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Johnson CC, Ownby DR. Allergies and Asthma: Do Atopic Disorders Result from Inadequate Immune Homeostasis arising from Infant Gut Dysbiosis? Expert Rev Clin Immunol 2016; 12:379-88. [PMID: 26776722 DOI: 10.1586/1744666x.2016.1139452] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Our global hypothesis is that atopic conditions and asthma develop because an individual's immune system is not able to appropriately resolve inflammation resulting from allergen exposures. We propose that the failure to appropriately down-regulate inflammation and produce a toleragenic state results primarily from less robust immune homeostatic processes rather than from a tendency to over-respond to allergenic stimuli. An individual with lower immune homeostatic capacity is unable to rapidly and completely terminate, on average over time, immune responses to innocuous allergens, increasing risk of allergic disease. A lack of robust homeostasis also increases the risk of other inflammatory conditions, such as prolonged respiratory viral infections and obesity, leading to the common co-occurrence of these conditions. Further, we posit that the development of vigorous immune homeostatic mechanisms is an evolutionary adaptation strongly influenced by both 1) exposure to a diverse maternal microbiota through the prenatal period, labor and delivery, and, 2) an orderly assemblage process of the infant's gut microbiota ecosystem shaped by breastfeeding and early exposure to a wide variety of ingested foods and environmental microbes. This early succession of microbial communities together with early allergen exposures orchestrate the development of an immune system with a robust ability to optimally control inflammatory responses and a lowered risk for atopic disorders.
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Affiliation(s)
- Christine C Johnson
- a Department of Public Health Sciences , Henry Ford Hospital , Detroit , MI , USA
| | - Dennis R Ownby
- b Department of Pediatrics , Georgia Regents University , Augusta , GA , USA
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102
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Huang X, Nie S, Xie M. Interaction between gut immunity and polysaccharides. Crit Rev Food Sci Nutr 2015; 57:2943-2955. [DOI: 10.1080/10408398.2015.1079165] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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103
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Pan M, Yuan D, Chen S, Xu A. Diversity and composition of the bacterial community in Amphioxus feces. J Basic Microbiol 2015; 55:1336-42. [PMID: 26173442 DOI: 10.1002/jobm.201500124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 06/23/2015] [Indexed: 12/12/2022]
Abstract
Amphioxus is a typical filter feeder animal and is confronted with a complex bacterial community in the seawater of its habitat. It has evolved a strong innate immune system to cope with the external bacterial stimulation, however, the ecological system of the bacterial community in Amphioxus remains unknown. Through massive parallel 16S rRNA gene tag pyrosequencing, the investigation indicated that the composition of wild and lab-cultured Amphioxus fecal bacteria was complex with more than 85,000 sequence tags being assigned to 12/13 phyla. The bacterial diversity between the two fecal samples was similar according to OTU richness of V4 tag, Chao1 index, Shannon index and Rarefaction curves, however, the most prominent bacteria in wild feces were genera Pseudoalteromonas (gamma Proteobacteria) and Arcobacter (epsilon Proteobacteria); the highly abundant bacteria in lab-cultured feces were other groups, including Leisingera, Phaeobacter (alpha Proteobacteria), and Vibrio (gamma Proteobacteria). Such difference indicates the complex fecal bacteria with the potential for multi-stability. The bacteria of habitat with 28 assigned phyla had the higher bacterial diversity and species richness than both fecal bacteria. Shared bacteria between wild feces and its habitat reached to approximately 90% (153/169 genera) and 28% (153/548 genera), respectively. As speculative, the less diversity of both fecal bacteria compared to its habitat partly because Amphioxus lives buried and the feces will ultimately end up in the sediment. Therefore, our study comprehensively investigates the complex bacterial community of Amphioxus and provides evidence for understanding the relationship of this basal chordate with the environment.
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Affiliation(s)
- Minming Pan
- Department of Biochemistry, College of Life Sciences, State Key Laboratory of Biocontrol, National Engineering Research Center of South China Sea Marine Biotechnology, Sun Yat-sen University, Guangzhou, P. R. China
| | - Dongjuan Yuan
- Department of Biochemistry, College of Life Sciences, State Key Laboratory of Biocontrol, National Engineering Research Center of South China Sea Marine Biotechnology, Sun Yat-sen University, Guangzhou, P. R. China.,Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, P. R. China
| | - Shangwu Chen
- Department of Biochemistry, College of Life Sciences, State Key Laboratory of Biocontrol, National Engineering Research Center of South China Sea Marine Biotechnology, Sun Yat-sen University, Guangzhou, P. R. China
| | - Anlong Xu
- Department of Biochemistry, College of Life Sciences, State Key Laboratory of Biocontrol, National Engineering Research Center of South China Sea Marine Biotechnology, Sun Yat-sen University, Guangzhou, P. R. China.,Beijing University of Chinese Medicine, 11 Bei San Huan Dong Road, Chao-yang District, Beijing 100029, P. R. China
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104
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Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota. Curr Biol 2015; 25:1682-93. [PMID: 25981789 DOI: 10.1016/j.cub.2015.04.055] [Citation(s) in RCA: 248] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/09/2015] [Accepted: 04/29/2015] [Indexed: 12/21/2022]
Abstract
Through human microbiome sequencing, we can better understand how host evolutionary and ontogenetic history is reflected in the microbial function. However, there has been no information on the gut metagenome configuration in hunter-gatherer populations, posing a gap in our knowledge of gut microbiota (GM)-host mutualism arising from a lifestyle that describes over 90% of human evolutionary history. Here, we present the first metagenomic analysis of GM from Hadza hunter-gatherers of Tanzania, showing a unique enrichment in metabolic pathways that aligns with the dietary and environmental factors characteristic of their foraging lifestyle. We found that the Hadza GM is adapted for broad-spectrum carbohydrate metabolism, reflecting the complex polysaccharides in their diet. Furthermore, the Hadza GM is equipped for branched-chain amino acid degradation and aromatic amino acid biosynthesis. Resistome functionality demonstrates the existence of antibiotic resistance genes in a population with little antibiotic exposure, indicating the ubiquitous presence of environmentally derived resistances. Our results demonstrate how the functional specificity of the GM correlates with certain environment and lifestyle factors and how complexity from the exogenous environment can be balanced by endogenous homeostasis. The Hadza gut metagenome structure allows us to appreciate the co-adaptive functional role of the GM in complementing the human physiology, providing a better understanding of the versatility of human life and subsistence.
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105
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Biagi E, Zama D, Nastasi C, Consolandi C, Fiori J, Rampelli S, Turroni S, Centanni M, Severgnini M, Peano C, de Bellis G, Basaglia G, Gotti R, Masetti R, Pession A, Brigidi P, Candela M. Gut microbiota trajectory in pediatric patients undergoing hematopoietic SCT. Bone Marrow Transplant 2015; 50:992-8. [PMID: 25893458 DOI: 10.1038/bmt.2015.16] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 01/19/2015] [Accepted: 01/20/2015] [Indexed: 12/27/2022]
Abstract
Acute GvHD (aGvHD) is the main complication of hematopoietic SCT (HSCT) during the treatment of hematological disorders. We carried out the first longitudinal study to follow the gut microbiota trajectory, from both the phylogenetic and functional points of view, in pediatric patients undergoing HSCT. Gut microbiota trajectories and short-chain fatty acid production profiles were followed starting from before HSCT and through the 3-4 months after transplant in children developing and not developing aGvHD. According to our findings, HSCT procedures temporarily cause a structural and functional disruption of the gut microbial ecosystem, describing a trajectory of recovery during the following 100 days. The onset of aGvHD is associated with specific gut microbiota signatures both along the course of gut microbiota reconstruction immediately after transplant and, most interestingly, prior to HSCT. Indeed, in pre-HSCT samples, non-aGvHD patients showed higher abundances of propionate-producing Bacteroidetes, highly adaptable microbiome mutualists that showed to persist during the HSCT-induced ecosystem disruption. Our data indicate that structure and temporal dynamics of the gut microbial ecosystem can be a relevant factor for the success of HSCT and opens the perspective to the manipulation of the pre-HSCT gut microbiota configuration to favor mutualistic persisters with immunomodulatory properties in the gut.
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Affiliation(s)
- E Biagi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - D Zama
- Pediatric Oncology and Haematology Unit "Lalla Seràgnoli", Department of Pediatrics, University of Bologna, Sant'Orsola Malpighi Hospital, Bologna, Italy
| | - C Nastasi
- Pediatric Oncology and Haematology Unit "Lalla Seràgnoli", Department of Pediatrics, University of Bologna, Sant'Orsola Malpighi Hospital, Bologna, Italy
| | - C Consolandi
- Institute of Biomedical Technologies, Italian National Research Council, Milan, Italy
| | - J Fiori
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - S Rampelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - S Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - M Centanni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - M Severgnini
- Institute of Biomedical Technologies, Italian National Research Council, Milan, Italy
| | - C Peano
- Institute of Biomedical Technologies, Italian National Research Council, Milan, Italy
| | - G de Bellis
- Institute of Biomedical Technologies, Italian National Research Council, Milan, Italy
| | - G Basaglia
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - R Gotti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - R Masetti
- Pediatric Oncology and Haematology Unit "Lalla Seràgnoli", Department of Pediatrics, University of Bologna, Sant'Orsola Malpighi Hospital, Bologna, Italy
| | - A Pession
- Pediatric Oncology and Haematology Unit "Lalla Seràgnoli", Department of Pediatrics, University of Bologna, Sant'Orsola Malpighi Hospital, Bologna, Italy
| | - P Brigidi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - M Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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106
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Tailford LE, Crost EH, Kavanaugh D, Juge N. Mucin glycan foraging in the human gut microbiome. Front Genet 2015; 6:81. [PMID: 25852737 PMCID: PMC4365749 DOI: 10.3389/fgene.2015.00081] [Citation(s) in RCA: 522] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 02/16/2015] [Indexed: 12/21/2022] Open
Abstract
The availability of host and dietary carbohydrates in the gastrointestinal (GI) tract plays a key role in shaping the structure-function of the microbiota. In particular, some gut bacteria have the ability to forage on glycans provided by the mucus layer covering the GI tract. The O-glycan structures present in mucin are diverse and complex, consisting predominantly of core 1-4 mucin-type O-glycans containing α- and β- linked N-acetyl-galactosamine, galactose and N-acetyl-glucosamine. These core structures are further elongated and frequently modified by fucose and sialic acid sugar residues via α1,2/3/4 and α2,3/6 linkages, respectively. The ability to metabolize these mucin O-linked oligosaccharides is likely to be a key factor in determining which bacterial species colonize the mucosal surface. Due to their proximity to the immune system, mucin-degrading bacteria are in a prime location to influence the host response. However, despite the growing number of bacterial genome sequences available from mucin degraders, our knowledge on the structural requirements for mucin degradation by gut bacteria remains fragmented. This is largely due to the limited number of functionally characterized enzymes and the lack of studies correlating the specificity of these enzymes with the ability of the strain to degrade and utilize mucin and mucin glycans. This review focuses on recent findings unraveling the molecular strategies used by mucin-degrading bacteria to utilize host glycans, adapt to the mucosal environment, and influence human health.
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Affiliation(s)
| | | | | | - Nathalie Juge
- The Gut Health and Food Safety Institute Strategic Programme, Institute of Food ResearchNorwich, UK
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107
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Thompson AL, Monteagudo-Mera A, Cadenas MB, Lampl ML, Azcarate-Peril MA. Milk- and solid-feeding practices and daycare attendance are associated with differences in bacterial diversity, predominant communities, and metabolic and immune function of the infant gut microbiome. Front Cell Infect Microbiol 2015; 5:3. [PMID: 25705611 PMCID: PMC4318912 DOI: 10.3389/fcimb.2015.00003] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 01/05/2015] [Indexed: 01/14/2023] Open
Abstract
The development of the infant intestinal microbiome in response to dietary and other exposures may shape long-term metabolic and immune function. We examined differences in the community structure and function of the intestinal microbiome between four feeding groups, exclusively breastfed infants before introduction of solid foods (EBF), non-exclusively breastfed infants before introduction of solid foods (non-EBF), EBF infants after introduction of solid foods (EBF+S), and non-EBF infants after introduction of solid foods (non-EBF+S), and tested whether out-of-home daycare attendance was associated with differences in relative abundance of gut bacteria. Bacterial 16S rRNA amplicon sequencing was performed on 49 stool samples collected longitudinally from a cohort of 9 infants (5 male, 4 female). PICRUSt metabolic inference analysis was used to identify metabolic impacts of feeding practices on the infant gut microbiome. Sequencing data identified significant differences across groups defined by feeding and daycare attendance. Non-EBF and daycare-attending infants had higher diversity and species richness than EBF and non-daycare attending infants. The gut microbiome of EBF infants showed increased proportions of Bifidobacterium and lower abundance of Bacteroidetes and Clostridiales than non-EBF infants. PICRUSt analysis indicated that introduction of solid foods had a marginal impact on the microbiome of EBF infants (24 enzymes overrepresented in EBF+S infants). In contrast, over 200 bacterial gene categories were overrepresented in non-EBF+S compared to non-EBF infants including several bacterial methyl-accepting chemotaxis proteins (MCP) involved in signal transduction. The identified differences between EBF and non-EBF infants suggest that breast milk may provide the gut microbiome with a greater plasticity (despite having a lower phylogenetic diversity) that eases the transition into solid foods.
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Affiliation(s)
- Amanda L. Thompson
- Department of Anthropology, University of North CarolinaChapel Hill, NC, USA
| | - Andrea Monteagudo-Mera
- Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, University of North CarolinaChapel Hill, NC, USA
| | - Maria B. Cadenas
- Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, University of North CarolinaChapel Hill, NC, USA
| | - Michelle L. Lampl
- Department of Anthropology and Center for the Study of Human Health, Emory UniversityAtlanta, GA, USA
| | - M. A. Azcarate-Peril
- Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, University of North CarolinaChapel Hill, NC, USA
- Department of Cell Biology and Physiology, School of Medicine, University of North CarolinaChapel Hill, NC, USA
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108
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Biedermann L, Rogler G. The intestinal microbiota: its role in health and disease. Eur J Pediatr 2015; 174:151-67. [PMID: 25563215 DOI: 10.1007/s00431-014-2476-2] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 12/08/2014] [Accepted: 12/10/2014] [Indexed: 12/13/2022]
Abstract
UNLABELLED The intestinal microbiota (previously referred to as "intestinal flora") has entered the focus of research interest not only in microbiology but also in medicine. Huge progress has been made with respect to the analysis of composition and functions of the human microbiota. An "imbalance" of the microbiota, frequently also called a "dysbiosis," has been associated with different diseases in recent years. Crohn's disease and ulcerative colitis as two major forms of inflammatory bowel disease, irritable bowel syndrome (IBS) and some infectious intestinal diseases such as Clostridium difficile colitis feature a dysbiosis of the intestinal flora. Whereas this is somehow expected or less surprising, an imbalance of the microbiota or an enrichment of specific bacterial strains in the flora has been associated with an increasing number of other diseases such as diabetes, metabolic syndrome, non-alcoholic fatty liver disease or steatohepatitis and even psychiatric disorders such as depression or multiple sclerosis. It is important to understand the different aspects of potential contributions of the microbiota to pathophysiology of the mentioned diseases. CONCLUSION With the present manuscript, we aim to summarize the current knowledge and provide an overview of the different concepts on how bacteria contribute to health and disease in animal models and-more importantly-humans. In addition, it has to be borne in mind that we are only at the very beginning to understand the complex mechanisms of host-microbial interactions.
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Affiliation(s)
- Luc Biedermann
- Division of Gastroenterology and Hepatology, University Hospital Zürich, Rämistrasse 100, 8091, Zürich, Switzerland,
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109
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Consolandi C, Turroni S, Emmi G, Severgnini M, Fiori J, Peano C, Biagi E, Grassi A, Rampelli S, Silvestri E, Centanni M, Cianchi F, Gotti R, Emmi L, Brigidi P, Bizzaro N, De Bellis G, Prisco D, Candela M, D'Elios MM. Behçet's syndrome patients exhibit specific microbiome signature. Autoimmun Rev 2014; 14:269-76. [PMID: 25435420 DOI: 10.1016/j.autrev.2014.11.009] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 11/15/2014] [Indexed: 02/07/2023]
Abstract
BACKGROUND AND AIMS Behçet syndrome is a systemic inflammatory condition characterized by muco-cutaneous and ocular manifestations, with central nervous system, vascular and/or gastro-intestinal involvement. The association of microbiota with Behçet syndrome has not been shown yet. Our work was aimed to compare the gut microbiota structure and the profiles of short-chain fatty acids production in Behçet syndrome patients and healthy control relatives. METHODS Here, we compared the fecal microbiota of 22 patients with Behçet syndrome and that of 16 healthy co-habiting controls, sharing the same diet and lifestyle by pyrosequencing of the V3-V4 hypervariable regions of the 16 rDNA gene and biochemical analyses. RESULTS Our analyses showed significant differences in gut microbiota between Behçet patients and healthy cohabitants. In particular we found that Behçet's patients were significantly depleted in the genera Roseburia and Subdoligranulum. Roseburia showed a relative abundance value of 10.45±6.01% in healthy relatives and 4.97±5.09% in Behçet's patients, and Subdoligranulum, which reached a relative abundance of 3.28±2.20% in healthy controls, was only at 1.93±1.75% of abundance in Behçet's patients. Here we report, for the first time, that a peculiar dysbiosis of the gut microbiota is present in patients with Behçet syndrome and this corresponds to specific changes in microbiome profile. A significant decrease of butyrate production (P=0.0033) in Behçet's patients was demonstrated. Butyrate is able to promote differentiation of T-regulatory cells, and consequently the results obtained prompt us to speculate that a defect of butyrate production might lead to both reduced T-reg responses and activation of immuno-pathological T-effector responses. CONCLUSIONS Altogether, our results indicate that both a peculiar dysbiosis of the gut microbiota and a significant decrease of butyrate production are present in patients with Behçet syndrome.
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Affiliation(s)
- Clarissa Consolandi
- Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate, Milan, Italy.
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giacomo Emmi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Marco Severgnini
- Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate, Milan, Italy
| | - Jessica Fiori
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Clelia Peano
- Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate, Milan, Italy
| | - Elena Biagi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Alessia Grassi
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Simone Rampelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Elena Silvestri
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Manuela Centanni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Fabio Cianchi
- Department of Surgery and Translational Medicine, University of Florence, Italy
| | - Roberto Gotti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Lorenzo Emmi
- Medical Pathology, Center for Autoimmune Systemic Diseases, Behçet Center and Lupus Clinic, AOU Careggi, Florence, Italy.
| | - Patrizia Brigidi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Nicola Bizzaro
- Laboratory of Clinical Pathology, Diagnostic Department, San Antonio Hospital, Tolmezzo, Italy
| | - Gianluca De Bellis
- Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate, Milan, Italy
| | - Domenico Prisco
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy; Medical Pathology, Center for Autoimmune Systemic Diseases, Behçet Center and Lupus Clinic, AOU Careggi, Florence, Italy
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Mario M D'Elios
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy; Medical Pathology, Center for Autoimmune Systemic Diseases, Behçet Center and Lupus Clinic, AOU Careggi, Florence, Italy
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110
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Sandionigi A, Vicario S, Prosdocimi EM, Galimberti A, Ferri E, Bruno A, Balech B, Mezzasalma V, Casiraghi M. Towards a better understanding of Apis mellifera and Varroa destructor microbiomes: introducing 'phyloh' as a novel phylogenetic diversity analysis tool. Mol Ecol Resour 2014; 15:697-710. [PMID: 25367306 DOI: 10.1111/1755-0998.12341] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 10/23/2014] [Accepted: 10/24/2014] [Indexed: 12/01/2022]
Abstract
The study of diversity in biological communities is an intriguing field. Huge amount of data are nowadays available (provided by the innovative DNA sequencing techniques), and management, analysis and display of results are not trivial. Here, we propose for the first time the use of phylogenetic entropy as a measure of bacterial diversity in studies of microbial community structure. We then compared our new method (i.e. the web tool phyloh) for partitioning phylogenetic diversity with the traditional approach in diversity analyses of bacteria communities. We tested phyloh to characterize microbiome in the honeybee (Apis mellifera, Insecta: Hymenoptera) and its parasitic mite varroa (Varroa destructor, Arachnida: Parasitiformes). The rationale is that the comparative analysis of honeybee and varroa microbiomes could open new perspectives concerning the role of the parasites on honeybee colonies health. Our results showed a dramatic change of the honeybee microbiome when varroa occurs, suggesting that this parasite is able to influence host microbiome. Among the different approaches used, only the entropy method, in conjunction with phylogenetic constraint as implemented in phyloh, was able to discriminate varroa microbiome from that of parasitized honeybees. In conclusion, we foresee that the use of phylogenetic entropy could become a new standard in the analyses of community structure, in particular to prove the contribution of each biological entity to the overall diversity.
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Affiliation(s)
- A Sandionigi
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - S Vicario
- Institute of Biomedical and Technologies (ITB), National Research Council (CNR), Via Giovanni Amendola, 122/D, 70126, Bari, Italy
| | - E M Prosdocimi
- DEFENS, University of Milan, Via Mangiagalli, 25, 20133, Milan, Italy
| | - A Galimberti
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - E Ferri
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - A Bruno
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - B Balech
- Institute of Biomembrane and Bioenergetics (IBBE), National Research Council (CNR), Via Giovanni Amendola, 165/A, 70126, Bari, Italy
| | - V Mezzasalma
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - M Casiraghi
- ZooPlantLab, Department of Biotechnology and Biosciences, University of Milan-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
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Quercia S, Candela M, Giuliani C, Turroni S, Luiselli D, Rampelli S, Brigidi P, Franceschi C, Bacalini MG, Garagnani P, Pirazzini C. From lifetime to evolution: timescales of human gut microbiota adaptation. Front Microbiol 2014; 5:587. [PMID: 25408692 PMCID: PMC4219431 DOI: 10.3389/fmicb.2014.00587] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 10/17/2014] [Indexed: 12/21/2022] Open
Abstract
Human beings harbor gut microbial communities that are essential to preserve human health. Molded by the human genome, the gut microbiota (GM) is an adaptive component of the human superorganisms that allows host adaptation at different timescales, optimizing host physiology from daily life to lifespan scales and human evolutionary history. The GM continuously changes from birth up to the most extreme limits of human life, reconfiguring its metagenomic layout in response to daily variations in diet or specific host physiological and immunological needs at different ages. On the other hand, the microbiota plasticity was strategic to face changes in lifestyle and dietary habits along the course of the recent evolutionary history, that has driven the passage from Paleolithic hunter-gathering societies to Neolithic agricultural farmers to modern Westernized societies.
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Affiliation(s)
- Sara Quercia
- Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
| | - Cristina Giuliani
- BiGEA, Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna Bologna, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
| | - Donata Luiselli
- BiGEA, Department of Biological, Geological and Environmental Sciences, Laboratory of Molecular Anthropology & Centre for Genome Biology, University of Bologna Bologna, Italy
| | - Simone Rampelli
- Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
| | - Patrizia Brigidi
- Department of Pharmacy and Biotechnology, University of Bologna Bologna, Italy
| | - Claudio Franceschi
- DIMES, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna Bologna, Italy ; CIG, Interdepartmental Centre "L. Galvani" CIG, University of Bologna Bologna, Italy ; IRCSS, Institute of Neurological Sciences of Bologna Bologna, Italy ; IGM-CNR, Institute of Molecular Genetics, Unit of Bologna IOR Bologna, Italy ; CNR, Institute of Organic Synthesis and Photoreactivity (ISOF) Bologna, Italy
| | - Maria Giulia Bacalini
- DIMES, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna Bologna, Italy ; CIG, Interdepartmental Centre "L. Galvani" CIG, University of Bologna Bologna, Italy
| | - Paolo Garagnani
- DIMES, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna Bologna, Italy ; CIG, Interdepartmental Centre "L. Galvani" CIG, University of Bologna Bologna, Italy ; CRBA, Center for Applied Biomedical Research, St. Orsola-Malpighi University Hospital Bologna, Italy
| | - Chiara Pirazzini
- DIMES, Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna Bologna, Italy ; CIG, Interdepartmental Centre "L. Galvani" CIG, University of Bologna Bologna, Italy
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112
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Abstract
Although the prevalence of main idiopathic forms of inflammatory bowel disease (IBD) has risen considerably over the last decades, their clinical features do not allow accurate prediction of prognosis, likelihood of disease progression, or response to specific therapy. Through a better understanding of the molecular pathways involved in IBD and the promise of more targeted therapies, the personalized approach to the management of IBD shows potential. To achieve this, there remains a significant need to better understand the disease process at cellular and molecular levels for any given individual with IBD. The complexity of biological functional networks behind the etiology of IBD highlights the need for their comprehensive analysis. In this, omics technologies can generate a systemic view of IBD pathogenesis on which to base novel, multiple pathway-integrated therapies. Omics sciences have just started to contribute here by generating gene, protein expression, metabolite data at global level and large scale, and more recently by offering new opportunities to explore gut functional ecology. In particular, there is much expectation regarding the putative role of the gut microbiome in IBD. No doubt it will provide additional insights and lead to the development of alternative, hopefully better, diagnostic, prognostic, and monitoring tools in the management of IBD. This review discusses perspectives of relevance to clinical translation with emphasis on gut microbial metabolic activities.
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Kennedy PJ, Cryan JF, Dinan TG, Clarke G. Irritable bowel syndrome: A microbiome-gut-brain axis disorder? World J Gastroenterol 2014; 20:14105-14125. [PMID: 25339800 PMCID: PMC4202342 DOI: 10.3748/wjg.v20.i39.14105] [Citation(s) in RCA: 201] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/18/2014] [Accepted: 05/26/2014] [Indexed: 02/07/2023] Open
Abstract
Irritable bowel syndrome (IBS) is an extremely prevalent but poorly understood gastrointestinal disorder. Consequently, there are no clear diagnostic markers to help diagnose the disorder and treatment options are limited to management of the symptoms. The concept of a dysregulated gut-brain axis has been adopted as a suitable model for the disorder. The gut microbiome may play an important role in the onset and exacerbation of symptoms in the disorder and has been extensively studied in this context. Although a causal role cannot yet be inferred from the clinical studies which have attempted to characterise the gut microbiota in IBS, they do confirm alterations in both community stability and diversity. Moreover, it has been reliably demonstrated that manipulation of the microbiota can influence the key symptoms, including abdominal pain and bowel habit, and other prominent features of IBS. A variety of strategies have been taken to study these interactions, including probiotics, antibiotics, faecal transplantations and the use of germ-free animals. There are clear mechanisms through which the microbiota can produce these effects, both humoral and neural. Taken together, these findings firmly establish the microbiota as a critical node in the gut-brain axis and one which is amenable to therapeutic interventions.
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Taneyo Saa D, Turroni S, Serrazanetti DI, Rampelli S, Maccaferri S, Candela M, Severgnini M, Simonetti E, Brigidi P, Gianotti A. Impact of Kamut® Khorasan on gut microbiota and metabolome in healthy volunteers. Food Res Int 2014. [DOI: 10.1016/j.foodres.2014.04.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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115
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Centanni M, Turroni S, Rampelli S, Biagi E, Quercia S, Consolandi C, Severgnini M, Brigidi P, Candela M. Bifidobacterium animalisssp.lactisBI07 modulates the tumor necrosis factor alpha-dependent imbalances of the enterocyte-associated intestinal microbiota fraction. FEMS Microbiol Lett 2014; 357:157-63. [DOI: 10.1111/1574-6968.12515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 06/06/2014] [Accepted: 06/18/2014] [Indexed: 12/12/2022] Open
Affiliation(s)
- Manuela Centanni
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Simone Rampelli
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Elena Biagi
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Sara Quercia
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Clarissa Consolandi
- Institute of Biomedical Technologies - Italian National Research Council; Milan Italy
| | - Marco Severgnini
- Institute of Biomedical Technologies - Italian National Research Council; Milan Italy
| | - Patrizia Brigidi
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
| | - Marco Candela
- Department of Pharmacy and Biotechnology; University of Bologna; Bologna Italy
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116
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Schnorr SL, Candela M, Rampelli S, Centanni M, Consolandi C, Basaglia G, Turroni S, Biagi E, Peano C, Severgnini M, Fiori J, Gotti R, De Bellis G, Luiselli D, Brigidi P, Mabulla A, Marlowe F, Henry AG, Crittenden AN. Gut microbiome of the Hadza hunter-gatherers. Nat Commun 2014; 5:3654. [PMID: 24736369 PMCID: PMC3996546 DOI: 10.1038/ncomms4654] [Citation(s) in RCA: 807] [Impact Index Per Article: 80.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 03/14/2014] [Indexed: 02/06/2023] Open
Abstract
Human gut microbiota directly influences health and provides an extra means of adaptive potential to different lifestyles. To explore variation in gut microbiota and to understand how these bacteria may have co-evolved with humans, here we investigate the phylogenetic diversity and metabolite production of the gut microbiota from a community of human hunter-gatherers, the Hadza of Tanzania. We show that the Hadza have higher levels of microbial richness and biodiversity than Italian urban controls. Further comparisons with two rural farming African groups illustrate other features unique to Hadza that can be linked to a foraging lifestyle. These include absence of Bifidobacterium and differences in microbial composition between the sexes that probably reflect sexual division of labour. Furthermore, enrichment in Prevotella, Treponema and unclassified Bacteroidetes, as well as a peculiar arrangement of Clostridiales taxa, may enhance the Hadza’s ability to digest and extract valuable nutrition from fibrous plant foods. Gut microbes influence our health and may contribute to human adaptation to different lifestyles. Here, the authors describe the gut microbiome of a community of hunter-gatherers and identify unique features that could be linked to a foraging lifestyle.
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Affiliation(s)
- Stephanie L Schnorr
- 1] Plant Foods in Hominin Dietary Ecology Research Group, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany [2]
| | - Marco Candela
- 1] Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy [2]
| | - Simone Rampelli
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Manuela Centanni
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Clarissa Consolandi
- Institute of Biomedical Technologies, Italian National Research Council, Via Fratelli Cervi 93, 20090 Segrate, Milan, Italy
| | - Giulia Basaglia
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Elena Biagi
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Clelia Peano
- Institute of Biomedical Technologies, Italian National Research Council, Via Fratelli Cervi 93, 20090 Segrate, Milan, Italy
| | - Marco Severgnini
- Institute of Biomedical Technologies, Italian National Research Council, Via Fratelli Cervi 93, 20090 Segrate, Milan, Italy
| | - Jessica Fiori
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Roberto Gotti
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Gianluca De Bellis
- Institute of Biomedical Technologies, Italian National Research Council, Via Fratelli Cervi 93, 20090 Segrate, Milan, Italy
| | - Donata Luiselli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, Bologna 40126, Italy
| | - Patrizia Brigidi
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Audax Mabulla
- College of Arts and Social Sciences, University of Dar es Salaam, 35091 Dar es Salaam, Tanzania
| | - Frank Marlowe
- Division of Biological Anthropology, University of Cambridge, Cambridge CB2 1TN, UK
| | - Amanda G Henry
- Plant Foods in Hominin Dietary Ecology Research Group, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Alyssa N Crittenden
- Metabolism, Anthropometry, and Nutrition Laboratory, Department of Anthropology, University of Nevada, Las Vegas, Nevada 89154-5003, USA
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Candela M, Turroni S, Biagi E, Carbonero F, Rampelli S, Fiorentini C, Brigidi P. Inflammation and colorectal cancer, when microbiota-host mutualism breaks. World J Gastroenterol 2014; 20:908-922. [PMID: 24574765 PMCID: PMC3921544 DOI: 10.3748/wjg.v20.i4.908] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 11/26/2013] [Accepted: 12/13/2013] [Indexed: 02/06/2023] Open
Abstract
Structural changes in the gut microbial community have been shown to accompany the progressive development of colorectal cancer. In this review we discuss recent hypotheses on the mechanisms involved in the bacteria-mediated carcinogenesis, as well as the triggering factors favoring the shift of the gut microbiota from a mutualistic to a pro-carcinogenic configuration. The possible role of inflammation, bacterial toxins and toxic microbiota metabolites in colorectal cancer onset is specifically discussed. On the other hand, the strategic role of inflammation as the keystone factor in driving microbiota to become carcinogenic is suggested. As a common outcome of different environmental and endogenous triggers, such as diet, aging, pathogen infection or genetic predisposition, inflammation can compromise the microbiota-host mutualism, forcing the increase of pathobionts at the expense of health-promoting groups, and allowing the microbiota to acquire an overall pro-inflammatory configuration. Consolidating inflammation in the gut, and favoring the bloom of toxigenic bacterial drivers, these changes in the gut microbial ecosystem have been suggested as pivotal in promoting carcinogenesis. In this context, it will become of primary importance to implement dietary or probiotics-based interventions aimed at preserving the microbiota-host mutualism along aging, counteracting deviations that favor a pro-carcinogenic microbiota asset.
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118
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Current understanding on the role of standard and immunoproteasomes in inflammatory/immunological pathways of multiple sclerosis. Autoimmune Dis 2014; 2014:739705. [PMID: 24523959 PMCID: PMC3910067 DOI: 10.1155/2014/739705] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 11/12/2013] [Indexed: 12/30/2022] Open
Abstract
The ubiquitin-proteasome system is the major intracellular molecular machinery for protein degradation and maintenance of protein homeostasis in most human cells. As ubiquitin-proteasome system plays a critical role in the regulation of the immune system, it might also influence the development and progression of multiple sclerosis (MS). Both ex vivo analyses and animal models suggest that activity and composition of ubiquitin-proteasome system are altered in MS. Proteasome isoforms endowed of immunosubunits may affect the functionality of different cell types such as CD8+ and CD4+ T cells and B cells as well as neurons during MS development. Furthermore, the study of proteasome-related biomarkers, such as proteasome antibodies and circulating proteasomes, may represent a field of interest in MS. Proteasome inhibitors are already used as treatment for cancer and the recent development of inhibitors selective for immunoproteasome subunits may soon represent novel therapeutic approaches to the different forms of MS. In this review we describe the current knowledge on the potential role of proteasomes in MS and discuss the pro et contra of possible therapies for MS targeting proteasome isoforms.
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119
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Candela M, Biagi E, Brigidi P, O'Toole PW, De Vos WM. Maintenance of a healthy trajectory of the intestinal microbiome during aging: a dietary approach. Mech Ageing Dev 2013; 136-137:70-5. [PMID: 24373997 DOI: 10.1016/j.mad.2013.12.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 12/05/2013] [Accepted: 12/16/2013] [Indexed: 12/21/2022]
Abstract
Sharing an intense transgenomic metabolism with the host, the intestinal microbiota is an essential factor for several aspects of the human physiology. However, several age-related factors, such as changes diet, lifestyle, inflammation and frailty, force the deterioration of this intestinal microbiota-host mutualistic interaction, compromising the possibility to reach longevity. In this scenario, the NU-AGE project involves the development of dietary interventions specifically tailored to the maintenance of a healthy trajectory of the intestinal microbiome, counteracting all processes connected to the pathophysiology of the human aging.
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Affiliation(s)
- Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
| | - Elena Biagi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Patrizia Brigidi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Paul W O'Toole
- Department of Microbiology & Alimentary Pharmabiotic Centre, University College Cork, Ireland
| | - Willem M De Vos
- Laboratory of Microbiology, Wageningen University, The Netherlands, and Departments of Veterinary Biosciences and Bacteriology & Immunology, Helsinki University, Finland
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120
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Marlow G, Ellett S, Ferguson IR, Zhu S, Karunasinghe N, Jesuthasan AC, Han DY, Fraser AG, Ferguson LR. Transcriptomics to study the effect of a Mediterranean-inspired diet on inflammation in Crohn's disease patients. Hum Genomics 2013; 7:24. [PMID: 24283712 PMCID: PMC4174666 DOI: 10.1186/1479-7364-7-24] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 11/16/2013] [Indexed: 12/13/2022] Open
Abstract
Background Inflammation is an essential immune response; however, chronic inflammation results in disease including Crohn's disease. Therefore, reducing the inflammation can yield a significant health benefit, and one way to achieve this is through diet. We developed a Mediterranean-inspired anti-inflammatory diet and used this diet in a 6-week intervention in a Crohn's disease population. We examined changes in inflammation and also in the gut microbiota. We compared the results of established biomarkers, C-reactive protein and the micronuclei assay, of inflammation with results from a transcriptomic approach. Results Data showed that being on our diet for 6 weeks was able to reduce the established biomarkers of inflammation. However, using transcriptomics, we observed significant changes in gene expression. Although no single gene stood out, the cumulative effect of small changes in many genes combined to have a beneficial effect. Data also showed that our diet resulted in a trend of normalising the microbiota. Conclusions This study showed that our Mediterranean-inspired diet appeared to benefit the health of people with Crohn's disease. Our participants showed a trend for reduced markers of inflammation and normalising of the microbiota. The significant changes in gene expression after 6 weeks highlighted the increased sensitivity of using transcriptomics when compared to the established biomarkers and open up a new era of dietary intervention studies.
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Affiliation(s)
- Gareth Marlow
- Discipline of Nutrition, Faculty of Medical and Health Sciences, The University of Auckland Private Bag 92019, Auckland 1142, New Zealand.
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Centanni M, Turroni S, Consolandi C, Rampelli S, Peano C, Severgnini M, Biagi E, Caredda G, De Bellis G, Brigidi P, Candela M. The enterocyte-associated intestinal microbiota of breast-fed infants and adults responds differently to a TNF-α-mediated pro-inflammatory stimulus. PLoS One 2013; 8:e81762. [PMID: 24303069 PMCID: PMC3841132 DOI: 10.1371/journal.pone.0081762] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 10/16/2013] [Indexed: 12/20/2022] Open
Abstract
Co-evolved as an integral component of our immune system, the gut microbiota provides specific immunological services at different ages, supporting the immune education during our infancy and sustaining a well-balanced immunological homeostasis during the course of our life. In order to figure out whether this involves differences in the microbial groups primarily interacting with the host immune system, we developed a non-invasive HT29 cell-based minimal model to fingerprint the enterocyte-associated microbiota fraction in infants and adults. After depicting the fecal microbial community of 12 breast-fed infants and 6 adults by 16S rDNA amplicon pools 454 pyrosequencing, their respective HT29 cell-associated gut microbiota fractions were characterized by the universal phylogenetic array platform HTF-Microbi.Array, both in the presence and absence of a tumor necrosis factor-alpha (TNF-α)-mediated pro-inflammatory stimulus. Our data revealed remarkable differences between the enterocyte-associated microbiota fractions in breast-fed infants and adults, being dominated by Bifidobacterium and Enterobacteriaceae the first and Bacteroides-Prevotella and Clostridium clusters IV and XIVa the second. While in adults TNF-α resulted in a profound impairment of the structure of the enterocyte-associated microbiota fraction, in infants it remained unaffected. Differently from the adult-type gut microbial community, the infant-type microbiota is structured to cope with inflammation, being co-evolved to prime the early immune response by means of transient inflammatory signals from gut microorganisms.
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Affiliation(s)
- Manuela Centanni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Clarissa Consolandi
- Institute of Biomedical Technologies - Italian National Research Council, Milan, Italy
| | - Simone Rampelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Clelia Peano
- Institute of Biomedical Technologies - Italian National Research Council, Milan, Italy
| | - Marco Severgnini
- Institute of Biomedical Technologies - Italian National Research Council, Milan, Italy
| | - Elena Biagi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giada Caredda
- Institute of Biomedical Technologies - Italian National Research Council, Milan, Italy
| | - Gianluca De Bellis
- Institute of Biomedical Technologies - Italian National Research Council, Milan, Italy
| | - Patrizia Brigidi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- * E-mail:
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122
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Vitetta L, Coulson S, Linnane AW, Butt H. The gastrointestinal microbiome and musculoskeletal diseases: a beneficial role for probiotics and prebiotics. Pathogens 2013; 2:606-26. [PMID: 25437335 PMCID: PMC4235701 DOI: 10.3390/pathogens2040606] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 11/04/2013] [Accepted: 11/07/2013] [Indexed: 12/11/2022] Open
Abstract
Natural medicines are an attractive option for patients diagnosed with common and debilitating musculoskeletal diseases such as Osteoarthritis (OA) or Rheumatoid Arthritis (RA). The high rate of self-medication with natural products is due to (1) lack of an available cure and (2) serious adverse events associated with chronic use of pharmaceutical medications in particular non-steroidal anti-inflammatory drugs (NSAIDs) and high dose paracetamol. Pharmaceuticals to treat pain may disrupt gastrointestinal (GIT) barrier integrity inducing GIT inflammation and a state of and hyper-permeability. Probiotics and prebiotics may comprise plausible therapeutic options that can restore GIT barrier functionality and down regulate pro-inflammatory mediators by modulating the activity of, for example, Clostridia species known to induce pro-inflammatory mediators. The effect may comprise the rescue of gut barrier physiological function. A postulated requirement has been the abrogation of free radical formation by numerous natural antioxidant molecules in order to improve musculoskeletal health outcomes, this notion in our view, is in error. The production of reactive oxygen species (ROS) in different anatomical environments including the GIT by the epithelial lining and the commensal microbe cohort is a regulated process, leading to the formation of hydrogen peroxide which is now well recognized as an essential second messenger required for normal cellular homeostasis and physiological function. The GIT commensal profile that tolerates the host does so by regulating pro-inflammatory and anti-inflammatory GIT mucosal actions through the activity of ROS signaling thereby controlling the activity of pathogenic bacterial species.
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Affiliation(s)
| | - Samantha Coulson
- School of Medicine, The University of Queensland, Brisbane 4102, Australia.
| | | | - Henry Butt
- Bioscreen, Bio21, The University of Melbourne, Melbourne 3010, Australia.
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Candela M, Biagi E, Turroni S, Maccaferri S, Figini P, Brigidi P. Dynamic efficiency of the human intestinal microbiota. Crit Rev Microbiol 2013; 41:165-71. [DOI: 10.3109/1040841x.2013.813900] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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125
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Ursell LK, Van Treuren W, Metcalf JL, Pirrung M, Gewirtz A, Knight R. Replenishing our defensive microbes. Bioessays 2013; 35:810-7. [PMID: 23836415 DOI: 10.1002/bies.201300018] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Large-scale characterization of the human microbiota has largely focused on Western adults, yet these populations may be uncharacteristic because of their diets and lifestyles. In particular, the rise of "Western diseases" may in part stem from reduced exposure to, or even loss of, microbes with which humans have coevolved. Here, we review beneficial microbes associated with pathogen resistance, highlighting the emerging role of complex microbial communities in protecting against disease. We discuss ways in which modern lifestyles and practices may deplete physiologically important microbiota, and explore prospects for reintroducing or encouraging the growth of beneficial microbes to promote the restoration of healthy microbial ecosystems.
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Affiliation(s)
- Luke K Ursell
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
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