzzi RL, Fierro V, Riccardi C, Napolitano T, Fiocchi AG, Putignani L. Gut Microbiota Profile in Children with IgE-Mediated Cow's Milk Allergy and Cow's Milk Sensitization and Probiotic Intestinal Persistence Evaluation. Int J Mol Sci 2021; 22:ijms22041649. [PMID: 33562104 PMCID: PMC7915344 DOI: 10.3390/ijms22041649] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 12/23/2022] Open
Abstract
Food allergy (FA) and, in particular, IgE-mediated cow's milk allergy is associated with compositional and functional changes of gut microbiota. In this study, we compared the gut microbiota of cow's milk allergic (CMA) infants with that of cow's milk sensitized (CMS) infants and Healthy controls. The effect of the intake of a mixture of Bifidobacterium longum subsp. longum BB536, Bifidobacterium breve M-16V and Bifidobacterium longum subsp. infantis M-63 on gut microbiota modulation of CMA infants and probiotic persistence was also investigated. Gut microbiota of CMA infants resulted to be characterized by a dysbiotic status with a prevalence of some bacteria as Haemophilus, Klebsiella, Prevotella, Actinobacillus and Streptococcus. Among the three strains administered, B.longum subsp. infantis colonized the gastrointestinal tract and persisted in the gut microbiota of infants with CMA for 60 days. This colonization was associated with perturbations of the gut microbiota, specifically with the increase of Akkermansia and Ruminococcus. Multi-strain probiotic formulations can be studied for their persistence in the intestine by monitoring specific bacterial probes persistence and exploiting microbiota profiling modulation before the evaluation of their therapeutic effects.
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Affiliation(s)
- Maurizio Mennini
- Translational Research in Pediatric Specialities Area, Allergy Unit, Bambino Gesù Children’s Hospital, IRCCS, 00147 Rome, Italy; (M.M.); (R.L.V.); (V.F.); (C.R.); (T.N.); (A.G.F.)
| | - Sofia Reddel
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00147 Rome, Italy; (S.R.); (F.D.C.); (A.Q.); (P.V.)
| | - Federica Del Chierico
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00147 Rome, Italy; (S.R.); (F.D.C.); (A.Q.); (P.V.)
| | | | - Andrea Quagliariello
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00147 Rome, Italy; (S.R.); (F.D.C.); (A.Q.); (P.V.)
| | - Pamela Vernocchi
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00147 Rome, Italy; (S.R.); (F.D.C.); (A.Q.); (P.V.)
| | - Rocco Luigi Valluzzi
- Translational Research in Pediatric Specialities Area, Allergy Unit, Bambino Gesù Children’s Hospital, IRCCS, 00147 Rome, Italy; (M.M.); (R.L.V.); (V.F.); (C.R.); (T.N.); (A.G.F.)
| | - Vincenzo Fierro
- Translational Research in Pediatric Specialities Area, Allergy Unit, Bambino Gesù Children’s Hospital, IRCCS, 00147 Rome, Italy; (M.M.); (R.L.V.); (V.F.); (C.R.); (T.N.); (A.G.F.)
| | - Carla Riccardi
- Translational Research in Pediatric Specialities Area, Allergy Unit, Bambino Gesù Children’s Hospital, IRCCS, 00147 Rome, Italy; (M.M.); (R.L.V.); (V.F.); (C.R.); (T.N.); (A.G.F.)
| | - Tania Napolitano
- Translational Research in Pediatric Specialities Area, Allergy Unit, Bambino Gesù Children’s Hospital, IRCCS, 00147 Rome, Italy; (M.M.); (R.L.V.); (V.F.); (C.R.); (T.N.); (A.G.F.)
| | - Alessandro Giovanni Fiocchi
- Translational Research in Pediatric Specialities Area, Allergy Unit, Bambino Gesù Children’s Hospital, IRCCS, 00147 Rome, Italy; (M.M.); (R.L.V.); (V.F.); (C.R.); (T.N.); (A.G.F.)
| | - Lorenza Putignani
- Department of Diagnostic and Laboratory Medicine, Unit of Parasitology and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00147 Rome, Italy
- Correspondence:
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12
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D’Onofrio V, Del Chierico F, Belci P, Vernocchi P, Quagliariello A, Reddel S, Conta G, Mancino MV, Fadda M, Scigliano MC, Morelli R, De Francesco A, Guagnini F, Fassio F, Galletti R, Putignani L. Effects of a Synbiotic Formula on Functional Bowel Disorders and Gut Microbiota Profile during Long-Term Home Enteral Nutrition (LTHEN): A Pilot Study. Nutrients 2020; 13:nu13010087. [PMID: 33383954 PMCID: PMC7824736 DOI: 10.3390/nu13010087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/17/2020] [Accepted: 12/24/2020] [Indexed: 02/07/2023] Open
Abstract
Long-term enteral nutrition (LTEN) can induce gut microbiota (GM) dysbiosis and gastrointestinal related symptoms, such as constipation or diarrhoea. To date, the treatment of constipation is based on the use of laxatives and prebiotics. Only recently have probiotics and synbiotics been considered, the latter modulating the GM and regulating intestinal functions. This randomized open-label intervention study evaluated the effects of synbiotic treatment on the GM profile, its functional activity and on intestinal functions in long-term home EN (LTHEN) patients. Twenty LTHEN patients were recruited to take enteral formula plus one sachet/day of synbiotic (intervention group, IG) or enteral formula (control group, CG) for four months and evaluated for constipation, stool consistency, and GM and metabolite profiles. In IG patients, statistically significant reduction of constipation and increase of stool consistency were observed after four months (T1), compared to CG subjects. GM ecology analyses revealed a decrease in the microbial diversity of both IC and CG groups. Biodiversity increased at T1 for 5/11 IG patients and Methanobrevibacter was identified as the biomarker correlated to the richness increase. Moreover, the increase of short chain fatty acids and the reduction of harmful molecules have been correlated to synbiotic administration. Synbiotics improve constipation symptoms and influences Methanobrevibacter growth in LTHEN patients.
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Affiliation(s)
- Valentina D’Onofrio
- S.C. Dietetica e Nutrizione Clinica, AOU Città della Salute e della Scienza di Torino, 10126 Torino, Italy; (V.D.); (P.B.); (M.V.M.); (M.F.); (M.C.S.); (R.M.); (A.D.F.); (R.G.)
| | - Federica Del Chierico
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (F.D.C.); (P.V.); (A.Q.); (S.R.)
| | - Paola Belci
- S.C. Dietetica e Nutrizione Clinica, AOU Città della Salute e della Scienza di Torino, 10126 Torino, Italy; (V.D.); (P.B.); (M.V.M.); (M.F.); (M.C.S.); (R.M.); (A.D.F.); (R.G.)
| | - Pamela Vernocchi
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (F.D.C.); (P.V.); (A.Q.); (S.R.)
| | - Andrea Quagliariello
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (F.D.C.); (P.V.); (A.Q.); (S.R.)
| | - Sofia Reddel
- Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (F.D.C.); (P.V.); (A.Q.); (S.R.)
| | - Giorgia Conta
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy;
- NMR-Based Metabolomics Laboratory, Sapienza University of Rome, 00185 Rome, Italy
| | - Maria Vittoria Mancino
- S.C. Dietetica e Nutrizione Clinica, AOU Città della Salute e della Scienza di Torino, 10126 Torino, Italy; (V.D.); (P.B.); (M.V.M.); (M.F.); (M.C.S.); (R.M.); (A.D.F.); (R.G.)
| | - Maurizio Fadda
- S.C. Dietetica e Nutrizione Clinica, AOU Città della Salute e della Scienza di Torino, 10126 Torino, Italy; (V.D.); (P.B.); (M.V.M.); (M.F.); (M.C.S.); (R.M.); (A.D.F.); (R.G.)
| | - Maria Carmine Scigliano
- S.C. Dietetica e Nutrizione Clinica, AOU Città della Salute e della Scienza di Torino, 10126 Torino, Italy; (V.D.); (P.B.); (M.V.M.); (M.F.); (M.C.S.); (R.M.); (A.D.F.); (R.G.)
| | - Roberta Morelli
- S.C. Dietetica e Nutrizione Clinica, AOU Città della Salute e della Scienza di Torino, 10126 Torino, Italy; (V.D.); (P.B.); (M.V.M.); (M.F.); (M.C.S.); (R.M.); (A.D.F.); (R.G.)
| | - Antonella De Francesco
- S.C. Dietetica e Nutrizione Clinica, AOU Città della Salute e della Scienza di Torino, 10126 Torino, Italy; (V.D.); (P.B.); (M.V.M.); (M.F.); (M.C.S.); (R.M.); (A.D.F.); (R.G.)
| | - Fabio Guagnini
- Allergy Therapeutics Italia, Milan, Italy e GE Healthcare, 20019 Milan, Italy;
| | - Filippo Fassio
- Allergy and Clinical Immunology Unit, San Giovanni di Dio Hospital, Azienda USL Toscana Centro, 50143 Florence, Italy;
| | - Rosalba Galletti
- S.C. Dietetica e Nutrizione Clinica, AOU Città della Salute e della Scienza di Torino, 10126 Torino, Italy; (V.D.); (P.B.); (M.V.M.); (M.F.); (M.C.S.); (R.M.); (A.D.F.); (R.G.)
| | - Lorenza Putignani
- Department of Diagnostic and Laboratory Medicine, Unit of Parasitology and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00147 Rome, Italy
- Correspondence: ; Tel.: +39-68594127-2598
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13
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Vernocchi P, Gili T, Conte F, Del Chierico F, Conta G, Miccheli A, Botticelli A, Paci P, Caldarelli G, Nuti M, Marchetti P, Putignani L. Network Analysis of Gut Microbiome and Metabolome to Discover Microbiota-Linked Biomarkers in Patients Affected by Non-Small Cell Lung Cancer. Int J Mol Sci 2020; 21:ijms21228730. [PMID: 33227982 PMCID: PMC7699235 DOI: 10.3390/ijms21228730] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 02/07/2023] Open
Abstract
Several studies in recent times have linked gut microbiome (GM) diversity to the pathogenesis of cancer and its role in disease progression through immune response, inflammation and metabolism modulation. This study focused on the use of network analysis and weighted gene co-expression network analysis (WGCNA) to identify the biological interaction between the gut ecosystem and its metabolites that could impact the immunotherapy response in non-small cell lung cancer (NSCLC) patients undergoing second-line treatment with anti-PD1. Metabolomic data were merged with operational taxonomic units (OTUs) from 16S RNA-targeted metagenomics and classified by chemometric models. The traits considered for the analyses were: (i) condition: disease or control (CTRLs), and (ii) treatment: responder (R) or non-responder (NR). Network analysis indicated that indole and its derivatives, aldehydes and alcohols could play a signaling role in GM functionality. WGCNA generated, instead, strong correlations between short-chain fatty acids (SCFAs) and a healthy GM. Furthermore, commensal bacteria such as Akkermansia muciniphila, Rikenellaceae, Bacteroides, Peptostreptococcaceae, Mogibacteriaceae and Clostridiaceae were found to be more abundant in CTRLs than in NSCLC patients. Our preliminary study demonstrates that the discovery of microbiota-linked biomarkers could provide an indication on the road towards personalized management of NSCLC patients.
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MESH Headings
- Akkermansia/classification
- Akkermansia/genetics
- Akkermansia/isolation & purification
- Alcohols/metabolism
- Aldehydes/metabolism
- Antineoplastic Agents, Immunological/therapeutic use
- Bacteroides/classification
- Bacteroides/genetics
- Bacteroides/isolation & purification
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/immunology
- Carcinoma, Non-Small-Cell Lung/microbiology
- Clostridiaceae/classification
- Clostridiaceae/genetics
- Clostridiaceae/isolation & purification
- Databases, Genetic
- Disease Progression
- Drug Monitoring/methods
- Fatty Acids, Volatile/metabolism
- Gastrointestinal Microbiome/genetics
- Gastrointestinal Microbiome/immunology
- Gene Expression Regulation, Neoplastic
- Gene Regulatory Networks
- Humans
- Immunotherapy/methods
- Indoles/metabolism
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/immunology
- Lung Neoplasms/microbiology
- Metabolome/genetics
- Metabolome/immunology
- Metagenomics/methods
- Peptostreptococcus/classification
- Peptostreptococcus/genetics
- Peptostreptococcus/isolation & purification
- Precision Medicine/methods
- Programmed Cell Death 1 Receptor/antagonists & inhibitors
- Programmed Cell Death 1 Receptor/genetics
- Programmed Cell Death 1 Receptor/immunology
- RNA, Ribosomal, 16S/genetics
- Signal Transduction
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Affiliation(s)
- Pamela Vernocchi
- Area of Genetics and Rare Diseases, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy; (P.V.); (F.D.C.)
| | - Tommaso Gili
- IMT School for Advanced Studies Lucca, Networks Unit, 55100 Lucca, Italy;
| | - Federica Conte
- Institute for Systems Analysis and Computer Science “Antonio Ruberti”, National Research Council, 00185 Rome, Italy;
| | - Federica Del Chierico
- Area of Genetics and Rare Diseases, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy; (P.V.); (F.D.C.)
| | - Giorgia Conta
- Department of Chemistry, NMR-Based Metabolomics Laboratory Sapienza, University of Rome, 00185 Rome, Italy;
| | - Alfredo Miccheli
- Department of Environmental Biology and NMR-Based Metabolomics Laboratory, Sapienza University of Rome, 00185 Rome, Italy;
| | - Andrea Botticelli
- Department of Clinical and Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy; (A.B.); (P.M.)
- AOU Policlinico Umberto I, 00161 Rome, Italy
| | - Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, 00185 Rome, Italy;
| | - Guido Caldarelli
- Department of Molecular Sciences and Nanosystems, Ca’ Foscari, University of Venice, 30172 Venice, Italy;
- European Centre for Living Technologies, 30172 Venice, Italy
- Institute of Complex Systems (CNR), Department of Physics, University of Rome “Sapienza”, 00185 Rome, Italy
| | - Marianna Nuti
- Department of Experimental Medicine, University Sapienza of Rome, 00185 Rome, Italy;
| | - Paolo Marchetti
- Department of Clinical and Molecular Medicine, Sapienza University of Rome, 00185 Rome, Italy; (A.B.); (P.M.)
- AOU Policlinico Umberto I, 00161 Rome, Italy
- AOU Sant’ Andrea Hospital, 00189 Rome, Italy
| | - Lorenza Putignani
- Department of Diagnostic and Laboratory Medicine, Unit of Parasitology and Area of Genetics and Rare Diseases, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy
- Correspondence: ; Tel.: +39-066-859-2598 (ext. 8433)
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14
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Reddel S, Mennini M, Del Chierico F, Vernocchi P, Valluzzi R, Fierro V, Riccardi C, Fiocchi A, Putignani L. Gut microbiota profile in infants with milk and/or egg allergy and evaluation of intestinal colonization and persistence of a probiotic mixture. World Allergy Organ J 2020. [DOI: 10.1016/j.waojou.2020.100424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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15
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Piersigilli F, Syed M, Lam TT, Dotta A, Massoud M, Vernocchi P, Quagliariello A, Putignani L, Auriti C, Salvatori G, Bagolan P, Bhandari V. An omic approach to congenital diaphragmatic hernia: a pilot study of genomic, microRNA, and metabolomic profiling. J Perinatol 2020; 40:952-961. [PMID: 32080334 DOI: 10.1038/s41372-020-0623-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 01/20/2020] [Accepted: 02/06/2020] [Indexed: 11/09/2022]
Abstract
INTRODUCTION The omic approach can help identify a signature that can be potentially used as biomarkers in babies with congenital diaphragmatic hernia (CDH). OBJECTIVES To find a specific microRNA (miR) and metabolic fingerprint of the tracheal aspirates (TA) of CDH patients. We conducted a genetic analysis from blood samples. METHODS TA samples collected in the first 48 h of life in patients with CDH, compared with age-matched controls. Metabolomics done by a mass spectroscopy-based assay. Genomics done using chromosomal microarray analysis. RESULTS CDH (n = 17) and 16 control neonates enrolled. miR-16, miR-17, miR-18, miR-19b, and miR-20a had an increased expression, while miR-19a had a twofold decreased expression in CDH patients, compared with age-matched control patients. Specific metabolites separated neonates with CDH from controls. A genetic mutation found in a small subset of patients. CONCLUSIONS Specific patterns of metabolites and miR expression can be discerned in TA samples in infants with CDH.
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Affiliation(s)
- Fiammetta Piersigilli
- Division of Perinatal Medicine, Yale Child Health Research Center, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA.,Division of Medical and Surgical Neonatology, Bambino Gesù Children's Hospital, Rome, Italy
| | - Mansoor Syed
- Division of Perinatal Medicine, Yale Child Health Research Center, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA.,Section of Neonatal-Perinatal Medicine, Department of Pediatrics, St. Christopher's Hospital for Children, Drexel University College of Medicine, 160 East Erie Avenue, Philadelphia, PA, 19134, USA
| | - TuKiet T Lam
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA.,Keck MS & Proteomics Resource, WM Keck Foundation Biotechnology Resource Laboratory, New Haven, CT, USA
| | - Andrea Dotta
- Division of Medical and Surgical Neonatology, Bambino Gesù Children's Hospital, Rome, Italy
| | - Michela Massoud
- Division of Medical and Surgical Neonatology, Bambino Gesù Children's Hospital, Rome, Italy
| | - Pamela Vernocchi
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, Rome, Italy
| | - Andrea Quagliariello
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, Rome, Italy
| | - Lorenza Putignani
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, Rome, Italy.,Unit of Parasitology, Department of Laboratory and Immunological, Diagnostics Bambino Gesù Children's Hospital, Rome, Italy
| | - Cinzia Auriti
- Division of Medical and Surgical Neonatology, Bambino Gesù Children's Hospital, Rome, Italy
| | - Guglielmo Salvatori
- Division of Medical and Surgical Neonatology, Bambino Gesù Children's Hospital, Rome, Italy
| | - Pietro Bagolan
- Division of Medical and Surgical Neonatology, Bambino Gesù Children's Hospital, Rome, Italy
| | - Vineet Bhandari
- Division of Perinatal Medicine, Yale Child Health Research Center, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA. .,Section of Neonatal-Perinatal Medicine, Department of Pediatrics, St. Christopher's Hospital for Children, Drexel University College of Medicine, 160 East Erie Avenue, Philadelphia, PA, 19134, USA. .,Division of Neonatology, Department of Pediatrics, The Children's Regional Hospital at Cooper, Cooper Medical School of Rowan University, One Cooper Plaza, Camden, NJ, 08103, USA.
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16
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Vernocchi P, Del Chierico F, Putignani L. Gut Microbiota Metabolism and Interaction with Food Components. Int J Mol Sci 2020; 21:ijms21103688. [PMID: 32456257 PMCID: PMC7279363 DOI: 10.3390/ijms21103688] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 12/13/2022] Open
Abstract
The human gut contains trillions of microbes that play a central role in host biology, including the provision of key nutrients from the diet. Food is a major source of precursors for metabolite production; in fact, diet modulates the gut microbiota (GM) as the nutrients, derived from dietary intake, reach the GM, affecting both the ecosystem and microbial metabolic profile. GM metabolic ability has an impact on human nutritional status from childhood. However, there is a wide variability of dietary patterns that exist among individuals. The study of interactions with the host via GM metabolic pathways is an interesting field of research in medicine, as microbiota members produce myriads of molecules with many bioactive properties. Indeed, much evidence has demonstrated the importance of metabolites produced by the bacterial metabolism from foods at the gut level that dynamically participate in various biochemical mechanisms of a cell as a reaction to environmental stimuli. Hence, the GM modulate homeostasis at the gut level, and the alteration in their composition can concur in disease onset or progression, including immunological, inflammatory, and metabolic disorders, as well as cancer. Understanding the gut microbe–nutrient interactions will increase our knowledge of how diet affects host health and disease, thus enabling personalized therapeutics and nutrition.
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Affiliation(s)
- Pamela Vernocchi
- Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Viale San Paolo 15, 00146 Rome, Italy;
- Correspondence: ; Tel.: +39-0668-594061; Fax: +39-0668-592218
| | - Federica Del Chierico
- Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Viale San Paolo 15, 00146 Rome, Italy;
| | - Lorenza Putignani
- Unit of Parasitology and Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Piazza Sant’ Onofrio 4, 00165 Rome, Italy;
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17
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Marzano V, Tilocca B, Fiocchi AG, Vernocchi P, Levi Mortera S, Urbani A, Roncada P, Putignani L. Perusal of food allergens analysis by mass spectrometry-based proteomics. J Proteomics 2020; 215:103636. [DOI: 10.1016/j.jprot.2020.103636] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/19/2019] [Accepted: 01/05/2020] [Indexed: 12/30/2022]
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18
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Botticelli A, Vernocchi P, Marini F, Quagliariello A, Cerbelli B, Reddel S, Del Chierico F, Di Pietro F, Giusti R, Tomassini A, Giampaoli O, Miccheli A, Zizzari IG, Nuti M, Putignani L, Marchetti P. Gut metabolomics profiling of non-small cell lung cancer (NSCLC) patients under immunotherapy treatment. J Transl Med 2020; 18:49. [PMID: 32014010 PMCID: PMC6998840 DOI: 10.1186/s12967-020-02231-0] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/16/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Despite the efficacy of immune checkpoint inhibitors (ICIs) only the 20-30% of treated patients present long term benefits. The metabolic changes occurring in the gut microbiota metabolome are herein proposed as a factor potentially influencing the response to immunotherapy. METHODS The metabolomic profiling of gut microbiota was characterized in 11 patients affected by non-small cell lung cancer (NSCLC) treated with nivolumab in second-line treatment with anti-PD-1 nivolumab. The metabolomics analyses were performed by GC-MS/SPME and 1H-NMR in order to detect volatile and non-volatile metabolites. Metabolomic data were processed by statistical profiling and chemometric analyses. RESULTS Four out of 11 patients (36%) presented early progression, while the remaining 7 out of 11 (64%) presented disease progression after 12 months. 2-Pentanone (ketone) and tridecane (alkane) were significantly associated with early progression, and on the contrary short chain fatty acids (SCFAs) (i.e., propionate, butyrate), lysine and nicotinic acid were significantly associated with long-term beneficial effects. CONCLUSIONS Our preliminary data suggest a significant role of gut microbiota metabolic pathways in affecting response to immunotherapy. The metabolic approach could be a promising strategy to contribute to the personalized management of cancer patients by the identification of microbiota-linked "indicators" of early progressor and long responder patients.
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Affiliation(s)
- Andrea Botticelli
- Department of Clinical and Molecular Medicine, Sapienza University of Rome, Rome, Italy.,AOU Policlinico Umberto I, Rome, Italy
| | - Pamela Vernocchi
- Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Federico Marini
- Department of Chemistry, Sapienza University of Rome, Rome, Italy.,NMR-based Metabolomics Laboratory, Sapienza University of Rome, Rome, Italy
| | | | - Bruna Cerbelli
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Rome, Italy
| | - Sofia Reddel
- Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | | | | | - Alberta Tomassini
- Department of Chemistry, Sapienza University of Rome, Rome, Italy.,NMR-based Metabolomics Laboratory, Sapienza University of Rome, Rome, Italy
| | | | - Alfredo Miccheli
- NMR-based Metabolomics Laboratory, Sapienza University of Rome, Rome, Italy.,Department of Enviromental Biology, University of Rome, Rome, Italy
| | | | - Marianna Nuti
- Department of Experimental Medicine, University Sapienza, Rome, Italy
| | - Lorenza Putignani
- Unit of Parasitology and Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
| | - Paolo Marchetti
- Department of Clinical and Molecular Medicine, Sapienza University of Rome, Rome, Italy.,AOU Policlinico Umberto I, Rome, Italy.,AOU Sant'Andrea Hospital, Rome, Italy
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Bianchi M, Alisi A, Fabrizi M, Vallone C, Ravà L, Giannico R, Vernocchi P, Signore F, Manco M. Maternal Intake of n-3 Polyunsaturated Fatty Acids During Pregnancy Is Associated With Differential Methylation Profiles in Cord Blood White Cells. Front Genet 2019; 10:1050. [PMID: 31708974 PMCID: PMC6824245 DOI: 10.3389/fgene.2019.01050] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 09/30/2019] [Indexed: 12/14/2022] Open
Abstract
A healthy diet during pregnancy is pivotal for the offspring health at birth and later in life. N-3 polyunsaturated fatty acids (n-3 PUFAs) are not endogenously produced in humans and are exclusively derived from the diet. They are pivotal for the fetus growth and neuronal development and seem beneficial in reducing the risk of cardiometabolic diseases and preventing later allergic disorders in the offspring by modulating the inflammatory immune response. In the present study, we investigated the association between maternal intakes of n-3PUFAs, profiled on maternal erythrocyte membranes at pregnancy term, and offspring DNA methylation on cord blood mononuclear cells in a sample of 118 mother–newborn pairs randomly drawn from the “Feeding fetus’ low-grade inflammation and insulin-resistance” study cohort. N-3 PUFA content on erythrocyte membranes is a validated biomarker to measure objectively medium term intake of n-3 PUFAs. Based on distribution of n-3 PUFA in the whole cohort of mothers, we identified mothers with low (n-3 PUFA concentration <25th percentile), medium (n-3 PUFAs between 25th and 75th percentiles), and high n-3 PUFA content (>75th percentile). The HumanMethylation450 BeadChip (Illumina) was used for the epigenome-wide association study using the Infinium Methylation Assay. The overall DNA methylation level was not different between the three groups while there was significant difference in methylation levels at certain sites. Indeed, 8,503 sites had significantly different methylations between low and high n-3 PUFA groups, 12,716 between low and medium n-3 PUFA groups, and 18,148 between high and medium n-3 PUFA groups. We found differentially methylated genes that belong prevalently to pathways of signal transduction, metabolism, downstream signaling of G protein-coupled receptors, and gene expression. Within these pathways, we identified four differentially methylated genes, namely, MSTN, IFNA13, ATP8B3, and GABBR2, that are involved in the onset of insulin resistance and adiposity, innate immune response, phospholipid translocation across cell membranes, and mechanisms of addiction to high fat diet, alcohol, and sweet taste. In conclusion, findings of this preliminary investigation suggest that maternal intake of n-3 PUFAs during pregnancy has potential to influence the offspring DNA methylation. Validation of results in a larger cohort and investigation of biological significance and impact on the phenotype are warranted.
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Affiliation(s)
- Marzia Bianchi
- Research Unit for Multifactorial Diseases, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Anna Alisi
- Research Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marta Fabrizi
- Research Unit for Multifactorial Diseases, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Cristina Vallone
- Department of Obstetrics and Gynecology, Misericordia Hospital, Grosseto, Italy
| | - Lucilla Ravà
- Clinical Epidemiology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Riccardo Giannico
- Research Unit for Multifactorial Diseases, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Pamela Vernocchi
- Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Fabrizio Signore
- Department of Obstetrics and Gynecology, Misericordia Hospital, Grosseto, Italy
| | - Melania Manco
- Research Unit for Multifactorial Diseases, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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20
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Levi Mortera S, Soggiu A, Vernocchi P, Del Chierico F, Piras C, Carsetti R, Marzano V, Britti D, Urbani A, Roncada P, Putignani L. Metaproteomic investigation to assess gut microbiota shaping in newborn mice: A combined taxonomic, functional and quantitative approach. J Proteomics 2019; 203:103378. [PMID: 31102759 DOI: 10.1016/j.jprot.2019.103378] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/23/2019] [Accepted: 05/13/2019] [Indexed: 12/16/2022]
Abstract
Breastfeeding is nowadays known to be one of the most critical factors contributing to the development of an efficient immune system. In the last decade, a consistent number of pieces of evidence demonstrated the relationship between a healthy organism and its gut microbiota. However, this link is still not fully understood and requires further investigation. We recently adopted a murine model to describe the impact of either maternal milk or parental genetic background, on the composition of the gut microbial population in the first weeks of life. A metaproteomic approach to such complex environments is a big challenge that requires a strong effort in both data production and analysis, including the set-up of dedicated multitasking bioinformatics pipelines. Herein we present an LC-MS/MS based investigation to monitor mouse gut microbiota in the early life, aiming at characterizing its functions and metabolic activities together with a taxonomic description in terms of operational taxonomic units. We provided a quantitative evaluation of bacterial metaproteins, taking into account differential expression results in relation to the functional and taxonomic classification, particularly with proteins from orthologues groups. This allowed the reduction of the bias arising from the presence of a high number of shared peptides, and proteins, among different bacterial species. We also focused on host mucosal proteome and its modulation, according to different microbiota composition. SIGNIFICANCE: This paper would represent a reference work for investigations on gut microbiota in early life, from both a microbiological and a functional proteomic point of view. We focused on the shaping of the mouse gut microbiota in dependence on the feeding modality, defining a reliable taxonomic description, highlighting some functional characteristics of the microbial community, and performing a first quantitative evaluation by data independent analysis in metaproteomics.
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Affiliation(s)
| | - Alessio Soggiu
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - Pamela Vernocchi
- Human Microbiome Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Cristian Piras
- Department of Veterinary Medicine, University of Milan, Milan, Italy
| | - Rita Carsetti
- B cell Pathophysiology Unit, Immunology Research Area and Unit of Diagnostic Immunology, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Valeria Marzano
- Human Microbiome Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Domenico Britti
- C.I.S. - Interdepartmental Services Centre of Veterinary for Human and Animal Health, University of Catanzaro "Magna Græcia", Catanzaro, Italy.; Department of Health Sciences, University of Catanzaro "Magna Græcia", Catanzaro, Italy
| | - Andrea Urbani
- Catholic University of Sacred Heart, Rome, Italy; Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Paola Roncada
- Department of Health Sciences, University of Catanzaro "Magna Græcia", Catanzaro, Italy
| | - Lorenza Putignani
- Parasitology Unit and Human Microbiome Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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21
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Reddel S, Del Chierico F, Quagliariello A, Giancristoforo S, Vernocchi P, Russo A, Fiocchi A, Rossi P, Putignani L, El Hachem M. Gut microbiota profile in children affected by atopic dermatitis and evaluation of intestinal persistence of a probiotic mixture. Sci Rep 2019; 9:4996. [PMID: 30899033 PMCID: PMC6428866 DOI: 10.1038/s41598-019-41149-6] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 02/11/2019] [Indexed: 12/17/2022] Open
Abstract
Atopic dermatitis (AD) has been hypothesised to be associated with gut microbiota (GM) composition. We performed a comparative study of the GM profile of 19 AD children and 18 healthy individuals aimed at identifying bacterial biomarkers associated with the disease. The effect of probiotic intake (Bifidobacterium breve plus Lactobacillus salivarius) on the modulation of GM and the probiotic persistence in the GM were also evaluated. Faecal samples were analysed by real-time PCR and 16S rRNA targeted metagenomics. Although the probiotics, chosen for this study, did not shape the entire GM profile, we observed the ability of these species to pass through the gastrointestinal tract and to persist (only B. breve) in the GM. Moreover, the GM of patients compared to CTRLs showed a dysbiotic status characterised by an increase of Faecalibacterium, Oscillospira, Bacteroides, Parabacteroides and Sutterella and a reduction of short-chain fatty acid (SCFA)-producing bacteria (i.e., Bifidobacterium, Blautia, Coprococcus, Eubacterium and Propionibacterium). Taken togheter these results show an alteration in AD microbiota composition with the depletion or absence of some species, opening the way to future probiotic intervention studies.
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Affiliation(s)
- Sofia Reddel
- Human Microbiome Unit, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | | | | | | | - Pamela Vernocchi
- Human Microbiome Unit, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Alessandra Russo
- Human Microbiome Unit, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Alessandro Fiocchi
- Unit of Allergology, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Paolo Rossi
- University Department of Pediatrics, Unit of Immune and Infectious Diseases, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Lorenza Putignani
- Human Microbiome Unit and Parasitology Unit, Bambino Gesù Children's Hospital IRCCS, Rome, Italy.
| | - May El Hachem
- Dermatology Unit, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
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22
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Piersigilli F, Lam TT, Vernocchi P, Quagliariello A, Putignani L, Aghai ZH, Bhandari V. Identification of new biomarkers of bronchopulmonary dysplasia using metabolomics. Metabolomics 2019; 15:20. [PMID: 30830433 DOI: 10.1007/s11306-019-1482-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/21/2019] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To identify new biomarkers of bronchopulmonary dysplasia (BPD) in preterm neonates. STUDY DESIGN Metabolomic study of prospectively collected tracheal aspirate (TA) samples from preterm neonates admitted in 2 neonatal intensive care units measured by a mass spectroscopy-based assay and analysed using partial least squares-discriminant analysis. RESULTS We evaluated 160 TA samples from 68 neonates, 44 with BPD and 24 without BPD in the first week of life. A cluster of 53 metabolites was identified as characteristic of BPD, with 18 select metabolites being highly significant in the separation of BPD versus No BPD. To control for the gestational age (GA) differences, we did a sub-group analyses, and noted that the amino acids histidine, glutamic acid, citrulline, glycine and isoleucine levels were higher in neonates with BPD. In addition, acylcarnitines C16-OH and C18:1-OH were also higher in neonates who developed BPD, but especially in the most preterm infants (neonates with GA < 27 weeks). CONCLUSION Metabolomics is a promising approach to identify novel specific biomarkers for BPD.
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Affiliation(s)
- Fiammetta Piersigilli
- Division of Perinatal Medicine, and Yale Child Health Research Center, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
- Division of Neonatology, Bambino Gesù Children's Hospital, Rome, Italy
| | - TuKiet T Lam
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
- Keck MS & Proteomics Resource, WM Keck Foundation Biotechnology Resource Laboratory, New Haven, CT, USA
| | - Pamela Vernocchi
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, Rome, Italy
| | - Andrea Quagliariello
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, Rome, Italy
| | - Lorenza Putignani
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, Rome, Italy
- Unit of Parasitology, Department of Laboratory and Immunological Diagnostics, Bambino Gesù Children's Hospital, Rome, Italy
| | - Zubair H Aghai
- Section of Neonatology, Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA, USA
| | - Vineet Bhandari
- Division of Perinatal Medicine, and Yale Child Health Research Center, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA.
- Section of Neonatal-Perinatal Medicine, Department of Pediatrics, St. Christopher's Hospital for Children, Drexel University College of Medicine, 160 East Erie Avenue, 19134, Philadelphia, PA, USA.
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23
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Mennini M, Reddel S, Arasi S, Del Chierico F, Napolitano T, Riccardi C, Fierro V, Vernocchi P, Putignani L, Fiocchi AG. Colonization and persistence capacity of a multi-strain probiotic in food allergy. J Allergy Clin Immunol 2019. [DOI: 10.1016/j.jaci.2018.12.699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Vernocchi P, Del Chierico F, Russo A, Majo F, Rossitto M, Valerio M, Casadei L, La Storia A, De Filippis F, Rizzo C, Manetti C, Paci P, Ercolini D, Marini F, Fiscarelli EV, Dallapiccola B, Lucidi V, Miccheli A, Putignani L. Gut microbiota signatures in cystic fibrosis: Loss of host CFTR function drives the microbiota enterophenotype. PLoS One 2018; 13:e0208171. [PMID: 30521551 PMCID: PMC6283533 DOI: 10.1371/journal.pone.0208171] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 11/13/2018] [Indexed: 02/08/2023] Open
Abstract
Background Cystic fibrosis (CF) is a disorder affecting the respiratory, digestive, reproductive systems and sweat glands. This lethal hereditary disease has known or suspected links to the dysbiosis gut microbiota. High-throughput meta-omics-based approaches may assist in unveiling this complex network of symbiosis modifications. Objectives The aim of this study was to provide a predictive and functional model of the gut microbiota enterophenotype of pediatric patients affected by CF under clinical stability. Methods Thirty-one fecal samples were collected from CF patients and healthy children (HC) (age range, 1–6 years) and analysed using targeted-metagenomics and metabolomics to characterize the ecology and metabolism of CF-linked gut microbiota. The multidimensional data were low fused and processed by chemometric classification analysis. Results The fused metagenomics and metabolomics based gut microbiota profile was characterized by a high abundance of Propionibacterium, Staphylococcus and Clostridiaceae, including Clostridium difficile, and a low abundance of Eggerthella, Eubacterium, Ruminococcus, Dorea, Faecalibacterium prausnitzii, and Lachnospiraceae, associated with overexpression of 4-aminobutyrate (GABA), choline, ethanol, propylbutyrate, and pyridine and low levels of sarcosine, 4-methylphenol, uracil, glucose, acetate, phenol, benzaldehyde, and methylacetate. The CF gut microbiota pattern revealed an enterophenotype intrinsically linked to disease, regardless of age, and with dysbiosis uninduced by reduced pancreatic function and only partially related to oral antibiotic administration or lung colonization/infection. Conclusions All together, the results obtained suggest that the gut microbiota enterophenotypes of CF, together with endogenous and bacterial CF biomarkers, are direct expression of functional alterations at the intestinal level. Hence, it’s possible to infer that CFTR impairment causes the gut ecosystem imbalance.This new understanding of CF host-gut microbiota interactions may be helpful to rationalize novel clinical interventions to improve the affected children’s nutritional status and intestinal function.
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Affiliation(s)
- Pamela Vernocchi
- Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Alessandra Russo
- Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Fabio Majo
- Cystic Fibrosis Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Martina Rossitto
- Diagnostics of Cystic Fibrosis, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Luca Casadei
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | - Antonietta La Storia
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Napoli, Italy
| | - Francesca De Filippis
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Napoli, Italy
| | - Cristiano Rizzo
- Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Cesare Manetti
- Department of Environmental Biology; Sapienza University of Rome, Rome, Italy
| | - Paola Paci
- CNR-Institute for Systems Analysis and Computer Science (IASI), Rome, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Napoli, Italy
| | - Federico Marini
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | | | - Bruno Dallapiccola
- Scientific Directorate, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Vincenzina Lucidi
- Cystic Fibrosis Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Alfredo Miccheli
- Department of Chemistry, Sapienza University of Rome, Rome, Italy
| | - Lorenza Putignani
- Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Unit of Parasitology Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- * E-mail:
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25
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Nobili V, Putignani L, Mosca A, Del Chierico F, Vernocchi P, Alisi A, Stronati L, Cucchiara S, Toscano M, Drago L. Bifidobacteria and lactobacilli in the gut microbiome of children with non-alcoholic fatty liver disease: which strains act as health players? Arch Med Sci 2018; 14:81-87. [PMID: 29379536 PMCID: PMC5778421 DOI: 10.5114/aoms.2016.62150] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/22/2016] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION Non-alcoholic fatty liver disease (NAFLD), considered the leading cause of chronic liver disease in children, can often progress from non-alcoholic fatty liver (NAFL) to non-alcoholic steatohepatitis (NASH). It is clear that obesity is one of the main risk factors involved in NAFLD pathogenesis, even if specific mechanisms have yet to be elucidated. We investigated the distribution of intestinal bifidobacteria and lactobacilli in the stools of four groups of children: obese, obese with NAFL, obese with NASH, and healthy, age-matched controls (CTRLs). MATERIAL AND METHODS Sixty-one obese, NAFL and NASH children and 54 CTRLs were enrolled in the study. Anthropometric and metabolic parameters were measured for all subjects. All children with suspected NASH underwent liver biopsy. Bifidobacteria and lactobacilli were analysed in children's faecal samples, during a broader, 16S rRNA-based pyrosequencing analysis of the gut microbiome. RESULTS Three Bifidobacterium spp. (Bifidobacterium longum, Bifidobacterium bifidum, and Bifidobacterium adolescentis) and five Lactobacillus spp. (L. zeae, L. vaginalis, L. brevis, L. ruminis, and L. mucosae) frequently recurred in metagenomic analyses. Lactobacillus spp. increased in NAFL, NASH, or obese children compared to CTRLs. Particularly, L. mucosae was significantly higher in obese (p = 0.02426), NAFLD (p = 0.01313) and NASH (p = 0.01079) than in CTRLs. In contrast, Bifidobacterium spp. were more abundant in CTRLs, suggesting a protective and beneficial role of these microorganisms against the aforementioned diseases. CONCLUSIONS Bifidobacteria seem to have a protective role against the development of NAFLD and obesity, highlighting their possible use in developing novel, targeted and effective probiotics.
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Affiliation(s)
- Valerio Nobili
- Hepato-Metabolic Disease Unit, “Bambino Gesù” Children’s Hospital, IRCCS, Rome, Italy
- Liver Research Unit, “Bambino Gesù” Children’s Hospital, IRCCS, Rome, Italy
| | - Lorenza Putignani
- Unit of Parasitology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Antonella Mosca
- Hepato-Metabolic Disease Unit, “Bambino Gesù” Children’s Hospital, IRCCS, Rome, Italy
| | | | - Pamela Vernocchi
- Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Anna Alisi
- Liver Research Unit, “Bambino Gesù” Children’s Hospital, IRCCS, Rome, Italy
| | - Laura Stronati
- Department of Cellular Biotechnology and Hematology, Sapienza University of Rome, Italy
| | - Salvatore Cucchiara
- Pediatric Gastroenterology and Liver Unit, Department of Pediatrics, Sapienza University, Rome, Italy
| | - Marco Toscano
- Laboratory of Clinical Chemistry and Microbiology, IRCCS Galeazzi Orthopaedic Institute, Milan, Italy
| | - Lorenzo Drago
- Laboratory of Clinical Chemistry and Microbiology, IRCCS Galeazzi Orthopaedic Institute, Milan, Italy
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26
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Siroli L, Patrignani F, Serrazanetti DI, Vernocchi P, Del Chierico F, Russo A, Torriani S, Putignani L, Gardini F, Lanciotti R. Effect of thyme essential oil and Lactococcus lactis CBM21 on the microbiota composition and quality of minimally processed lamb's lettuce. Food Microbiol 2017; 68:61-70. [PMID: 28800826 DOI: 10.1016/j.fm.2017.06.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 05/10/2017] [Accepted: 06/26/2017] [Indexed: 11/24/2022]
Abstract
The main aim of this work was to evaluate, at pilot scale in an industrial environment, the effects of the biocontrol agent Lactococcus lactis CBM21 and thyme essential oil compared to chlorine, used in the washing step of fresh-cut lamb's lettuce, on the microbiota and its changes in relation to the time of storage. The modification of the microbial population was studied through pyrosequencing in addition to the traditional plate counts. In addition, the volatile molecule and sensory profiles were evaluated during the storage. The results showed no significant differences in terms of total aerobic mesophilic cell loads in relation to the washing solution adopted. However, the pyrosequencing data permitted to identify the genera and species able to dominate the spoilage associations over storage in relation to the treatment applied. Also, the analyses of the volatile molecule profiles of the samples during storage allowed the identification of specific molecules as markers of the spoilage for each different treatment. The sensory analyses after 3 and 5 days of storage showed the preference of the panelists for samples washed with the combination thyme EO and the biocontrol agent. These samples were preferred for attributes such as flavor, acceptability and overall quality. These results highlighted the effect of the innovative washing solutions on the quality of lettuce through the shift of microbiota towards genera and species with lower potential in decreasing the sensory properties of the product.
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Affiliation(s)
- Lorenzo Siroli
- Department of Agricultural and Food Sciences, Alma Mater Studiorum, University of Bologna, Campus of Food Science, Piazza Goidanich 60, 47521 Cesena, Italy
| | - Francesca Patrignani
- Department of Agricultural and Food Sciences, Alma Mater Studiorum, University of Bologna, Campus of Food Science, Piazza Goidanich 60, 47521 Cesena, Italy
| | - Diana I Serrazanetti
- Interdepartmental Center for Industrial Agri-food Research, University of Bologna, Piazza Goidanich 60, 47521 Cesena FC, Italy
| | - Pamela Vernocchi
- Department of Agricultural and Food Sciences, Alma Mater Studiorum, University of Bologna, Campus of Food Science, Piazza Goidanich 60, 47521 Cesena, Italy; Human Microbiome Unit, Bambino Gesù Children Hospital, IRCCS, Viale di San Paolo 15, 00146 Rome, Italy
| | - Federica Del Chierico
- Human Microbiome Unit, Bambino Gesù Children Hospital, IRCCS, Viale di San Paolo 15, 00146 Rome, Italy
| | - Alessandra Russo
- Human Microbiome Unit, Bambino Gesù Children Hospital, IRCCS, Viale di San Paolo 15, 00146 Rome, Italy
| | - Sandra Torriani
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Lorenza Putignani
- Human Microbiome Unit, Bambino Gesù Children Hospital, IRCCS, Viale di San Paolo 15, 00146 Rome, Italy; Unit of Parasitology, Bambino Gesù Children Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome Italy
| | - Fausto Gardini
- Department of Agricultural and Food Sciences, Alma Mater Studiorum, University of Bologna, Campus of Food Science, Piazza Goidanich 60, 47521 Cesena, Italy; Interdepartmental Center for Industrial Agri-food Research, University of Bologna, Piazza Goidanich 60, 47521 Cesena FC, Italy
| | - Rosalba Lanciotti
- Department of Agricultural and Food Sciences, Alma Mater Studiorum, University of Bologna, Campus of Food Science, Piazza Goidanich 60, 47521 Cesena, Italy; Interdepartmental Center for Industrial Agri-food Research, University of Bologna, Piazza Goidanich 60, 47521 Cesena FC, Italy.
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27
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Traina G, Valluzzi RL, Fierro V, Riccardi C, Artesani MC, De Vuono A, Fiocchi A, Martelli AG, Ríos LA, Alcocer CR, Navarrete E, Del Rio Navarro BE, Gonzalez V, Velasco B, Perez Aviles HJ, Fernandez RJ, Pozo FC, Farhan AJ, Arshad H, Hussain A, Sharikadze O, Okhotnikova O, Alcover J, Rodriguez D, Pineda F, Dalal I, Weinbrand-Goichberg J, Benor S, Rottem M, Kivity S, Sato S, Yanagida N, Ebisawa M, Umanets T, Pineda F, Antipkin Y, Barzylovich V, Lapshyn V, Umanets T, Umanets M, Yuriev S, Pineda F, Rodriguez D, Alcover J, Bekir S, Pincock T, Vieira Hernandez A, Capriles Hulett A, Sánchez Borges M, Fabiano F, Albarran C, Goyal R, Gupta S, Gaurav G, Luskin AT, Griffin NM, Wagelie-Steffen A, Trzaskoma BL, Limb SL, Busse WW, Zeiger RS, Gonzalez-Reyes E, Casale TB, Chipps BE, Sugizaki C, Goto F, Sato S, Yanagida N, Ebisawa M, Yamaide A, Mitsunaga K, Tomiita M, Hoshioka A, Shimojo N, Pop LL, Ciucǎ IM, Tǎmaş L, Lazarescu M, Pienar C, Yamaide F, Fikri B, Sato H, Shimojo N, Okishima N, Kobayashi M, Takai M, Nishigata K, Yoda R, Oana YT, Kajiwara C, Shimodaira M, Suzuki T, Iizawa H, Kamijo K, Karmakar B, Bhattacharya SG, Blohlávková S, Kopelentová E, Víšek P, Štádler J, Šetinová I, Novobílská J, Lundelin K, Salminen S, Isolauri E, Pitt T, Flanders T, Peñalver M, Martínez P, Lluch M, Malet A, Nam YH, Jin HJ, Lee SK, Kulalert P, Sritipsukho P, Pathumanond J, Baynova K, Labella M, De Aramburu T, Prados M, Haanpää L, Aarnio J, Nermes M, Af Ursin P, Kaljonen A, Isolauri E, Bala N, Bhagwat K, Hindley J, Chapman M, Baalasubramanian S, Besednjak-Kocijančič L, SenGupta K, Bhattacharya SG, Chipps BE, Antonova E, Kong AM, Iqbal A, Teague WG, Chipps BE, Antonova E, Trzaskoma B, Ortiz B, Paknis B, Iqbal A, Rosen K, Szefler S, Alblooshi A, Al-Hammadi S, Vega A, Gutiérrez-Rivas R, Alonso AM, Beitia JM, Belén Mateo M, Cárdenas R, García-Domínguez JJ, Pitchon Dos Reis R, Gonçalves Alvim C, Andrade C, Reis A, Ribeiro H, Panaitescu Bunu C, Marusciac L, Paralescu S, Tamas P, Panitescu Bunu C, Marusciac L, Paralescu S, Tamas P, Martí Guadaño E, Escobar Bolaños C, Martí José N, Pau Casanovas P, Biarnés Rib G, Castells M, de Vicente Jiménez T, Mennini M, Riccardi C, De Angelis P, Rea F, Malamisura M, Tambucci R, Fiocchi A, Dall'Oglio L, Mennini M, Del Chierico F, Napolitano T, Reddel S, Vernocchi P, D'Ambrosio A, Putignani L, Artesani MC, Dahdah L, Fierro V, Banzato C, Echeverría Zudaire LA, Plaza AM, Bosque García M, Íbero M, Mazzina O, Fierro V, Marzano V, Riccardi C, Mazzina O, Dahdah L, Mennini M, Artesani MC, Mazzina O, Pecora V, Koch P, Valluzzi RL, Fierro V, Fiocchi A, Pecora V, Valentini D, Mennini M, Dahdah L, Mazzina O, Santamaria F, Valluzzi R, Mukherjee A, Kandhare A, Bodhankar S. Proceedings of the 2017 WAO Symposium on Hot Topics in Allergy: Pediatric & Regulatory Aspects: Rome, Italy/Vatican City. 27-29 April 2017. World Allergy Organ J 2017; 10:39. [PMID: 29444193 PMCID: PMC5773904 DOI: 10.1186/s40413-017-0170-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Giovanni Traina
- U.O.C Pediatria, Ospedale G. Salvini, Garbagnate Milanese, Milan, Italy
| | - Rocco Luigi Valluzzi
- 2Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Italy
| | - Vincenzo Fierro
- 2Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Italy
| | - Carla Riccardi
- 2Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Italy
| | - Maria Cristina Artesani
- 2Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Italy
| | - Andrea De Vuono
- Ufficio Statistica, Ospedale G. Salvini, Garbagnate Milanese, Milan, Italy
| | - Alessandro Fiocchi
- 2Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Italy
| | | | - Luis Alberto Ríos
- 4Pediatric Allergy and Clinical Immunology, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Christian R Alcocer
- 4Pediatric Allergy and Clinical Immunology, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Elsy Navarrete
- 4Pediatric Allergy and Clinical Immunology, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | | | - Victor Gonzalez
- 4Pediatric Allergy and Clinical Immunology, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Berenice Velasco
- 4Pediatric Allergy and Clinical Immunology, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Herberth J Perez Aviles
- 4Pediatric Allergy and Clinical Immunology, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Roberto Jose Fernandez
- 4Pediatric Allergy and Clinical Immunology, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - F Cesar Pozo
- 4Pediatric Allergy and Clinical Immunology, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | | | - Hasan Arshad
- 6Faculty of Medicine, Southampton University, Southampton, UK
| | | | - Olena Sharikadze
- 8Shupyk National Medical Academy of Postgraduate Education, Kyiv, Ukraine
| | - Olena Okhotnikova
- 8Shupyk National Medical Academy of Postgraduate Education, Kyiv, Ukraine
| | | | | | | | - Ilan Dalal
- 10Pediatric Allergy Unit, E. Wolfson Medical Center, Pediatric Department, E. Wolfson Medical Center, Sackler faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Shira Benor
- 12Allergy and Clinical Immunology Unit, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Menachem Rottem
- 13Allergy Asthma and Immunology Unit, Emek Medical Center, Afula, Israel
| | - Shmuel Kivity
- 12Allergy and Clinical Immunology Unit, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sakura Sato
- 14Department of Allergy, Clinical Research Center for Allergy and Rheumatology, Sagamihara National Hospital, Kanagawa, Japan
| | - Noriyuki Yanagida
- 15Department of Pediatrics, Sagamihara National Hospital, Kanagawa, Japan
| | - Motohiro Ebisawa
- 14Department of Allergy, Clinical Research Center for Allergy and Rheumatology, Sagamihara National Hospital, Kanagawa, Japan
| | - Tetiana Umanets
- Institute of Pediatrics, Obstetrics and Gynecology, Kyiv, Ukraine
| | | | - Youriy Antipkin
- Institute of Pediatrics, Obstetrics and Gynecology, Kyiv, Ukraine
| | | | | | - Tetiana Umanets
- Institute of Pediatrics, Obstetrics and Gynecology, Kyiv, Ukraine
| | | | - Sergey Yuriev
- Ukrainian School of Molecular Allergy and Immunology, Kyiv, Ukraine
| | | | | | | | - Suzan Bekir
- Collective.care Allergy Clinic, Sydney, Australia.,Australian Allergy Centre, Sydney, Australia
| | - Tobias Pincock
- Collective.care Allergy Clinic, Sydney, Australia.,Australian Allergy Centre, Sydney, Australia
| | | | | | - Mario Sánchez Borges
- 26Departamento de Pediatria, Centro Medico Docente La Trinidad, Caracas, Venezuela
| | | | - Carlos Albarran
- 25Departamento de Alergologia, Hospital de San Juan De Dios, Caracas, Venezuela
| | - Rohit Goyal
- 28Max Super Speciality Hospital, Bathinda, India
| | | | - Garg Gaurav
- 30Deen Dayal Upadhyay Hospital, New Delhi, India
| | | | | | | | | | | | - William W Busse
- 34University of Wisconsin School of Medicine and Public Health, Madison, WI USA
| | - Robert S Zeiger
- 35Deptartment of Allergy and Research and Evaluation, Kaiser Permanente Southern California, San Diego, CA USA
| | - Erika Gonzalez-Reyes
- 36The Children's Hospital of San Antonio, Baylor College of Medicine, San Antonio, TX USA
| | - Thomas B Casale
- 37Division of Allergy and Immunology, University of South Florida, Tampa, FL USA
| | - Bradley E Chipps
- 38Capital Allergy and Respiratory Disease Center, Sacramento, CA USA
| | - Chizuko Sugizaki
- 39Clinical Research Center, Sagamihara National Hospital, Sagamihara, Japan
| | - Fumiko Goto
- 39Clinical Research Center, Sagamihara National Hospital, Sagamihara, Japan
| | - Sakura Sato
- 39Clinical Research Center, Sagamihara National Hospital, Sagamihara, Japan
| | - Noriyuki Yanagida
- 39Clinical Research Center, Sagamihara National Hospital, Sagamihara, Japan
| | - Motohiro Ebisawa
- 39Clinical Research Center, Sagamihara National Hospital, Sagamihara, Japan
| | - Akiko Yamaide
- 40Department of Allergy and Rheumatology, Chiba Children's Hospital, Chiba, Japan
| | - Kanako Mitsunaga
- 40Department of Allergy and Rheumatology, Chiba Children's Hospital, Chiba, Japan
| | - Minako Tomiita
- 40Department of Allergy and Rheumatology, Chiba Children's Hospital, Chiba, Japan
| | - Akira Hoshioka
- 40Department of Allergy and Rheumatology, Chiba Children's Hospital, Chiba, Japan
| | - Naoki Shimojo
- 41Department of Pediatrics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Liviu L Pop
- 42Department of Pediatrics II, Victor Babeş University of Medicine and Pharmacy Timisora, Timisoara, Romania.,National Cystic Fibrosis Center, Timisoara, Romania
| | - Ioana-Mihaela Ciucǎ
- 42Department of Pediatrics II, Victor Babeş University of Medicine and Pharmacy Timisora, Timisoara, Romania.,National Cystic Fibrosis Center, Timisoara, Romania
| | - Liviu Tǎmaş
- 43Department of Biochemistry, Victor Babeş University of Medicine and Pharmacy Timisora, Timisoara, Romania
| | | | - Corina Pienar
- 42Department of Pediatrics II, Victor Babeş University of Medicine and Pharmacy Timisora, Timisoara, Romania
| | - Fumiya Yamaide
- 45Department of Pediatrics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Bahrul Fikri
- 45Department of Pediatrics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hironori Sato
- 45Department of Pediatrics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Naoki Shimojo
- 45Department of Pediatrics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Naoko Okishima
- 46Department of Health and Nutritional Science, Matsumoto University, Matsumoto, Japan
| | - Miyabi Kobayashi
- 46Department of Health and Nutritional Science, Matsumoto University, Matsumoto, Japan
| | - Mizuki Takai
- 46Department of Health and Nutritional Science, Matsumoto University, Matsumoto, Japan
| | - Kotarou Nishigata
- 46Department of Health and Nutritional Science, Matsumoto University, Matsumoto, Japan
| | - Ryou Yoda
- 46Department of Health and Nutritional Science, Matsumoto University, Matsumoto, Japan
| | - Yu-Ta Oana
- 46Department of Health and Nutritional Science, Matsumoto University, Matsumoto, Japan
| | - Chifu Kajiwara
- 46Department of Health and Nutritional Science, Matsumoto University, Matsumoto, Japan
| | - Moe Shimodaira
- 46Department of Health and Nutritional Science, Matsumoto University, Matsumoto, Japan
| | - Tomoka Suzuki
- 46Department of Health and Nutritional Science, Matsumoto University, Matsumoto, Japan
| | - Hiromi Iizawa
- 47Health Support Station, Matsumoto University, Matsumoto, Japan
| | | | | | | | - Simona Blohlávková
- Immuno-flow, s.r.o., Prague, Czech Republic.,52Medical Faculty, Charles University, Pilsen, Czech Republic
| | - Eliška Kopelentová
- Allergology Department, Kolín Hospital, Kolín, Czech Republic.,54Allergology and Immunology Department, Faculty Hospital Motol, Prague, Czech Republic
| | - Petr Víšek
- Allergology and Immunology Department, Litomyšl, Czech Republic
| | | | | | | | - Krisa Lundelin
- 58Department of Paediatrics, Turku University Hospital, Turku, Finland
| | - Seppo Salminen
- 58Department of Paediatrics, Turku University Hospital, Turku, Finland.,59Functional Foods Forum, University of Turku, Turku, Finland
| | - Erika Isolauri
- 58Department of Paediatrics, Turku University Hospital, Turku, Finland
| | - Tracy Pitt
- Department of Paediatrics, Humber River Hospital, Toronto, ON Canada.,61Deptartment of Paediatrics, Queen's University, Kingston, ON Canada
| | | | | | - Patricia Martínez
- Allergy and Clinical Immunology Service, Hospital de Nens de Barcelona, Barcelona, Spain
| | - Magdalena Lluch
- Allergy and Clinical Immunology Service, Hospital de Nens de Barcelona, Barcelona, Spain
| | - Alfonso Malet
- Allergy and Clinical Immunology Service, Hospital de Nens de Barcelona, Barcelona, Spain
| | - Young-Hee Nam
- 65Department of Internal Medicine, College of Medicine, Dong-A University, Busan, Korea
| | - Hyun Jung Jin
- 66Department of Internal Medicine, Yeungnam University Medical School, Daegu, Korea
| | - Soo-Keol Lee
- 65Department of Internal Medicine, College of Medicine, Dong-A University, Busan, Korea
| | - Prapasri Kulalert
- 67Division of Clinical Epidemiology, and Division of Allergy and Immunology, Deptartment of Pediatrics, Faculty of Medicine, Thammasat University (Rungsit Campus), Pathum Thani, Thailand.,68Thammasat University Center of Excellence of Asthma, Allergy and Immunology, Thammasat University Hospital, Pathum Thani, Thailand
| | - Paskorn Sritipsukho
- 69Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine, Thammasat University (Rungsit Campus), Pathum Thani, Thailand.,70Center of Excellence in Applied Epidemiology, Thammasat University (Rungsit campus), Pathum Thani, Thailand
| | - Jayanton Pathumanond
- 71Division of Clinical Epidemiology, Faculty of Medicine, Thammasat University (Rungsit Campus), Pathum Thani, Thailand
| | - Krasimira Baynova
- 72Allergy Unit, University Hospital Virgen del Rocío, Seville, Spain
| | - Marina Labella
- 72Allergy Unit, University Hospital Virgen del Rocío, Seville, Spain
| | | | - Manuel Prados
- 72Allergy Unit, University Hospital Virgen del Rocío, Seville, Spain
| | - Leena Haanpää
- 73Child and Youth Research Institute, Department of Clinical Medicine, University of Turku, Turku, Finland
| | - Jasmin Aarnio
- 75Faculty of Medicine, Department of Clinical Medicine, University of Turku, Turku, Finland
| | - Merja Nermes
- 74Department of Pediatrics and Adolescent Medicine, Turku University Hospital, Turku, Finland
| | - Piia Af Ursin
- 73Child and Youth Research Institute, Department of Clinical Medicine, University of Turku, Turku, Finland
| | - Anne Kaljonen
- 75Faculty of Medicine, Department of Clinical Medicine, University of Turku, Turku, Finland
| | - Erika Isolauri
- 74Department of Pediatrics and Adolescent Medicine, Turku University Hospital, Turku, Finland
| | - Nandana Bala
- 77Rainbow Children's Hospital, Bangalore, India.,79Indoor Biotechnologies Inc, Charlottesville, VA USA
| | | | | | | | | | | | - Koyel SenGupta
- 81Division of Plant Biology, Bose Institute, Kolkata, India
| | | | - Bradley E Chipps
- 82Capital Allergy and Respiratory Disease Center, Sacramento, CA USA
| | | | - Amanda M Kong
- Truven Health Analytics, an IBM Company, Cambridge, MA USA
| | - Ahmar Iqbal
- 83Genentech, Inc., South San Francisco, CA USA
| | - W Gerald Teague
- 85Child Health Research Center, University of Virginia School of Medicine, Charlottesville, VA USA
| | - Bradley E Chipps
- 86Capital Allergy and Respiratory Disease Center, Sacramento, CA USA
| | | | | | - Benjamin Ortiz
- 88Novartis Pharmaceuticals Corporation, East Hanover, NJ USA
| | - Brandee Paknis
- 88Novartis Pharmaceuticals Corporation, East Hanover, NJ USA
| | - Amar Iqbal
- 87Genentech, Inc., South San Francisco, CA USA
| | - Karin Rosen
- 87Genentech, Inc., South San Francisco, CA USA
| | - Stanley Szefler
- 89Pediatric Asthma Research Program, Children's Hospital and University of Colorado School of Medicine, Colorado, Aurora, CO USA
| | - Afaf Alblooshi
- 90Deptartment of Pediatrics, UAE University, Al-Ain, United Arab Emirates
| | | | - Arantza Vega
- 91Allergy Service, Hospital Universitario de Guadalajara, Guadalajara, Spain
| | | | - Ana Maria Alonso
- 91Allergy Service, Hospital Universitario de Guadalajara, Guadalajara, Spain
| | - Juan Maria Beitia
- 91Allergy Service, Hospital Universitario de Guadalajara, Guadalajara, Spain
| | - Maria Belén Mateo
- 91Allergy Service, Hospital Universitario de Guadalajara, Guadalajara, Spain
| | - Remedios Cárdenas
- 91Allergy Service, Hospital Universitario de Guadalajara, Guadalajara, Spain
| | | | - Raquel Pitchon Dos Reis
- 93Department of Pediatrics, Federal University of Minas Gerais, Belo Horizonte, Brazil.,94Allergy Department, Mater Dei Hospital, Belo Horizonte, Brazil
| | | | - Claudia Andrade
- 93Department of Pediatrics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Adriana Reis
- 93Department of Pediatrics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Henrique Ribeiro
- 93Department of Pediatrics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Laura Marusciac
- OncoGen Research Center, Emergency Clinical County Hospital, Timisoara, Romania
| | - Sorin Paralescu
- 95Victor Babes University of Medicine and Pharmacy, Timisoara, Romania
| | - Paul Tamas
- OncoGen Research Center, Emergency Clinical County Hospital, Timisoara, Romania
| | | | - Laura Marusciac
- OncoGen Research Center, Emergency Clinical County Hospital, Timisoara, Romania
| | - Sorin Paralescu
- 97Victor Babes University of Medicine and Pharmacy, Timisoara, Romania
| | - Paul Tamas
- OncoGen Research Center, Emergency Clinical County Hospital, Timisoara, Romania
| | | | | | | | | | | | - Mariana Castells
- 101Desensitization Unit, Brigham and Women's Hospital, Boston, MA USA
| | | | - Maurizio Mennini
- 103Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Carla Riccardi
- 103Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Papola De Angelis
- 104Digestive Surgery and Endoscopy Unit, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Francesca Rea
- 104Digestive Surgery and Endoscopy Unit, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Monica Malamisura
- 104Digestive Surgery and Endoscopy Unit, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Renato Tambucci
- 104Digestive Surgery and Endoscopy Unit, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Alessandro Fiocchi
- 103Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Luigi Dall'Oglio
- 104Digestive Surgery and Endoscopy Unit, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Maurizio Mennini
- 105Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | | | - Tania Napolitano
- 105Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Silvia Reddel
- 106Human Microbiome Unit, Bambino Gesù Children Hospital, Rome, Italy
| | - Pamela Vernocchi
- 106Human Microbiome Unit, Bambino Gesù Children Hospital, Rome, Italy
| | - Angelo D'Ambrosio
- 106Human Microbiome Unit, Bambino Gesù Children Hospital, Rome, Italy
| | - Lorenza Putignani
- 106Human Microbiome Unit, Bambino Gesù Children Hospital, Rome, Italy
| | | | - Lamia Dahdah
- 107Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Vincenzo Fierro
- 107Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Claudia Banzato
- 108Department of Life and Reproduction Sciences, Section of Pediatrics, University of Verona, Verona, Italy
| | | | - Ana María Plaza
- 110Pediatric Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Montserrat Bosque García
- 111Division of Pneumology, Hospital Parc Taulí, Autonomous University of Barcelona, Barcelona, Spain
| | - Marcel Íbero
- 112Allergy Unit, Hospital de Terrassa, Barcelona, Spain
| | - Oscar Mazzina
- 107Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Vincenzo Fierro
- 113Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Valeria Marzano
- 114Human Microbiome Unit, Bambino Gesù Children Hospital, Rome, Italy
| | - Carla Riccardi
- 113Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Oscar Mazzina
- 113Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Lamia Dahdah
- 113Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Maurizio Mennini
- 115Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Maria Cristina Artesani
- 115Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Oscar Mazzina
- 115Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Valeria Pecora
- 115Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Pierluigi Koch
- 115Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Rocco Luigi Valluzzi
- 115Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Vincenzo Fierro
- 115Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Alessandro Fiocchi
- 115Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Valentina Pecora
- 116Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Diletta Valentini
- 117Division of Infectious disease, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Maurizio Mennini
- 116Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Lamia Dahdah
- 116Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Oscar Mazzina
- 116Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Francesca Santamaria
- 116Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Rocco Valluzzi
- 116Division of Allergy, University Department of Pediatrics, Pediatric Hospital Bambino Gesù, Rome, Vatican City Italy
| | - Anwesha Mukherjee
- Department of Pharmacology, Poona College of Pharmacy, Bharati Videyapeeth Deemed University, Pune, India
| | - Amit Kandhare
- Department of Pharmacology, Poona College of Pharmacy, Bharati Videyapeeth Deemed University, Pune, India
| | - Subhash Bodhankar
- Department of Pharmacology, Poona College of Pharmacy, Bharati Videyapeeth Deemed University, Pune, India
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Marzano V, Mancinelli L, Bracaglia G, Del Chierico F, Vernocchi P, Di Girolamo F, Garrone S, Tchidjou Kuekou H, D’Argenio P, Dallapiccola B, Urbani A, Putignani L. "Omic" investigations of protozoa and worms for a deeper understanding of the human gut "parasitome". PLoS Negl Trop Dis 2017; 11:e0005916. [PMID: 29095820 PMCID: PMC5667730 DOI: 10.1371/journal.pntd.0005916] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The human gut has been continuously exposed to a broad spectrum of intestinal organisms, including viruses, bacteria, fungi, and parasites (protozoa and worms), over millions of years of coevolution, and plays a central role in human health. The modern lifestyles of Western countries, such as the adoption of highly hygienic habits, the extensive use of antimicrobial drugs, and increasing globalisation, have dramatically altered the composition of the gut milieu, especially in terms of its eukaryotic “citizens.” In the past few decades, numerous studies have highlighted the composition and role of human intestinal bacteria in physiological and pathological conditions, while few investigations exist on gut parasites and particularly on their coexistence and interaction with the intestinal microbiota. Studies of the gut “parasitome” through “omic” technologies, such as (meta)genomics, transcriptomics, proteomics, and metabolomics, are herein reviewed to better understand their role in the relationships between intestinal parasites, host, and resident prokaryotes, whether pathogens or commensals. Systems biology–based profiles of the gut “parasitome” under physiological and severe disease conditions can indeed contribute to the control of infectious diseases and offer a new perspective of omics-assisted tropical medicine.
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Affiliation(s)
- Valeria Marzano
- Human Microbiome Unit, Bambino Gesù Children’s Hospital IRCCS, Rome, Italy
| | - Livia Mancinelli
- Laboratory Medicine, Bambino Gesù Children’s Hospital IRCCS, Rome, Italy
| | - Giorgia Bracaglia
- Laboratory Medicine, Bambino Gesù Children’s Hospital IRCCS, Rome, Italy
| | | | - Pamela Vernocchi
- Human Microbiome Unit, Bambino Gesù Children’s Hospital IRCCS, Rome, Italy
| | | | - Stefano Garrone
- Laboratory Medicine, Bambino Gesù Children’s Hospital IRCCS, Rome, Italy
| | | | - Patrizia D’Argenio
- Pediatric Immuno-infectivology, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Bruno Dallapiccola
- Scientific Directorate, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Andrea Urbani
- Institute of Biochemistry and Biochemical Clinic, Faculty of Medicine and Surgery–Policlinico A. Gemelli, Catholic University of Sacred Heart, Rome, Italy
- Proteomic and Metabonomic Unit, Fondazione Santa Lucia IRCCS, Rome, Italy
| | - Lorenza Putignani
- Human Microbiome Unit, Bambino Gesù Children’s Hospital IRCCS, Rome, Italy
- Parasitology Unit, Bambino Gesù Children’s Hospital IRCCS, Rome, Italy
- * E-mail:
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29
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Vernocchi P, Del Chierico F, Russo A, Majo F, Valerio M, Casadei L, La Storia A, De Filippis F, Rizzo C, Manetti C, Paci P, Ercolini D, Marini F, Fiscarelli E, Dallapiccola B, Lucidi V, Miccheli A, Putignani L. 168 Loss of CFTR function drives the host-gut microbiota interaction: from omics data to clinical cue. J Cyst Fibros 2017. [DOI: 10.1016/s1569-1993(17)30532-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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30
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Del Chierico F, Nobili V, Vernocchi P, Russo A, De Stefanis C, Gnani D, Furlanello C, Zandonà A, Paci P, Capuani G, Dallapiccola B, Miccheli A, Alisi A, Putignani L. Gut microbiota profiling of pediatric nonalcoholic fatty liver disease and obese patients unveiled by an integrated meta-omics-based approach. Hepatology 2017; 65:451-464. [PMID: 27028797 DOI: 10.1002/hep.28572] [Citation(s) in RCA: 464] [Impact Index Per Article: 66.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 03/19/2016] [Indexed: 12/11/2022]
Abstract
UNLABELLED There is evidence that nonalcoholic fatty liver disease (NAFLD) is affected by gut microbiota. Therefore, we investigated its modifications in pediatric NAFLD patients using targeted metagenomics and metabolomics. Stools were collected from 61 consecutive patients diagnosed with nonalcoholic fatty liver (NAFL), nonalcoholic steatohepatitis (NASH), or obesity and 54 healthy controls (CTRLs), matched in a case-control fashion. Operational taxonomic units were pyrosequenced targeting 16S ribosomal RNA and volatile organic compounds determined by solid-phase microextraction gas chromatography-mass spectrometry. The α-diversity was highest in CTRLs, followed by obese, NASH, and NAFL patients; and β-diversity distinguished between patients and CTRLs but not NAFL and NASH. Compared to CTRLs, in NAFLD patients Actinobacteria were significantly increased and Bacteroidetes reduced. There were no significant differences among the NAFL, NASH, and obese groups. Overall NAFLD patients had increased levels of Bradyrhizobium, Anaerococcus, Peptoniphilus, Propionibacterium acnes, Dorea, and Ruminococcus and reduced proportions of Oscillospira and Rikenellaceae compared to CTRLs. After reducing metagenomics and metabolomics data dimensionality, multivariate analyses indicated a decrease of Oscillospira in NAFL and NASH groups and increases of Ruminococcus, Blautia, and Dorea in NASH patients compared to CTRLs. Of the 292 volatile organic compounds, 26 were up-regulated and 2 down-regulated in NAFLD patients. Multivariate analyses found that combination of Oscillospira, Rickenellaceae, Parabacteroides, Bacteroides fragilis, Sutterella, Lachnospiraceae, 4-methyl-2-pentanone, 1-butanol, and 2-butanone could discriminate NAFLD patients from CTRLs. Univariate analyses found significantly lower levels of Oscillospira and higher levels of 1-pentanol and 2-butanone in NAFL patients compared to CTRLs. In NASH, lower levels of Oscillospira were associated with higher abundance of Dorea and Ruminococcus and higher levels of 2-butanone and 4-methyl-2-pentanone compared to CTRLs. CONCLUSION An Oscillospira decrease coupled to a 2-butanone up-regulation and increases in Ruminococcus and Dorea were identified as gut microbiota signatures of NAFL onset and NAFL-NASH progression, respectively. (Hepatology 2017;65:451-464).
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Affiliation(s)
| | - Valerio Nobili
- Hepato-Metabolic Disease Unit, "Bambino Gesù" Children's Hospital, IRCCS, Rome, Italy.,Liver Research Unit, "Bambino Gesù" Children's Hospital, IRCCS, Rome, Italy
| | - Pamela Vernocchi
- Human Microbiome Unit, "Bambino Gesù" Children's Hospital, IRCCS, Rome, Italy
| | - Alessandra Russo
- Human Microbiome Unit, "Bambino Gesù" Children's Hospital, IRCCS, Rome, Italy
| | | | - Daniela Gnani
- Liver Research Unit, "Bambino Gesù" Children's Hospital, IRCCS, Rome, Italy
| | - Cesare Furlanello
- Predictive Models for Biomedicine and Environment Unit, Fondazione Bruno Kessler, Trento, Italy
| | - Alessandro Zandonà
- Predictive Models for Biomedicine and Environment Unit, Fondazione Bruno Kessler, Trento, Italy
| | - Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, 00185, Rome, Italy.,SysBio Centre for Systems Biology, 00185, Rome, Italy
| | | | - Bruno Dallapiccola
- Scientific Directorate, "Bambino Gesù" Children's Hospital, IRCCS, Rome, Italy
| | | | - Anna Alisi
- Liver Research Unit, "Bambino Gesù" Children's Hospital, IRCCS, Rome, Italy
| | - Lorenza Putignani
- Human Microbiome Unit, "Bambino Gesù" Children's Hospital, IRCCS, Rome, Italy.,Parasitology Unit, "Bambino Gesù" Children's Hospital, IRCCS, Rome, Italy
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31
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Patrignani F, Montanari C, Serrazanetti DI, Braschi G, Vernocchi P, Tabanelli G, Parpinello GP, Versari A, Gardini F, Lanciotti R. Characterisation of yeast microbiota, chemical and sensory properties of organic and biodynamic Sangiovese red wines. ANN MICROBIOL 2016. [DOI: 10.1007/s13213-016-1241-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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32
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Fiocchi A, Napolitano T, Reddel S, Vernocchi P, D'Ambrosio A, Putignani L. P295 Bifidobacterium longum & breve colonize and persist in microflora of infants with food allergy. Ann Allergy Asthma Immunol 2016. [DOI: 10.1016/j.anai.2016.09.308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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33
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Levi Mortera S, Del Chierico F, Vernocchi P, Rosado MM, Cavola A, Chierici M, Pieroni L, Urbani A, Carsetti R, Lante I, Dallapiccola B, Putignani L. Monitoring Perinatal Gut Microbiota in Mouse Models by Mass Spectrometry Approaches: Parental Genetic Background and Breastfeeding Effects. Front Microbiol 2016; 7:1523. [PMID: 27725814 PMCID: PMC5036385 DOI: 10.3389/fmicb.2016.01523] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 09/12/2016] [Indexed: 01/22/2023] Open
Abstract
At birth, contact with external stimuli, such as nutrients derived from food, is necessary to modulate the symbiotic balance between commensal and pathogenic bacteria, protect against bacterial dysbiosis, and initiate the development of the mucosal immune response. Among a variety of different feeding patterns, breastfeeding represents the best modality. In fact, the capacity of breast milk to modulate the composition of infants’ gut microbiota leads to beneficial effects on their health. In this study, we used newborn mice as a model to evaluate the effect of parental genetic background (i.e., IgA-producing mice and IgA-deficient mice) and feeding modulation (i.e., maternal feeding and cross-feeding) on the onset and shaping of gut microbiota after birth. To investigate these topics, we used either a culturomic approach that employed Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MS), or bottom–up Liquid Chromatography, with subsequent MSMS shotgun metaproteomic analysis that compared and assembled results of the two techniques. We found that the microbial community was enriched by lactic acid bacteria when pups were breastfed by wild-type (WT) mothers, while IgA-deficient milk led to an increase in the opportunistic bacterial pathogen (OBP) population. Cross-feeding results suggested that IgA supplementation promoted the exclusion of some OBPs and the temporary appearance of beneficial species in pups fed by WT foster mothers. Our results show that both techniques yield a picture of microbiota from different angles and with varying depths. In particular, our metaproteomic pipeline was found to be a reliable tool in the description of microbiota. Data from these studies are available via ProteomeXchange, with identifier PXD004033.
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Affiliation(s)
- Stefano Levi Mortera
- Human Microbiome Unit, Area of Genetic and Rare Diseases, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Federica Del Chierico
- Human Microbiome Unit, Area of Genetic and Rare Diseases, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Pamela Vernocchi
- Human Microbiome Unit, Area of Genetic and Rare Diseases, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Maria M Rosado
- Immunology Research Area, B-cell Physiopathology Unit and Diagnostic Immunology Unit, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Agnese Cavola
- Department of Experimental Medicine, University of Rome Tor Vergata Rome, Italy
| | | | | | - Andrea Urbani
- IRCCS-Santa Lucia FoundationRome, Italy; Istituto di Biochimica e Biochimica Clinica, Università Cattolica del Sacro CuoreRome, Italy
| | - Rita Carsetti
- Immunology Research Area, B-cell Physiopathology Unit and Diagnostic Immunology Unit, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Isabella Lante
- Laboratory Medicine Department, San Camillo Hospital Treviso, Italy
| | | | - Lorenza Putignani
- Human Microbiome Unit, Area of Genetic and Rare Diseases, Bambino Gesù Children's Hospital, IRCCSRome, Italy; Unit of Parasitology, Department of Laboratory, Bambino Gesù Children's Hospital, IRCCSRome, Italy
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34
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Vernocchi P, Del Chierico F, Putignani L. Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health. Front Microbiol 2016. [PMID: 27507964 DOI: 10.3389/fmicb.2016.01144]+[] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The gut microbiota is composed of a huge number of different bacteria, that produce a large amount of compounds playing a key role in microbe selection and in the construction of a metabolic signaling network. The microbial activities are affected by environmental stimuli leading to the generation of a wide number of compounds, that influence the host metabolome and human health. Indeed, metabolite profiles related to the gut microbiota can offer deep insights on the impact of lifestyle and dietary factors on chronic and acute diseases. Metagenomics, metaproteomics and metabolomics are some of the meta-omics approaches to study the modulation of the gut microbiota. Metabolomic research applied to biofluids allows to: define the metabolic profile; identify and quantify classes and compounds of interest; characterize small molecules produced by intestinal microbes; and define the biochemical pathways of metabolites. Mass spectrometry and nuclear magnetic resonance spectroscopy are the principal technologies applied to metabolomics in terms of coverage, sensitivity and quantification. Moreover, the use of biostatistics and mathematical approaches coupled with metabolomics play a key role in the extraction of biologically meaningful information from wide datasets. Metabolomic studies in gut microbiota-related research have increased, focusing on the generation of novel biomarkers, which could lead to the development of mechanistic hypotheses potentially applicable to the development of nutritional and personalized therapies.
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Affiliation(s)
- Pamela Vernocchi
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Federica Del Chierico
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Lorenza Putignani
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCSRome, Italy; Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCSRome, Italy
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35
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Vernocchi P, Del Chierico F, Putignani L. Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health. Front Microbiol 2016. [PMID: 27507964 DOI: 10.3389/fmicb.2016.01144] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota is composed of a huge number of different bacteria, that produce a large amount of compounds playing a key role in microbe selection and in the construction of a metabolic signaling network. The microbial activities are affected by environmental stimuli leading to the generation of a wide number of compounds, that influence the host metabolome and human health. Indeed, metabolite profiles related to the gut microbiota can offer deep insights on the impact of lifestyle and dietary factors on chronic and acute diseases. Metagenomics, metaproteomics and metabolomics are some of the meta-omics approaches to study the modulation of the gut microbiota. Metabolomic research applied to biofluids allows to: define the metabolic profile; identify and quantify classes and compounds of interest; characterize small molecules produced by intestinal microbes; and define the biochemical pathways of metabolites. Mass spectrometry and nuclear magnetic resonance spectroscopy are the principal technologies applied to metabolomics in terms of coverage, sensitivity and quantification. Moreover, the use of biostatistics and mathematical approaches coupled with metabolomics play a key role in the extraction of biologically meaningful information from wide datasets. Metabolomic studies in gut microbiota-related research have increased, focusing on the generation of novel biomarkers, which could lead to the development of mechanistic hypotheses potentially applicable to the development of nutritional and personalized therapies.
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Affiliation(s)
- Pamela Vernocchi
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Federica Del Chierico
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Lorenza Putignani
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCSRome, Italy; Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCSRome, Italy
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36
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Vernocchi P, Del Chierico F, Putignani L. Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health. Front Microbiol 2016; 7:1144. [PMID: 27507964 PMCID: PMC4960240 DOI: 10.3389/fmicb.2016.01144] [Citation(s) in RCA: 219] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 07/08/2016] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota is composed of a huge number of different bacteria, that produce a large amount of compounds playing a key role in microbe selection and in the construction of a metabolic signaling network. The microbial activities are affected by environmental stimuli leading to the generation of a wide number of compounds, that influence the host metabolome and human health. Indeed, metabolite profiles related to the gut microbiota can offer deep insights on the impact of lifestyle and dietary factors on chronic and acute diseases. Metagenomics, metaproteomics and metabolomics are some of the meta-omics approaches to study the modulation of the gut microbiota. Metabolomic research applied to biofluids allows to: define the metabolic profile; identify and quantify classes and compounds of interest; characterize small molecules produced by intestinal microbes; and define the biochemical pathways of metabolites. Mass spectrometry and nuclear magnetic resonance spectroscopy are the principal technologies applied to metabolomics in terms of coverage, sensitivity and quantification. Moreover, the use of biostatistics and mathematical approaches coupled with metabolomics play a key role in the extraction of biologically meaningful information from wide datasets. Metabolomic studies in gut microbiota-related research have increased, focusing on the generation of novel biomarkers, which could lead to the development of mechanistic hypotheses potentially applicable to the development of nutritional and personalized therapies.
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Affiliation(s)
- Pamela Vernocchi
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCSRome, Italy
| | - Federica Del Chierico
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCSRome, Italy
| | - Lorenza Putignani
- Unit of Human Microbiome, Genetic and Rare Diseases Area, Bambino Gesù Children's Hospital, IRCCSRome, Italy
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCSRome, Italy
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Patrignani F, Chinnici F, Serrazanetti DI, Vernocchi P, Ndagijimana M, Riponi C, Lanciotti R. Production of Volatile and Sulfur Compounds by 10 Saccharomyces cerevisiae Strains Inoculated in Trebbiano Must. Front Microbiol 2016; 7:243. [PMID: 26973621 PMCID: PMC4777720 DOI: 10.3389/fmicb.2016.00243] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/15/2016] [Indexed: 11/13/2022] Open
Abstract
In wines, the presence of sulfur compounds is the resulting of several contributions among which yeast metabolism. The characterization of the starter Saccharomyces cerevisiae needs to be performed also taking into account this ability even if evaluated together with the overall metabolic profile. In this perspective, principal aim of this experimental research was the evaluation of the volatile profiles, throughout GC/MS technique coupled with solid phase micro extraction, of wines obtained throughout the fermentation of 10 strains of S. cerevisiae. In addition, the production of sulfur compounds was further evaluated by using a gas-chromatograph coupled with a Flame Photometric Detector. Specifically, the 10 strains were inoculated in Trebbiano musts and the fermentations were monitored for 19 days. In the produced wines, volatile and sulfur compounds as well as amino acid concentrations were investigated. Also the physico-chemical characteristics of the wines and their electronic nose profiles were evaluated.
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Affiliation(s)
- Francesca Patrignani
- Department of Agricultural and Food Sciences, University of BolognaBologna, Italy; Interdepartmental Centres for Industrial Research, University of BolognaCesena, Italy
| | - Fabio Chinnici
- Department of Agricultural and Food Sciences, University of Bologna Bologna, Italy
| | - Diana I Serrazanetti
- Interdepartmental Centres for Industrial Research, University of Bologna Cesena, Italy
| | - Pamela Vernocchi
- Department of Agricultural and Food Sciences, University of BolognaBologna, Italy; Human Microbiome Unit, Genetic and Rare Diseases Area, Bambino Gesu Research Hospital IRCCSRome, Italy
| | - Maurice Ndagijimana
- Department of Agricultural Food and Nutritional Science, Agriculture/Forestry Centre, University of Alberta Edmonton, AB, Canada
| | - Claudio Riponi
- Department of Agricultural and Food Sciences, University of Bologna Bologna, Italy
| | - Rosalba Lanciotti
- Department of Agricultural and Food Sciences, University of BolognaBologna, Italy; Interdepartmental Centres for Industrial Research, University of BolognaCesena, Italy
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Tabanelli G, Vernocchi P, Patrignani F, Del Chierico F, Putignani L, Vinderola G, Reinheimer JA, Gardini F, Lanciotti R. Effects of sub-lethal high-pressure homogenization treatment on the outermost cellular structures and the volatile-molecule profiles of two strains of probiotic lactobacilli. Front Microbiol 2015; 6:1006. [PMID: 26441931 PMCID: PMC4585067 DOI: 10.3389/fmicb.2015.01006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 09/07/2015] [Indexed: 11/23/2022] Open
Abstract
Applying sub-lethal levels of high-pressure homogenization (HPH) to lactic acid bacteria has been proposed as a method of enhancing some of their functional properties. Because the principal targets of HPH are the cell-surface structures, the aim of this study was to examine the effect of sub-lethal HPH treatment on the outermost cellular structures and the proteomic profiles of two known probiotic bacterial strains. Moreover, the effect of HPH treatment on the metabolism of probiotic cells within a dairy product during its refrigerated storage was investigated using SPME-GC-MS. Transmission electron microscopy was used to examine the microstructural changes in the outermost cellular structures due to HPH treatment. These alterations may be involved in the changes in some of the technological and functional properties of the strains that were observed after pressure treatment. Moreover, the proteomic profiles of the probiotic strains treated with HPH and incubated at 37°C for various periods showed different peptide patterns compared with those of the untreated cells. In addition, there were differences in the peaks that were observed in the low-mass spectral region (2000–3000 Da) of the spectral profiles of the control and treated samples. Due to pressure treatment, the volatile-molecule profiles of buttermilk inoculated with treated or control cells and stored at 4°C for 30 days exhibited overall changes in the aroma profile and in the production of molecules that improved its sensory profile, although the two different species imparted specific fingerprints to the product. The results of this study will contribute to understanding the changes that occur in the outermost cellular structures and the metabolism of LAB in response to HPH treatment. The findings of this investigation may contribute to elucidating the relationships between these changes and the alterations of the technological and functional properties of LAB induced by pressure treatment.
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Affiliation(s)
- Giulia Tabanelli
- Centro Interdipartimentale di Ricerca Industriale Agroalimentare, Università degli Studi di Bologna Cesena, Italy
| | - Pamela Vernocchi
- Centro Interdipartimentale di Ricerca Industriale Agroalimentare, Università degli Studi di Bologna Cesena, Italy ; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Francesca Patrignani
- Dipartimento di Scienze e Tecnologie Agro-alimentari, Università degli Studi di Bologna - Sede di Cesena Cesena, Italy
| | | | - Lorenza Putignani
- Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS Rome, Italy ; Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
| | - Gabriel Vinderola
- Facultad de Ingeniería Química, Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Universidad Nacional del Litoral Santa Fe, Argentina
| | - Jorge A Reinheimer
- Facultad de Ingeniería Química, Instituto de Lactología Industrial (INLAIN, UNL-CONICET), Universidad Nacional del Litoral Santa Fe, Argentina
| | - Fausto Gardini
- Centro Interdipartimentale di Ricerca Industriale Agroalimentare, Università degli Studi di Bologna Cesena, Italy ; Dipartimento di Scienze e Tecnologie Agro-alimentari, Università degli Studi di Bologna - Sede di Cesena Cesena, Italy
| | - Rosalba Lanciotti
- Centro Interdipartimentale di Ricerca Industriale Agroalimentare, Università degli Studi di Bologna Cesena, Italy ; Dipartimento di Scienze e Tecnologie Agro-alimentari, Università degli Studi di Bologna - Sede di Cesena Cesena, Italy
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Del Chierico F, Vernocchi P, Petrucca A, Paci P, Fuentes S, Praticò G, Capuani G, Masotti A, Reddel S, Russo A, Vallone C, Salvatori G, Buffone E, Signore F, Rigon G, Dotta A, Miccheli A, de Vos WM, Dallapiccola B, Putignani L. Phylogenetic and Metabolic Tracking of Gut Microbiota during Perinatal Development. PLoS One 2015; 10:e0137347. [PMID: 26332837 PMCID: PMC4557834 DOI: 10.1371/journal.pone.0137347] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 08/14/2015] [Indexed: 12/28/2022] Open
Abstract
The colonization and development of gut microbiota immediately after birth is highly variable and depends on several factors, such as delivery mode and modality of feeding during the first months of life. A cohort of 31 mother and neonate pairs, including 25 at-term caesarean (CS) and 6 vaginally (V) delivered neonates (DNs), were included in this study and 121 meconium/faecal samples were collected at days 1 through 30 following birth. Operational taxonomic units (OTUs) were assessed in 69 stool samples by phylogenetic microarray HITChip and inter- and intra-individual distributions were established by inter-OTUs correlation matrices and OTUs co-occurrence or co-exclusion networks. 1H-NMR metabolites were determined in 70 stool samples, PCA analysis was performed on 55 CS DNs samples, and metabolome/OTUs co-correlations were assessed in 45 CS samples, providing an integrated map of the early microbiota OTUs-metabolome. A microbiota "core" of OTUs was identified that was independent of delivery mode and lactation stage, suggesting highly specialized communities that act as seminal colonizers of microbial networks. Correlations among OTUs, metabolites, and OTUs-metabolites revealed metabolic profiles associated with early microbial ecological dynamics, maturation of milk components, and host physiology.
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Affiliation(s)
| | - Pamela Vernocchi
- Unit of Metagenomics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Interdipartimental Centre for Industrial Research-CIRI-AGRIFOOD, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Andrea Petrucca
- Unit of Metagenomics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Department of Diagnostic Science, Sant’Andrea Hospital, Rome, Italy
| | - Paola Paci
- CNR, Institute of Systems Analysis and Informatics Antonio Ruberti, Rome, Italy
| | - Susana Fuentes
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Giulia Praticò
- Department of Chemistry, Sapienza University, Rome, Italy
| | | | | | - Sofia Reddel
- Unit of Metagenomics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Alessandra Russo
- Unit of Metagenomics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Cristina Vallone
- Department of Obstetrics and Gyneacology, San Camillo Hospital, Rome, Italy
| | - Guglielmo Salvatori
- Department of Neonatology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Elsa Buffone
- Department of Neonatology, San Camillo Hospital, Rome, Italy
| | - Fabrizio Signore
- Department of Obstetrics and Gyneacology, San Camillo Hospital, Rome, Italy
| | - Giuliano Rigon
- Department of Obstetrics and Gyneacology, San Camillo Hospital, Rome, Italy
| | - Andrea Dotta
- Department of Neonatology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | | | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Departments of Veterinary Biosciences and Bacteriology & Immunology, Helsinki University, Helsinki, Finland
| | - Bruno Dallapiccola
- Scientific Directorate, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Lorenza Putignani
- Unit of Metagenomics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Unit of Parasitology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- * E-mail:
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Del Chierico F, Vernocchi P, Dallapiccola B, Putignani L. Mediterranean diet and health: food effects on gut microbiota and disease control. Int J Mol Sci 2014; 15:11678-99. [PMID: 24987952 PMCID: PMC4139807 DOI: 10.3390/ijms150711678] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 06/04/2014] [Accepted: 06/11/2014] [Indexed: 02/07/2023] Open
Abstract
The Mediterranean diet (MD) is considered one of the healthiest dietary models. Many of the characteristic components of the MD have functional features with positive effects on health and wellness. The MD adherence, calculated through various computational scores, can lead to a reduction of the incidence of major diseases (e.g., cancers, metabolic and cardiovascular syndromes, neurodegenerative diseases, type 2 diabetes and allergy). Furthermore, eating habits are the main significant determinants of the microbial multiplicity of the gut, and dietary components influence both microbial populations and their metabolic activities from the early stages of life. For this purpose, we present a study proposal relying on the generation of individual gut microbiota maps from MD-aware children/adolescents. The maps, based on meta-omics approaches, may be considered as new tools, acting as a systems biology-based proof of evidence to evaluate MD effects on gut microbiota homeostasis. Data integration of food metabotypes and gut microbiota “enterotypes” may allow one to interpret MD adherence and its effects on health in a new way, employable for the design of targeted diets and nutraceutical interventions in childcare and clinical management of food-related diseases, whose onset has been significantly shifted early in life.
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Affiliation(s)
- Federica Del Chierico
- Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio, Rome 400165, Italy.
| | - Pamela Vernocchi
- Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio, Rome 400165, Italy.
| | - Bruno Dallapiccola
- Scientific Directorate, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio, Rome 400165, Italy.
| | - Lorenza Putignani
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio, Rome 400165, Italy.
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Pietrantoni E, Del Chierico F, Rigon G, Vernocchi P, Salvatori G, Manco M, Signore F, Putignani L. Docosahexaenoic acid supplementation during pregnancy: a potential tool to prevent membrane rupture and preterm labor. Int J Mol Sci 2014; 15:8024-36. [PMID: 24810692 PMCID: PMC4057716 DOI: 10.3390/ijms15058024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 04/24/2014] [Accepted: 04/29/2014] [Indexed: 01/18/2023] Open
Abstract
Polyunsaturated fatty acids (PUFAs) are required to maintain the fluidity, permeability and integrity of cell membranes. Maternal dietary supplementation with ω-3 PUFAs during pregnancy has beneficial effects, including increased gestational length and reduced risk of pregnancy complications. Significant amounts of ω-3 docosahexaenoic acid (DHA) are transferred from maternal to fetal blood, hence ensuring high levels of DHA in the placenta and fetal bloodstream and tissues. Fetal DHA demand increases exponentially with gestational age, especially in the third trimester, due to fetal development. According to the World Health Organization (WHO) and the Food and Agriculture Organization of the United Nations (FAO), a daily intake of DHA is recommended during pregnancy. Omega-3 PUFAs are involved in several anti-inflammatory, pro-resolving and anti-oxidative pathways. Several placental disorders, such as intrauterine growth restriction, premature rupture of membranes (PROM) and preterm-PROM (pPROM), are associated with placental inflammation and oxidative stress. This pilot study reports on a preliminary evaluation of the significance of the daily DHA administration on PROM and pPROM events in healthy pregnant women. Further extensive clinical trials will be necessary to fully elucidate the correlation between DHA administration during pregnancy and PROM/pPROM occurrence, which is related in turn to gestational duration and overall fetal health.
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Affiliation(s)
- Emanuela Pietrantoni
- Department of Obstetrics and Gynaecology, San Camillo Forlanini Hospital, Circonvallazione Gianicolense, 87, Rome 00151, Italy.
| | - Federica Del Chierico
- Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio, 4, Rome 00165, Italy.
| | - Giuliano Rigon
- Department of Obstetrics and Gynaecology, San Camillo Forlanini Hospital, Circonvallazione Gianicolense, 87, Rome 00151, Italy.
| | - Pamela Vernocchi
- Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio, 4, Rome 00165, Italy.
| | - Guglielmo Salvatori
- Unit of Neonatology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio, 4, Rome 00165, Italy.
| | - Melania Manco
- Scientific Directorate, Research Unit for Multifactorial Disease, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio, 4, Rome 00165, Italy.
| | - Fabrizio Signore
- Department of Obstetrics and Gynaecology, San Camillo Forlanini Hospital, Circonvallazione Gianicolense, 87, Rome 00151, Italy.
| | - Lorenza Putignani
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio, 4, Rome 00165, Italy.
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Del Chierico F, Petrucca A, Mortera SL, Vernocchi P, Rosado MM, Pieroni L, Carsetti R, Urbani A, Putignani L. A metaproteomic pipeline to identify newborn mouse gut phylotypes. J Proteomics 2013; 97:17-26. [PMID: 24176786 DOI: 10.1016/j.jprot.2013.10.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 09/20/2013] [Accepted: 10/18/2013] [Indexed: 12/12/2022]
Abstract
UNLABELLED In order to characterize newborn mouse gut microbiota phylotypes in very early-life stages, an original metaproteomic pipeline, based on LC-MS(2)-spectra and Mascot driven NCBI non-redundant repository database interrogation was developed. An original computational analysis assisted in the generation of a taxonomic gut architecture from protein hits to operational taxonomic units (OTUs) and related functional categories. Regardless of the mouse's genetic background, a prevalence of Firmicutes (Lactobacillaceae) and Proteobacteria (Enterobacteriaceae) was observed among the entire Eubacteria taxonomic node. However, a higher abundance of Firmicutes was retrieved for Balb/c gut microbiota compared to Rag2(ko) mice, the latter was mainly characterized by a Proteobacteria enriched microbiota. The metaproteomic-obtained OTUs were supported, for the identification (ID) of the cultivable bacteria fraction, corroborated by axenic culture-based MALDI-TOF MS IDs. Particularly, functional analysis of Rag2(ko) mice gut microbiota proteins revealed the presence of abundant glutathione, riboflavin metabolism and pentose phosphate pathway components, possibly related to genetic background. The metaproteomic pipeline herein presented may represent a useful tool to investigate the highly debated onset of the human gut microbiota in the first days of life, when the bacterial composition, despite its very low diversity (complexity), is still very far from an exhaustive description and other complex microbial consortia. BIOLOGICAL SIGNIFICANCE The manuscript deals with a "frontier" topic regarding the study of the gut microbiota and the application of a metaproteomic pipeline to unveil the complexity of this fascinating ecosystem at the very early stages of life. Indeed during these phases, its diversity is very low but the bacterial content is highly "instable", and the relative balance between mucosal and fecal bacteria starts its dynamics of "fight" to get homeostasis. However, in the neonatal period, especially immediately after birth, a comprehensive description of this microbial eco-organ is still lacking, while it should be mandatory to highlight its first mechanisms of homeostasis and perturbation, while it co-develops with and within the host species. In order to unravel its low but almost unknown microbial community multiplicity, the newborn mouse gut, characterized by a "very" low complexity, was herein selected as model to design a LC-MS(2)-based shotgun metaproteomic approach, potentially suitable to study onset and shaping in human newborns. A microbiological semi-automatic computational analysis was performed to infer gut phylotypes; such as proof of evidence, related OTUs were compared to axenic-culture-based MALDI-TOF MS IDs showing consistency at family and phyla levels for the bacterial cultivable fraction. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Federica Del Chierico
- Parasitology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Metagenomics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Petrucca
- Parasitology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Metagenomics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Department of Diagnostic Science, Sant'Andrea Hospital, Rome, Italy
| | - Stefano Levi Mortera
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy; IRCCS-Santa Lucia Foundation, Rome, Italy
| | - Pamela Vernocchi
- Parasitology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Metagenomics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Interdipartimental Centre for Industrial Research, Alma Mater Studiorum, University of Bologna, Italy
| | - Maria M Rosado
- B-cell development Unit and Immunological Diagnosis Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Luisa Pieroni
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy; IRCCS-Santa Lucia Foundation, Rome, Italy
| | - Rita Carsetti
- B-cell development Unit and Immunological Diagnosis Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Andrea Urbani
- Department of Experimental Medicine, University of Rome "Tor Vergata", Rome, Italy; IRCCS-Santa Lucia Foundation, Rome, Italy.
| | - Lorenza Putignani
- Parasitology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Metagenomics Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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Del Chierico F, Petrucca A, Vernocchi P, Bracaglia G, Fiscarelli E, Bernaschi P, Muraca M, Urbani A, Putignani L. Proteomics boosts translational and clinical microbiology. J Proteomics 2013; 97:69-87. [PMID: 24145144 DOI: 10.1016/j.jprot.2013.10.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 07/28/2013] [Accepted: 10/09/2013] [Indexed: 01/17/2023]
Abstract
The application of proteomics to translational and clinical microbiology is one of the most advanced frontiers in the management and control of infectious diseases and in the understanding of complex microbial systems within human fluids and districts. This new approach aims at providing, by dedicated bioinformatic pipelines, a thorough description of pathogen proteomes and their interactions within the context of human host ecosystems, revolutionizing the vision of infectious diseases in biomedicine and approaching new viewpoints in both diagnostic and clinical management of the patient. Indeed, in the last few years, many laboratories have matured a series of advanced proteomic applications, aiming at providing individual proteome charts of pathogens, with respect to their morph and/or cell life stages, antimicrobial or antimycotic resistance profiling, epidemiological dispersion. Herein, we aim at reviewing the current state-of-the-art on proteomic protocols designed and set-up for translational and diagnostic microbiological purposes, from axenic pathogens' characterization to microbiota ecosystems' full description. The final goal is to describe applications of the most common MALDI-TOF MS platforms to advanced diagnostic issues related to emerging infections, increasing of fastidious bacteria, and generation of patient-tailored phylotypes. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- F Del Chierico
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - A Petrucca
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Department of Diagnostic Science, Sant'Andrea Hospital, Via di Grottarossa 1035, 00185 Rome, Italy
| | - P Vernocchi
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Interdipartimental Centre for Industrial Research-CIRI-AGRIFOOD, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - G Bracaglia
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - E Fiscarelli
- Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - P Bernaschi
- Unit of Microbiology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - M Muraca
- Laboratory Medicine, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - A Urbani
- Department of Experimental Medicine and Surgery, University "Tor Vergata", Rome, Italy; IRCCS-Santa Lucia Foundation, Rome, Italy
| | - L Putignani
- Unit of Parasitology, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy; Unit of Metagenomics, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy.
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Vernocchi P, Vannini L, Gottardi D, Del Chierico F, Serrazanetti DI, Ndagijimana M, Guerzoni ME. Integration of datasets from different analytical techniques to assess the impact of nutrition on human metabolome. Front Cell Infect Microbiol 2012; 2:156. [PMID: 23248777 PMCID: PMC3518793 DOI: 10.3389/fcimb.2012.00156] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Accepted: 11/25/2012] [Indexed: 12/14/2022] Open
Abstract
Bacteria colonizing the human intestinal tract exhibit a high phylogenetic diversity that reflects their immense metabolic potentials. The catalytic activity of gut microbes has an important impact on gastrointestinal (GI) functions and host health. The microbial conversion of carbohydrates and other food components leads to the formation of a large number of compounds that affect the host metabolome and have beneficial or adverse effects on human health. Metabolomics is a metabolic-biology system approach focused on the metabolic responses understanding of living systems to physio-pathological stimuli by using multivariate statistical data on human body fluids obtained by different instrumental techniques. A metabolomic approach based on an analytical platform could be able to separate, detect, characterize and quantify a wide range of metabolites and its metabolic pathways. This approach has been recently applied to study the metabolic changes triggered in the gut microbiota by specific diet components and diet variations, specific diseases, probiotic and synbiotic food intake. This review describes the metabolomic data obtained by analyzing human fluids by using different techniques and particularly Gas Chromatography Mass Spectrometry Solid-phase Micro Extraction (GC-MS/SPME), Proton Nuclear Magnetic Resonance (1H-NMR) Spectroscopy and Fourier Transform Infrared (FTIR) Spectroscopy. This instrumental approach has a good potential in the identification and detection of specific food intake and diseases biomarkers.
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Affiliation(s)
- Pamela Vernocchi
- Interdipartimental Centre for Industrial Research-CIRI-AGRIFOOD, Alma Mater Studiorum, University of Bologna Bologna, Italy ; Parasitology Unit, Department of Laboratories, Bambino Gesù Children's Hospital, IRCCS Rome, Italy
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Francavilla R, Calasso M, Calace L, Siragusa S, Ndagijimana M, Vernocchi P, Brunetti L, Mancino G, Tedeschi G, Guerzoni E, Indrio F, Laghi L, Miniello VL, Gobbetti M, De Angelis M. Effect of lactose on gut microbiota and metabolome of infants with cow's milk allergy. Pediatr Allergy Immunol 2012; 23:420-7. [PMID: 22435727 DOI: 10.1111/j.1399-3038.2012.01286.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Allergic infants have an unusual gastrointestinal microbiota with low numbers of Bifidobacterium/Lactobacilli and high levels of Clostridium, staphylococci and Escherichia coli. Hydrolyzed formula used to treat these infants is deprived of lactose that instead may influence the gut microbial composition. The aim of the present study is to investigate the influence of lactose on the composition of the gut microbiota and metabolome of infants with cow's milk allergy. Infants prospectively enrolled received an extensively hydrolyzed formula with no lactose for 2 months followed by an identical lactose-containing formula for an additional 2 months. Healthy, age-gender-matched infants were used as controls. The following determinations were performed before and after the introduction of lactose in the diet: enumeration of cells present in the feces using FISH, counts of viable bacterial cells and gas-chromatography mass spectrometry/solid-phase microextraction analysis. The addition of lactose to the diet significantly increases the counts of Bifidobacteria and lactic acid bacteria (p < 0.01), decreases that of Bacteroides/clostridia (p < 0.05) reaching counts found in healthy controls; lactose significantly increases the concentration of total short-chain fatty acids (p < 0.05). The addition of lactose to an extensively hydrolyzed formula is able to positively modulate the composition of gut microbiota by increasing the total fecal counts of Lactobacillus/Bifidobacteria and decreasing that of Bacteroides/Clostridia. The positive effect is completed by the increase of median concentration of short chain fatty acids, especially for acetic and butyric acids demonstrated by the metabolomic analysis.
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Del Chierico F, Vernocchi P, Bonizzi L, Carsetti R, Castellazzi AM, Dallapiccola B, de Vos W, Guerzoni ME, Manco M, Marseglia GL, Muraca M, Roncada P, Salvatori G, Signore F, Urbani A, Putignani L. Early-life gut microbiota under physiological and pathological conditions: The central role of combined meta-omics-based approaches. J Proteomics 2012; 75:4580-7. [DOI: 10.1016/j.jprot.2012.02.018] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Revised: 01/28/2012] [Accepted: 02/14/2012] [Indexed: 01/01/2023]
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Patrignani F, Ndagijimana M, Belletti N, Gardini F, Vernocchi P, Lanciotti R. Biogenic amines and ethyl carbamate in primitivo wine: survey of their concentrations in commercial products and relationship with the use of malolactic starter. J Food Prot 2012; 75:591-6. [PMID: 22410237 DOI: 10.4315/0362-028x.jfp-11-311] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
This research was conducted to determine the biogenic amine (BA) and ethyl carbamate (EC) concentrations in commercial Primitivo wine samples and the influence of the use of malolactic starter culture on concentrations of these potentially hazardous compounds in this wine. One hundred sixty bottles of wine from eight producers in the Apulia region of southern Italy were purchased at retail and analyzed. The most common BAs were histamine, 2-phenylethylamine, tyramine, cadaverine, putrescine, spermine, and spermidine. Putrescine (derived from ornithine) was the most abundant BA in all commercial Primitivo wines (5.41 to 9.51 mg/liter), 2-phenylethylamine was detected in only two commercial wines (at less than 2.12 mg/liter), and histamine was found at concentrations of 1.49 to 16.34 mg/liter. The concentration of EC in commercial Primitivo wine was 6.81 to 15.62 ppb, which is not considered dangerous for human health. Malolactic fermentation (MLF) affected the concentrations of BAs and EC differently. For EC, no significant differences were detected between samples of wine produced by spontaneous fermentation and wine that was inoculated malolactic starter. Mean EC concentrations were 12 and 14 ppb in two batches tested (always 18 ppb or less), regardless of whether the malolactic starter was added. Although present at trace levels in wine before the MLF, histamine accumulated during the MLF process, regardless of whether the malolactic starter was added. However, the increase in histamine was higher in wines without the malolactic starter. The concentrations of putrescine and cadaverine increased after MLF, especially in the wine that spontaneously fermented. The use of a selected malolactic starter resulted in reductions in BA concentrations in wine produced by this guided MLF compared with wine produced by spontaneous MLF.
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Affiliation(s)
- F Patrignani
- Department of Food Science, University of Bologna, Piazza Goidanich 60, 47521 Cesena, Italy
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Di Cagno R, De Angelis M, De Pasquale I, Ndagijimana M, Vernocchi P, Ricciuti P, Gagliardi F, Laghi L, Crecchio C, Guerzoni ME, Gobbetti M, Francavilla R. Duodenal and faecal microbiota of celiac children: molecular, phenotype and metabolome characterization. BMC Microbiol 2011; 11:219. [PMID: 21970810 PMCID: PMC3206437 DOI: 10.1186/1471-2180-11-219] [Citation(s) in RCA: 209] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 10/04/2011] [Indexed: 12/14/2022] Open
Abstract
Background Epidemiology of celiac disease (CD) is increasing. CD mainly presents in early childhood with small intestinal villous atrophy and signs of malabsorption. Compared to healthy individuals, CD patients seemed to be characterized by higher numbers of Gram-negative bacteria and lower numbers Gram-positive bacteria. Results This study aimed at investigating the microbiota and metabolome of 19 celiac disease children under gluten-free diet (treated celiac disease, T-CD) and 15 non-celiac children (HC). PCR-denaturing gradient gel electrophoresis (DGGE) analyses by universal and group-specific primers were carried out in duodenal biopsies and faecal samples. Based on the number of PCR-DGGE bands, the diversity of Eubacteria was the higher in duodenal biopsies of T-CD than HC children. Bifidobacteria were only found in faecal samples. With a few exceptions, PCR-DGGE profiles of faecal samples for Lactobacillus and Bifidobacteria differed between T-CD and HC. As shown by culture-dependent methods, the levels of Lactobacillus, Enterococcus and Bifidobacteria were confirmed to be significantly higher (P = 0.028; P = 0.019; and P = 0.023, respectively) in fecal samples of HC than in T-CD children. On the contrary, cell counts (CFU/ml) of presumptive Bacteroides, Staphylococcus, Salmonella, Shighella and Klebsiella were significantly higher (P = 0.014) in T-CD compared to HC children. Enterococcus faecium and Lactobacillus plantarum were the species most diffusely identified. This latter species was also found in all duodenal biopsies of T-CD and HC children. Other bacterial species were identified only in T-CD or HC faecal samples. As shown by Randomly Amplified Polymorphic DNA-PCR analysis, the percentage of strains identified as lactobacilli significantly (P = 0.011) differed between T-CD (ca. 26.5%) and HC (ca. 34.6%) groups. The metabolome of T-CD and HC children was studied using faecal and urine samples which were analyzed by gas-chromatography mass spectrometry-solid-phase microextraction and 1H-Nuclear Magnetic Resonance. As shown by Canonical Discriminant Analysis of Principal Coordinates, the levels of volatile organic compounds and free amino acids in faecal and/or urine samples were markedly affected by CD. Conclusion As shown by the parallel microbiology and metabolome approach, the gluten-free diet lasting at least two years did not completely restore the microbiota and, consequently, the metabolome of CD children. Some molecules (e.g., ethyl-acetate and octyl-acetate, some short chain fatty acids and free amino acids, and glutamine) seems to be metabolic signatures of CD.
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Affiliation(s)
- Raffaella Di Cagno
- Department of Biologia e Chimica Agro-Forestale ed Ambientale, University of Bari Aldo Moro, via Amendola 165/A, Bari, 70126 Italy
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Ercolini D, Ferrocino I, Nasi A, Ndagijimana M, Vernocchi P, La Storia A, Laghi L, Mauriello G, Guerzoni ME, Villani F. Monitoring of microbial metabolites and bacterial diversity in beef stored under different packaging conditions. Appl Environ Microbiol 2011; 77:7372-81. [PMID: 21803905 PMCID: PMC3194879 DOI: 10.1128/aem.05521-11] [Citation(s) in RCA: 188] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Accepted: 07/19/2011] [Indexed: 12/17/2022] Open
Abstract
Beef chops were stored at 4°C under different conditions: in air (A), modified-atmosphere packaging (MAP), vacuum packaging (V), or bacteriocin-activated antimicrobial packaging (AV). After 0 to 45 days of storage, analyses were performed to determine loads of spoilage microorganisms, microbial metabolites (by solid-phase microextraction [SPME]-gas chromatography [GC]-mass spectrometry [MS] and proton nuclear magnetic resonance [(1)H NMR]), and microbial diversity (by PCR-denaturing gradient gel electrophoresis [DGGE] and pyrosequencing). The microbiological shelf life of meat increased with increasing selectivity of storage conditions. Culture-independent analysis by pyrosequencing of DNA extracted directly from meat showed that Brochothrix thermosphacta dominated during the early stages of storage in A and MAP, while Pseudomonas spp. took over during further storage in A. Many different bacteria, several of which are usually associated with soil rather than meat, were identified in V and AV; however, lactic acid bacteria (LAB) dominated during the late phases of storage, and Carnobacterium divergens was the most frequent microorganism in AV. Among the volatile metabolites, butanoic acid was associated with the growth of LAB under V and AV storage conditions, while acetoin was related to the other spoilage microbial groups and storage conditions. (1)H NMR analysis showed that storage in air was associated with decreases in lactate, glycogen, IMP, and ADP levels and with selective increases in levels of 3-methylindole, betaine, creatine, and other amino acids. The meat microbiota is significantly affected by storage conditions, and its changes during storage determine complex shifts in the metabolites produced, with a potential impact on meat quality.
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Affiliation(s)
- Danilo Ercolini
- Dipartimento di Scienza degli Alimenti, Università degli Studi di Napoli Federico II, Via Università 100, 80055 Portici (NA), Italy.
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Vernocchi P, Ndagijimana M, Serrazanetti DI, López CC, Fabiani A, Gardini F, Elisabetta Guerzoni M, Lanciotti R. Use of Saccharomyces cerevisiae strains endowed with β-glucosidase activity for the production of Sangiovese wine. World J Microbiol Biotechnol 2010; 27:1423-33. [PMID: 25187142 DOI: 10.1007/s11274-010-0594-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 10/12/2010] [Indexed: 10/18/2022]
Abstract
The aim of this work was to evaluate the suitability of four strains of Saccharomyces cerevisiae endowed with in vitro β-glucosidase activity to improve the Sangiovese wine aroma profiles. In particular the effects of the strains on fermentation kinetics, wine sugar and acid concentrations, volatile molecule profiles and colour parameters were evaluated. Moreover their effects on anthocyanins, anthocyanidins and poliphenols were evaluated. These four strains of S. cerevisiae were tested in comparison with one commercial strain and with a spontaneous fermentation in the presence and in the absence of paraffin oil. The results showed that the four wild strains had high fermentation rates and an efficient conversion of grape sugars to alcohol. However, each strain imparted specific features to the wine. AS11 and AS15 gave rise to wine having low volatile acidity values associated to high levels of linalool and nerolidol. They provoked decrease of anthocyanins accompanied by the increase of some anthocyanidins. S. cerevisiae BV12 and BV14 showed the best performances producing wines with the lowest residual sugar contents and volatile acidity values, high levels of nerolidol and citronellol without detrimental effects on wine colour.
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Affiliation(s)
- Pamela Vernocchi
- Dipartimento di Scienze degli Alimenti, Università degli Studi di Bologna, Piazza Goidanich 60, 47023, Cesena, Italy
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