151
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Durack J, Lynch SV. The gut microbiome: Relationships with disease and opportunities for therapy. J Exp Med 2019; 216:20-40. [PMID: 30322864 PMCID: PMC6314516 DOI: 10.1084/jem.20180448] [Citation(s) in RCA: 499] [Impact Index Per Article: 99.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 06/12/2018] [Accepted: 09/05/2018] [Indexed: 12/12/2022] Open
Abstract
Over the past decade, our view of human-associated microbes has expanded beyond that of a few species toward an appreciation of the diverse and niche-specialized microbial communities that develop in the human host with chronological age. The largest reservoir of microbes exists in the distal gastrointestinal tract, both in the lumen, where microbes facilitate primary and secondary metabolism, and on mucosal surfaces, where they interact with host immune cell populations. While local microbial-driven immunomodulation in the gut is well described, more recent studies have demonstrated a role for the gut microbiome in influencing remote organs and mucosal and hematopoietic immune function. Unsurprisingly, therefore, perturbation to the composition and function of the gut microbiota has been associated with chronic diseases ranging from gastrointestinal inflammatory and metabolic conditions to neurological, cardiovascular, and respiratory illnesses. Considerable effort is currently focused on understanding the natural history of microbiome development in humans in the context of health outcomes, in parallel with improving our knowledge of microbiome-host molecular interactions. These efforts ultimately aim to develop effective approaches to rehabilitate perturbed human microbial ecosystems as a means to restore health or prevent disease. This review details the role of the gut microbiome in modulating host health with a focus on immunomodulation and discusses strategies for manipulating the gut microbiome for the management or prevention of chronic inflammatory conditions.
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Affiliation(s)
- Juliana Durack
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Susan V Lynch
- Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA
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152
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Putting microbiota-gut-brain research in a systemic developmental context: Focus on breast milk. Behav Brain Sci 2019. [DOI: 10.1017/s0140525x1800290x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Abstract
The microbiota-gut-brain (MGB) field holds huge potential for understanding behavioral development and informing effective early interventions for psychological health. To realize this potential, factors that shape the MGB axis in infancy (i.e., breast milk) must be integrated into a systemic framework that considers salient behavioral outcomes. This is best accomplished applying network analyses in large prospective, longitudinal investigations in humans.
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153
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Chen R, Wu P, Cai Z, Fang Y, Zhou H, Lasanajak Y, Tang L, Ye L, Hou C, Zhao J. Puerariae Lobatae Radix with chuanxiong Rhizoma for treatment of cerebral ischemic stroke by remodeling gut microbiota to regulate the brain-gut barriers. J Nutr Biochem 2018; 65:101-114. [PMID: 30710886 DOI: 10.1016/j.jnutbio.2018.12.004] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 12/13/2018] [Accepted: 12/14/2018] [Indexed: 02/07/2023]
Abstract
The combination of Puerariae Lobatae Radix (PLR) and Chuanxiong Rhizoma (CXR) is commonly used to treat cerebrovascular diseases. This work aimed to clarify the mechanisms of their action in treating cerebral ischemic stroke from the perspective of gut microecology. The PLR and CXR combination effectively improved the neurological function, reduced the cerebral infarction and relieved the complications of cerebral ischemic stroke, including dyslipidemia, increased blood viscosity and thrombotic risk. Cerebral ischemic stroke triggered gut microbial disturbances by enriching pathogens and opportunistic microorganisms, including Bacteroides, Escherichia_Shigella, Haemophilus, Eubacterium_nodatum_group, Collinsella, Enterococcus, Proteus, Alistipes, Klebsiella, Shuttleworthia and Faecalibacterium. Cerebral ischemic stroke also increased the intestinal permeability, disrupted the gut barrier and caused intestinal microbial translocation. Occludin, claudin-5 and ZO-1 levels in the brain-gut barriers showed a high positive correlation. However, the combination remodeled the gut microecology by modulating endogenous bacteria whose effects may mitigate cerebral damage, such as Alloprevotella, Ruminococcaceae, Oscillospira, Lachnospiraceae_NK4B4_group, Akkermansia and Megasphaera, protected the brain-gut barriers by increasing claudin-5 and ZO-1 levels; and weakened the gut microbiota translocation by decreasing diamine oxidase, lipopolysaccharide and d-lactate. Although nimodipine effectively reduced the cerebral infarction, it did not relieve the gut microbiota dysbiosis and instead aggravated the gut barrier disruption and microbiota translocation. In conclusion, cerebral ischemic stroke caused gut microbiota dysbiosis, increased intestinal permeability, disrupted the gut barrier and triggered gut microbiota translocation. The PLR and CXR combination was an effective treatment for cerebral ischemic stroke that relieved the gut microbiota dysbiosis and brain-gut barriers disruption.
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Affiliation(s)
- Runzhi Chen
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Peng Wu
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zheng Cai
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Yingying Fang
- Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Hao Zhou
- Department of Hospital Infection Management of Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yi Lasanajak
- Emory Comprehensive Glycomics Core, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Lan Tang
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Ling Ye
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Chuqi Hou
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Jie Zhao
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of New Drug Screening, Biopharmaceutics, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
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154
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Baumann-Dudenhoeffer AM, D'Souza AW, Tarr PI, Warner BB, Dantas G. Infant diet and maternal gestational weight gain predict early metabolic maturation of gut microbiomes. Nat Med 2018; 24:1822-1829. [PMID: 30374198 PMCID: PMC6294307 DOI: 10.1038/s41591-018-0216-2] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 09/10/2018] [Indexed: 12/17/2022]
Abstract
Commensal gut bacterial communities (microbiomes) are predicted to influence human health and disease1,2. Neonatal gut microbiomes are colonized with maternal and environmental flora and mature toward a stable composition over 2-3 years3,4. To study pre- and postnatal determinants of infant microbiome development, we analyzed 402 fecal metagenomes from 60 infants aged 0-8 months, using longitudinal generalized linear mixed models (GLMMs). Distinct microbiome signatures correlated with breastfeeding, formula ingredients, and maternal gestational weight gain (GWG). Amino acid synthesis pathway accretion in breastfed microbiomes complemented normative breastmilk composition. Prebiotic oligosaccharides, designed to promote breastfed-like microflora5, predicted functional pathways distinct from breastfed infant microbiomes. Soy formula in six infants was positively associated with Lachnospiraceae and pathways suggesting a short-chain fatty acid (SCFA)-rich environment, including glycerol to 1-butanol fermentation, which is potentially dysbiotic. GWG correlated with altered carbohydrate degradation and enriched vitamin synthesis pathways. Maternal and postnatal antibiotics predicted microbiome alterations, while delivery route had no persistent effects. Domestic water source correlates suggest water may be an underappreciated determinant of microbiome acquisition. Clinically important microbial pathways with statistically significant dietary correlates included dysbiotic markers6,7, core enterotype features8, and synthesis pathways for enteroprotective9 and immunomodulatory10,11 metabolites, epigenetic mediators1, and developmentally critical vitamins12, warranting further investigation.
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Affiliation(s)
- Aimee M Baumann-Dudenhoeffer
- Division of Newborn Medicine, Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
| | - Alaric W D'Souza
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Phillip I Tarr
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
- Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Barbara B Warner
- Division of Newborn Medicine, Department of Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
- Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA.
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155
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Bhagavata Srinivasan SP, Raipuria M, Bahari H, Kaakoush NO, Morris MJ. Impacts of Diet and Exercise on Maternal Gut Microbiota Are Transferred to Offspring. Front Endocrinol (Lausanne) 2018; 9:716. [PMID: 30559716 PMCID: PMC6284474 DOI: 10.3389/fendo.2018.00716] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 11/13/2018] [Indexed: 12/18/2022] Open
Abstract
Background: It is well established that maternal exercise during pregnancy improves metabolic outcomes associated with obesity in mothers and offspring, however, its effects on the gut microbiota of both mother and offspring, are unknown. Here, we investigated whether wheel running exercise prior to and during pregnancy and prolonged feeding of an obesogenic diet were associated with changes in the gut microbiomes of Sprague-Dawley rat dams and their offspring. Female rats were fed either chow or obesogenic diet, and half of each diet group were given access to a running wheel 10 days before mating until delivery, while others remained sedentary. 16S rRNA gene amplicon sequencing was used to assess gut microbial communities in dams and their male and female offspring around the time of weaning. Results: Statistical analyses at the operational taxonomic unit (OTU) level revealed that maternal obesogenic diet decreased gut microbial alpha diversity and altered abundances of bacterial taxa previously associated with obesity such as Bacteroides and Blautia in dams, and their offspring of both sexes. Distance based linear modeling revealed that the relative abundances of Bacteroides OTUs were associated with adiposity measures in both dams and offspring. We identified no marked effects of maternal exercise on the gut microbiota of obesogenic diet dams or their offspring. In contrast, maternal exercise decreased gut microbial alpha diversity and altered the abundance of 88 microbial taxa in offspring of control dams. Thirty of these taxa were altered in a similar direction in offspring of sedentary obesogenic vs. control diet dams. In particular, the relative abundances of Oscillibacter OTUs were decreased in offspring of both exercised control dams and sedentary obesogenic diet dams, and associated with blood glucose concentrations and adiposity measures. Analyses of predicted bacterial metabolic pathways inferred decreased indole alkaloid biosynthesis in offspring of both obesogenic diet and exercised control dams. Conclusions: Our data suggest that maternal exercise prior to and during pregnancy resulted in gut dysbiosis in offspring of control dams. Importantly, alterations in the maternal gut microbiota by obesogenic diet or obesity were transferred to their offspring.
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Affiliation(s)
| | | | | | | | - Margaret J. Morris
- School of Medical Sciences, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
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156
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Eissa N, Kittana H, Gomes-Neto JC, Hussein H. Mucosal immunity and gut microbiota in dogs with chronic enteropathy. Res Vet Sci 2018; 122:156-164. [PMID: 30504001 DOI: 10.1016/j.rvsc.2018.11.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 11/19/2018] [Accepted: 11/23/2018] [Indexed: 12/18/2022]
Abstract
Chronic enteropathy (CE) in dogs is a chronic and relapsing immunopathology, of unknown etiology, that usually manifests with a plethora of clinical signs reflecting the underlying heterogeneity in its pathogenesis. Alterations of the mucosal immune responses and the gut microbiota composition are thought to play an essential role in CE. Similar to humans, it is hypothesized that the breakdown in mucosal tolerance leads to aberrant and pathological immune responses toward the gut microbiota, that in turn, may contribute to the severity of disease, at least for certain CE subsets. Therefore, in this review, we discuss some of the most relevant and recent insights microbiological and immunological aspects characterizing CE in dogs.
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Affiliation(s)
- Nour Eissa
- Department of Immunology, University of Manitoba, Winnipeg, MB, Canada.
| | - Hatem Kittana
- Department of Food Science and Technology, University of Nebraska-, Lincoln, NE, USA
| | - João Carlos Gomes-Neto
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA
| | - Hayam Hussein
- Department of Parasitology and Animal Diseases, Veterinary Research Division, National Research Centre, Giza, Egypt
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157
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Shigeno Y, Zhang H, Banno T, Usuda K, Nochi T, Inoue R, Watanabe G, Jin W, Benno Y, Nagaoka K. Gut microbiota development in mice is affected by hydrogen peroxide produced from amino acid metabolism during lactation. FASEB J 2018; 33:3343-3352. [PMID: 30433825 DOI: 10.1096/fj.201801462r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The development of gut microbiota during infancy is an important event that affects the health status of the host; however, the mechanism governing it is not fully understood. l-Amino acid oxidase 1 (LAO1) is a flavoprotein that catalyzes the oxidative deamination of particular l-amino acids and converts them into keto acids, ammonia, and H2O2. Our previous study showed that LAO1 is present in mouse milk and exerts protection against bacteria by its production of H2O2. The data led us to consider whether LAO1, H2O2, or both could impact infant gut microbiota development via mother's milk consumption in mice. Different gut microbiota profiles were observed in the wild-type (WT) and LAO1-knockout mouse pups. The WT pups' microbiota was relatively simple and composed of only a few dominant bacteria, such as Lactobacillus, whereas the lactating knockout pups had high microbiota diversity. Cross-fostering experiments indicated that WT milk (containing LAO1) has the ability to suppress the diversity of microbiota in pups. We observed that the stomach content of pups fed WT milk had LAO1 proteins and the ability to produce H2O2. Moreover, culture experiments showed that Lactobacillus was abundant in the feces of pups fed WT milk and that Lactobacillus was more resistant to H2O2 than Bifidobacterium and Escherichia. Human breast milk produces very little H2O2, which could be the reason for Lactobacillus not being dominant in the feces of breast-fed human infants. In mouse mother's milk, H2O2 is generated from the process of free amino acid metabolism, and H2O2 may be a key player in regulating the initial acquisition and development of gut microbiota, especially growth of Lactobacillus, during infancy.-Shigeno, Y., Zhang, H., Banno, T., Usuda, K., Nochi, T., Inoue, R., Watanabe, G., Jin, W., Benno, Y., Nagaoka, K. Gut microbiota development in mice is affected by hydrogen peroxide produced from amino acid metabolism during lactation.
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Affiliation(s)
- Yuko Shigeno
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo, Japan.,Benno Laboratory, RIKEN Innovation Center, Wako, Japan
| | - Haolin Zhang
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Taihei Banno
- Benno Laboratory, RIKEN Innovation Center, Wako, Japan
| | - Kento Usuda
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Tomonori Nochi
- Laboratory of Mucosal Immunology, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Ryo Inoue
- Laboratory of Animal Science, Department of Agricultural and Life Sciences, Kyoto Prefectural University, Kyoto, Japan; and
| | - Gen Watanabe
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Wanzhu Jin
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yoshimi Benno
- Benno Laboratory, RIKEN Innovation Center, Wako, Japan
| | - Kentaro Nagaoka
- Laboratory of Veterinary Physiology, Department of Veterinary Medicine, Tokyo University of Agriculture and Technology, Tokyo, Japan
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158
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Exposure to heat-stress environment affects the physiology, circulation levels of cytokines, and microbiome in dairy cows. Sci Rep 2018; 8:14606. [PMID: 30279428 PMCID: PMC6168502 DOI: 10.1038/s41598-018-32886-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/13/2018] [Indexed: 12/13/2022] Open
Abstract
The microbiome has emerged as a new player on behavior, physiology and stress because of its significant effects on the brain-gut axis. The aim of this study was to increase our understanding of brain-gut function in dairy cows. We investigated the effects of a heat-stress (HS) environment and individual differences of heat sensitivity (IH) on bovine physiological characteristics and microbial composition. Results indicate that both HS and IH increased rectal temperature (RT) (P < 0.05). An HS environment increased plasma, as well as milk cortisol and cytokines in plasma; however, it decreased plasma, and milk oxytocin, triiodothyronine, and thyroxine (P < 0.05) levels. Exposure to an HS environment reduced the diversity of the fecal microbial population, and resulted in a higher expression of diseases, the environmental adaptation pathway, and the immune related pathway, whereas it lowered the expression of metabolic pathways (P < 0.05). High heat sensitive cows have upregulated metabolisms, environmental adaptation and cellular process pathways, and a downregulated neurodegenerative disease pathway (P < 0.05). Thus, we conclude that exposure to an HS environment modulates physiological characteristics, which may interplay with microbial activity, and in turn, alter the circulation levels of cytokines, implicating the role of the brain-gut axis in dairy cows. The HS environment affected physiological characteristics, cytokine levels, and microbial composition, but IH influenced RT and fecal microbial functions.
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159
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Vogelzang A, Guerrini MM, Minato N, Fagarasan S. Microbiota - an amplifier of autoimmunity. Curr Opin Immunol 2018; 55:15-21. [PMID: 30248521 DOI: 10.1016/j.coi.2018.09.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/07/2018] [Indexed: 02/08/2023]
Abstract
Many studies describe dysbiosis as a change in the microbiota that accompanies autoimmune illnesses, but little is known about whether these changes are a cause or consequence of an altered immune state. The immune system actively shapes the composition of the microbiota, with divergent outcomes in healthy or autoimmune-prone individuals. The gut microbiota in turn acts as an acquired endocrine organ, influencing the physiology of the host via release of nutrients and chemical messengers. Dysbiosis arising from abnormal immune function can initiate or amplify autoimmunity through multiple mechanisms. We examine how the bidirectional relationship between resident microbes and the immune system contributes to autoimmune diseases.
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Affiliation(s)
- Alexis Vogelzang
- Laboratory for Mucosal Immunity, Center for Integrative Medical Sciences, RIKEN Yokohama Institute, Tsurumi Ward, Suehirocho, 1 Chome-7-22, Yokohama, Kanagawa Prefecture, 230-0045, Japan
| | - Matteo M Guerrini
- Laboratory for Mucosal Immunity, Center for Integrative Medical Sciences, RIKEN Yokohama Institute, Tsurumi Ward, Suehirocho, 1 Chome-7-22, Yokohama, Kanagawa Prefecture, 230-0045, Japan
| | - Nagahiro Minato
- Medical Innovation Center, Kyoto University Graduate School of Medicine, Sakyo Ward, Yoshida-Konoe, Kyoto, Kyoto Prefecture, 606-8501, Japan
| | - Sidonia Fagarasan
- Laboratory for Mucosal Immunity, Center for Integrative Medical Sciences, RIKEN Yokohama Institute, Tsurumi Ward, Suehirocho, 1 Chome-7-22, Yokohama, Kanagawa Prefecture, 230-0045, Japan.
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160
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Tytgat HLP, Nobrega FL, van der Oost J, de Vos WM. Bowel Biofilms: Tipping Points between a Healthy and Compromised Gut? Trends Microbiol 2018; 27:17-25. [PMID: 30219265 DOI: 10.1016/j.tim.2018.08.009] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/29/2018] [Accepted: 08/15/2018] [Indexed: 02/06/2023]
Abstract
Bacterial communities are known to impact human health and disease. Mixed species biofilms, mostly pathogenic in nature, have been observed in dental and gastric infections as well as in intestinal diseases, chronic gut wounds and colon cancer. Apart from the appendix, the presence of thick polymicrobial biofilms in the healthy gut mucosa is still debated. Polymicrobial biofilms containing potential pathogens appear to be an early-warning signal of developing disease and can be regarded as a tipping point between a healthy and a diseased state of the gut mucosa. Key biofilm-forming pathogens and associated molecules hold promise as biomarkers. Criteria to distinguish microcolonies from biofilms are crucial to provide clarity when reporting biofilm-related phenomena in health and disease in the gut.
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Affiliation(s)
- Hanne L P Tytgat
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, The Netherlands; Institute of Microbiology, Swiss Federal Institute of Technology, ETH Zurich, 8093 Zurich, Switzerland.
| | - Franklin L Nobrega
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, The Netherlands; Kavli Institute of Nanoscience and Department of BioNanoscience, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, The Netherlands; Faculty of Medicine, Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, 00290 Helsinki, Finland.
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161
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Desselberger U. The Mammalian Intestinal Microbiome: Composition, Interaction with the Immune System, Significance for Vaccine Efficacy, and Potential for Disease Therapy. Pathogens 2018; 7:E57. [PMID: 29933546 PMCID: PMC6161280 DOI: 10.3390/pathogens7030057] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 06/11/2018] [Accepted: 06/15/2018] [Indexed: 12/28/2022] Open
Abstract
The mammalian gut is colonized by a large variety of microbes, collectively termed ‘the microbiome’. The gut microbiome undergoes rapid changes during the first few years of life and is highly variable in adulthood depending on various factors. With the gut being the largest organ of immune responses, the composition of the microbiome of the gut has been found to be correlated with qualitative and quantitative differences of mucosal and systemic immune responses. Animal models have been very useful to unravel the relationship between gut microbiome and immune responses and for the understanding of variations of immune responses to vaccination in different childhood populations. However, the molecular mechanisms underlying optimal immune responses to infection or vaccination are not fully understood. The gut virome and gut bacteria can interact, with bacteria facilitating viral infectivity by different mechanisms. Some gut bacteria, which have a beneficial effect on increasing immune responses or by overgrowing intestinal pathogens, are considered to act as probiotics and can be used for therapeutic purposes (as in the case of fecal microbiome transplantation).
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162
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Abstract
Mammalian immune systems evolved within a diverse world dominated by microbes, making interactions between these two life-forms inevitable. Adaptive immunity protects against microbes through antigen-specific responses. In classical studies, these responses were investigated in the context of pathogenicity; however, we now know that they have significant effects on our resident microbes. In turn, microbes employ an arsenal of mechanisms to influence development and specificity of host immunity. Understanding these complex reactions will be necessary to develop microbiota-based strategies to prevent or treat disease. Here we review the literature detailing the cross talk between resident microbes with a focus on the specificity of host responses and the microbial molecules that influence them.
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Affiliation(s)
- Kyla S Ost
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Utah 84211, USA;
| | - June L Round
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Utah 84211, USA;
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163
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Common ground: shared risk factors for type 1 diabetes and celiac disease. Nat Immunol 2018; 19:685-695. [DOI: 10.1038/s41590-018-0130-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 04/27/2018] [Indexed: 02/07/2023]
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164
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Flandroy L, Poutahidis T, Berg G, Clarke G, Dao MC, Decaestecker E, Furman E, Haahtela T, Massart S, Plovier H, Sanz Y, Rook G. The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 627:1018-1038. [PMID: 29426121 DOI: 10.1016/j.scitotenv.2018.01.288] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/28/2018] [Accepted: 01/28/2018] [Indexed: 05/03/2023]
Abstract
Plants, animals and humans, are colonized by microorganisms (microbiota) and transiently exposed to countless others. The microbiota affects the development and function of essentially all organ systems, and contributes to adaptation and evolution, while protecting against pathogenic microorganisms and toxins. Genetics and lifestyle factors, including diet, antibiotics and other drugs, and exposure to the natural environment, affect the composition of the microbiota, which influences host health through modulation of interrelated physiological systems. These include immune system development and regulation, metabolic and endocrine pathways, brain function and epigenetic modification of the genome. Importantly, parental microbiotas have transgenerational impacts on the health of progeny. Humans, animals and plants share similar relationships with microbes. Research paradigms from humans and other mammals, amphibians, insects, planktonic crustaceans and plants demonstrate the influence of environmental microbial ecosystems on the microbiota and health of organisms, and indicate links between environmental and internal microbial diversity and good health. Therefore, overlapping compositions, and interconnected roles of microbes in human, animal and plant health should be considered within the broader context of terrestrial and aquatic microbial ecosystems that are challenged by the human lifestyle and by agricultural and industrial activities. Here, we propose research priorities and organizational, educational and administrative measures that will help to identify safe microbe-associated health-promoting modalities and practices. In the spirit of an expanding version of "One health" that includes environmental health and its relation to human cultures and habits (EcoHealth), we urge that the lifestyle-microbiota-human health nexus be taken into account in societal decision making.
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Affiliation(s)
- Lucette Flandroy
- Federal Public Service Health, Food Chain Safety and Environment, Belgium
| | - Theofilos Poutahidis
- Laboratory of Pathology, Faculty of Health Sciences, School of Veterinary Medicine, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - Gabriele Berg
- Environmental Biotechnology, Graz University of Technology, Petersgasse 12, A-8010 Graz, Austria
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioural Science, APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Maria-Carlota Dao
- ICAN, Institute of Cardiometabolism and Nutrition, Assistance Publique Hôpitaux de Paris, Pitié-Salpêtrière Hospital, Paris, France; INSERM, UMRS U1166 (Eq 6) Nutriomics, Paris 6, France; UPMC, Sorbonne University, Pierre et Marie Curie-Paris 6, France
| | - Ellen Decaestecker
- Aquatic Biology, Department Biology, Science, Engineering & Technology Group, KU Leuven, Campus Kortrijk. E. Sabbelaan 53, B-8500 Kortrijk, Belgium
| | - Eeva Furman
- Finnish Environment Institute (SYKE), Helsinki, Finland
| | - Tari Haahtela
- Skin and Allergy Hospital, Helsinki University Hospital, University of Helsinki, Finland
| | - Sébastien Massart
- Laboratory of Integrated and Urban Phytopathology, TERRA, Gembloux Agro-Bio Tech, University of Liège, Passage des deportes, 2, 5030 Gembloux, Belgium
| | - Hubert Plovier
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Yolanda Sanz
- Microbial Ecology, Nutrition & Health Research Unit, Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Valencia, Spain
| | - Graham Rook
- Centre for Clinical Microbiology, Department of Infection, UCL (University College London), London, UK.
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165
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McGrath CJ, Arndt MB, Walson JL. Biomarkers to Stratify Risk Groups among Children with Malnutrition in Resource-Limited Settings and to Monitor Response to Intervention. Horm Res Paediatr 2018; 88:111-117. [PMID: 28486222 DOI: 10.1159/000471875] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 03/21/2017] [Indexed: 11/19/2022] Open
Abstract
Despite global efforts to reduce childhood undernutrition, current interventions have had little impact on stunting and wasting, and the mechanisms underlying growth faltering are poorly understood. There is a clear need to distinguish populations of children most likely to benefit from any given intervention and to develop tools to monitor response to therapy prior to the development of morbid sequelae. In resource-limited settings, environmental enteric dysfunction (EED) is common among children, contributing to malnutrition and increasing childhood morbidity and mortality risk. In addition to EED, early alterations in the gut microbiota can adversely affect growth through nutrient malabsorption, altered metabolism, gut inflammation, and dysregulation of the growth hormone axis. We examined the evidence linking EED and the gut microbiome to growth faltering and explored novel biomarkers to identify subgroups of children at risk of malnutrition due to underlying pathology. These and other biomarkers could be used to identify specific groups of children at risk of malnutrition and monitor response to targeted interventions.
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Affiliation(s)
- Christine J McGrath
- Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, Texas, USA
| | | | - Judd L Walson
- Department of Global Health, University of Washington, Seattle, Washington, USA.,Department of Pediatrics, University of Washington, Seattle, Washington, USA.,Department of Medicine, University of Washington, Seattle, Washington, USA.,Department of Epidemiology, University of Washington, Seattle, Washington, USA.,The Childhood Acute Illness and Nutrition Network (CHAIN), Nairobi, Kenya
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166
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Rios-Arce ND, Collins FL, Schepper JD, Steury MD, Raehtz S, Mallin H, Schoenherr DT, Parameswaran N, McCabe LR. Epithelial Barrier Function in Gut-Bone Signaling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1033:151-183. [PMID: 29101655 DOI: 10.1007/978-3-319-66653-2_8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The intestinal epithelial barrier plays an essential role in maintaining host homeostasis. The barrier regulates nutrient absorption as well as prevents the invasion of pathogenic bacteria in the host. It is composed of epithelial cells, tight junctions, and a mucus layer. Several factors, such as cytokines, diet, and diseases, can affect this barrier. These factors have been shown to increase intestinal permeability, inflammation, and translocation of pathogenic bacteria. In addition, dysregulation of the epithelial barrier can result in inflammatory diseases such as inflammatory bowel disease. Our lab and others have also shown that barrier disruption can have systemic effects including bone loss. In this chapter, we will discuss the current literature to understand the link between intestinal barrier and bone. We will discuss how inflammation, aging, dysbiosis, and metabolic diseases can affect intestinal barrier-bone link. In addition, we will highlight the current suggested mechanism between intestinal barrier and bone.
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Affiliation(s)
- Naiomy Deliz Rios-Arce
- Comparative Medicine and Integrative Biology Program, East Lansing, MI, USA.,Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Fraser L Collins
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | | | - Michael D Steury
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Sandi Raehtz
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Heather Mallin
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Danny T Schoenherr
- Department of Physiology, Michigan State University, East Lansing, MI, USA
| | - Narayanan Parameswaran
- Comparative Medicine and Integrative Biology Program, East Lansing, MI, USA. .,Department of Physiology, Michigan State University, East Lansing, MI, USA.
| | - Laura R McCabe
- Department of Physiology and Department of Radiology, Biomedical Imaging Research Centre, Michigan State University, East Lansing, MI, USA.
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167
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Sprockett D, Fukami T, Relman DA. Role of priority effects in the early-life assembly of the gut microbiota. Nat Rev Gastroenterol Hepatol 2018; 15:197-205. [PMID: 29362469 PMCID: PMC6813786 DOI: 10.1038/nrgastro.2017.173] [Citation(s) in RCA: 217] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Understanding how microbial communities develop is essential for predicting and directing their future states. Ecological theory suggests that community development is often influenced by priority effects, in which the order and timing of species arrival determine how species affect one another. Priority effects can have long-lasting consequences, particularly if species arrival history varies during the early stage of community development, but their importance to the human gut microbiota and host health remains largely unknown. Here, we explore how priority effects might influence microbial communities in the gastrointestinal tract during early childhood and how the strength of priority effects can be estimated from the composition of the microbial species pool. We also discuss factors that alter microbial transmission, such as delivery mode, diet and parenting behaviours such as breastfeeding, which can influence the likelihood of priority effects. An improved knowledge of priority effects has the potential to inform microorganism-based therapies, such as prebiotics and probiotics, which are aimed at guiding the microbiota towards a healthy state.
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Affiliation(s)
- Daniel Sprockett
- Department of Microbiology and Immunology, Stanford University School ofMedicine, 291 Campus Drive, Stanford, California 94305, USA
| | - Tadashi Fukami
- Department of Biology, Stanford University, 371 Serra Mall, Stanford, California 94305, USA
| | - David A Relman
- Department of Microbiology and Immunology, Stanford University School ofMedicine, 291 Campus Drive, Stanford, California 94305, USA
- Department of Medicine, Stanford University School of Medicine, 291 Campus Drive, Stanford, California 94305, USA
- Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo Alto, California 94304, USA
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168
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John GK, Wang L, Nanavati J, Twose C, Singh R, Mullin G. Dietary Alteration of the Gut Microbiome and Its Impact on Weight and Fat Mass: A Systematic Review and Meta-Analysis. Genes (Basel) 2018; 9:genes9030167. [PMID: 29547587 PMCID: PMC5867888 DOI: 10.3390/genes9030167] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/07/2018] [Accepted: 03/07/2018] [Indexed: 02/07/2023] Open
Abstract
Dietary alteration of the gut microbiome is an important target in the treatment of obesity. Animal and human studies have shown bidirectional weight modulation based on the probiotic formulation used. In this study, we systematically reviewed the literature and performed a meta-analysis to assess the impact of prebiotics, probiotics and synbiotics on body weight, body mass index (BMI) and fat mass in adult human subjects. We searched Medline (PubMed), Embase, the Cochrane Library and the Web of Science to identify 4721 articles, of which 41 were subjected to full-text screening, yielding 21 included studies with 33 study arms. Probiotic use was associated with significant decreases in BMI, weight and fat mass. Studies of subjects consuming prebiotics demonstrated a significant reduction in body weight, whereas synbiotics did not show an effect. Overall, when the utilization of gut microbiome-modulating dietary agents (prebiotic/probiotic/synbiotic) was compared to placebo, there were significant decreases in BMI, weight and fat mass. In summary, dietary agents for the modulation of the gut microbiome are essential tools in the treatment of obesity and can lead to significant decreases in BMI, weight and fat mass. Further studies are needed to identify the ideal dose and duration of supplementation and to assess the durability of this effect.
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Affiliation(s)
| | - Lin Wang
- Johns Hopkins School of Public Health, Baltimore, MD 21205, USA.
| | - Julie Nanavati
- Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Claire Twose
- Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | | | - Gerard Mullin
- Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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169
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Wang X, Zhang L, Wang Y, Liu X, Zhang H, Liu Y, Shen N, Yang J, Gai Z. Gut microbiota dysbiosis is associated with Henoch-Schönlein Purpura in children. Int Immunopharmacol 2018. [PMID: 29525681 DOI: 10.1016/j.intimp.2018.03.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND Alterations in the intestinal microbiota have been associated with the development of allergic diseases, such as asthma and food allergies. However, there is no report detailing the role of microbiota alterations in Henoch-Schönlein Purpura (HSP) development. METHOD A total of 85 children with HSP and 70 healthy children were recruited for this study. Intestinal microbiota composition was analyzed by 16S rRNA gene-based pyrosequencing. Fecal microbial diversity and composition were compared. RESULT We compared the gut microbiota of 155 subjects and found that children with HSP exhibited gut microbial dysbiosis. Lower microbial diversity and richness were found in HSP patients when compared to the control group. Based on an analysis of similarities, the composition of the microbiota in HSP patients was also different from that of the control group (r = 0.306, P = 0.001). The relative abundance of the bacterial genera Dialister (P < 0.0001), Roseburia (P < 0.0001), and Parasutterella (P < 0.0001) was significantly decreased in HSP children, while the relative abundance of Parabacteroides (P < 0.006) and Enterococcus (P < 0.0001) in these children was significantly increased. Based on Spearman correlation analysis, the LOS showed a significant negative (P < 0.05) correlation with the genera Paraprevotella and Roseburia. Meanwhile, IgA levels exhibited a significant negative (P < 0.01) correlation with the genus Bifidobacterium. CONCLUSIONS Our results indicate that HSP is associated with significant compositional and structural changes in the gut microbiota. These results enhance the potential for future microbial-based therapies to improve the clinical outcome of HSP in children.
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Affiliation(s)
- Xingcui Wang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Jinan 250022, China; Department of Nephrology, Qilu Children's Hospital of Shandong University, Jinan 250022, China
| | - Lei Zhang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Jinan 250022, China; Shandong Children's Microbiome Center, Qilu Children's Hospital of Shandong University, Jinan 250022, China; Shandong Human Microbiome Initiative: College of Life Science, Shandong Normal University, Jinan 250200, China
| | - Ying Wang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Jinan 250022, China
| | - Xuemei Liu
- Department of Nephrology, Qilu Children's Hospital of Shandong University, Jinan 250022, China
| | - Hongxia Zhang
- Department of Nephrology, Qilu Children's Hospital of Shandong University, Jinan 250022, China
| | - Yi Liu
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Jinan 250022, China
| | - Nan Shen
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Jinan 250022, China
| | - Junjie Yang
- Shandong Children's Microbiome Center, Qilu Children's Hospital of Shandong University, Jinan 250022, China; Shandong Human Microbiome Initiative: College of Life Science, Shandong Normal University, Jinan 250200, China.
| | - Zhongtao Gai
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Jinan 250022, China; Shandong Children's Microbiome Center, Qilu Children's Hospital of Shandong University, Jinan 250022, China.
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170
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Jahnsen FL, Bækkevold ES, Hov JR, Landsverk OJ. Do Long-Lived Plasma Cells Maintain a Healthy Microbiota in the Gut? Trends Immunol 2018; 39:196-208. [DOI: 10.1016/j.it.2017.10.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/25/2017] [Accepted: 10/25/2017] [Indexed: 02/07/2023]
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171
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Gut Microbial Changes, Interactions, and Their Implications on Human Lifecycle: An Ageing Perspective. BIOMED RESEARCH INTERNATIONAL 2018; 2018:4178607. [PMID: 29682542 PMCID: PMC5846367 DOI: 10.1155/2018/4178607] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 01/23/2018] [Indexed: 02/07/2023]
Abstract
Gut microbiota is established during birth and evolves with age, mostly maintaining the commensal relationship with the host. A growing body of clinical evidence suggests an intricate relationship between the gut microbiota and the immune system. With ageing, the gut microbiota develops significant imbalances in the major phyla such as the anaerobic Firmicutes and Bacteroidetes as well as a diverse range of facultative organisms, resulting in impaired immune responses. Antimicrobial therapy is commonly used for the treatment of infections; however, this may also result in the loss of normal gut flora. Advanced age, antibiotic use, underlying diseases, infections, hormonal differences, circadian rhythm, and malnutrition, either alone or in combination, contribute to the problem. This nonbeneficial gastrointestinal modulation may be reversed by judicious and controlled use of antibiotics and the appropriate use of prebiotics and probiotics. In certain persistent, recurrent settings, the option of faecal microbiota transplantation can be explored. The aim of the current review is to focus on the establishment and alteration of gut microbiota, with ageing. The review also discusses the potential role of gut microbiota in regulating the immune system, together with its function in healthy and diseased state.
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172
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Round JL, Palm NW. Causal effects of the microbiota on immune-mediated diseases. Sci Immunol 2018; 3:3/20/eaao1603. [DOI: 10.1126/sciimmunol.aao1603] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 12/23/2017] [Indexed: 12/24/2022]
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173
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Macpherson AJ, Yilmaz B, Limenitakis JP, Ganal-Vonarburg SC. IgA Function in Relation to the Intestinal Microbiota. Annu Rev Immunol 2018; 36:359-381. [PMID: 29400985 DOI: 10.1146/annurev-immunol-042617-053238] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
IgA is the dominant immunoglobulin isotype produced in mammals, largely secreted across the intestinal mucosal surface. Although induction of IgA has been a hallmark feature of microbiota colonization following colonization in germ-free animals, until recently appreciation of the function of IgA in host-microbial mutualism has depended mainly on indirect evidence of alterations in microbiota composition or penetration of microbes in the absence of somatic mutations in IgA (or compensatory IgM). Highly parallel sequencing techniques that enable high-resolution analysis of either microbial consortia or IgA sequence diversity are now giving us new perspectives on selective targeting of microbial taxa and the trajectory of IgA diversification according to induction mechanisms, between different individuals and over time. The prospects are to link the range of diversified IgA clonotypes to specific antigenic functions in modulating the microbiota composition, position and metabolism to ensure host mutualism.
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Affiliation(s)
- Andrew J Macpherson
- Maurice Müller Laboratories (Department of Biomedical Research), University of Bern, 3008 Bern, Switzerland.,University Clinic of Visceral Surgery and Medicine, Inselspital, 3010 Bern, Switzerland;
| | - Bahtiyar Yilmaz
- Maurice Müller Laboratories (Department of Biomedical Research), University of Bern, 3008 Bern, Switzerland.,University Clinic of Visceral Surgery and Medicine, Inselspital, 3010 Bern, Switzerland;
| | - Julien P Limenitakis
- Maurice Müller Laboratories (Department of Biomedical Research), University of Bern, 3008 Bern, Switzerland.,University Clinic of Visceral Surgery and Medicine, Inselspital, 3010 Bern, Switzerland;
| | - Stephanie C Ganal-Vonarburg
- Maurice Müller Laboratories (Department of Biomedical Research), University of Bern, 3008 Bern, Switzerland.,University Clinic of Visceral Surgery and Medicine, Inselspital, 3010 Bern, Switzerland;
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174
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Carlson AL, Xia K, Azcarate-Peril MA, Goldman BD, Ahn M, Styner MA, Thompson AL, Geng X, Gilmore JH, Knickmeyer RC. Infant Gut Microbiome Associated With Cognitive Development. Biol Psychiatry 2018; 83:148-159. [PMID: 28793975 PMCID: PMC5724966 DOI: 10.1016/j.biopsych.2017.06.021] [Citation(s) in RCA: 304] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 05/31/2017] [Accepted: 06/12/2017] [Indexed: 12/22/2022]
Abstract
BACKGROUND Studies in rodents provide compelling evidence that microorganisms inhabiting the gut influence neurodevelopment. In particular, experimental manipulations that alter intestinal microbiota impact exploratory and communicative behaviors and cognitive performance. In humans, the first years of life are a dynamic time in gut colonization and brain development, but little is known about the relationship between these two processes. METHODS We tested whether microbial composition at 1 year of age is associated with cognitive outcomes using the Mullen Scales of Early Learning and with global and regional brain volumes using structural magnetic resonance imaging at 1 and 2 years of age. Fecal samples were collected from 89 typically developing 1-year-olds. 16S ribosomal RNA amplicon sequencing was used for identification and relative quantification of bacterial taxa. RESULTS Cluster analysis identified 3 groups of infants defined by their bacterial composition. Mullen scores at 2 years of age differed significantly between clusters. In addition, higher alpha diversity was associated with lower scores on the overall composite score, visual reception scale, and expressive language scale at 2 years of age. Exploratory analyses of neuroimaging data suggest the gut microbiome has minimal effects on regional brain volumes at 1 and 2 years of age. CONCLUSIONS This is the first study to demonstrate associations between the gut microbiota and cognition in human infants. As such, it represents an essential first step in translating animal data into the clinic.
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Affiliation(s)
- Alexander L Carlson
- Neuroscience Curriculum, University of North Carolina, Chapel Hill, North Carolina
| | - Kai Xia
- Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina
| | - M Andrea Azcarate-Peril
- Department of Medicine, University of North Carolina, Chapel Hill, North Carolina; Microbiome Core Facility, University of North Carolina, Chapel Hill, North Carolina
| | - Barbara D Goldman
- Department of Psychology and Neuroscience, University of North Carolina, Chapel Hill, North Carolina; Frank Porter Graham Child Development Institute, University of North Carolina, Chapel Hill, North Carolina
| | - Mihye Ahn
- Department of Mathematics and Statistics, University of Nevada, Reno, Nevada
| | - Martin A Styner
- Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina; Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina
| | - Amanda L Thompson
- Department of Anthropology, University of North Carolina, Chapel Hill, North Carolina; Department of Nutrition, University of North Carolina, Chapel Hill, North Carolina
| | - Xiujuan Geng
- Department of Psychology Lab of Neuropsychology and Lab of Social Cognitive Affective Neuroscience, University of Hong Kong, Hong Kong; State Key Lab of Brain and Cognitive Sciences, University of Hong Kong, Hong Kong
| | - John H Gilmore
- Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina
| | - Rebecca C Knickmeyer
- Department of Psychiatry, University of North Carolina, Chapel Hill, North Carolina.
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175
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Ventura M, O'Toole PW, de Vos WM, van Sinderen D. Selected aspects of the human gut microbiota. Cell Mol Life Sci 2018; 75:81-82. [PMID: 28986602 PMCID: PMC11105371 DOI: 10.1007/s00018-017-2669-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 09/29/2017] [Indexed: 02/06/2023]
Abstract
The gut microbiota represents a highly complex assembly of microbes, which interact with each other and with their host. These interactions have various implications in terms of health and disease, and this multi-author review issue will address a number of selected aspects pertaining to gut microbiota research.
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Affiliation(s)
- Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, Microbiome Research Hub, University of Parma, Parma, Italy
| | - Paul W O'Toole
- School of Microbiology, APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, 6708 PB, Wageningen, The Netherlands
- Department of Bacteriology and Immunology, University of Helsinki, 00100, Helsinki, Finland
| | - Douwe van Sinderen
- School of Microbiology, APC Microbiome Institute, University College Cork, Cork, Ireland.
- School of Microbiology, National University of Ireland, Western Road, Cork, Ireland.
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176
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Gálvez EJC, Iljazovic A, Gronow A, Flavell R, Strowig T. Shaping of Intestinal Microbiota in Nlrp6- and Rag2-Deficient Mice Depends on Community Structure. Cell Rep 2017; 21:3914-3926. [PMID: 29281837 DOI: 10.1016/j.celrep.2017.12.027] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 11/14/2017] [Accepted: 12/06/2017] [Indexed: 01/05/2023] Open
Abstract
Contradicting observations have been made regarding the relative contributions of immune sensors to shaping the microbiome, yet the reasons for these discrepancies are not fully understood. Here, we investigated the contribution of environmental factors in shaping the microbiome in mice deficient in adaptive immunity (Rag2-/-) and Nlrp6, an immune sensor proposed to be involved in regulation of microbiota composition. In conventionally housed Nlrp6-/- mice, familial transmission has a significant effect on microbiota composition, complicating the analysis of genotype-dependent effects. Notably, after rederivation into standardized specific pathogen-free (SPF) conditions devoid of pathobionts, microbiota composition was indistinguishable between WT, Rag2-/-, and Nlrp6-/- mice. However, upon reintroduction of a pathobiont-containing community host, genotype-dependent differences reappear, specifically affecting the relative abundance of pathobionts such as Helicobacter spp. Our results show that the impact of Nlrp6 and also of adaptive immunity on microbiota composition depends on community structure and primarily influences pathobionts but not commensals.
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Affiliation(s)
- Eric J C Gálvez
- Research Group Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Aida Iljazovic
- Research Group Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Achim Gronow
- Research Group Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Richard Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Till Strowig
- Research Group Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany.
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177
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Lynch JP, Werder RB, Loh Z, Sikder MAA, Curren B, Zhang V, Rogers MJ, Lane K, Simpson J, Mazzone SB, Spann K, Hayball J, Diener K, Everard ML, Blyth CC, Forstner C, Dennis PG, Murtaza N, Morrison M, Ó Cuív P, Zhang P, Haque A, Hill GR, Sly PD, Upham JW, Phipps S. Plasmacytoid dendritic cells protect from viral bronchiolitis and asthma through semaphorin 4a-mediated T reg expansion. J Exp Med 2017; 215:537-557. [PMID: 29273643 PMCID: PMC5789405 DOI: 10.1084/jem.20170298] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 08/21/2017] [Accepted: 11/27/2017] [Indexed: 12/16/2022] Open
Abstract
Lynch et al. provide evidence of a causal relationship between RSV-bronchiolitis and asthma development and highlight a common but age-related Sema4a-mediated pathway by which pDCs and microbial colonization induce T reg cell expansion to confer protection against severe bronchiolitis and asthma. Respiratory syncytial virus–bronchiolitis is a major independent risk factor for subsequent asthma, but the causal mechanisms remain obscure. We identified that transient plasmacytoid dendritic cell (pDC) depletion during primary Pneumovirus infection alone predisposed to severe bronchiolitis in early life and subsequent asthma in later life after reinfection. pDC depletion ablated interferon production and increased viral load; however, the heightened immunopathology and susceptibility to subsequent asthma stemmed from a failure to expand functional neuropilin-1+ regulatory T (T reg) cells in the absence of pDC-derived semaphorin 4a (Sema4a). In adult mice, pDC depletion predisposed to severe bronchiolitis only after antibiotic treatment. Consistent with a protective role for the microbiome, treatment of pDC-depleted neonates with the microbial-derived metabolite propionate promoted Sema4a-dependent T reg cell expansion, ameliorating both diseases. In children with viral bronchiolitis, nasal propionate levels were decreased and correlated with an IL-6high/IL-10low microenvironment. We highlight a common but age-related Sema4a-mediated pathway by which pDCs and microbial colonization induce T reg cell expansion to protect against severe bronchiolitis and subsequent asthma.
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Affiliation(s)
- Jason P Lynch
- School of Biomedical Sciences, The University of Queensland, St. Lucia, Queensland, Australia.,Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Cambridge, MA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA.,QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Rhiannon B Werder
- School of Biomedical Sciences, The University of Queensland, St. Lucia, Queensland, Australia.,QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Zhixuan Loh
- School of Biomedical Sciences, The University of Queensland, St. Lucia, Queensland, Australia.,The Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Md Al Amin Sikder
- School of Biomedical Sciences, The University of Queensland, St. Lucia, Queensland, Australia.,QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Bodie Curren
- School of Biomedical Sciences, The University of Queensland, St. Lucia, Queensland, Australia.,QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Vivian Zhang
- School of Biomedical Sciences, The University of Queensland, St. Lucia, Queensland, Australia.,QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Matthew J Rogers
- School of Biomedical Sciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Katie Lane
- School of Biomedical Sciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Jennifer Simpson
- School of Biomedical Sciences, The University of Queensland, St. Lucia, Queensland, Australia.,QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Stuart B Mazzone
- School of Biomedical Sciences, The University of Queensland, St. Lucia, Queensland, Australia.,Department of Anatomy and Neuroscience, The University of Melbourne, Melbourne, Victoria, Australia
| | - Kirsten Spann
- School of Biomedical Science, Queensland University of Technology, Brisbane, Queensland, Australia.,Institute of Health and Biomedical Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - John Hayball
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia.,Robinson Research Institute, Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Kerrilyn Diener
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, South Australia, Australia.,Robinson Research Institute, Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Mark L Everard
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia
| | - Christopher C Blyth
- School of Medicine, University of Western Australia, Perth, Western Australia, Australia.,Department of Infectious Diseases, Princess Margaret Hospital for Children, Perth, Western Australia, Australia.,Department of Microbiology, PathWest Laboratory Medicine WA, Princess Margaret Hospital for Children, Perth, Western Australia, Australia.,Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
| | - Christian Forstner
- School of Earth and Environmental Sciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Paul G Dennis
- School of Earth and Environmental Sciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Nida Murtaza
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Mark Morrison
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Páraic Ó Cuív
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Ping Zhang
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Ashraful Haque
- Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia.,QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Geoffrey R Hill
- Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia.,QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Peter D Sly
- Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia.,Child Health Research Centre, The University of Queensland, St. Lucia, Queensland, Australia
| | - John W Upham
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Simon Phipps
- School of Biomedical Sciences, The University of Queensland, St. Lucia, Queensland, Australia .,Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Queensland, Australia.,QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
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178
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de Groot PF, Belzer C, Aydin Ö, Levin E, Levels JH, Aalvink S, Boot F, Holleman F, van Raalte DH, Scheithauer TP, Simsek S, Schaap FG, Olde Damink SWM, Roep BO, Hoekstra JB, de Vos WM, Nieuwdorp M. Distinct fecal and oral microbiota composition in human type 1 diabetes, an observational study. PLoS One 2017; 12:e0188475. [PMID: 29211757 PMCID: PMC5718513 DOI: 10.1371/journal.pone.0188475] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/07/2017] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVE Environmental factors driving the development of type 1 diabetes (T1D) are still largely unknown. Both animal and human studies have shown an association between altered fecal microbiota composition, impaired production of short-chain fatty acids (SCFA) and T1D onset. However, observational evidence on SCFA and fecal and oral microbiota in adults with longstanding T1D vs healthy controls (HC) is lacking. RESEARCH DESIGN AND METHODS We included 53 T1D patients without complications or medication and 50 HC matched for age, sex and BMI. Oral and fecal microbiota, fecal and plasma SCFA levels, markers of intestinal inflammation (fecal IgA and calprotectin) and markers of low-grade systemic inflammation were measured. RESULTS Oral microbiota were markedly different in T1D (eg abundance of Streptococci) compared to HC. Fecal analysis showed decreased butyrate producing species in T1D and less butyryl-CoA transferase genes. Also, plasma levels of acetate and propionate were lower in T1D, with similar fecal SCFA. Finally, fecal strains Christensenella and Subdoligranulum correlated with glycemic control, inflammatory parameters and SCFA. CONCLUSIONS We conclude that T1D patients harbor a different amount of intestinal SCFA (butyrate) producers and different plasma acetate and propionate levels. Future research should disentangle cause and effect and whether supplementation of SCFA-producing bacteria or SCFA alone can have disease-modifying effects in T1D.
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Affiliation(s)
- Pieter F. de Groot
- Department of Internal and Vascular Medicine, Academic Medical Center–University of Amsterdam, Amsterdam, the Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands
| | - Ömrüm Aydin
- Department of Internal and Vascular Medicine, Academic Medical Center–University of Amsterdam, Amsterdam, the Netherlands
| | - Evgeni Levin
- Department of Internal and Vascular Medicine, Academic Medical Center–University of Amsterdam, Amsterdam, the Netherlands
| | - Johannes H. Levels
- Department of Internal and Vascular Medicine, Academic Medical Center–University of Amsterdam, Amsterdam, the Netherlands
| | - Steven Aalvink
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands
| | - Fransje Boot
- Department of Internal and Vascular Medicine, Academic Medical Center–University of Amsterdam, Amsterdam, the Netherlands
| | - Frits Holleman
- Department of Internal and Vascular Medicine, Academic Medical Center–University of Amsterdam, Amsterdam, the Netherlands
| | - Daniël H. van Raalte
- Department of Internal medicine, VU University Medical Center, Amsterdam, The Netherlands
- ICAR, VU University Medical Center, Amsterdam, The Netherlands
| | - Torsten P. Scheithauer
- Department of Internal and Vascular Medicine, Academic Medical Center–University of Amsterdam, Amsterdam, the Netherlands
- Department of Internal medicine, VU University Medical Center, Amsterdam, The Netherlands
- ICAR, VU University Medical Center, Amsterdam, The Netherlands
| | - Suat Simsek
- Department of Internal Medicine, Medisch Centrum Alkmaar, Alkmaar, the Netherlands
| | - Frank G. Schaap
- Department of Surgery, Maastricht University, Maastricht, The Netherlands
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht, the Netherlands
- Department of General, Visceral and Transplantation Surgery, RWTH University Hospital Aachen, Aachen, Germany
| | | | - Bart O. Roep
- Department of Immunohaematology & Blood Transfusion, Leiden University Medical Center, Leiden, the Netherlands
- Beckman Research Institute, DMRI, City of Hope, Duarte, CA, United States of America
| | - Joost B. Hoekstra
- Department of Internal and Vascular Medicine, Academic Medical Center–University of Amsterdam, Amsterdam, the Netherlands
| | - Willem M. de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands
- RPU Immunobiology, University of Helsinki, Helsinki, Finland
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Academic Medical Center–University of Amsterdam, Amsterdam, the Netherlands
- Department of Internal medicine, VU University Medical Center, Amsterdam, The Netherlands
- ICAR, VU University Medical Center, Amsterdam, The Netherlands
- Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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179
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Dietary Therapies in Pediatric Inflammatory Bowel Disease: An Evolving Inflammatory Bowel Disease Paradigm. Gastroenterol Clin North Am 2017; 46:731-744. [PMID: 29173518 DOI: 10.1016/j.gtc.2017.08.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Nutrition has long been recognized as a critical component in the treatment of pediatric inflammatory bowel disease (IBD). Formerly, nutritional interventions have focused on targeting improved weight gain and linear growth, as well as correction of micronutrient deficiencies. Recently, there has been growing interest and study of dietary interventions for induction and maintenance of remission. In addition to exclusive enteral nutrition, successes have been achieved with specific exclusion diets. This article evaluates current literature regarding the role of diet and nutrition in pathogenesis of disease, as well as the role of diet as primary therapy for pediatric IBD.
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180
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Nataro JP, Guerrant RL. Chronic consequences on human health induced by microbial pathogens: Growth faltering among children in developing countries. Vaccine 2017; 35:6807-6812. [DOI: 10.1016/j.vaccine.2017.05.035] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 03/28/2017] [Accepted: 05/10/2017] [Indexed: 02/07/2023]
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181
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Zheng S, Shao S, Qiao Z, Chen X, Piao C, Yu Y, Gao F, Zhang J, Du J. Clinical Parameters and Gut Microbiome Changes Before and After Surgery in Thoracic Aortic Dissection in Patients with Gastrointestinal Complications. Sci Rep 2017; 7:15228. [PMID: 29123168 PMCID: PMC5680333 DOI: 10.1038/s41598-017-15079-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 10/20/2017] [Indexed: 01/07/2023] Open
Abstract
Thoracic aortic dissection (TAAD) is one of the most common types of aortic diseases. Although surgery remains the main method of treatment, the high rate of postoperative gastrointestinal complications significantly influences the effects of surgery and the recovery process. Moreover, the mechanisms underlying this disease remain unclear. To address these problems, we examined changes in the gut microbiota in 40 thoracic aortic dissection patients with abdominal complications after surgery. Levels of white blood cells (WBC), neutrophile granulocytes (NE), alanine aminotransferase (ALT), and aspartate aminotransferase (AST) were higher in all patients after surgery. Levels of inflammatory cytokines, including interleukin (IL)-2, IL-6, IL-8, and IL-10, were also higher after surgery. A metagenome analysis revealed that levels of Oscillibacter, Anaerotruncus, Alistipes, and Clostridium difficile were higher after the operation. The abundance of functional genes, such as the spermidine/putrescine transport system permease protein, the flagellar motor switch protein, and branched-chain amino acid transport system proteins, was also higher post-surgery. These changes likely contribute to diarrhea, bloating, gastrointestinal bleeding, and other abdominal complications after surgery, and our research opens up new treatment possibilities for patients suffering from abdominal complications after surgical treatment.
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Affiliation(s)
- Shuai Zheng
- Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China.,Beijing Collaborative Innovation Centre for Cardiovascular Disorders, Beijing, 100029, China.,The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, 100029, China
| | - Shulin Shao
- Department of Gastroenterology, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
| | - Zhiyu Qiao
- Department of Cardiovascular Surgery, Beijing Aortic Disease Centre, Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing Engineering Research Centre for Vascular Prostheses, Beijing, 100029, China
| | - Xue Chen
- Department of Gastroenterology, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
| | - Chunmei Piao
- Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China.,Beijing Collaborative Innovation Centre for Cardiovascular Disorders, Beijing, 100029, China.,The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, 100029, China
| | - Ying Yu
- Department of Gastroenterology, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
| | - Feng Gao
- Department of Gastroenterology, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China
| | - Jie Zhang
- Department of Gastroenterology, Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China.
| | - Jie Du
- Beijing Anzhen Hospital, Capital Medical University, Beijing, 100029, China. .,Beijing Collaborative Innovation Centre for Cardiovascular Disorders, Beijing, 100029, China. .,The Key Laboratory of Remodeling-Related Cardiovascular Diseases, Ministry of Education, Beijing Institute of Heart Lung and Blood Vessel Diseases, Beijing, 100029, China.
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182
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Ramírez-Pérez O, Cruz-Ramón V, Chinchilla-López P, Méndez-Sánchez N. The Role of the Gut Microbiota in Bile Acid Metabolism. Ann Hepatol 2017; 16 Suppl 1:S21-S26. [PMID: 31196631 DOI: 10.5604/01.3001.0010.5672] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 09/09/2017] [Indexed: 02/04/2023]
Abstract
The gut microbiota has been considered a cornerstone of maintaining the health status of its human host because it not only facilitates harvesting of nutrients and energy from ingested food, but also produces numerous metabolites that can regulate host metabolism. One such class of metabolites, the bile acids, are synthesized from cholesterol in the liver and further metabolized by the gut microbiota into secondary bile acids. These bioconversions modulate the signaling properties of bile acids through the nuclear farnesoid X receptor and the G protein-coupled membrane receptor 5, which regulate diverse metabolic pathways in the host. In addition, bile acids can regulate gut microbial composition both directly and indirectly by activation of innate immune response genes in the small intestine. Therefore, host metabolism can be affected by both microbial modifications of bile acids, which leads to altered signaling via bile acid receptors, and by alterations in the composition of the microbiota. In this review, we mainly describe the interactions between bile acids and intestinal microbiota and their roles in regulating host metabolism, but we also examine the impact of bile acid composition in the gut on the intestinal microbiome and on host physiology.
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Affiliation(s)
| | - Vania Cruz-Ramón
- Liver Research Unit, Medica Sur Clinic & Foundation, Mexico City, Mexico
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183
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Affiliation(s)
- Johnathan R Lex
- a College of Medical and Dental Sciences , University of Birmingham , Birmingham , UK
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184
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Rosen CE, Palm NW. Functional Classification of the Gut Microbiota: The Key to Cracking the Microbiota Composition Code: Functional classifications of the gut microbiota reveal previously hidden contributions of indigenous gut bacteria to human health and disease. Bioessays 2017; 39. [PMID: 28976007 DOI: 10.1002/bies.201700032] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 09/03/2017] [Indexed: 12/21/2022]
Abstract
The last decade has seen an explosion of research on the gut microbiota-the trillions of microorganisms that colonize the human gut. It is now clear that interindividual diversity in microbiota composition plays an important role in determining susceptibility to a wide variety of diseases. However, identifying the precise changes in microbiota composition that play causal roles has remained a largely unrealized goal. Here, we propose that functional classifications of microbes based on their interactions with and effects on the host-particularly the host immune system-will illuminate the role of the microbiota in shaping human physiology. We outline the benefits of "functional" classification compared to phylogenetic classifications, and review current efforts at functional classification of the microbiota. Finally, we outline a theoretical framework for classifying host-microbiota interactions. Future advances enabling broader functional classifications of the microbiota promise to revolutionize our understanding of the role of gut microbes in health and disease.
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Affiliation(s)
- Connor E Rosen
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Noah W Palm
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
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185
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Bunker JJ, Erickson SA, Flynn TM, Henry C, Koval JC, Meisel M, Jabri B, Antonopoulos DA, Wilson PC, Bendelac A. Natural polyreactive IgA antibodies coat the intestinal microbiota. Science 2017; 358:science.aan6619. [PMID: 28971969 DOI: 10.1126/science.aan6619] [Citation(s) in RCA: 303] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/19/2017] [Indexed: 12/11/2022]
Abstract
Large quantities of immunoglobulin A (IgA) are constitutively secreted by intestinal plasma cells to coat and contain the commensal microbiota, yet the specificity of these antibodies remains elusive. Here we profiled the reactivities of single murine IgA plasma cells by cloning and characterizing large numbers of monoclonal antibodies. IgAs were not specific to individual bacterial taxa but rather polyreactive, with broad reactivity to a diverse, but defined, subset of microbiota. These antibodies arose at low frequencies among naïve B cells and were selected into the IgA repertoire upon recirculation in Peyer's patches. This selection process occurred independent of microbiota or dietary antigens. Furthermore, although some IgAs acquired somatic mutations, these did not substantially influence their reactivity. These findings reveal an endogenous mechanism driving homeostatic production of polyreactive IgAs with innate specificity to microbiota.
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Affiliation(s)
- Jeffrey J Bunker
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA.,Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Steven A Erickson
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA.,Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Theodore M Flynn
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Carole Henry
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA.,Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Jason C Koval
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Marlies Meisel
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA.,Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Bana Jabri
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA.,Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Dionysios A Antonopoulos
- Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.,Department of Medicine, University of Chicago, Chicago, IL 60637, USA.,Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Patrick C Wilson
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA.,Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Albert Bendelac
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA. .,Department of Pathology, University of Chicago, Chicago, IL 60637, USA
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186
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Anderson G, Vaillancourt C, Maes M, Reiter RJ. Breastfeeding and the gut-brain axis: is there a role for melatonin? Biomol Concepts 2017; 8:185-195. [DOI: 10.1515/bmc-2017-0009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/05/2017] [Indexed: 12/12/2022] Open
Abstract
AbstractThe benefits of breastfeeding over formula feed are widely appreciated. However, for many mothers breastfeeding is not possible, highlighting the need for a significant improvement in the contents of formula feed. In this article, the overlooked role of melatonin and the melatonergic pathways in breast milk and in the regulation of wider breast milk components are reviewed. There is a growing appreciation that the benefits of breastfeeding are mediated by its effects in the infant gut, with consequences for the development of the gut-brain axis and the immune system. The melatonergic pathways are intimately associated with highly researched processes in the gut, gut microbiome and gut-brain axis. As the melatonergic pathways are dependent on the levels of serotonin availability as a necessary precursor, decreased melatonin is linked to depression and depression-associated disorders. The association of breastfeeding and the gut-brain axis with a host of medical conditions may be mediated by their regulation of processes that modulate depression susceptibility. The biological underpinnings of depression include increased levels of pro-inflammatory cytokines, oxidative stress, kynurenine pathway activity and dysregulation of the hypothalamic-pituitary adrenal axis, all of which can decrease melatonergic pathway activity. The inclusion of the melatonergic pathways in the biological interactions of breast milk and gut development has significant theoretical and treatment implications, as well as being important to the prevention of a host of infant-, child- and adult-onset medical conditions.
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Affiliation(s)
- George Anderson
- CRC Scotland & London, Eccleston Square, London SWIV 1PG, UK
| | - Cathy Vaillancourt
- INRS-Armand-Frappier Institute and Center for Interdisciplinary Research on Well-Being, Health, Society and Environment (CINBIOSE), Laval, QC, Canada
| | - Michael Maes
- Deakin University, Department of Psychiatry, Geelong, Australia
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187
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Abstract
In a recent issue of Nature, Gordon and colleagues show that, during the first 2 years life, the assembly of the gut microbiota follows predictable architectural patterns that correlate with the development of commensal-specific immunoglobulin A responses.
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188
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Sugahara H, Okai S, Odamaki T, Wong CB, Kato K, Mitsuyama E, Xiao JZ, Shinkura R. Decreased Taxon-Specific IgA Response in Relation to the Changes of Gut Microbiota Composition in the Elderly. Front Microbiol 2017; 8:1757. [PMID: 28955323 PMCID: PMC5601059 DOI: 10.3389/fmicb.2017.01757] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/29/2017] [Indexed: 12/25/2022] Open
Abstract
Gut microbiota is known to change with aging; however, the underlying mechanisms have not been well elucidated. Immunoglobulin A (IgA) is the dominant class of antibody secreted by the intestinal mucosa, and are thought to play a key role in the regulation of the gut microbiota. T cells regulate the magnitude and nature of microbiota-specific IgA responses. However, it is also known that T cells become senescent in elderly people. Therefore, we speculated that the age-related changes of IgA response against the gut microbiota might be one of the mechanisms causing the age-associated changes of gut microbiota composition. To prove our hypothesis, fecal samples from 40 healthy subjects (adult group: n = 20, an average of 35 years old; elderly group: n = 20, an average of 76 years old) were collected, and the gut microbiota composition and the response of IgA to gut microbiota were investigated. The relative abundance of Bifidobacteriaceae was significantly lower, whereas those of Clostridiaceae, Clostridiales;f__ and Enterobacteriaceae were significantly higher in the elderly group than in the adult group. There was no significant difference in the fecal IgA concentration between the adult and elderly groups. However, the taxon-specific IgA response to some bacterial taxa was different between the adult and elderly groups. To evaluate inter-group differences in the taxon-specific IgA response to each bacterial taxon, the IgA-indices were calculated, and the IgA-indices of Clostridiaceae and Enterobacteriaceae were found to be significantly lower in the elderly group than the adult group. In addition, Clostridiales;f__ and Enterobacteriaceae were significantly enriched in the IgA+ fraction in the adult group but not in the elderly group, whereas Clostridiaceae was significantly enriched in the IgA- fraction in the elderly group but not in the adult group. Some species assigned to Clostridiaceae or Enterobacteriaceae are known to be pathogenic bacteria. Our results suggest the possible contribution of decreased IgA response in the increased abundance of bacterial taxa with potential pathogenicity in the intestinal environment of the elderly. Our findings contribute to the understanding of the regulatory factor for the changes in the gut microbiota composition with aging.
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Affiliation(s)
- Hirosuke Sugahara
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd.Zama, Japan
| | - Shinsaku Okai
- Applied Immunology, Graduate School of Biological Science, Nara Institute of Science and TechnologyIkoma, Japan
| | - Toshitaka Odamaki
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd.Zama, Japan
| | - Chyn B Wong
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd.Zama, Japan
| | - Kumiko Kato
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd.Zama, Japan
| | - Eri Mitsuyama
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd.Zama, Japan
| | - Jin-Zhong Xiao
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd.Zama, Japan
| | - Reiko Shinkura
- Applied Immunology, Graduate School of Biological Science, Nara Institute of Science and TechnologyIkoma, Japan
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189
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Regulation of inflammation by microbiota interactions with the host. Nat Immunol 2017; 18:851-860. [PMID: 28722709 DOI: 10.1038/ni.3780] [Citation(s) in RCA: 422] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 05/30/2017] [Indexed: 12/13/2022]
Abstract
The study of the intestinal microbiota has begun to shift from cataloging individual members of the commensal community to understanding their contributions to the physiology of the host organism in health and disease. Here, we review the effects of the microbiome on innate and adaptive immunological players from epithelial cells and antigen-presenting cells to innate lymphoid cells and regulatory T cells. We discuss recent studies that have identified diverse microbiota-derived bioactive molecules and their effects on inflammation within the intestine and distally at sites as anatomically remote as the brain. Finally, we highlight new insights into how the microbiome influences the host response to infection, vaccination and cancer, as well as susceptibility to autoimmune and neurodegenerative disorders.
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190
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Whelan FJ, Surette MG. A comprehensive evaluation of the sl1p pipeline for 16S rRNA gene sequencing analysis. MICROBIOME 2017; 5:100. [PMID: 28807046 PMCID: PMC5557527 DOI: 10.1186/s40168-017-0314-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/21/2017] [Indexed: 05/11/2023]
Abstract
BACKGROUND Advances in next-generation sequencing technologies have allowed for detailed, molecular-based studies of microbial communities such as the human gut, soil, and ocean waters. Sequencing of the 16S rRNA gene, specific to prokaryotes, using universal PCR primers has become a common approach to studying the composition of these microbiota. However, the bioinformatic processing of the resulting millions of DNA sequences can be challenging, and a standardized protocol would aid in reproducible analyses. METHODS The short-read library 16S rRNA gene sequencing pipeline (sl1p, pronounced "slip") was designed with the purpose of mitigating this lack of reproducibility by combining pre-existing tools into a computational pipeline. This pipeline automates the processing of raw 16S rRNA gene sequencing data to create human-readable tables, graphs, and figures to make the collected data more readily accessible. RESULTS Data generated from mock communities were compared using eight OTU clustering algorithms, two taxon assignment approaches, and three 16S rRNA gene reference databases. While all of these algorithms and options are available to sl1p users, through testing with human-associated mock communities, AbundantOTU+, the RDP Classifier, and the Greengenes 2011 reference database were chosen as sl1p's defaults based on their ability to best represent the known input communities. CONCLUSIONS sl1p promotes reproducible research by providing a comprehensive log file, and reduces the computational knowledge needed by the user to process next-generation sequencing data. sl1p is freely available at https://bitbucket.org/fwhelan/sl1p .
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Affiliation(s)
- Fiona J. Whelan
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St. W, Hamilton, Canada
| | - Michael G. Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main St. W, Hamilton, Canada
- Department of Medicine, McMaster University, 1280 Main St. W, Hamilton, Canada
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191
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Magri G, Comerma L, Pybus M, Sintes J, Lligé D, Segura-Garzón D, Bascones S, Yeste A, Grasset EK, Gutzeit C, Uzzan M, Ramanujam M, van Zelm MC, Albero-González R, Vazquez I, Iglesias M, Serrano S, Márquez L, Mercade E, Mehandru S, Cerutti A. Human Secretory IgM Emerges from Plasma Cells Clonally Related to Gut Memory B Cells and Targets Highly Diverse Commensals. Immunity 2017; 47:118-134.e8. [PMID: 28709802 PMCID: PMC5519504 DOI: 10.1016/j.immuni.2017.06.013] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 04/07/2017] [Accepted: 06/16/2017] [Indexed: 12/16/2022]
Abstract
Secretory immunoglobulin A (SIgA) enhances host-microbiota symbiosis, whereas SIgM remains poorly understood. We found that gut IgM+ plasma cells (PCs) were more abundant in humans than mice and clonally related to a large repertoire of memory IgM+ B cells disseminated throughout the intestine but rare in systemic lymphoid organs. In addition to sharing a gut-specific gene signature with memory IgA+ B cells, memory IgM+ B cells were related to some IgA+ clonotypes and switched to IgA in response to T cell-independent or T cell-dependent signals. These signals induced abundant IgM which, together with SIgM from clonally affiliated PCs, recognized mucus-embedded commensals. Bacteria recognized by human SIgM were dually coated by SIgA and showed increased richness and diversity compared to IgA-only-coated or uncoated bacteria. Thus, SIgM may emerge from pre-existing memory rather than newly activated naive IgM+ B cells and could help SIgA to anchor highly diverse commensal communities to mucus. IgM+ PCs generating SIgM are relatively abundant in human but not mouse gut IgM+ PCs clonally relate to a large gut repertoire of memory IgM+ B cells Gut memory IgM+ B cells express a tissue-specific signature and can switch to IgA Human but not mouse SIgM binds a highly diverse microbiota dually coated by SIgA
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Affiliation(s)
- Giuliana Magri
- Program for Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona 08003, Spain.
| | - Laura Comerma
- Program for Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona 08003, Spain
| | - Marc Pybus
- Program for Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona 08003, Spain
| | - Jordi Sintes
- Program for Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona 08003, Spain
| | - David Lligé
- Program for Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona 08003, Spain
| | - Daniel Segura-Garzón
- Program for Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona 08003, Spain
| | - Sabrina Bascones
- Program for Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona 08003, Spain
| | - Ada Yeste
- Program for Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona 08003, Spain
| | - Emilie K Grasset
- Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm 171 76, Sweden
| | - Cindy Gutzeit
- Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mathieu Uzzan
- Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Meera Ramanujam
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT 06877, USA
| | - Menno C van Zelm
- Department of Immunology and Pathology, Monash University and Alfred Hospital, Melbourne, VIC 3004, Australia
| | | | - Ivonne Vazquez
- Pathology Department, Hospital del Mar, Barcelona 08003, Spain
| | - Mar Iglesias
- Pathology Department, Hospital del Mar, Barcelona 08003, Spain; Universitat Autònoma de Barcelona, Barcelona 08003, Spain
| | - Sergi Serrano
- Pathology Department, Hospital del Mar, Barcelona 08003, Spain; Universitat Autònoma de Barcelona, Barcelona 08003, Spain
| | - Lucía Márquez
- Department of Gastroenterology, Hospital del Mar, Barcelona 08003, Spain
| | - Elena Mercade
- Department of Biology, Health and Environment, University of Barcelona, Barcelona 08028, Spain
| | - Saurabh Mehandru
- Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrea Cerutti
- Program for Inflammatory and Cardiovascular Disorders, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona 08003, Spain; Department of Medicine, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Catalan Institute for Research and Advanced Studies (ICREA), Barcelona 08003, Spain.
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192
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El Kafsi H, Gorochov G, Larsen M. [Not Available]. Biol Aujourdhui 2017; 211:39-49. [PMID: 28682226 DOI: 10.1051/jbio/2017010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Indexed: 06/07/2023]
Abstract
Genetic evolution of multicellular organisms occurred as a response to environmental challenges, in particular competition for nutrients, climatic change, physical and chemical stressors and pathogens. However organism fitness depends on both the efficiency of its defences and its capacities for benefiting from its symbiotic organisms. Indeed microbes not only engender pathogenies, but enable efficient uptake of host non-self biodegradable nutriments. Furthermore, microbes play an important role in the development of host immunity. We shall review here the associations between some specific genes of the host, microbiota and the immune system. Recent genome-wide association studies disclose that symbiosis between host and microbiota results from a stringent genetic co-evolution. On the other hand, a microbe subset isolated from murine and human microbiotes has been identified on the basis of its interaction with both the host genetics and immunity. Remarkably, microbes which have two such connections are taxonomically related. The best performing bacterial genuses in these two perspectives are Bifidobacterium, Lactobacillus and Akkermansia. We conclude that future therapies targeting microbiota within the framework of chronic inflammatory diseases must consider together host immune and genetic characters associated with microbiota homeostasis.
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Affiliation(s)
- Hela El Kafsi
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris UMRS1135), Sorbonne Universités, UPMC Univ Paris 06, INSERM, Paris, France
| | - Guy Gorochov
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris UMRS1135), Sorbonne Universités, UPMC Univ Paris 06, INSERM, Paris, France - Département d'Immunologie, AP-HP, Groupement Hospitalier Pitié - Salpêtrière, Paris, France
| | - Martin Larsen
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris UMRS1135), Sorbonne Universités, UPMC Univ Paris 06, INSERM, Paris, France - Département d'Immunologie, AP-HP, Groupement Hospitalier Pitié - Salpêtrière, Paris, France
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193
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Lane ER, Zisman TL, Suskind DL. The microbiota in inflammatory bowel disease: current and therapeutic insights. J Inflamm Res 2017; 10:63-73. [PMID: 28652796 PMCID: PMC5473501 DOI: 10.2147/jir.s116088] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel disease is a heterogeneous group of chronic disorders that result from the interaction of the intestinal immune system with the gut microbiome. Until recently, most investigative efforts and therapeutic breakthroughs were centered on understanding and manipulating the altered mucosal immune response that characterizes these diseases. However, more recent studies have highlighted the important role of environmental factors, and in particular the microbiota, in disease onset and disease exacerbation. Advances in genomic sequencing technology and bioinformatics have facilitated an explosion of investigative inquiries into the composition and function of the intestinal microbiome in health and disease and have advanced our understanding of the interplay between the gut microbiota and the host immune system. The gut microbiome is dynamic and changes with age and in response to diet, antibiotics and other environmental factors, and these alterations in the microbiome contribute to disease onset and exacerbation. Strategies to manipulate the microbiome through diet, probiotics, antibiotics or fecal microbiota transplantation may potentially be used therapeutically to influence modulate disease activity. This review will characterize the factors involved in the development of the intestinal microbiome and will describe the typical alterations in the microbiota that are characteristic of inflammatory bowel disease. Additionally, this manuscript will summarize the early but promising literature on the role of the gut microbiota in the pathogenesis of inflammatory bowel disease with implications for utilizing this data for diagnostic or therapeutic application in the clinical management of patients with these diseases.
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Affiliation(s)
- Erin R Lane
- Division of Gastroenterology and Hepatology, Seattle Children's Hospital
| | - Timothy L Zisman
- Division of Gastroenterology, University of Washington, Seattle, WA, USA
| | - David L Suskind
- Division of Gastroenterology and Hepatology, Seattle Children's Hospital
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194
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Young VB. Old and new models for studying host-microbe interactions in health and disease: C. difficile as an example. Am J Physiol Gastrointest Liver Physiol 2017; 312:G623-G627. [PMID: 28360030 DOI: 10.1152/ajpgi.00341.2016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 01/31/2023]
Abstract
There has been an explosion of interest in studying the indigenous microbiota, which plays an important role in human health and disease. Traditionally, the study of microbes in relationship to human health involved consideration of individual microbial species that caused classical infectious diseases. With the interest in the human microbiome, an appreciation of the influence that complex communities of microbes can have on their environment has developed. When considering either individual pathogenic microbes or a symbiotic microbial community, researchers have employed a variety of model systems with which they can study the host-microbe interaction. With the use of studies of infections with the toxin-producing bacterium Clostridium difficile as a model for both a pathogen and beneficial bacterial communities as an example, this review will summarize and compare various model systems that can be used to gain insight into the host-microbe interaction.
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Affiliation(s)
- Vincent B Young
- Department of Internal Medicine/Infectious Diseases Division, Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
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195
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Hibberd MC, Wu M, Rodionov DA, Li X, Cheng J, Griffin NW, Barratt MJ, Giannone RJ, Hettich RL, Osterman AL, Gordon JI. The effects of micronutrient deficiencies on bacterial species from the human gut microbiota. Sci Transl Med 2017; 9:eaal4069. [PMID: 28515336 PMCID: PMC5524138 DOI: 10.1126/scitranslmed.aal4069] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/14/2017] [Indexed: 12/13/2022]
Abstract
Vitamin and mineral (micronutrient) deficiencies afflict 2 billion people. Although the impact of these imbalances on host biology has been studied extensively, much less is known about their effects on the gut microbiota of developing or adult humans. Therefore, we established a community of cultured, sequenced human gut-derived bacterial species in gnotobiotic mice and fed the animals a defined micronutrient-sufficient diet, followed by a derivative diet devoid of vitamin A, folate, iron, or zinc, followed by return to the sufficient diet. Acute vitamin A deficiency had the largest effect on bacterial community structure and metatranscriptome, with Bacteroides vulgatus, a prominent responder, increasing its abundance in the absence of vitamin A. Applying retinol selection to a library of 30,300 B. vulgatus transposon mutants revealed that disruption of acrR abrogated retinol sensitivity. Genetic complementation studies, microbial RNA sequencing, and transcription factor-binding assays disclosed that AcrR is a repressor of an adjacent AcrAB-TolC efflux system. Retinol efflux measurements in wild-type and acrR-mutant strains plus treatment with a pharmacologic inhibitor of the efflux system revealed that AcrAB-TolC is a determinant of retinol and bile acid sensitivity in B. vulgatus Acute vitamin A deficiency was associated with altered bile acid metabolism in vivo, raising the possibility that retinol, bile acid metabolites, and AcrAB-TolC interact to influence the fitness of B. vulgatus and perhaps other microbiota members. This type of preclinical model can help to develop mechanistic insights about the effects of, and more effective treatment strategies for micronutrient deficiencies.
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Affiliation(s)
- Matthew C Hibberd
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Meng Wu
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dmitry A Rodionov
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127994, Russia
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Xiaoqing Li
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jiye Cheng
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicholas W Griffin
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael J Barratt
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Richard J Giannone
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Andrei L Osterman
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO 63110, USA
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196
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Lynch JP, Sikder MAA, Curren BF, Werder RB, Simpson J, Cuív PÓ, Dennis PG, Everard ML, Phipps S. The Influence of the Microbiome on Early-Life Severe Viral Lower Respiratory Infections and Asthma-Food for Thought? Front Immunol 2017; 8:156. [PMID: 28261214 PMCID: PMC5311067 DOI: 10.3389/fimmu.2017.00156] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 01/30/2017] [Indexed: 12/24/2022] Open
Abstract
Severe viral lower respiratory infections are a major cause of infant morbidity. In developing countries, respiratory syncytial virus (RSV)-bronchiolitis induces significant mortality, whereas in developed nations the disease represents a major risk factor for subsequent asthma. Susceptibility to severe RSV-bronchiolitis is governed by gene-environmental interactions that affect the host response to RSV infection. Emerging evidence suggests that the excessive inflammatory response and ensuing immunopathology, typically as a consequence of insufficient immunoregulation, leads to long-term changes in immune cells and structural cells that render the host susceptible to subsequent environmental incursions. Thus, the initial host response to RSV may represent a tipping point in the balance between long-term respiratory health or chronic disease (e.g., asthma). The composition and diversity of the microbiota, which in humans stabilizes in the first year of life, critically affects the development and function of the immune system. Hence, perturbations to the maternal and/or infant microbiota are likely to have a profound impact on the host response to RSV and susceptibility to childhood asthma. Here, we review recent insights describing the effects of the microbiota on immune system homeostasis and respiratory disease and discuss the environmental factors that promote microbial dysbiosis in infancy. Ultimately, this knowledge will be harnessed for the prevention and treatment of severe viral bronchiolitis as a strategy to prevent the onset and development of asthma.
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Affiliation(s)
- Jason P. Lynch
- Laboratory of Respiratory Mucosal Immunity, School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Md. Al Amin Sikder
- Laboratory of Respiratory Mucosal Immunity, School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Bodie F. Curren
- Laboratory of Respiratory Mucosal Immunity, School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Rhiannon B. Werder
- Laboratory of Respiratory Mucosal Immunity, School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Jennifer Simpson
- Laboratory of Respiratory Mucosal Immunity, School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Páraic Ó Cuív
- Translational Research Institute, The University of Queensland Diamantina Institute, The University of Queensland, St. Lucia, QLD, Australia
| | - Paul G. Dennis
- The School of Agriculture and Food Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Mark L. Everard
- School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia
| | - Simon Phipps
- Laboratory of Respiratory Mucosal Immunity, School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, QLD, Australia
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197
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Lewis JD, Abreu MT. Diet as a Trigger or Therapy for Inflammatory Bowel Diseases. Gastroenterology 2017; 152:398-414.e6. [PMID: 27793606 DOI: 10.1053/j.gastro.2016.10.019] [Citation(s) in RCA: 229] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/15/2016] [Accepted: 10/19/2016] [Indexed: 02/07/2023]
Abstract
The most common question asked by patients with inflammatory bowel disease (IBD) is, "Doctor, what should I eat?" Findings from epidemiology studies have indicated that diets high in animal fat and low in fruits and vegetables are the most common pattern associated with an increased risk of IBD. Low levels of vitamin D also appear to be a risk factor for IBD. In murine models, diets high in fat, especially saturated animal fats, also increase inflammation, whereas supplementation with omega 3 long-chain fatty acids protect against intestinal inflammation. Unfortunately, omega 3 supplements have not been shown to decrease the risk of relapse in patients with Crohn's disease. Dietary intervention studies have shown that enteral therapy, with defined formula diets, helps children with Crohn's disease and reduces inflammation and dysbiosis. Although fiber supplements have not been shown definitively to benefit patients with IBD, soluble fiber is the best way to generate short-chain fatty acids such as butyrate, which has anti-inflammatory effects. Addition of vitamin D and curcumin has been shown to increase the efficacy of IBD therapy. There is compelling evidence from animal models that emulsifiers in processed foods increase risk for IBD. We discuss current knowledge about popular diets, including the specific carbohydrate diet and diet low in fermentable oligo-, di-, and monosaccharides and polyols. We present findings from clinical and basic science studies to help gastroenterologists navigate diet as it relates to the management of IBD.
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Affiliation(s)
- James D Lewis
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| | - Maria T Abreu
- Crohn's and Colitis Center, Department of Medicine, Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida.
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198
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Sartor RB, Wu GD. Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches. Gastroenterology 2017; 152:327-339.e4. [PMID: 27769810 PMCID: PMC5511756 DOI: 10.1053/j.gastro.2016.10.012] [Citation(s) in RCA: 535] [Impact Index Per Article: 76.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 02/08/2023]
Abstract
Intestinal microbiota are involved in the pathogenesis of Crohn's disease, ulcerative colitis, and pouchitis. We review the mechanisms by which these gut bacteria, fungi, and viruses mediate mucosal homeostasis via their composite genes (metagenome) and metabolic products (metabolome). We explain how alterations to their profiles and functions under conditions of dysbiosis contribute to inflammation and effector immune responses that mediate inflammatory bowel diseases (IBD) in humans and enterocolitis in mice. It could be possible to engineer the intestinal environment by modifying the microbiota community structure or function to treat patients with IBD-either with individual agents, via dietary management, or as adjuncts to immunosuppressive drugs. We summarize the latest information on therapeutic use of fecal microbial transplantation and propose improved strategies to selectively normalize the dysbiotic microbiome in personalized approaches to treatment.
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Affiliation(s)
- R Balfour Sartor
- Departments of Medicine, Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.
| | - Gary D Wu
- Division of Gastroenterology, Perelman School of Medicine, the University of Pennsylvania, Philadelphia, Pennsylvania.
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199
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200
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An expanding stage for commensal microbes in host immune regulation. Cell Mol Immunol 2017; 14:339-348. [PMID: 28065939 DOI: 10.1038/cmi.2016.64] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/12/2016] [Accepted: 10/12/2016] [Indexed: 02/07/2023] Open
Abstract
Gastrointestinal commensal microbiota is a concentrated mix of microbial life forms, including bacteria, fungi, archaea and viruses. These life forms are targets of host antimicrobial defense in order to establish a homeostatic symbiosis inside the host. However, they are also instrumental in shaping the functions of our immune system via a diverse set of communication mechanisms. In the gut, T helper 17, regulatory T and B cells are continuously tuned by specific microbial strains and metabolic processes. These cells in return help to establish a mutually beneficial exchange with the gut microbial contents. Imbalances in this symbiosis lead to dysregulations in the host's ability to control infections and the development of autoimmune diseases. In addition, the commensal microbiota has a significant and obligatory role in shaping both gut intrinsic and distal lymphoid organs, casting a large impact on the overall immune landscape in the host. This review discusses the major components of the microbial community in the gut and how its members collectively and individually exert regulatory roles in the host immune system and lymphoid structure development, as well as the functions of several major immune cell types.
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