601
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Feehley T, Nagler CR. Cellular and molecular pathways through which commensal bacteria modulate sensitization to dietary antigens. Curr Opin Immunol 2014; 31:79-86. [PMID: 25458998 PMCID: PMC4255329 DOI: 10.1016/j.coi.2014.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 09/25/2014] [Accepted: 10/03/2014] [Indexed: 12/16/2022]
Abstract
Food allergies are a growing public health concern. The rapidly increasing prevalence of allergic disease cannot be explained by genetic variation alone, suggesting a role for gene-by-environment interactions. The bacteria that colonize barrier surfaces, often referred to as the commensal microbiota, are dramatically affected by environmental factors and have a major impact on host health and homeostasis. Increasing evidence suggests that alterations in the composition of the microbiota, caused by factors such as antibiotic use and diet, are contributing to increased sensitization to dietary antigens. This review will discuss the cellular and molecular pathways activated by commensal bacteria to protect against allergic sensitization. By understanding the interplay between the environment, the microbiota, and the host, we may uncover novel therapeutic targets that will allow us to control the allergy epidemic.
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Affiliation(s)
- Taylor Feehley
- Committee on Immunology, Department of Pathology, The University of Chicago, 924 E. 57th St. JFK R120, Chicago, IL 60637, USA
| | - Cathryn R Nagler
- Committee on Immunology, Department of Pathology, The University of Chicago, 924 E. 57th St. JFK R120, Chicago, IL 60637, USA.
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602
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Liang G, Malmuthuge N, Guan LL, Griebel P. Model systems to analyze the role of miRNAs and commensal microflora in bovine mucosal immune system development. Mol Immunol 2014; 66:57-67. [PMID: 25467799 DOI: 10.1016/j.molimm.2014.10.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/15/2014] [Accepted: 10/16/2014] [Indexed: 02/07/2023]
Abstract
Information is rapidly accumulating regarding the role of miRNAs as key regulators of immune system development and function. It is also increasingly evident that miRNAs play an important role in host-pathogen interactions through regulation of both innate and acquired immune responses. Little is known, however, about the specific role of miRNAs in regulating normal development of the mucosal immune system, especially during the neonatal period. Furthermore, there is limited knowledge regarding the possible role the commensal microbiome may play in regulating mucosal miRNAs expression, although evidence is emerging that a variety of enteric pathogens influence miRNA expression. The current review focuses on recent information that miRNAs play an important role in regulating early development of the bovine mucosal immune system. A possible role for the commensal microbiome in regulating mucosal development by altering miRNA expression is also discussed. Finally, we explore the potential advantages of using the newborn calf as a model to determine how interactions between developmental programming, maternal factors in colostrum, and colonization of the gastrointestinal tract by commensal bacteria may alter mucosal miRNA expression and immune development. Identifying the key factors that regulate mucosal miRNA expression is critical for understanding how the balance between protective immunity and inflammation is maintained to ensure optimal gastrointestinal tract function and health of the whole organism.
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Affiliation(s)
- Guanxiang Liang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Nilusha Malmuthuge
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta T6G 2P5, Canada
| | - Philip Griebel
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon S7N 5E3, Canada; School of Public Health, University of Saskatchewan, Saskatoon S7N 5E3, Canada.
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603
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Abstract
Although intestinal bacteria live deep within the body, they are topographically on the exterior surface and thus outside the host. According to the classic notion that the immune system targets non-self rather than self, these intestinal bacteria should be considered foreign and therefore attacked and eliminated. While this appears to be true for some commensal bacterial species, recent data suggest that the immune system actively becomes tolerant to many bacterial organisms. The induction or activation of regulatory T (Treg) cells that inhibit, rather than promote, inflammatory responses to commensal bacteria appears to be a central component of mucosal tolerance. Loss of this mechanism can lead to inappropriate immune reactivity toward commensal organisms, perhaps contributing to mucosal inflammation characteristic of disorders such as inflammatory bowel disease.
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Affiliation(s)
- Teresa L Ai
- Department of Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO, USA
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604
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Bowcutt R, Forman R, Glymenaki M, Carding SR, Else KJ, Cruickshank SM. Heterogeneity across the murine small and large intestine. World J Gastroenterol 2014; 20:15216-15232. [PMID: 25386070 PMCID: PMC4223255 DOI: 10.3748/wjg.v20.i41.15216] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 03/18/2014] [Accepted: 06/17/2014] [Indexed: 02/06/2023] Open
Abstract
The small and large intestine of the gastrointestinal tract (GIT) have evolved to have discrete functions with distinct anatomies and immune cell composition. The importance of these differences is underlined when considering that different pathogens have uniquely adapted to live in each region of the gut. Furthermore, different regions of the GIT are also associated with differences in susceptibility to diseases such as cancer and chronic inflammation. The large and small intestine, given their anatomical and functional differences, should be seen as two separate immunological sites. However, this distinction is often ignored with findings from one area of the GIT being inappropriately extrapolated to the other. Focussing largely on the murine small and large intestine, this review addresses the literature relating to the immunology and biology of the two sites, drawing comparisons between them and clarifying similarities and differences. We also highlight the gaps in our understanding and where further research is needed.
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605
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Joice R, Yasuda K, Shafquat A, Morgan XC, Huttenhower C. Determining microbial products and identifying molecular targets in the human microbiome. Cell Metab 2014; 20:731-741. [PMID: 25440055 PMCID: PMC4254638 DOI: 10.1016/j.cmet.2014.10.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Human-associated microbes are the source of many bioactive microbial products (proteins and metabolites) that play key functions both in human host pathways and in microbe-microbe interactions. Culture-independent studies now provide an accelerated means of exploring novel bioactives in the human microbiome; however, intriguingly, a substantial fraction of the microbial metagenome cannot be mapped to annotated genes or isolate genomes and is thus of unknown function. Meta'omic approaches, including metagenomic sequencing, metatranscriptomics, metabolomics, and integration of multiple assay types, represent an opportunity to efficiently explore this large pool of potential therapeutics. In combination with appropriate follow-up validation, high-throughput culture-independent assays can be combined with computational approaches to identify and characterize novel and biologically interesting microbial products. Here we briefly review the state of microbial product identification and characterization and discuss possible next steps to catalog and leverage the large uncharted fraction of the microbial metagenome.
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Affiliation(s)
- Regina Joice
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Koji Yasuda
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Afrah Shafquat
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xochitl C Morgan
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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606
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Sharon G, Garg N, Debelius J, Knight R, Dorrestein PC, Mazmanian SK. Specialized metabolites from the microbiome in health and disease. Cell Metab 2014; 20:719-730. [PMID: 25440054 PMCID: PMC4337795 DOI: 10.1016/j.cmet.2014.10.016] [Citation(s) in RCA: 387] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The microbiota, and the genes that comprise its microbiome, play key roles in human health. Host-microbe interactions affect immunity, metabolism, development, and behavior, and dysbiosis of gut bacteria contributes to disease. Despite advances in correlating changes in the microbiota with various conditions, specific mechanisms of host-microbiota signaling remain largely elusive. We discuss the synthesis of microbial metabolites, their absorption, and potential physiological effects on the host. We propose that the effects of specialized metabolites may explain present knowledge gaps in linking the gut microbiota to biological host mechanisms during initial colonization, and in health and disease.
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Affiliation(s)
- Gil Sharon
- Division of Biology and Biological Engineering, California institute of Technology, Pasadena, CA 91125, USA
| | - Neha Garg
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA
| | - Justine Debelius
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA; Howard Hughes Medical Institute, Boulder, CO 80309, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093, USA; Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093, USA
| | - Sarkis K Mazmanian
- Division of Biology and Biological Engineering, California institute of Technology, Pasadena, CA 91125, USA.
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607
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Epigenomic regulation of host-microbiota interactions. Trends Immunol 2014; 35:518-25. [PMID: 25443494 DOI: 10.1016/j.it.2014.09.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 09/21/2014] [Accepted: 09/22/2014] [Indexed: 02/07/2023]
Abstract
The trillions of beneficial commensal microorganisms that normally reside in the gastrointestinal tract have emerged as a critical source of environmentally-derived stimuli that can impact health and disease. However, the underlying cellular and molecular mechanisms that recognize commensal bacteria-derived signals and regulate mammalian homeostasis are just beginning to be defined. Highly coordinated epigenomic modifications allow mammals to alter the transcriptional program of a cell in response to environmental cues. These modifications may play a key role in regulating the dynamic relationship between mammals and their microbiota. We review recent advances in understanding the interplay between the microbiota and mammalian epigenomic pathways, and highlight emerging findings that implicate a central role for histone deacetylases (HDACs) in orchestrating host-microbiota interactions.
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608
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Furusawa Y, Obata Y, Hase K. Commensal microbiota regulates T cell fate decision in the gut. Semin Immunopathol 2014; 37:17-25. [PMID: 25315350 DOI: 10.1007/s00281-014-0455-3] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 10/02/2014] [Indexed: 12/15/2022]
Abstract
Commensal microbiota shapes the intestinal immune system by regulating T helper (TH) cell lineage differentiation. For example, Bacteroides fragilis colonization not only optimizes the systemic TH1/TH2 balance, but also can induce regulatory T (Treg) cell differentiation in the gut. In addition, segmented filamentous bacteria (SFB) facilitate the development of TH17 cells in the small intestine. The 17 strains within clusters IV, XIVa, and XVIII of Clostridiales found in human feces can also induce the differentiation and expansion of Treg cells in the colon. Thus, the regulation of TH cell differentiation by commensal bacteria is evident; however, the molecular mechanisms underlying these processes remain uncertain. Recent studies have demonstrated that bacterial components, as well as their metabolites, play a central role in regulating TH cell development. Furthermore, these metabolites can elicit changes in histone posttranslational modification to modify the expression of critical regulators of T cell fate. In this review, we discuss the mechanisms and biological significance of microbiota-dependent TH differentiation.
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Affiliation(s)
- Yukihiro Furusawa
- Department of Biochemistry, Graduate School of Pharmaceutical Science, Keio University, Tokyo, 105-8512, Japan
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609
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Cassidy L, Tholey A. Model organism proteomics as a tool for the study of host-microbiome interactions. Proteomics Clin Appl 2014; 8:665-76. [DOI: 10.1002/prca.201300083] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 10/25/2013] [Accepted: 12/03/2013] [Indexed: 01/05/2023]
Affiliation(s)
- Liam Cassidy
- Institut für Experimentelle Medizin - AG Systematische Proteomforschung; Christian-Albrechts-Universität zu Kiel; Kiel Germany
| | - Andreas Tholey
- Institut für Experimentelle Medizin - AG Systematische Proteomforschung; Christian-Albrechts-Universität zu Kiel; Kiel Germany
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610
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You H, Lee WJ, Lee WJ. Homeostasis between gut-associated microorganisms and the immune system in Drosophila. Curr Opin Immunol 2014; 30:48-53. [DOI: 10.1016/j.coi.2014.06.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 06/08/2014] [Accepted: 06/09/2014] [Indexed: 12/18/2022]
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611
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Runtsch MC, Round JL, O'Connell RM. MicroRNAs and the regulation of intestinal homeostasis. Front Genet 2014; 5:347. [PMID: 25324861 PMCID: PMC4181235 DOI: 10.3389/fgene.2014.00347] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 09/16/2014] [Indexed: 12/11/2022] Open
Abstract
The mammalian intestinal tract is a unique site in which a large portion of our immune system and the 1014 commensal organisms that make up the microbiota reside in intimate contact with each other. Despite the potential for inflammatory immune responses, this complex interface contains host immune cells and epithelial cells interacting with the microbiota in a manner that promotes symbiosis. Due to the complexity of the cell types and microorganisms involved, this process requires elaborate regulatory mechanisms to ensure mutualism and prevent disease. While many studies have described critical roles for protein regulators of intestinal homeostasis, recent reports indicate that non-coding RNAs are also major contributors to optimal host-commensal interactions. In particular, there is emerging evidence that microRNAs (miRNAs) have evolved to fine tune host gene expression networks and signaling pathways that modulate cellular physiology in the intestinal tract. Here, we review our present knowledge of the influence miRNAs have on both immune and epithelial cell biology in the mammalian intestines and the impact this has on the microbiota. We also discuss a need for further studies to decipher the functions of specific miRNAs within the gut to better understand cellular mechanisms that promote intestinal homeostasis and to identify potential molecular targets underlying diseases such as inflammatory bowel disease and colorectal cancer.
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Affiliation(s)
- Marah C Runtsch
- Department of Pathology, University of Utah Salt Lake City, UT, USA
| | - June L Round
- Department of Pathology, University of Utah Salt Lake City, UT, USA
| | - Ryan M O'Connell
- Department of Pathology, University of Utah Salt Lake City, UT, USA
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612
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The probiotic mixture VSL#3 mediates both pro- and anti-inflammatory responses in bone marrow-derived dendritic cells from C57BL/6 and BALB/c mice. Br J Nutr 2014; 112:1088-97. [PMID: 25181025 DOI: 10.1017/s000711451400169x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Probiotic bacteria express a wide range of molecular structures that bind to receptors on innate immune cells and mediate health-promoting effects in the host. We have recently demonstrated in a colitis model that favourable effects of the probiotic mixture VSL#3 may in part be due to the suppression of intestinal chemokine expression. To obtain more insights into the underlying mechanisms, in the present study, we analysed the modulation of bone marrow-derived dendritic cells (BM-DC) from BALB/c (T helper (Th)2 biased) v. C57BL/6 (Th1 biased) mice. Our findings showed that VSL#3 differed from pure Toll-like receptor (TLR) ligands by inducing the production of various cytokines, including IL-12 p70 subunit (IL-12p70), IL-23 and IL-10. Dedicated TLR arrays were employed to profile mRNA from BM-DC cultured with lipopolysaccharide (LPS), VSL#3, or a combination of both. This approach led to the identification of (1) a cluster of genes that were up- or down-regulated, irrespective of the stimulus, (2) a cluster of genes that were synergistically up-regulated by LPS and VSL#3 in BM-DC from C57BL/6 mice, but not in those from BALB/c mice, and (3) a cluster of LPS-induced genes that were suppressed by VSL#3, in particular chemokine genes. These data show that this probiotic mixture has both pro- and anti-inflammatory effects on BM-DC and suggest that their immune-modulating properties in vivo may depend on the genetic background of the host.
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613
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High-fat-diet-mediated dysbiosis promotes intestinal carcinogenesis independently of obesity. Nature 2014; 514:508-12. [PMID: 25174708 DOI: 10.1038/nature13398] [Citation(s) in RCA: 331] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Accepted: 04/22/2014] [Indexed: 12/25/2022]
Abstract
Several features common to a Western lifestyle, including obesity and low levels of physical activity, are known risk factors for gastrointestinal cancers. There is substantial evidence suggesting that diet markedly affects the composition of the intestinal microbiota. Moreover, there is now unequivocal evidence linking dysbiosis to cancer development. However, the mechanisms by which high-fat diet (HFD)-mediated changes in the microbial community affect the severity of tumorigenesis in the gut remain to be determined. Here we demonstrate that an HFD promotes tumour progression in the small intestine of genetically susceptible, K-ras(G12Dint), mice independently of obesity. HFD consumption, in conjunction with K-ras mutation, mediated a shift in the composition of the gut microbiota, and this shift was associated with a decrease in Paneth-cell-mediated antimicrobial host defence that compromised dendritic cell recruitment and MHC class II molecule presentation in the gut-associated lymphoid tissues. When butyrate was administered to HFD-fed K-ras(G12Dint) mice, dendritic cell recruitment in the gut-associated lymphoid tissues was normalized, and tumour progression was attenuated. Importantly, deficiency in MYD88, a signalling adaptor for pattern recognition receptors and Toll-like receptors, blocked tumour progression. The transfer of faecal samples from HFD-fed mice with intestinal tumours to healthy adult K-ras(G12Dint) mice was sufficient to transmit disease in the absence of an HFD. Furthermore, treatment with antibiotics completely blocked HFD-induced tumour progression, suggesting that distinct shifts in the microbiota have a pivotal role in aggravating disease. Collectively, these data underscore the importance of the reciprocal interaction between host and environmental factors in selecting a microbiota that favours carcinogenesis, and they suggest that tumorigenesis is transmissible among genetically predisposed individuals.
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614
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Abstract
Over the past decade, it has become apparent that bile acids are involved in a host of activities beyond their classic functions in bile formation and fat absorption. The identification of the farnesoid X receptor (FXR) as a nuclear receptor directly activated by bile acids and the discovery that bile acids are also ligands for the membrane-bound, G-protein coupled bile acid receptor 1 (also known as TGR5) have opened new avenues of research. Both FXR and TGR5 regulate various elements of glucose, lipid and energy metabolism. Consequently, a picture has emerged of bile acids acting as modulators of (postprandial) metabolism. Therefore, strategies that interfere with either bile acid metabolism or signalling cascades mediated by bile acids may represent novel therapeutic approaches for metabolic diseases. Synthetic modulators of FXR have been designed and tested, primarily in animal models. Furthermore, the use of bile acid sequestrants to reduce plasma cholesterol levels has unexpected benefits. For example, treatment of patients with type 2 diabetes mellitus (T2DM) with sequestrants causes substantial reductions in plasma levels of glucose and HbA1c. This Review aims to provide an overview of the molecular mechanisms by which bile acids modulate glucose and energy metabolism, particularly focusing on the glucose-lowering actions of bile acid sequestrants in insulin resistant states and T2DM.
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Affiliation(s)
- Folkert Kuipers
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700RB Groningen, Netherlands
| | - Vincent W Bloks
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700RB Groningen, Netherlands
| | - Albert K Groen
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9700RB Groningen, Netherlands
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615
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Lee KN, Lee OY. Intestinal microbiota in pathophysiology and management of irritable bowel syndrome. World J Gastroenterol 2014; 20:8886-8897. [PMID: 25083061 PMCID: PMC4112865 DOI: 10.3748/wjg.v20.i27.8886] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 04/02/2014] [Accepted: 06/17/2014] [Indexed: 02/07/2023] Open
Abstract
Irritable bowel syndrome (IBS) is a functional bowel disorder without any structural or metabolic abnormalities that sufficiently explain the symptoms, which include abdominal pain and discomfort, and bowel habit changes such as diarrhea and constipation. Its pathogenesis is multifactorial: visceral hypersensitivity, dysmotility, psychosocial factors, genetic or environmental factors, dysregulation of the brain-gut axis, and altered intestinal microbiota have all been proposed as possible causes. The human intestinal microbiota are composed of more than 1000 different bacterial species and 1014 cells, and are essential for the development, function, and homeostasis of the intestine, and for individual health. The putative mechanisms that explain the role of microbiota in the development of IBS include altered composition or metabolic activity of the microbiota, mucosal immune activation and inflammation, increased intestinal permeability and impaired mucosal barrier function, sensory-motor disturbances provoked by the microbiota, and a disturbed gut-microbiota-brain axis. Therefore, modulation of the intestinal microbiota through dietary changes, and use of antibiotics, probiotics, and anti-inflammatory agents has been suggested as strategies for managing IBS symptoms. This review summarizes and discusses the accumulating evidence that intestinal microbiota play a role in the pathophysiology and management of IBS.
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616
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Gut microbiota-generated metabolites in animal health and disease. Nat Chem Biol 2014; 10:416-24. [PMID: 24838170 DOI: 10.1038/nchembio.1535] [Citation(s) in RCA: 464] [Impact Index Per Article: 46.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 04/22/2014] [Indexed: 12/27/2022]
Abstract
Gut microbiota is found in virtually any metazoan, from invertebrates to vertebrates. It has long been believed that gut microbiota, more specifically, the activity of the microbiome and its metabolic products, directly influence a variety of aspects in metazoan physiology. However, the exact molecular relationship among microbe-derived gut metabolites, host signaling pathways, and host physiology remains to be elucidated. Here we review recent discoveries regarding the molecular links between gut metabolites and host physiology in different invertebrate and vertebrate animal models. We describe the different roles of gut microbiome activity and their metabolites in regulating distinct host physiology and the molecular mechanisms by which gut metabolites cause physiological homeostasis via regulating specific host signaling pathways. Future studies in this direction using different animal models will provide the key concepts to understanding the evolutionarily conserved chemical dialogues between gut microbiota and metazoan cells and also human diseases associated with gut microbiota and metabolites.
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617
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Tikhonov M, Leach RW, Wingreen NS. Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution. ISME JOURNAL 2014; 9:68-80. [PMID: 25012900 DOI: 10.1038/ismej.2014.117] [Citation(s) in RCA: 115] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 06/02/2014] [Accepted: 06/06/2014] [Indexed: 02/08/2023]
Abstract
The standard approach to analyzing 16S tag sequence data, which relies on clustering reads by sequence similarity into Operational Taxonomic Units (OTUs), underexploits the accuracy of modern sequencing technology. We present a clustering-free approach to multi-sample Illumina data sets that can identify independent bacterial subpopulations regardless of the similarity of their 16S tag sequences. Using published data from a longitudinal time-series study of human tongue microbiota, we are able to resolve within standard 97% similarity OTUs up to 20 distinct subpopulations, all ecologically distinct but with 16S tags differing by as little as one nucleotide (99.2% similarity). A comparative analysis of oral communities of two cohabiting individuals reveals that most such subpopulations are shared between the two communities at 100% sequence identity, and that dynamical similarity between subpopulations in one host is strongly predictive of dynamical similarity between the same subpopulations in the other host. Our method can also be applied to samples collected in cross-sectional studies and can be used with the 454 sequencing platform. We discuss how the sub-OTU resolution of our approach can provide new insight into factors shaping community assembly.
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Affiliation(s)
- Mikhail Tikhonov
- 1] Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ, USA [2] Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Robert W Leach
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Ned S Wingreen
- 1] Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA [2] Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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618
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Chai JN, Zhou YW, Hsieh CS. T cells and intestinal commensal bacteria--ignorance, rejection, and acceptance. FEBS Lett 2014; 588:4167-75. [PMID: 24997344 DOI: 10.1016/j.febslet.2014.06.040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 06/23/2014] [Accepted: 06/24/2014] [Indexed: 02/01/2023]
Abstract
Trillions of commensal bacteria cohabit our bodies to mutual benefit. In the past several years, it has become clear that the adaptive immune system is not ignorant of intestinal commensal bacteria, but is constantly interacting with them. For T cells, the response to commensal bacteria does not appear uniform, as certain commensal bacterial species appear to trigger effector T cells to reject and control them, whereas other species elicit Foxp3(+) regulatory T (Treg) cells to accept and be tolerant of them. Here, we review our current knowledge of T cell differentiation in response to commensal bacteria, and how this process leads to immune homeostasis in the intestine.
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Affiliation(s)
- Jiani N Chai
- Department of Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63132, United States
| | - You W Zhou
- Department of Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63132, United States
| | - Chyi-Song Hsieh
- Department of Medicine, Division of Rheumatology, Washington University School of Medicine, St. Louis, MO 63132, United States.
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619
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Abstract
Gut bacteria is now considered as an additional host organ, and it has been shown that they have important influences on host developmental and physiological processes. More recently gut bacteria have additionally been implicated in behavioral processes. We showed that in two species of Drosophila, gut bacteria variation affects behavior, altering partner investment in copulation in relation to whether individuals were familiar (i.e., having developed in the same environment), or were related. This suggests that gut bacteria play a role in kin recognition in these species. We suggest that this phenomenon is associated with gut bacteria influencing the scent profiles used by Drosophila in mate choice.
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Affiliation(s)
- Zenobia Lewis
- Institute of Integrative Biology; School of Life Sciences; University of Liverpool; Liverpool, UK
| | - Chloe Heys
- Institute of Integrative Biology; School of Life Sciences; University of Liverpool; Liverpool, UK
| | - Mark Prescott
- Institute of Integrative Biology; School of Life Sciences; University of Liverpool; Liverpool, UK
| | - Anne Lizé
- UMR 6553 ECOBIO; University of Rennes 1, 35042; Rennes, France
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620
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Reynolds LA, Smith KA, Filbey KJ, Harcus Y, Hewitson JP, Redpath SA, Valdez Y, Yebra MJ, Finlay BB, Maizels RM. Commensal-pathogen interactions in the intestinal tract: lactobacilli promote infection with, and are promoted by, helminth parasites. Gut Microbes 2014; 5:522-32. [PMID: 25144609 PMCID: PMC4822684 DOI: 10.4161/gmic.32155] [Citation(s) in RCA: 185] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The intestinal microbiota are pivotal in determining the developmental, metabolic and immunological status of the mammalian host. However, the intestinal tract may also accommodate pathogenic organisms, including helminth parasites which are highly prevalent in most tropical countries. Both microbes and helminths must evade or manipulate the host immune system to reside in the intestinal environment, yet whether they influence each other's persistence in the host remains unknown. We now show that abundance of Lactobacillus bacteria correlates positively with infection with the mouse intestinal nematode parasite, Heligmosomoides polygyrus, as well as with heightened regulatory T cell (Treg) and Th17 responses. Moreover, H. polygyrus raises Lactobacillus species abundance in the duodenum of C57BL/6 mice, which are highly susceptible to H. polygyrus infection, but not in BALB/c mice, which are relatively resistant. Sequencing of samples at the bacterial gyrB locus identified the principal Lactobacillus species as L. taiwanensis, a previously characterized rodent commensal. Experimental administration of L. taiwanensis to BALB/c mice elevates regulatory T cell frequencies and results in greater helminth establishment, demonstrating a causal relationship in which commensal bacteria promote infection with an intestinal parasite and implicating a bacterially-induced expansion of Tregs as a mechanism of greater helminth susceptibility. The discovery of this tripartite interaction between host, bacteria and parasite has important implications for both antibiotic and anthelmintic use in endemic human populations.
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Affiliation(s)
- Lisa A Reynolds
- Centre for Immunity, Infection and Evolution, and Institute of Immunology and Infection Research; Ashworth Laboratories; University of Edinburgh; Edinburgh, UK
- Michael Smith Laboratories; University of British Columbia; Vancouver, BC Canada
| | - Katherine A Smith
- Centre for Immunity, Infection and Evolution, and Institute of Immunology and Infection Research; Ashworth Laboratories; University of Edinburgh; Edinburgh, UK
| | - Kara J Filbey
- Centre for Immunity, Infection and Evolution, and Institute of Immunology and Infection Research; Ashworth Laboratories; University of Edinburgh; Edinburgh, UK
| | - Yvonne Harcus
- Centre for Immunity, Infection and Evolution, and Institute of Immunology and Infection Research; Ashworth Laboratories; University of Edinburgh; Edinburgh, UK
| | - James P Hewitson
- Centre for Immunity, Infection and Evolution, and Institute of Immunology and Infection Research; Ashworth Laboratories; University of Edinburgh; Edinburgh, UK
| | - Stephen A Redpath
- Department of Microbiology and Immunology; University of British Columbia; Vancouver, BC Canada
| | - Yanet Valdez
- Michael Smith Laboratories; University of British Columbia; Vancouver, BC Canada
| | - María J Yebra
- Laboratorio de Bacterias Lácticas y Probióticos; Instituto de Agroquímica y Tecnología de los Alimentos; IATA-CSIC; Valencia, Spain
| | - B Brett Finlay
- Michael Smith Laboratories; University of British Columbia; Vancouver, BC Canada
- Department of Microbiology and Immunology; University of British Columbia; Vancouver, BC Canada
- Department of Biochemistry and Molecular Biology; University of British Columbia; Vancouver, BC Canada
| | - Rick M Maizels
- Centre for Immunity, Infection and Evolution, and Institute of Immunology and Infection Research; Ashworth Laboratories; University of Edinburgh; Edinburgh, UK
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621
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Markle JGM, Frank DN, Adeli K, von Bergen M, Danska JS. Microbiome manipulation modifies sex-specific risk for autoimmunity. Gut Microbes 2014; 5:485-93. [PMID: 25007153 DOI: 10.4161/gmic.29795] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Despite growing evidence for a causal role of environmental factors in autoimmune diseases including the rise in disease frequencies over the past several decades we lack an understanding of how particular environmental exposures modify disease risk. In addition, many autoimmune diseases display sex-biased incidence, with females being disproportionately affected but the mechanisms underlying this sex bias remain elusive. Emerging evidence suggests that both host metabolism and immune function is crucially regulated by the intestinal microbiome. Recently, we showed that in the non-obese diabetic (NOD) mouse model of Type 1 Diabetes (T1D), the gut commensal microbial community strongly impacts the pronounced sex bias in T1D risk by controlling serum testosterone and metabolic phenotypes (1). Here we present new data in the NOD model that explores the correlations between microbial phylogeny, testosterone levels, and metabolic phenotypes, and discuss the future of microbiome-centered analysis and microbe-based therapeutic approaches in autoimmune diseases.
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Affiliation(s)
- Janet G M Markle
- Department of Immunology; University of Toronto; Toronto, ON Canada; Program in Genetics and Genomic Biology; The Hospital for Sick Children; Toronto, ON Canada
| | - Daniel N Frank
- Division of Infectious Diseases; University of Colorado; Aurora, CO USA
| | - Khosrow Adeli
- Department of Laboratory Medicine; The Hospital for Sick Children; Toronto, ON Canada; Department of Biochemistry; University of Toronto; Toronto, ON Canada
| | - Martin von Bergen
- Department of Metabolomics and Department of Proteomics; Helmholtz Center for Environmental Research; Leipzig, Germany; Department of Biotechnology, Chemistry, and Environmental Engineering; Aalborg University; Aalborg, Denmark
| | - Jayne S Danska
- Department of Immunology; University of Toronto; Toronto, ON Canada; Program in Genetics and Genomic Biology; The Hospital for Sick Children; Toronto, ON Canada; Department of Medical Biophysics; University of Toronto; Toronto, ON Canada
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622
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Abstract
The human gastrointestinal tract hosts a large number of microbial cells which exceed their mammalian counterparts by approximately 3-fold. The genes expressed by these microorganisms constitute the gut microbiome and may participate in diverse functions that are essential to the host, including digestion, regulation of energy metabolism, and modulation of inflammation and immunity. The gut microbiome can be modulated by dietary changes, antibiotic use, or disease. Different ailments have distinct associated microbiomes in which certain species or genes are present in different relative quantities. Thus, identifying specific disease-associated signatures in the microbiome as well as the factors that alter microbial populations and gene expression will lead to the development of new products such as prebiotics, probiotics, antimicrobials, live biotherapeutic products, or more traditional drugs to treat these disorders. Gained knowledge on the microbiome may result in molecular lab tests that may serve as personalized tools to guide the use of the aforementioned products and monitor interventional progress.
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Affiliation(s)
| | | | | | | | - Satya Prakash
- Micropharma Limited; Montreal, QC Canada; Biomedical Technology and Cell Therapy Research Laboratory; Department of Biomedical Engineering; Faculty of Medicine; McGill University; Montreal, QC Canada
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623
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Abstract
Human gastrointestinal bacteria often share their environment with parasitic worms, allowing physical and physiological interaction between the two groups. Such associations have the potential to affect host health as well as the bacterial and helminth populations. Although still in its early stages, research on the interaction between the microbiome and parasitic helminths in humans offers the potential to improve health by manipulating the microbiome. Previously, supplementation with various nutritional compounds has been found to increase the abundance of potentially beneficial gut commensal bacteria. Thus, nutritional microbiome manipulation to produce an environment which may decrease malnutrition associated with helminth infection and/or aid host recovery from disease is conceivable. This review discusses the influence of the gut microbiota and helminths on host nutrition and immunity and the subsequent effects on the human host's overall health. It also discusses changes occurring in the microbiota upon helminth infections and the underlying mechanisms leading to these changes. There are still significant knowledge gaps which need to be filled before meaningful progress can be made in translating knowledge from studying the human gut microbiome into therapeutic strategies. Ultimately this review aims to discuss our current knowledge as well as highlight areas requiring further investigation.
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624
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Protection from hypertension in mice by the Mediterranean diet is mediated by nitro fatty acid inhibition of soluble epoxide hydrolase. Proc Natl Acad Sci U S A 2014; 111:8167-72. [PMID: 24843165 DOI: 10.1073/pnas.1402965111] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Soluble epoxide hydrolase (sEH) is inhibited by electrophilic lipids by their adduction to Cys521 proximal to its catalytic center. This inhibition prevents hydrolysis of the enzymes' epoxyeicosatrienoic acid (EET) substrates, so they accumulate inducing vasodilation to lower blood pressure (BP). We generated a Cys521Ser sEH redox-dead knockin (KI) mouse model that was resistant to this mode of inhibition. The electrophilic lipid 10-nitro-oleic acid (NO2-OA) inhibited hydrolase activity and also lowered BP in an angiotensin II-induced hypertension model in wild-type (WT) but not KI mice. Furthermore, EET/dihydroxy-epoxyeicosatrienoic acid isomer ratios were elevated in plasma from WT but not KI mice following NO2-OA treatment, consistent with the redox-dead mutant being resistant to inhibition by lipid electrophiles. sEH was inhibited in WT mice fed linoleic acid and nitrite, key constituents of the Mediterranean diet that elevates electrophilic nitro fatty acid levels, whereas KIs were unaffected. These observations reveal that lipid electrophiles such as NO2-OA mediate antihypertensive signaling actions by inhibiting sEH and suggest a mechanism accounting for protection from hypertension afforded by the Mediterranean diet.
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625
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Dworkin J. The medium is the message: interspecies and interkingdom signaling by peptidoglycan and related bacterial glycans. Annu Rev Microbiol 2014; 68:137-54. [PMID: 24847956 DOI: 10.1146/annurev-micro-091213-112844] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Peptidoglycan serves as a key structure of the bacterial cell by determining cell shape and providing resistance to internal turgor pressure. However, in addition to these essential and well-studied functions, bacterial signaling by peptidoglycan fragments, or muropeptides, has been demonstrated by recent work. Actively growing bacteria release muropeptides as a consequence of cell wall remodeling during elongation and division. Therefore, the presence of muropeptide synthesis is indicative of growth-promoting conditions and may serve as a broadly conserved signal for nongrowing cells to reinitiate growth. In addition, muropeptides serve as signals between bacteria and eukaryotic organisms during both pathogenic and symbiotic interactions. The increasingly appreciated role of the microbiota in metazoan organisms suggests that muropeptide signaling likely has important implications for homeostatic mammalian physiology.
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Affiliation(s)
- Jonathan Dworkin
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032;
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626
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Sanders ME, Lenoir-Wijnkoop I, Salminen S, Merenstein DJ, Gibson GR, Petschow BW, Nieuwdorp M, Tancredi DJ, Cifelli CJ, Jacques P, Pot B. Probiotics and prebiotics: prospects for public health and nutritional recommendations. Ann N Y Acad Sci 2014; 1309:19-29. [PMID: 24571254 DOI: 10.1111/nyas.12377] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Probiotics and prebiotics are useful interventions for improving human health through direct or indirect effects on the colonizing microbiota. However, translation of these research findings into nutritional recommendations and public health policy endorsements has not been achieved in a manner consistent with the strength of the evidence. More progress has been made with clinical recommendations. Conclusions include that beneficial cultures, including probiotics and live cultures in fermented foods, can contribute towards the health of the general population; prebiotics, in part due to their function as a special type of soluble fiber, can contribute to the health of the general population; and a number of challenges must be addressed in order to fully realize probiotic and prebiotic benefits, including the need for greater awareness of the accumulated evidence on probiotics and prebiotics among policy makers, strategies to cope with regulatory roadblocks to research, and high-quality human trials that address outstanding research questions in the field.
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Affiliation(s)
- Mary Ellen Sanders
- International Scientific Association for Probiotics and Prebiotics, Centennial, Colorado
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627
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Randall TD, Mebius RE. The development and function of mucosal lymphoid tissues: a balancing act with micro-organisms. Mucosal Immunol 2014; 7:455-66. [PMID: 24569801 DOI: 10.1038/mi.2014.11] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 01/24/2014] [Indexed: 02/06/2023]
Abstract
Mucosal surfaces are constantly exposed to environmental antigens, colonized by commensal organisms and used by pathogens as points of entry. As a result, the immune system has devoted the bulk of its resources to mucosal sites to maintain symbiosis with commensal organisms, prevent pathogen entry, and avoid unnecessary inflammatory responses to innocuous antigens. These functions are facilitated by a variety of mucosal lymphoid organs that develop during embryogenesis in the absence of microbial stimulation as well as ectopic lymphoid tissues that develop in adults following microbial exposure or inflammation. Each of these lymphoid organs samples antigens from different mucosal sites and contributes to immune homeostasis, commensal containment, and immunity to pathogens. Here we discuss the mechanisms, mostly based on mouse studies, that control the development of mucosal lymphoid organs and how the various lymphoid tissues cooperate to maintain the integrity of the mucosal barrier.
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Affiliation(s)
- T D Randall
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham Alabama, USA
| | - R E Mebius
- Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, The Netherlands
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628
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Reid G, Nduti N, Sybesma W, Kort R, Kollmann TR, Adam R, Boga H, Brown EM, Einerhand A, El-Nezami H, Gloor GB, Kavere II, Lindahl J, Manges A, Mamo W, Martin R, McMillan A, Obiero J, Ochieng’ PA, Onyango A, Rulisa S, Salminen E, Salminen S, Sije A, Swann JR, van Treuren W, Waweru D, Kemp SJ. Harnessing microbiome and probiotic research in sub-Saharan Africa: recommendations from an African workshop. MICROBIOME 2014; 2:12. [PMID: 24739094 PMCID: PMC3996947 DOI: 10.1186/2049-2618-2-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 03/06/2014] [Indexed: 05/07/2023]
Abstract
To augment capacity-building for microbiome and probiotic research in Africa, a workshop was held in Nairobi, Kenya, at which researchers discussed human, animal, insect, and agricultural microbiome and probiotics/prebiotics topics. Five recommendations were made to promote future basic and translational research that benefits Africans.
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Affiliation(s)
- Gregor Reid
- Lawson Health Research Institute and Departments of Microbiology & Immunology, and Surgery, University of Western Ontario, 268 Grosvenor Street, London, Ontario N6A 4V2, Canada
| | - Nicholas Nduti
- Ministry of Agriculture, Waruhiu Agriculture training Center, P.O. Box 800, Githunguri, Kenya
| | - Wilbert Sybesma
- Yoba for Life Foundation, Hunzestraat 133-A, 1079 WB Amsterdam, The Netherlands
| | - Remco Kort
- Yoba for Life Foundation, Hunzestraat 133-A, 1079 WB Amsterdam, The Netherlands
- TNO Microbiology and Systems Biology, Utrechtseweg 48, 3704 HE Zeist, and Molecular Cell Physiology, De Boelelaan 1085, 1081 HV, VU University, Amsterdam, The Netherlands
| | - Tobias R Kollmann
- Department of Pediatrics, Division of Infectious Diseases, University of British Columbia, CFRI A5-147, 950 W28th Ave, Vancouver, BC V5Z 4H4, Canada
| | - Rod Adam
- Department of Pathology, Aga Khan University Hospital, Nairobi, Kenya
| | - Hamadi Boga
- Taita Taveta University College, P.O. Box 635–80300, Voi, Kenya
| | - Eric M Brown
- Michael Smith Laboratories and Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | | | - Hani El-Nezami
- School of Biological Sciences, University of Hong Kong, Pokfulam Rd, Hong Kong, Hong Kong SAR
| | - Gregory B Gloor
- Department of Biochemistry, University of Western Ontario, London, ON, Canada
| | - Irene I Kavere
- Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000, (00200) Nairobi, Kenya
| | - Johanna Lindahl
- Consultative Group on International Agricultural Research, ILRI, Nairobi, Kenya
| | - Amee Manges
- School of Population and Public Health, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Wondu Mamo
- Department of Animal Production, College of Veterinary Medicine and Agriculture, Addis Ababa University, Debre Zeyte, Ethiopia
| | - Rocio Martin
- Danone Nutricia Research, Uppsalalaan 12, 3584 CT Utrecht, The Netherlands
| | - Amy McMillan
- Lawson Health Research Institute and Departments of Microbiology & Immunology, and Surgery, University of Western Ontario, 268 Grosvenor Street, London, Ontario N6A 4V2, Canada
| | - Jael Obiero
- Department of Reproductive Health/Biology, Institute of Primate Research, Karen, Nairobi, Kenya
| | - Pamela A Ochieng’
- Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000, (00200) Nairobi, Kenya
| | - Arnold Onyango
- Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000, (00200) Nairobi, Kenya
| | - Stephen Rulisa
- University Teaching Hospital of Kigali, National University of Rwanda, Kigali, Rwanda
| | - Eeva Salminen
- Functional Foods Forum, The Medical School, University of Turku, 20014 Turku, Finland
| | - Seppo Salminen
- Department of Oncology, Turku University Hospital, 20520 Turku, Finland
| | - Antony Sije
- Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000, (00200) Nairobi, Kenya
| | - Jonathan R Swann
- Department of Food and Nutritional Sciences, School of Chemistry, Food and Pharmacy, University of Reading, Reading RG6 6AP, United Kingdom
| | - William van Treuren
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado at Boulder, Boulder, CO 80309, USA
| | - Daniel Waweru
- Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000, (00200) Nairobi, Kenya
| | - Steve J Kemp
- International Livestock Research Institute, Nairobi, Kenya
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629
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Abstract
Cell metabolism is closely related to the host immunity in many respects. We herein briefly summarized the recent progress on the roles of cellular metabolism in T-cell development, homeostasis, differentiation and functions. Relatively quiescent naïve T cells only require energy for survival and migration, and they mainly metabolize glucose to carbon dioxide through oxidative phosphorylation. However, activated T cells engage in robust cell proliferation, produce of a range of effector molecules and migrate through peripheral tissues, so they utilizes glycolysis to convert glucose to lactate (termed aerobic glycolysis) to meet the significantly increased metabolic demands. Importantly, the differentiation of T-cell subsets and memory T cells (Tm) was also significantly shaped by distinct cellular metabolic pathways including glucose, amino acids (AA), fatty acids (FA), and others. Understanding the regulatory metabolic networks on immunity may offer new insights into the immune-related disorders and open novel potential therapies to prevent and treat immune diseases.
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Affiliation(s)
- Hui Chen
- Transplantation Biology Research Division, State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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630
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Shafquat A, Joice R, Simmons SL, Huttenhower C. Functional and phylogenetic assembly of microbial communities in the human microbiome. Trends Microbiol 2014; 22:261-6. [PMID: 24618403 DOI: 10.1016/j.tim.2014.01.011] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 01/29/2014] [Accepted: 01/31/2014] [Indexed: 12/28/2022]
Abstract
Microbial communities associated with the human body, that is, the human microbiome, are complex ecologies critical for normal development and health. The taxonomic and phylogenetic composition of these communities tends to significantly differ among individuals, precluding the definition of a simple, shared set of 'core' microbes. Here, we review recent evidence and ecological theory supporting the assembly of host-associated microbial communities in terms of functional traits rather than specific organisms. That is, distinct microbial species may be responsible for specific host-associated functions and phenotypes in distinct hosts. We discuss how ecological processes (selective and stochastic forces) governing the assembly of metazoan communities can be adapted to describe microbial ecologies in host-associated environments, resulting in both niche-specific and 'core' metabolic and other pathways maintained throughout the human microbiome. The extent to which phylogeny and functional traits are linked in host-associated microbes, as opposed to unlinked by mechanisms, such as lateral transfer, remains to be determined. However, the definition of these functional assembly rules within microbial communities using controlled model systems and integrative 'omics' represents a fruitful opportunity for molecular systems ecology.
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Affiliation(s)
- Afrah Shafquat
- Department of Biostatistics, Harvard School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA
| | - Regina Joice
- Department of Biostatistics, Harvard School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA
| | - Sheri L Simmons
- Bay Paul Center, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard School of Public Health, 655 Huntington Ave, Boston, MA 02115, USA; The Broad Institute of Harvard and Massachusetts Institute of Technology (MIT), 301 Binney Street, Cambridge, MA 02142, USA.
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631
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Lu K, Abo RP, Schlieper KA, Graffam ME, Levine S, Wishnok JS, Swenberg JA, Tannenbaum SR, Fox JG. Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis. ENVIRONMENTAL HEALTH PERSPECTIVES 2014; 122:284-91. [PMID: 24413286 PMCID: PMC3948040 DOI: 10.1289/ehp.1307429] [Citation(s) in RCA: 378] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 01/09/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND The human intestine is host to an enormously complex, diverse, and vast microbial community-the gut microbiota. The gut microbiome plays a profound role in metabolic processing, energy production, immune and cognitive development, epithelial homeostasis, and so forth. However, the composition and diversity of the gut microbiome can be readily affected by external factors, which raises the possibility that exposure to toxic environmental chemicals leads to gut microbiome alteration, or dysbiosis. Arsenic exposure affects large human populations worldwide and has been linked to a number of diseases, including cancer, diabetes, and cardiovascular disorders. OBJECTIVES We investigated the impact of arsenic exposure on the gut microbiome composition and its metabolic profiles. METHODS We used an integrated approach combining 16S rRNA gene sequencing and mass spectrometry-based metabolomics profiling to examine the functional impact of arsenic exposure on the gut microbiome. RESULTS 16S rRNA gene sequencing revealed that arsenic significantly perturbed the gut microbiome composition in C57BL/6 mice after exposure to 10 ppm arsenic for 4 weeks in drinking water. Moreover, metabolomics profiling revealed a concurrent effect, with a number of gut microflora-related metabolites being perturbed in multiple biological matrices. CONCLUSIONS Arsenic exposure not only alters the gut microbiome community at the abundance level but also substantially disturbs its metabolic profiles at the function level. These findings may provide novel insights regarding perturbations of the gut microbiome and its functions as a potential new mechanism by which arsenic exposure leads to or exacerbates human diseases. CITATION Lu K, Abo RP, Schlieper KA, Graffam ME, Levine S, Wishnok JS, Swenberg JA, Tannenbaum SR, Fox JG. 2014. Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis. Environ Health Perspect 122:284-291; http://dx.doi.org/10.1289/ehp.1307429.
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Affiliation(s)
- Kun Lu
- Department of Biological Engineering
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632
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Foley KA, Ossenkopp KP, Kavaliers M, MacFabe DF. Pre- and neonatal exposure to lipopolysaccharide or the enteric metabolite, propionic acid, alters development and behavior in adolescent rats in a sexually dimorphic manner. PLoS One 2014; 9:e87072. [PMID: 24466331 PMCID: PMC3899377 DOI: 10.1371/journal.pone.0087072] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 12/22/2013] [Indexed: 02/08/2023] Open
Abstract
Alterations in the composition of the gut microbiome and/or immune system function may have a role in the development of autism spectrum disorders (ASD). The current study examined the effects of prenatal and early life administration of lipopolysaccharide (LPS), a bacterial mimetic, and the short chain fatty acid, propionic acid (PPA), a metabolic fermentation product of enteric bacteria, on developmental milestones, locomotor activity, and anxiety-like behavior in adolescent male and female offspring. Pregnant Long-Evans rats were subcutaneously injected once a day with PPA (500 mg/kg) on gestation days G12–16, LPS (50 µg/kg) on G15–16, or vehicle control on G12–16 or G15–16. Male and female offspring were injected with PPA (500 mg/kg) or vehicle twice a day, every second day from postnatal days (P) 10–18. Physical milestones and reflexes were monitored in early life with prenatal PPA and LPS inducing delays in eye opening. Locomotor activity and anxiety were assessed in adolescence (P40–42) in the elevated plus maze (EPM) and open-field. Prenatal and postnatal treatments altered behavior in a sex-specific manner. Prenatal PPA decreased time spent in the centre of the open-field in males and females while prenatal and postnatal PPA increased anxiety behavior on the EPM in female rats. Prenatal LPS did not significantly influence those behaviors. Evidence for the double hit hypothesis was seen as females receiving a double hit of PPA (prenatal and postnatal) displayed increased repetitive behavior in the open-field. These results provide evidence for the hypothesis that by-products of enteric bacteria metabolism such as PPA may contribute to ASD, altering development and behavior in adolescent rats similar to that observed in ASD and other neurodevelopmental disorders.
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Affiliation(s)
- Kelly A. Foley
- Graduate Program in Neuroscience, The University of Western Ontario, London, Ontario, Canada
- Department of Psychology, The University of Western Ontario, London, Ontario, Canada
- * E-mail:
| | - Klaus-Peter Ossenkopp
- Graduate Program in Neuroscience, The University of Western Ontario, London, Ontario, Canada
- Department of Psychology, The University of Western Ontario, London, Ontario, Canada
- The Kilee Patchell-Evans Autism Research Group, Department of Psychology, The University of Western Ontario, London, Ontario, Canada
| | - Martin Kavaliers
- Graduate Program in Neuroscience, The University of Western Ontario, London, Ontario, Canada
- Department of Psychology, The University of Western Ontario, London, Ontario, Canada
- The Kilee Patchell-Evans Autism Research Group, Department of Psychology, The University of Western Ontario, London, Ontario, Canada
| | - Derrick F. MacFabe
- Department of Psychology, The University of Western Ontario, London, Ontario, Canada
- The Kilee Patchell-Evans Autism Research Group, Division of Developmental Disabilities, Departments of Psychology and Psychiatry, The University of Western Ontario, London, Ontario, Canada
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633
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Villena J, Kitazawa H. Modulation of Intestinal TLR4-Inflammatory Signaling Pathways by Probiotic Microorganisms: Lessons Learned from Lactobacillus jensenii TL2937. Front Immunol 2014; 4:512. [PMID: 24459463 PMCID: PMC3890654 DOI: 10.3389/fimmu.2013.00512] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 12/26/2013] [Indexed: 12/21/2022] Open
Abstract
The intestinal mucosa plays a critical role in the host’s interactions with innocuous commensal microbiota and invading pathogenic microorganisms. Intestinal epithelial cells (IECs) and gut associated immune cells recognize the bacterial components via pattern-recognition receptors (PRRs) and are responsible for maintaining tolerance to the large communities of resident luminal bacteria while being also able to mount inflammatory responses against pathogens. Toll-like receptors (TLRs) are a major class of PRRs that are present on IECs and immune cells which are involved in the induction of both tolerance and inflammation. A growing body of experimental and clinical evidence supports the therapeutic and preventive application of probiotics for several gastrointestinal inflammatory disorders in which TLRs exert a significant role. This review aims to summarize the current knowledge of the beneficial effects of probiotic microorganisms with the capacity to modulate the immune system (immunobiotics) in the regulation of intestinal inflammation in pigs, which are very important as both livestock and human model. Especially we discuss the role of TLRs, their signaling pathways, and their negative regulators in both the inflammatory intestinal injury and the beneficial effects of immunobiotics in general, and Lactobacillus jensenii TL2937 in particular. This review article emphasizes the cellular and molecular interactions of immunobiotics with IECs and immune cells through TLRs and their application for improving animal and human health.
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Affiliation(s)
- Julio Villena
- Immunobiotics Research Group , Tucuman , Argentina ; Laboratory of Immunobiotechnology, Reference Centre for Lactobacilli (CERELA-CONICET) , Tucuman , Argentina
| | - Haruki Kitazawa
- Food and Feed Immunology Group, Laboratory of Animal Products Chemistry, Department of Science of Food Function and Health, Graduate School of Agricultural Science, Tohoku University , Sendai , Japan
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634
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Reynolds LA, Finlay BB. A case for antibiotic perturbation of the microbiota leading to allergy development. Expert Rev Clin Immunol 2014; 9:1019-30. [DOI: 10.1586/1744666x.2013.851603] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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635
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Abstract
The bacterial microbiota of the human large bowel is a complex ecosystem consisting of several hundred, mostly anaerobic, species. To maintain colonization of the gut lumen and maximize growth in the presence of nutritional competitors, highly diverse metabolic pathways have evolved, with each microbe utilizing a different "winning strategy" for nutrient acquisition and utilization. Conditions and diseases leading to intestinal inflammation are accompanied by a severe disruption the microbiota composition characterized by an expansion of facultative anaerobic Enterobacteriaceae. Here, we review evidence that the local inflammatory response creates a unique nutritional environment that is conducive to a bloom of bacterial species whose genomes encode the capability of utilizing inflammation-derived nutrients.
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636
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Winter SE, Bäumler AJ. Why related bacterial species bloom simultaneously in the gut: principles underlying the 'Like will to like' concept. Cell Microbiol 2013; 16:179-84. [PMID: 24286560 DOI: 10.1111/cmi.12245] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 10/11/2013] [Accepted: 10/14/2013] [Indexed: 12/17/2022]
Abstract
The large intestine is host to a complex ecological community composed predominantly of obligate anaerobic bacteria belonging to the classes Bacteroidia and Clostridia. This community confers benefits through its metabolic activities and host interactions. However, a microbial imbalance (dysbiosis) characterized by a decreased abundance of Clostridia and a bloom of facultative anaerobic Proteobacteria is commonly observed during inflammation in the large bowel. Here we review recent insights into the principles that favour simultaneous increases in the abundance of closely related species belonging to the Proteobacteria during inflammation, which provides important clues for the rational design of strategies to treat dysbiosis.
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Affiliation(s)
- Sebastian E Winter
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, One Shields Ave, Davis, CA, 95616, USA
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637
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Abstract
The genetic and cellular alterations that define cancer provide the immune system with the means to generate T cell responses that recognize and eradicate cancer cells. However, elimination of cancer by T cells is only one step in the Cancer-Immunity Cycle, which manages the delicate balance between the recognition of nonself and the prevention of autoimmunity. Identification of cancer cell T cell inhibitory signals, including PD-L1, has prompted the development of a new class of cancer immunotherapy that specifically hinders immune effector inhibition, reinvigorating and potentially expanding preexisting anticancer immune responses. The presence of suppressive factors in the tumor microenvironment may explain the limited activity observed with previous immune-based therapies and why these therapies may be more effective in combination with agents that target other steps of the cycle. Emerging clinical data suggest that cancer immunotherapy is likely to become a key part of the clinical management of cancer.
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638
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McHardy IH, Li X, Tong M, Ruegger P, Jacobs J, Borneman J, Anton P, Braun J. HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota. MICROBIOME 2013; 1:26. [PMID: 24451087 PMCID: PMC3971626 DOI: 10.1186/2049-2618-1-26] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 10/03/2013] [Indexed: 05/05/2023]
Abstract
BACKGROUND Regardless of infection route, the intestine is the primary site for HIV-1 infection establishment and results in significant mucosal CD4+ T lymphocyte depletion, induces an inflammatory state that propagates viral dissemination, facilitates microbial translocation, and fosters establishment of one of the largest HIV reservoirs. Here we test the prediction that HIV infection modifies the composition and function of the mucosal commensal microbiota. RESULTS Rectal mucosal microbiota were collected from human subjects using a sponge-based sampling methodology. Samples were collected from 20 HIV-positive men not receiving combination anti-retroviral therapy (cART), 20 HIV-positive men on cART and 20 healthy, HIV-negative men. Microbial composition of samples was analyzed using barcoded 16S Illumina deep sequencing (85,900 reads per sample after processing). Microbial metagenomic information for the samples was imputed using the bioinformatic tools PICRUST and HUMAnN. Microbial composition and imputed function in HIV-positive individuals not receiving cART was significantly different from HIV-negative individuals. Genera including Roseburia, Coprococcus, Ruminococcus, Eubacterium, Alistipes and Lachnospira were depleted in HIV-infected subjects not receiving cART, while Fusobacteria, Anaerococcus, Peptostreptococcus and Porphyromonas were significantly enriched. HIV-positive subjects receiving cART exhibited similar depletion and enrichment for these genera, but were of intermediate magnitude and did not achieve statistical significance. Imputed metagenomic functions, including amino acid metabolism, vitamin biosynthesis, and siderophore biosynthesis differed significantly between healthy controls and HIV-infected subjects not receiving cART. CONCLUSIONS HIV infection was associated with rectal mucosal changes in microbiota composition and imputed function that cART failed to completely reverse. HIV infection was associated with depletion of some commensal species and enrichment of a few opportunistic pathogens. Many imputed metagenomic functions differed between samples from HIV-negative and HIV-positive subjects not receiving cART, possibly reflecting mucosal metabolic changes associated with HIV infection. Such functional pathways may represent novel interventional targets for HIV therapy if normalizing the microbial composition or functional activity of the microbiota proves therapeutically useful.
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Affiliation(s)
- Ian H McHardy
- Pathology and Laboratory Medicine, UCLA, 10833 Le Conte Ave 13-188 CHS, Los Angeles, CA 90095, USA
| | - Xiaoxiao Li
- Inflammatory Bowel Disease & Immunobiology Research Institute, Cedars Sinai Medical Center, Los Angeles 90048, USA
| | | | - Paul Ruegger
- Plant Pathology, UC Riverside, Riverside, CA, USA
| | - Jonathan Jacobs
- Pathology and Laboratory Medicine, UCLA, 10833 Le Conte Ave 13-188 CHS, Los Angeles, CA 90095, USA
- Department of Medicine, UCLA, Los Angeles, CA, USA
| | | | - Peter Anton
- Department of Medicine, UCLA, Los Angeles, CA, USA
- Center for HIV Prevention Research, UCLA AIDS Institute, Los Angeles, CA, USA
| | - Jonathan Braun
- Pathology and Laboratory Medicine, UCLA, 10833 Le Conte Ave 13-188 CHS, Los Angeles, CA 90095, USA
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639
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Denning TL, Parkos CA. Neutrophils enlist IL-22 to restore order in the gut. Proc Natl Acad Sci U S A 2013; 110:12509-10. [PMID: 23872844 PMCID: PMC3732960 DOI: 10.1073/pnas.1310907110] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Timothy L. Denning
- Departments of Pathology and Laboratory Medicine and
- Pediatrics, Emory University School of Medicine, Atlanta, GA 30322
| | - Charles A. Parkos
- Departments of Pathology and Laboratory Medicine and
- Pediatrics, Emory University School of Medicine, Atlanta, GA 30322
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640
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White AK, Smith RJ, Bigler CR, Brooke WF, Schauer PR. Head and neck manifestations of neurofibromatosis. Laryngoscope 1986; 47:75-85. [PMID: 3088347 DOI: 10.1249/jes.0000000000000183] [Citation(s) in RCA: 248] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Neurofibromatosis is a neurocutaneous systemic disease that occurs in 1:2500 to 3300 live births. Prevalence figures have shown it to be as common as cystic fibrosis or Down's syndrome and more than twice as common as muscular dystrophy. In this study, our experience with 257 cases of neurofibromatosis seen since 1972 is reviewed. Intracranial, bony, and extracranial anomalies are described in the 223 patients (87%) who presented with, or ultimately developed, head and neck manifestations of the disease. The most common intracranial tumor was optic glioma, found in 35 patients (14%), 19 younger than 10 years of age. Acoustic neuromas were diagnosed in eight individuals (3%) and were bilateral in three. The most common skull anomaly was macrocephaly, noted 78 times (30%). Absence of the sphenoid wing occurred in 11 patients (4%) and 19 others (7%) had facial asymmetry due to other skull abnormalities. Extracranial manifestations included neurofibromas of the plexiform and nonplexiform type, Lisch nodules, and cafe-au-lait spots.
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