151
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Huang Z, Pan Z, Yang R, Bi Y, Xiong X. The canine gastrointestinal microbiota: early studies and research frontiers. Gut Microbes 2020; 11:635-654. [PMID: 31992112 PMCID: PMC7524387 DOI: 10.1080/19490976.2019.1704142] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The canine gut microbiota is a complex microbial population that is potentially related to metabolism, immunologic activity and gastrointestinal (GI) diseases. Early studies revealed that the canine gut microbiota was dynamic, and bacterial populations in the adjacent gut segments were similar, with anaerobes predominating. Metagenomics analysis revealed that nutrient contents in the diet modulated bacterial populations and metabolites in the canine gut. Further research revealed significant correlations between dietary factors and canine gut core microbiomes. Canine GI diseases are closely correlated with gut microbiota dysbiosis and metabolic disorders. Probiotic-related therapies can effectively treat canine GI diseases. Recent studies have revealed that the canine gut microbiota is similar to the human gut microbiota, and dietary factors affect both. Studying canine intestinal microorganisms enables clarifying changes in the canine intestinal bacteria under different conditions, simulating human diseases in dog models, and conducting in-depth studies of the interactions between intestinal bacteria and disease.
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Affiliation(s)
- Zongyu Huang
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zhiyuan Pan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yujing Bi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China,CONTACT Yujing Bi State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiaohui Xiong
- College of Food Science and Light Industry, Nanjing Tech University, Nanjing, China,Xiaohui Xiong Nanjing Tech University, Nanjing, China
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152
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Piggott DA, Tuddenham S. The gut microbiome and frailty. Transl Res 2020; 221:23-43. [PMID: 32360945 PMCID: PMC8487348 DOI: 10.1016/j.trsl.2020.03.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 12/12/2022]
Abstract
The human microbiome is constituted by an extensive network of organisms that lie at the host/environment interface and transduce signals that play vital roles in human health and disease across the lifespan. Frailty is a critical aging-related syndrome marked by diminished physiological reserve and heightened vulnerability to stress, predictive of major adverse clinical outcomes including death. While recent studies suggest the microbiome may impact key pathways critical to frailty pathophysiology, direct evaluation of the microbiome-frailty relationship remains limited. In this article, we review the complex interplay of biological, behavioral, and environmental factors that may influence shifts in gut microbiome composition and function in aging populations and the putative implications of such shifts for progression to frailty. We discuss HIV infection as a key prototype for elucidating the complex pathways via which the microbiome may precipitate frailty. Finally, we review considerations for future research efforts.
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Affiliation(s)
- Damani A Piggott
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Epidemiology, Johns Hopkins University School of Public Health, Baltimore, Maryland.
| | - Susan Tuddenham
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
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153
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The microbiome in inflammatory bowel diseases: from pathogenesis to therapy. Protein Cell 2020; 12:331-345. [PMID: 32601832 PMCID: PMC8106558 DOI: 10.1007/s13238-020-00745-3] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/30/2020] [Indexed: 02/08/2023] Open
Abstract
Inflammatory bowel disease (IBD) has become a global disease with accelerating incidence worldwide in the 21st century while its accurate etiology remains unclear. In the past decade, gut microbiota dysbiosis has consistently been associated with IBD. Although many IBD-associated dysbiosis have not been proven to be a cause or an effect of IBD, it is often hypothesized that at least some of alteration in microbiome is protective or causative. In this article, we selectively reviewed the hypothesis supported by both association studies in human and pathogenesis studies in biological models. Specifically, we reviewed the potential protective bacterial pathways and species against IBD, as well as the potential causative bacterial pathways and species of IBD. We also reviewed the potential roles of some members of mycobiome and virome in IBD. Lastly, we covered the current status of therapeutic approaches targeting microbiome, which is a promising strategy to alleviate and cure this inflammatory disease.
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154
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Wang L, Ai C, Wen C, Qin Y, Liu Z, Wang L, Gong Y, Su C, Wang Z, Song S. Fucoidan isolated from Ascophyllum nodosum alleviates gut microbiota dysbiosis and colonic inflammation in antibiotic-treated mice. Food Funct 2020; 11:5595-5606. [PMID: 32525182 DOI: 10.1039/d0fo00668h] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Antibiotic treatment, as an important therapeutic intervention, can cause damage to the host microbiome and the intestinal mucosal barrier. In order to find a way to alleviate the side effects of antibiotics, the present study investigated the effects of fucoidan (ANP) isolated from Ascophyllum nodosum on gut microbiota dysbiosis and colonic inflammation induced by ciprofloxacin-metronidazole (CiMe) in C57BL/6J mice. Our results showed that dietary ANP prevented colon shortening, alleviated the colonic tissue damages, and partially reversed the alteration of gut microbiota by increasing the abundance of potentially beneficial bacteria, e.g., Ruminococcaceae_UCG_014 and Akkermansia and decreasing the abundance of harmful bacteria, e.g., Proteus and Enterococcus. ANP also suppressed the overproduction of TNF-α, IL-1β, and IL-6 and promoted the expression of IL-10. In addition, ANP reversed the decreased production of short-chain fatty acids in CiMe-treated mice. Furthermore, correlation analysis indicated the presence of critical gut microbiota, which played important roles in reducing the inflammation-related indices. Thus, the present study suggests that fucoidan isolated from Ascophyllum nodosum is effective in providing protection against the negative effects of antibiotics on gut microbiota and colonic health.
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Affiliation(s)
- Lilong Wang
- National Engineering Research Center of Seafood, School of Food Science and Technology, Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, P. R. China.
| | - Chunqing Ai
- National Engineering Research Center of Seafood, School of Food Science and Technology, Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, P. R. China. and National & Local Joint Engineering Laboratory for Marine Bioactive Polysaccharide Development and Application, Dalian Polytechnic University, Dalian 116034, P. R. China
| | - Chengrong Wen
- National Engineering Research Center of Seafood, School of Food Science and Technology, Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, P. R. China. and National & Local Joint Engineering Laboratory for Marine Bioactive Polysaccharide Development and Application, Dalian Polytechnic University, Dalian 116034, P. R. China
| | - Yimin Qin
- Qingdao Brightmoon Seaweed Group Co Ltd, Qingdao 266400, P. R. China and State Key Laboratory of Bioactive Seaweed Substances, Qingdao 266400, P. R. China
| | - Zhengqi Liu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Linlin Wang
- National Engineering Research Center of Seafood, School of Food Science and Technology, Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, P. R. China.
| | - Yue Gong
- National Engineering Research Center of Seafood, School of Food Science and Technology, Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, P. R. China.
| | - Changyu Su
- National Engineering Research Center of Seafood, School of Food Science and Technology, Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, P. R. China.
| | - Zhongfu Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education and Provincial Key Laboratory of Biotechnology, College of Life Sciences, Northwest University, Xi'an 710069, P. R. China
| | - Shuang Song
- National Engineering Research Center of Seafood, School of Food Science and Technology, Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, P. R. China. and National & Local Joint Engineering Laboratory for Marine Bioactive Polysaccharide Development and Application, Dalian Polytechnic University, Dalian 116034, P. R. China
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155
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Gut Epithelial Metabolism as a Key Driver of Intestinal Dysbiosis Associated with Noncommunicable Diseases. Infect Immun 2020; 88:IAI.00939-19. [PMID: 32122941 DOI: 10.1128/iai.00939-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In high-income countries, the leading causes of death are noncommunicable diseases (NCDs), such as obesity, cancer, and cardiovascular disease. An important feature of most NCDs is inflammation-induced gut dysbiosis characterized by a shift in the microbial community structure from obligate to facultative anaerobes such as Proteobacteria This microbial imbalance can contribute to disease pathogenesis by either a depletion in or the production of microbiota-derived metabolites. However, little is known about the mechanism by which inflammation-mediated changes in host physiology disrupt the microbial ecosystem in our large intestine leading to disease. Recent work by our group suggests that during gut homeostasis, epithelial hypoxia derived from peroxisome proliferator-activated receptor γ (PPAR-γ)-dependent β-oxidation of microbiota-derived short-chain fatty acids limits oxygen availability in the colon, thereby maintaining a balanced microbial community. During inflammation, disruption in gut anaerobiosis drives expansion of facultative anaerobic Enterobacteriaceae, regardless of their pathogenic potential. Therefore, our research group is currently exploring the concept that dysbiosis-associated expansion of Enterobacteriaceae can be viewed as a microbial signature of epithelial dysfunction and may play a greater role in different models of NCDs, including diet-induced obesity, atherosclerosis, and inflammation-associated colorectal cancer.
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156
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Di Gioia D, Bozzi Cionci N, Baffoni L, Amoruso A, Pane M, Mogna L, Gaggìa F, Lucenti MA, Bersano E, Cantello R, De Marchi F, Mazzini L. A prospective longitudinal study on the microbiota composition in amyotrophic lateral sclerosis. BMC Med 2020; 18:153. [PMID: 32546239 PMCID: PMC7298784 DOI: 10.1186/s12916-020-01607-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 04/27/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND A connection between amyotrophic lateral sclerosis (ALS) and altered gut microbiota composition has previously been reported in animal models. This work is the first prospective longitudinal study addressing the microbiota composition in ALS patients and the impact of a probiotic supplementation on the gut microbiota and disease progression. METHODS Fifty patients and 50 matched controls were enrolled. The microbial profile of stool samples from patients and controls was analyzed via PCR-Denaturing Gradient Gel Electrophoresis, and the main microbial groups quantified via qPCR. The whole microbiota was then analyzed via next generation sequencing after amplification of the V3-V4 region of 16S rDNA. Patients were then randomized to receive probiotic treatment or placebo and followed up for 6 months with ALSFRS-R, BMI, and FVC%. RESULTS The results demonstrate that the gut microbiota of ALS patients is characterized by some differences with respect to controls, regardless of the disability degree. Moreover, the gut microbiota composition changes during the course of the disease as demonstrated by the significant decrease in the number of observed operational taxonomic unit during the follow-up. Interestingly, an unbalance between potentially protective microbial groups, such as Bacteroidetes, and other with potential neurotoxic or pro-inflammatory activity, such as Cyanobacteria, has been shown. The 6-month probiotic treatment influenced the gut microbial composition; however, it did not bring the biodiversity of intestinal microbiota of patients closer to that of control subjects and no influence on the progression of the disease measured by ALSFRS-R was demonstrated. CONCLUSIONS Our study poses the bases for larger clinical studies to characterize the microbiota changes as a novel ALS biomarker and to test new microbial strategy to ameliorate the health status of the gut. TRIAL REGISTRATION CE 107/14, approved by the Ethics Committee of the "Maggiore della Carità" University Hospital, Italy.
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Affiliation(s)
- Diana Di Gioia
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 42, Bologna, Italy
| | - Nicole Bozzi Cionci
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 42, Bologna, Italy
| | - Loredana Baffoni
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 42, Bologna, Italy
| | - Angela Amoruso
- BIOLAB RESEARCH srl, via E. Mattei 3, 28100, Novara, Italy
| | - Marco Pane
- BIOLAB RESEARCH srl, via E. Mattei 3, 28100, Novara, Italy
| | - Luca Mogna
- BIOLAB RESEARCH srl, via E. Mattei 3, 28100, Novara, Italy
| | - Francesca Gaggìa
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 42, Bologna, Italy
| | - Maria Ausiliatrice Lucenti
- Department of Neurology and ALS Centre, University of Piemonte Orientale, Maggiore della Carità Hospital, Corso Mazzini 18, 28100, Novara, Italy
| | - Enrica Bersano
- Department of Neurology and ALS Centre, University of Piemonte Orientale, Maggiore della Carità Hospital, Corso Mazzini 18, 28100, Novara, Italy
| | - Roberto Cantello
- Department of Neurology and ALS Centre, University of Piemonte Orientale, Maggiore della Carità Hospital, Corso Mazzini 18, 28100, Novara, Italy
| | - Fabiola De Marchi
- Department of Neurology and ALS Centre, University of Piemonte Orientale, Maggiore della Carità Hospital, Corso Mazzini 18, 28100, Novara, Italy
| | - Letizia Mazzini
- Department of Neurology and ALS Centre, University of Piemonte Orientale, Maggiore della Carità Hospital, Corso Mazzini 18, 28100, Novara, Italy.
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157
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Wang J, Chen WD, Wang YD. The Relationship Between Gut Microbiota and Inflammatory Diseases: The Role of Macrophages. Front Microbiol 2020; 11:1065. [PMID: 32582063 PMCID: PMC7296120 DOI: 10.3389/fmicb.2020.01065] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022] Open
Abstract
Gut microbiota, an integral part of the human body, comprise bacteria, fungi, archaea, and protozoa. There is consensus that the disruption of the gut microbiota (termed “gut dysbiosis”) is influenced by host genetics, diet, antibiotics, and inflammation, and it is closely linked to the pathogenesis of inflammatory diseases, such as obesity and inflammatory bowel disease (IBD). Macrophages are the key players in the maintenance of tissue homeostasis by eliminating invading pathogens and exhibit extreme plasticity of their phenotypes, such as M1 or M2, which have been demonstrated to exert pro- and anti-inflammatory functions. Microbiota-derived metabolites, short-chain fatty acids (SCFAs) and Gram-negative bacterial lipopolysaccharides (LPS), exert anti-inflammatory or pro-inflammatory effects by acting on macrophages. Understanding the role of macrophages in gut microbiota-inflammation interactions might provide us a novel method for preventing and treating inflammatory diseases. In this review, we summarize the recent research on the relationship between gut microbiota and inflammation and discuss the important role of macrophages in this context.
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Affiliation(s)
- Ji Wang
- State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Wei-Dong Chen
- Key Laboratory of Molecular Pathology, School of Basic Medical Science, Inner Mongolia Medical University, Hohhot, China.,Key Laboratory of Receptors-Mediated Gene Regulation and Drug Discovery, Hebi People's Hospital, School of Medicine, Henan University, Kaifeng, China
| | - Yan-Dong Wang
- State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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158
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Axelrad JE, Cadwell KH, Colombel JF, Shah SC. Systematic review: gastrointestinal infection and incident inflammatory bowel disease. Aliment Pharmacol Ther 2020; 51:1222-1232. [PMID: 32372471 PMCID: PMC7354095 DOI: 10.1111/apt.15770] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 03/24/2020] [Accepted: 04/14/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND The initiating events of chronic gastrointestinal (GI) inflammation in Crohn's disease (CD) and ulcerative colitis (UC) are not well-defined, but GI infections are implicated. AIMS To define the role of GI infections in risk of incident inflammatory bowel disease (IBD) and synthesise the current body of relevant translational data to provide biological context for associations between GI infections and IBD risk. METHODS We systematically reviewed electronic databases through February 2020. Clinical studies that provided risk estimates of the association between GI infections and incident IBD were included. Inclusion criteria were broader for translational studies aiming to define mechanisms of GI infections and predisposition to or protection from IBD. RESULTS Of the studies identified, 63 met full inclusion criteria. Among studies of clinical gastroenteritis, bacteria-specifically, Salmonella species, Campylobacter species and Clostridioides difficile-demonstrated consistent positive associations with risk of incident IBD. Of viruses, norovirus was associated with increased risk of incident CD. Regarding inverse associations with incident IBD, Helicobacter pylori and helminth infections were associated with a generally consistent reduced risk of IBD. Based on a qualitative analysis of the translational data, putative mechanisms involve multiple microbial and immunologic pathways. CONCLUSIONS Based on this systematic review, certain enteric pathogens are associated with an increased risk of incident IBD, while others are potentially protective. Prospective studies are required to clarify the clinical implications of these enteric pathogens on the risk and course of IBD, and possible therapeutic or preventative benefit.
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Affiliation(s)
- Jordan E Axelrad
- Division of Gastroenterology, Department of Medicine, NYU School of Medicine, New York, NY, USA
| | - Ken H Cadwell
- Division of Gastroenterology, Department of Medicine, NYU School of Medicine, New York, NY, USA
- Department of Microbiology, NYU School of Medicine, New York, NY, USA
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shailja C Shah
- Division of Gastroenterology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
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159
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Lamas B, Martins Breyner N, Houdeau E. Impacts of foodborne inorganic nanoparticles on the gut microbiota-immune axis: potential consequences for host health. Part Fibre Toxicol 2020; 17:19. [PMID: 32487227 PMCID: PMC7268708 DOI: 10.1186/s12989-020-00349-z] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 05/11/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In food toxicology, there is growing interest in studying the impacts of foodborne nanoparticles (NPs, originating from food additives, food supplements or food packaging) on the intestinal microbiome due to the important and complex physiological roles of these microbial communities in host health. Biocidal activities, as described over recent years for most inorganic and metal NPs, could favour chronic changes in the composition and/or metabolic activities of commensal bacteria (namely, intestinal dysbiosis) with consequences on immune functions. Reciprocally, direct interactions of NPs with the immune system (e.g., inflammatory responses, adjuvant or immunosuppressive properties) may in turn have effects on the gut microbiota. Many chronic diseases in humans are associated with alterations along the microbiota-immune system axis, such as inflammatory bowel diseases (IBD) (Crohn's disease and ulcerative colitis), metabolic disorders (e.g., obesity) or colorectal cancer (CRC). This raises the question of whether chronic dietary exposure to inorganic NPs may be viewed as a risk factor facilitating disease onset and/or progression. Deciphering the variety of effects along the microbiota-immune axis may aid the understanding of how daily exposure to inorganic NPs through various foodstuffs may potentially disturb the intricate dialogue between gut commensals and immunity, hence increasing the vulnerability of the host. In animal studies, dose levels and durations of oral treatment are key factors for mimicking exposure conditions to which humans are or may be exposed through the diet on a daily basis, and are needed for hazard identification and risk assessment of foodborne NPs. This review summarizes relevant studies to support the development of predictive toxicological models that account for the gut microbiota-immune axis. CONCLUSIONS The literature indicates that, in addition to evoking immune dysfunctions in the gut, inorganic NPs exhibit a moderate to extensive impact on intestinal microbiota composition and activity, highlighting a recurrent signature that favours colonization of the intestine by pathobionts at the expense of beneficial bacterial strains, as observed in IBD, CRC and obesity. Considering the long-term exposure via food, the effects of NPs on the gut microbiome should be considered in human health risk assessment, especially when a nanomaterial exhibits antimicrobial properties.
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Affiliation(s)
- Bruno Lamas
- INRAE Toxalim UMR 1331 (Research Center in Food Toxicology), Team Endocrinology and Toxicology of the Intestinal Barrier, INRAE, Toulouse University, ENVT, INP-Purpan, UPS, 180 Chemin de Tournefeuille, 31027, Toulouse cedex 3, France.
| | - Natalia Martins Breyner
- INRAE Toxalim UMR 1331 (Research Center in Food Toxicology), Team Endocrinology and Toxicology of the Intestinal Barrier, INRAE, Toulouse University, ENVT, INP-Purpan, UPS, 180 Chemin de Tournefeuille, 31027, Toulouse cedex 3, France
| | - Eric Houdeau
- INRAE Toxalim UMR 1331 (Research Center in Food Toxicology), Team Endocrinology and Toxicology of the Intestinal Barrier, INRAE, Toulouse University, ENVT, INP-Purpan, UPS, 180 Chemin de Tournefeuille, 31027, Toulouse cedex 3, France.
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160
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Abstract
Host-microbiota interactions are fundamental for the development of the immune system. Drastic changes in modern environments and lifestyles have led to an imbalance of this evolutionarily ancient process, coinciding with a steep rise in immune-mediated diseases such as autoimmune, allergic and chronic inflammatory disorders. There is an urgent need to better understand these diseases in the context of mucosal and skin microbiota. This Review discusses the mechanisms of how the microbiota contributes to the predisposition, initiation and perpetuation of immune-mediated diseases in the context of a genetically prone host. It is timely owing to the wealth of new studies that recently contributed to this field, ranging from metagenomic studies in humans and mechanistic studies of host-microorganism interactions in gnotobiotic models and in vitro systems, to molecular mechanisms with broader implications across immune-mediated diseases. We focus on the general principles, such as breaches in immune tolerance and barriers, leading to the promotion of immune-mediated diseases by gut, oral and skin microbiota. Lastly, the therapeutic avenues that either target the microbiota, the barrier surfaces or the host immune system to restore tolerance and homeostasis will be explored.
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161
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Mjelle R, Aass KR, Sjursen W, Hofsli E, Sætrom P. sMETASeq: Combined Profiling of Microbiota and Host Small RNAs. iScience 2020; 23:101131. [PMID: 32422595 PMCID: PMC7229328 DOI: 10.1016/j.isci.2020.101131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/20/2020] [Accepted: 04/28/2020] [Indexed: 11/30/2022] Open
Abstract
Understanding microbial communities' roles in human health and disease requires methods that accurately characterize the microbial composition and their activity and effects within human biological samples. We present sMETASeq (small RNA Metagenomics by Sequencing), a novel method that uses sequencing of small RNAs to jointly measure host small RNA expression and create metagenomic profiles and detect small bacterial RNAs. We evaluated the performance of sMETASeq on a mock bacterial community and demonstrated its use on different human samples, including colon cancer, oral leukoplakia, cervix cancer, and a panel of human biofluids. In all datasets, the detected microbes reflected the biology of the different sample types.
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Affiliation(s)
- Robin Mjelle
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Trondheim 7030, Norway; Bioinformatics Core Facility-BioCore, Norwegian University of Science and Technology, NTNU, Trondheim 7491, Norway; K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, NTNU, Trondheim 7491, Norway.
| | - Kristin Roseth Aass
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Trondheim 7030, Norway; Centre of Molecular Inflammation Research, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim 7030, Norway
| | - Wenche Sjursen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Trondheim 7030, Norway; Department of Medical Genetics, St. Olavs Hospital, Trondheim 7030, Norway
| | - Eva Hofsli
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Trondheim 7030, Norway; The Cancer Clinic, St. Olavs Hospital, Trondheim University Hospital, Trondheim 7030, Norway
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Trondheim 7030, Norway; Department of Computer and Information Science, Norwegian University of Science and Technology, NTNU, Trondheim 7491, Norway; Bioinformatics Core Facility-BioCore, Norwegian University of Science and Technology, NTNU, Trondheim 7491, Norway; K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, NTNU, Trondheim 7491, Norway
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162
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HIV-associated gut dysbiosis is independent of sexual practice and correlates with noncommunicable diseases. Nat Commun 2020; 11:2448. [PMID: 32415070 PMCID: PMC7228978 DOI: 10.1038/s41467-020-16222-8] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 04/15/2020] [Indexed: 02/08/2023] Open
Abstract
Loss of gut mucosal integrity and an aberrant gut microbiota are proposed mechanisms contributing to chronic inflammation and increased morbidity and mortality during antiretroviral-treated HIV disease. Sexual practice has recently been uncovered as a major source of microbiota variation, potentially confounding prior observations of gut microbiota alterations among persons with HIV (PWH). To overcome this and other confounding factors, we examine a well-powered subset of AGEhIV Cohort participants comprising antiretroviral-treated PWH and seronegative controls matched for age, body-mass index, sex, and sexual practice. We report significant gut microbiota differences in PWH regardless of sex and sexual practice including Gammaproteobacteria enrichment, Lachnospiraceae and Ruminococcaceae depletion, and decreased alpha diversity. Men who have sex with men (MSM) exhibit a distinct microbiota signature characterized by Prevotella enrichment and increased alpha diversity, which is linked with receptive anal intercourse in both males and females. Finally, the HIV-associated microbiota signature correlates with inflammatory markers including suPAR, nadir CD4 count, and prevalence of age-associated noncommunicable comorbidities.
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163
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Gao B, Zhong M, Shen Q, Wu Y, Cao M, Ju S, Chen L. Gut microbiota in early pregnancy among women with Hyperglycaemia vs. Normal blood glucose. BMC Pregnancy Childbirth 2020; 20:284. [PMID: 32393255 PMCID: PMC7216510 DOI: 10.1186/s12884-020-02961-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 04/21/2020] [Indexed: 02/07/2023] Open
Abstract
Background Recent studies suggest that there is a link between the gut microbiota and glucose metabolism. This study aimed to compare the gut microbiota during early pregnancy of women with hyperglycymia to those with normal blood glucose. Methods Gut microbial composition was analysed in 22 women with hyperglycaemia and 28 age-matched healthy controls during their first prenatal visits (< 20 weeks) using high throughput sequencing of the V3-V4 region of the 16S ribosomal RNA gene. Hyperglycemia was diagnosed based on the criteria recommended by the International Association of Diabetes and Pregnancy Study Groups in 2010. Results Women with hyperglycemia in pregnancy (HIP) had significantly lower microbial richness and diversity compared with healthy pregnant women. The proportions of the Firmicutes and Bacteroidetes phyla and the ratio of Firmicutes:Bacteroidetes were not different between the two groups. We observed that individuals with HIP had an increased abundance of Nocardiaceae, Fusobacteriaceae, etc., whereas healthy controls had significantly higher levels of Christensenellaceae, Clostridiales_vadinBB60_group, Coriobacteriaceae, etc. Similarly, levels of the members of the Ruminococcaceae family, including Ruminococcaceae_UCG-014, Ruminococcaceae_UCG-003, and Ruminococcaceae_UCG-002, were significantly reduced in the HIP group and were negatively correlated with HbA1c. HbA1c levels were positively correlated with Bacteroidaceae and Enterobacteriaceae and negatively correlated with Christensenellaceae, etc. CRP was positively correlated with the Bacteroidaceae and Fusobacteriaceae families and the Fusobacterium genus. Conclusions Our study revealed that individuals with HIP have gut microbial dysbiosis and that certain bacterial groups are associated with glucose metabolism during pregnancy. Further study is needed to provide new ideas to control glucose by modifying the gut microbiota.
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Affiliation(s)
- Beibei Gao
- Department of Endocrinology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, 215000, China
| | - Mengdan Zhong
- Department of Endocrinology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, 215000, China
| | - Qiong Shen
- Department of Endocrinology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, 215000, China
| | - Ying Wu
- Department of Endocrinology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, 215000, China
| | - Mengdie Cao
- Department of Endocrinology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, 215000, China
| | - Songwen Ju
- Central Laboratory, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, 215000, China
| | - Lei Chen
- Department of Endocrinology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, 215000, China.
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164
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Chen D, Chen G, Chen C, Zeng X, Ye H. Prebiotics effects in vitro of polysaccharides from tea flowers on gut microbiota of healthy persons and patients with inflammatory bowel disease. Int J Biol Macromol 2020; 158:968-976. [PMID: 32371134 DOI: 10.1016/j.ijbiomac.2020.04.248] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/24/2020] [Accepted: 04/28/2020] [Indexed: 12/12/2022]
Abstract
Polysaccharides from the flowers of tea (Camellia sinensis L.) plant (TFPS) were considered as potential functional components mainly playing the role in the distal intestines. In the present study, effects of TFPS on compositions of gut microbiota of feces from healthy persons and patients with inflammatory bowel disease (IBD) were investigated in vitro. Microbial communities in normal feces were more diverse than those in IBD feces. After fermentation of TFPS for 24 h under simulated anaerobic conditions, significant changes were observed in the composition of intestinal microbes (enhanced the relative abundances of Klebsiella, Dialister, Megasphaera, Collinsella, Lactobacillus and Bifidobacterium while decreased Prevotella, Clostridium XlVa, Alistipes, Clostridium XlVb, Akkermansia, Ruminococcus, Butyricimonas, Clostridium XVIII, Ruminococcus and Butyricicoccus for the normal feces; increased Escherichia/Shigella, Enterococcus, Collinsella, Lactobacillus and Bifidobacterium while decreased Enterobacter, Streptococcus, Bacteroides, Clostridium XlVa, Megasphaera, Roseburia, Granulicatella, Akkermansia and Fusobacterium for the IBD feces) and their metabolites, short-chain fatty acids (from 4.54 ± 0.43 to 12.88 ± 1.59 mM for the normal feces and from 5.21 ± 0.51 to 7.61 ± 0.81 mM for the IBD feces). The results illustrated that TFPS had probiotics promoting effect on the normal and IBD intestinal environments, however, might have a pro-inflammatory effect on IBD.
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Affiliation(s)
- Dan Chen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Guijie Chen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Chunxu Chen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Xiaoxiong Zeng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
| | - Hong Ye
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China.
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165
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Huang Y, Yu Y, Zhan S, Tomberlin JK, Huang D, Cai M, Zheng L, Yu Z, Zhang J. Dual oxidase Duox and Toll-like receptor 3 TLR3 in the Toll pathway suppress zoonotic pathogens through regulating the intestinal bacterial community homeostasis in Hermetia illucens L. PLoS One 2020; 15:e0225873. [PMID: 32352968 PMCID: PMC7192390 DOI: 10.1371/journal.pone.0225873] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 03/26/2020] [Indexed: 01/26/2023] Open
Abstract
Black soldier fly (BSF; Hermetia illucens L.) larvae can convert fresh pig manure into protein and fat-rich biomass, which can then be used as aquafeed for select species. Currently, BSF is the only approved insect for such purposes in Canada, USA, and the European Union. Pig manure could serve as a feed substrate for BSF; however, it is contaminated with zoonotic pathogens (e.g., Staphylococcus aureus and Salmonella spp.). Fortunately, BSF larvae inhibit many of these zoonotic pathogens; however, the mechanisms employed are unclear. We employed RNAi, qRT-PCR, and Illumina MiSeq 16S rDNA high-throughput sequencing to examine the interaction between two immune genes (Duox in Duox-reactive oxygen species [ROS] immune system and TLR3 in the Toll signaling pathway) and select pathogens common in pig manure to decipher the mechanisms resulting in pathogen suppression. Results indicate Bsf Duox-TLR3 RNAi increased bacterial load but decreased relative abundance of Providencia and Dysgonomonas, which are thought to be commensals in the BSF larval gut. Bsf Duox-TLR3 RNAi also inactivated the NF-κB signaling pathway, downregulated the expression of antimicrobial peptides, and diminished inhibitory effects on zoonotic pathogen. The resulting dysbiosis stimulated an immune response by activating BsfDuox and promoting ROS, which regulated the composition and structure of the gut bacterial community. Thus, BsfDuox and BsfTLR3 are important factors in regulating these key gut microbes, while inhibiting target zoonotic pathogens.
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Affiliation(s)
- Yaqing Huang
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yongqiang Yu
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shuai Zhan
- Institute of Plant Physiology & Ecology, SIBS, CAS, Shanghai, China
| | | | - Dian Huang
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Minmin Cai
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Longyu Zheng
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ziniu Yu
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jibin Zhang
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- * E-mail:
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166
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Zhang X, Zou Q, Zhao B, Zhang J, Zhao W, Li Y, Liu R, Liu X, Liu Z. Effects of alternate-day fasting, time-restricted fasting and intermittent energy restriction DSS-induced on colitis and behavioral disorders. Redox Biol 2020; 32:101535. [PMID: 32305005 PMCID: PMC7162980 DOI: 10.1016/j.redox.2020.101535] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/27/2020] [Accepted: 04/04/2020] [Indexed: 12/18/2022] Open
Abstract
Intermittent fasting (IF) has been reported to have beneficial effects on improving gut function via lowering gut inflammation and altering the gut microbiome diversity. In this study, we aimed to investigate the differential effects of three different common IF treatments, alternate day fasting (ADF), time-restricted fasting (TRF), and intermittent energy restriction (IER), on a dextran sodium sulfate (DSS)-induced colitis mouse model. The results indicated that TRF and IER, but not ADF improved the survival rates of the colitis mice. TRF and IER, but not ADF, reversed the colitis pathological development by improving the gut barrier integrity and colon length. Importantly, TRF and IER suppressed the inflammatory responses and oxidative stress in colon tissues. Interestingly, TRF and IER also attenuated colitis-related anxiety-like and obsessive-compulsive disorder behavior and alleviated the neuroinflammation and oxidative stress. TRF and IER also altered the gut microbiota composition, including the decrease of the enrichments of colitis-related microbes such as Shigella and Escherichia Coli, and increase of the enrichments of anti-inflammatory-related microbes. TRF and IER also improved the short chain fatty acid formation in colitis mice. In conclusion, the TRF and IER but not ADF exhibited the protective effects against colitis and related behavioral disorders, which could be partly explained by improving the gut microbiome compositions and preventing gut leak, and consequently suppressing the inflammation and oxidative damages in both colon and brain. The current research indicates that proper IF regimens could be effective strategies for nutritional intervention for the prevention and treatment of colitis.
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Affiliation(s)
- Xin Zhang
- Laboratory of Functional Chemistry and Nutrition of Food, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaan Xi, China
| | - Qianhui Zou
- Laboratory of Functional Chemistry and Nutrition of Food, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaan Xi, China
| | - Beita Zhao
- Laboratory of Functional Chemistry and Nutrition of Food, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaan Xi, China
| | - Jingwen Zhang
- Laboratory of Functional Chemistry and Nutrition of Food, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaan Xi, China
| | - Weiyang Zhao
- Department of Food Science, Cornell University, Ithaca, NY, 14853, United States
| | - Yitong Li
- Department of Food Science, Cornell University, Ithaca, NY, 14853, United States
| | - Ruihai Liu
- Department of Food Science, Cornell University, Ithaca, NY, 14853, United States
| | - Xuebo Liu
- Laboratory of Functional Chemistry and Nutrition of Food, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaan Xi, China
| | - Zhigang Liu
- Laboratory of Functional Chemistry and Nutrition of Food, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaan Xi, China; Department of Food Science, Cornell University, Ithaca, NY, 14853, United States.
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167
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Kayama H, Tani H, Kitada S, Opasawatchai A, Okumura R, Motooka D, Nakamura S, Takeda K. BATF2 prevents T-cell-mediated intestinal inflammation through regulation of the IL-23/IL-17 pathway. Int Immunol 2020; 31:371-383. [PMID: 30753547 PMCID: PMC6528702 DOI: 10.1093/intimm/dxz014] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 02/19/2019] [Indexed: 12/15/2022] Open
Abstract
Inappropriate activation of the IL-23 signaling pathway causes chronic inflammation through the induction of immunopathological Th17 cells in several tissues including the intestine, whereas adequate Th17 responses are essential for host defense against harmful organisms. In the intestinal lamina propria, IL-23 is primarily produced by innate myeloid cells including dendritic cells (DCs) and macrophages (Mϕs). However, the molecular mechanisms underlying the regulation of IL-23 production by these cells remains poorly understood. In this study, we demonstrated that BATF2 regulates intestinal homeostasis by inhibiting IL-23-driven T-cell responses. Batf2 was highly expressed in intestinal innate myeloid subsets, such as monocytes, CD11b+ CD64+ Mϕs and CD103+ DCs. Batf2-/- mice spontaneously developed colitis and ileitis with altered microbiota composition. In this context, IL-23, but not TNF-α and IL-10, was produced in high quantities by intestinal CD11b+ CD64+ Mϕs from Batf2-/- mice compared with wild-type mice. Moreover, increased numbers of IFN-γ+, IL-17+ and IFN-γ+ IL-17+ CD4+ T cells, but not IL-10+ CD4+ T cells, accumulated in the colons and small intestines of Batf2-/- mice. In addition, RORγt-expressing innate lymphoid cells were increased in Batf2-/- mice. Batf2-/-Rag2-/- mice showed a reduction in intestinal inflammation present in Batf2-/- mice. Furthermore, the high numbers of intestinal IL-17+ and IFN-γ+ IL-17+ CD4+ T cells were markedly reduced in Batf2-/- mice when introducing Il23a deficiency, which was associated with the abrogation of intestinal inflammation. These results indicated that BATF2 in innate myeloid cells is a key molecule for the suppression of IL-23/IL-17 pathway-mediated adaptive intestinal pathology.
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Affiliation(s)
- Hisako Kayama
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan.,WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Core Research for Evolutional Science and Technology, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Haruka Tani
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan.,WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Core Research for Evolutional Science and Technology, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Shoko Kitada
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan.,WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Core Research for Evolutional Science and Technology, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Anunya Opasawatchai
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan.,Faculty of Dentistry, Mahidol University, Bangkok, Thailand
| | - Ryu Okumura
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan.,WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Core Research for Evolutional Science and Technology, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shota Nakamura
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Kiyoshi Takeda
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan.,WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Core Research for Evolutional Science and Technology, Japan Agency for Medical Research and Development, Tokyo, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
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168
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Caruso R, Mathes T, Martens EC, Kamada N, Nusrat A, Inohara N, Núñez G. A specific gene-microbe interaction drives the development of Crohn's disease-like colitis in mice. Sci Immunol 2020; 4:4/34/eaaw4341. [PMID: 31004013 DOI: 10.1126/sciimmunol.aaw4341] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/07/2019] [Indexed: 12/12/2022]
Abstract
Bacterial dysbiosis is associated with Crohn's disease (CD), a chronic intestinal inflammatory disorder thought to result from an abnormal immune response against intestinal bacteria in genetically susceptible individuals. However, it is unclear whether dysbiosis is a cause or consequence of intestinal inflammation and whether overall dysbiosis or specific bacteria trigger the disease. Here, we show that the combined deficiency of NOD2 and phagocyte NADPH oxidase, two CD susceptibility genes, triggers early-onset spontaneous TH1-type intestinal inflammation in mice with the pathological hallmarks of CD. Disease was induced by Mucispirillum schaedleri, a Gram-negative mucus-dwelling anaerobe. NOD2 and CYBB deficiencies led to marked accumulation of Mucispirillum, which was associated with impaired neutrophil recruitment and killing of the bacterium by luminal neutrophils. Maternal immunoglobulins against Mucispirillum protected mutant mice from disease during breastfeeding. Our results indicate that a specific intestinal microbe triggers CD-like disease in the presence of impaired clearance of the bacterium by innate immunity.
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Affiliation(s)
- R Caruso
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - T Mathes
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - E C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - N Kamada
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - A Nusrat
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - N Inohara
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - G Núñez
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA. .,Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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169
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Relationship between hyperlipidemia and the gut microbiome of rats, characterized using high-throughput sequencing. JOURNAL OF TRADITIONAL CHINESE MEDICAL SCIENCES 2020. [DOI: 10.1016/j.jtcms.2020.04.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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170
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Association of colitis with gut-microbiota dysbiosis in clathrin adapter AP-1B knockout mice. PLoS One 2020; 15:e0228358. [PMID: 32208434 PMCID: PMC7093000 DOI: 10.1371/journal.pone.0228358] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/13/2020] [Indexed: 12/21/2022] Open
Abstract
Inflammatory bowel disease results from alterations in the immune system and intestinal microbiota. The role of intestinal epithelial cells (IECs) in maintaining gut homeostasis is well known and its perturbation often causes gastrointestinal disorders including IBD. The epithelial specific adaptor protein (AP)-1B is involved in the establishment of the polarity of IECs. Deficiency of the AP-1B μ subunit (Ap1m2-/-) leads to the development of chronic colitis in mice. However, how this deficiency affects the gut microbes and its potential functions remains elusive. To gain insights into the gut microbiome of Ap1m2-/- mice having the colitis phenotype, we undertook shotgun metagenomic sequencing analysis of knockout mice. We found important links to the microbial features involved in altering various physiological pathways, including carbohydrate metabolism, nutrient transportation, oxidative stress, and bacterial pathogenesis (cell motility). In addition, an increased abundance of sulfur-reducing and lactate-producing bacteria has been observed which may aggravate the colitis condition.
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171
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Vujkovic-Cvijin I, Somsouk M. HIV and the Gut Microbiota: Composition, Consequences, and Avenues for Amelioration. Curr HIV/AIDS Rep 2020; 16:204-213. [PMID: 31037552 DOI: 10.1007/s11904-019-00441-w] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW We discuss recent advances in understanding of gut bacterial microbiota composition in HIV-infected subjects and comment on controversies. We discuss the putative effects of microbiota shifts on systemic inflammation and HIV disease progression and potential mechanisms, as well as ongoing strategies being developed to modulate the gut microbiota in humans for amelioration of infectious and inflammatory diseases. RECENT FINDINGS Lifestyle and behavioral factors relevant to HIV infection studies have independent effects on the microbiota. Microbial metabolism of immunomodulatory compounds and direct immune stimulation by translocation of microbes are putative mechanisms contributing to HIV disease. Fecal microbiota transplantation, microbial enzyme inhibition, phage therapy, and rationally selected probiotic cocktails have emerged as promising strategies for microbiota modulation. Numerous surveys of the HIV gut microbiota matched for lifestyle factors suggest consistent shifts in gut microbiota composition among HIV-infected subjects. Evidence exists for a complex pathogenic role of the gut microbiota in HIV disease progression, warranting further study.
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Affiliation(s)
- Ivan Vujkovic-Cvijin
- Metaorganism Immunity Section, National Institute of Allergy & Infectious Disease, National Institutes of Health, Bethesda, MD, USA.
| | - Ma Somsouk
- Division of Gastroenterology, University of California, San Francisco, CA, USA.
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172
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IL-8 and LYPD8 expression levels are associated with the inflammatory response in the colon of patients with ulcerative colitis. Biomed Rep 2020; 12:193-198. [PMID: 32190307 DOI: 10.3892/br.2020.1280] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022] Open
Abstract
Ulcerative colitis (UC) is an idiopathic chronic inflammatory disorder affecting the large intestine, which may involve mucosal degeneration. Glycoproteins, mucin2 (MUC2) and the LY6/PLAUR domain containing 8 (LYPD8) are present on the mucous layer of the colon and can hinder the invasion of bacteria, thus contributing to the prevention of colitis. The present study investigated the expression levels of interleukin-8 (IL-8), MUC2 and LYPD8 on the mucous membranes of patients with UC. A total of 18 patients with UC (6 females and 12 males) were examined. Biopsies of the lesions as well as matching normal membranes were obtained and the mRNA expression levels of IL-8, MUC2 and LYPD8 were compared. LYPD8 expression was downregulated in the lesions and the relapsing-remitting subtype of lesions was associated with higher levels of MUC2 expression compared with single attack and chronic lesions subtypes. A positive correlation between Matts' histopathological grade and IL-8, as well as a negative correlation between Matts' histopathological grade and LYPD8 were observed. The expression levels of LYPD8 were lower in highly active lesions and these levels decreased according to the intensity of the mucosal inflammation. Conversely, an increase in MUC2 expression levels may reflect the recovery of the outer mucus layer in the remission phase. Therefore, the examination of MUC2 and LYPD8 expression levels may be useful indicators of mucosal healing in patients with UC.
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173
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Schirmer M, Garner A, Vlamakis H, Xavier RJ. Microbial genes and pathways in inflammatory bowel disease. Nat Rev Microbiol 2020; 17:497-511. [PMID: 31249397 DOI: 10.1038/s41579-019-0213-6] [Citation(s) in RCA: 413] [Impact Index Per Article: 103.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Perturbations in the intestinal microbiome are implicated in inflammatory bowel disease (IBD). Studies of treatment-naive patients have identified microbial taxa associated with disease course and treatment efficacy. To gain a mechanistic understanding of how the microbiome affects gastrointestinal health, we need to move from census to function. Bacteria, including those that adhere to epithelial cells as well as several Clostridium species, can alter differentiation of T helper 17 cells and regulatory T cells. Similarly, microbial products such as short-chain fatty acids and sphingolipids also influence immune responses. Metagenomics and culturomics have identified strains of Ruminococcus gnavus and adherent invasive Escherichia coli that are linked to IBD and gut inflammation. Integrated analysis of multiomics data, including metagenomics, metatranscriptomics and metabolomics, with measurements of host response and culturomics, have great potential in understanding the role of the microbiome in IBD. In this Review, we highlight current knowledge of gut microbial factors linked to IBD pathogenesis and discuss how multiomics data from large-scale population studies in health and disease have been used to identify specific microbial strains, transcriptional changes and metabolic alterations associated with IBD.
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Affiliation(s)
| | - Ashley Garner
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.
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174
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Zhu W, Winter MG, Spiga L, Hughes ER, Chanin R, Mulgaonkar A, Pennington J, Maas M, Behrendt CL, Kim J, Sun X, Beiting DP, Hooper LV, Winter SE. Xenosiderophore Utilization Promotes Bacteroides thetaiotaomicron Resilience during Colitis. Cell Host Microbe 2020; 27:376-388.e8. [PMID: 32075741 DOI: 10.1016/j.chom.2020.01.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 12/02/2019] [Accepted: 01/16/2020] [Indexed: 02/06/2023]
Abstract
During short-lived perturbations, such as inflammation, the gut microbiota exhibits resilience and reverts to its original configuration. Although microbial access to the micronutrient iron is decreased during colitis, pathogens can scavenge iron by using siderophores. How commensal bacteria acquire iron during gut inflammation is incompletely understood. Curiously, the human commensal Bacteroides thetaiotaomicron does not produce siderophores but grows under iron-limiting conditions using enterobacterial siderophores. Using RNA-seq, we identify B. thetaiotaomicron genes that were upregulated during Salmonella-induced gut inflammation and were predicted to be involved in iron uptake. Mutants in the xusABC locus (BT2063-2065) were defective for xenosiderophore-mediated iron uptake in vitro. In the normal mouse gut, the XusABC system was dispensable, while a xusA mutant colonized poorly during colitis. This work identifies xenosiderophore utilization as a critical mechanism for B. thetaiotaomicron to sustain colonization during inflammation and suggests a mechanism of how interphylum iron metabolism contributes to gut microbiota resilience.
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Affiliation(s)
- Wenhan Zhu
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Maria G Winter
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Luisella Spiga
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Elizabeth R Hughes
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rachael Chanin
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Aditi Mulgaonkar
- Radiology and Advanced Imaging Research Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jenelle Pennington
- Radiology and Advanced Imaging Research Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Michelle Maas
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cassie L Behrendt
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiwoong Kim
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiankai Sun
- Radiology and Advanced Imaging Research Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Daniel P Beiting
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lora V Hooper
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sebastian E Winter
- Department of Microbiology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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175
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Yeh NL, Hsu CY, Tsai TF, Chiu HY. Gut Microbiome in Psoriasis is Perturbed Differently During Secukinumab and Ustekinumab Therapy and Associated with Response to Treatment. Clin Drug Investig 2020; 39:1195-1203. [PMID: 31549347 DOI: 10.1007/s40261-019-00849-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND OBJECTIVE Immunotherapy could change the complex host-microbial interactions. We aimed to investigate the dynamics of gut microbiome in response to secukinumab [an interleukin (IL)-17 inhibitor] and ustekinumab (an IL-12/23 inhibitor) therapy and its association with treatment response in psoriasis. METHODS This observational, longitudinal study collected a total of 114 fecal samples from 12 healthy controls and 34 patients with psoriasis at baseline and 3 and 6 months after secukinumab (n = 24) or ustekinumab treatment (n = 10) and gut microbiomes were investigated using next-generation sequencing targeting 16S ribosomal RNA. RESULTS Secukinumab treatment causes more profound alterations in gut microbiome, including increases in the relative abundance of phylum Proteobacteria and decreases in Bacteroidetes and Firmicutes, than ustekinumab treatment. The relative abundance of family Pseudomonadaceae, family Enterobacteriaceae and order Pseudomonadales also increased significantly following secukinumab therapy. In contrast, there was no significant change in gut microbiome composition following ustekinumab treatment, and only genus Coprococcus significantly increased after 6 months of ustekinumab therapy. Moreover, we observed significant differences in baseline gut microbiome between responders and non-responders to secukinumab treatment. CONCLUSION These results indicate that gut microbiome is altered differently after anti-IL17 and anti-IL12/23 treatment. Secukinumab (anti-IL17) therapy is associated with distinct and more profound gut microbiome shifts than ustekinumab therapy (anti-IL 12/23) in patients with psoriasis. Moreover, gut microbiome would serve as potential biomarkers of response to secukinumab treatment.
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Affiliation(s)
- Nai-Lun Yeh
- Department of Community and Family Medicine, National Taiwan University Hospital Hsinchu Branch, Hsinchu, Taiwan
| | - Che-Yuan Hsu
- Department of Dermatology, National Taiwan University Hospital Hsinchu Branch, No. 25, Lane 442, Sec. 1, Jingguo Rd., Hsinchu, 300, Taiwan
| | - Tsen-Fang Tsai
- Department of Dermatology, National Taiwan University Hospital, Taipei, Taiwan.,Department of Dermatology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsien-Yi Chiu
- Department of Dermatology, National Taiwan University Hospital Hsinchu Branch, No. 25, Lane 442, Sec. 1, Jingguo Rd., Hsinchu, 300, Taiwan. .,Department of Dermatology, National Taiwan University Hospital, Taipei, Taiwan. .,Department of Dermatology, College of Medicine, National Taiwan University, Taipei, Taiwan. .,Institute of Biomedical Engineering, College of Medicine and College of Engineering, National Taiwan University, Taipei, Taiwan.
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176
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Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease. Nat Microbiol 2020; 5:486-497. [PMID: 31959971 PMCID: PMC7047597 DOI: 10.1038/s41564-019-0655-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 12/06/2019] [Indexed: 12/12/2022]
Abstract
Inflammatory bowel diseases (IBD) are associated with alterations in gut microbial abundances and lumenal metabolite concentrations, but the effects of specific metabolites on the gut microbiota in health and disease remain largely unknown. Here, we analysed the influences of metabolites that are differentially abundant in IBD on the growth and physiology of gut bacteria that are also differentially abundant in IBD. We found that N-acylethanolamines (NAEs), a class of endogenously produced signalling lipids elevated in the stool of IBD patients and a T-cell transfer model of colitis, stimulated growth of species over-represented in IBD and inhibited that of species depleted in IBD in vitro. Using metagenomic sequencing, we recapitulated the effects of NAEs in complex microbial communities ex vivo, with Proteobacteria blooming and Bacteroidetes declining in the presence of NAEs. Metatranscriptomic analysis of the same communities identified components of the respiratory chain as important for the metabolism of NAEs, and this was verified using a mutant deficient for respiratory complex I. In this study, we identified NAEs as a class of metabolites that are elevated in IBD and have the potential to shift gut microbiota towards an IBD-like composition.
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177
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Ahern PP, Maloy KJ. Understanding immune-microbiota interactions in the intestine. Immunology 2020; 159:4-14. [PMID: 31777071 PMCID: PMC6904641 DOI: 10.1111/imm.13150] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 12/13/2022] Open
Abstract
The past two decades have seen an explosion in research that aims to understand how the dynamic interplay with the gut microbiota impacts host health and disease, establishing a role for the gut microbiota in a plethora of pathologies. Understanding how health-promoting microbiota are established and how beneficial host-microbiota interactions are maintained is of immense biomedical importance. Despite the enormous progress that has been made, our knowledge of the specific microbiota members that mediate these effects and the mechanisms underlying these interactions is rudimentary. The dearth of information regarding the nature of advantageous host-microbiota interactions, and the factors that cause these relationships to go awry, has hampered our ability to realize the therapeutic potential of the microbiota. Here we discuss key issues that limit current knowledge and describe a path forwards to improving our understanding of the contributions of the microbiota to host health.
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Affiliation(s)
- Philip P. Ahern
- Department of Cardiovascular and Metabolic SciencesCleveland Clinic Lerner Research InstituteClevelandOHUSA
| | - Kevin J. Maloy
- Institute of Infection, Immunity and InflammationCollege of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowUK
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178
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Dong L, Xie J, Wang Y, Zuo D. Gut Microbiota and Immune Responses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1238:165-193. [PMID: 32323185 DOI: 10.1007/978-981-15-2385-4_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The gut microbiota consists of a dynamic multispecies community living within a particular niche in a mutual synergy with the host organism. Recent findings have revealed roles for the gut microbiota in the modulation of host immunity and the development and progression of immune-mediated diseases. Besides, growing evidence supports the concept that some metabolites mainly originated from gut microbiota are linked to the immune regulation implicated in systemic inflammatory and autoimmune disorders. In this chapter, we describe the recent advances in our understanding of how host-microbiota interactions shape the immune system, how they affect the pathogenesis of immune-associated diseases and the impact of these mechanisms in the efficacy of disease therapy.
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Affiliation(s)
- Lijun Dong
- The Fifth Affiliated Hospital, Southern Medical University, Guangzhou, 510900, China
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Jingwen Xie
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Youyi Wang
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
- School of Laboratory Medicine and Biotechnology, Institute of Molecular Immunology, Southern Medical University, Guangzhou, 510515, China
| | - Daming Zuo
- School of Laboratory Medicine and Biotechnology, Institute of Molecular Immunology, Southern Medical University, Guangzhou, 510515, China.
- Microbiome Medicine Center, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China.
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179
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The impact of gut microbiota manipulation with antibiotics on colon tumorigenesis in a murine model. PLoS One 2019; 14:e0226907. [PMID: 31860645 PMCID: PMC6924659 DOI: 10.1371/journal.pone.0226907] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/07/2019] [Indexed: 12/30/2022] Open
Abstract
It has been suggested that manipulation of gut microbiota using antibiotics can inhibit colitis-associated colorectal cancer (CAC) in a mouse model. We investigated whether timing of gut microbial manipulation using antibiotics affects colon tumorigenesis in the azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced CAC model. CAC was induced in C57BL/6 mice by injection of 12.5 mg/kg AOM followed by three rounds of 1.7% DSS exposure. There were six groups based on timing of antibiotic administration. Colonic inflammation, proliferation, and tumorigenesis were evaluated after animal sacrifice. High-throughput sequencing of the mice feces was performed to characterize changes in gut microbiota. Full-time antibiotic treatment significantly decreased the number and size of tumors, histological scores, and expression of pro-inflammatory cytokines compared to the AOM/DSS group without antibiotic treatment. The early and late antibiotic groups, antibiotic administration from the first and second rounds of DSS to the end of the study, showed significantly lower histological scores and tumor burden. In contrast, the pretreatment antibiotic group, antibiotic administration from 3 weeks prior to AOM to the first round of DSS, did not exhibit decreased tumorigenesis. Principal coordinate analysis showed similar gut microbial community structures among the full-time, early, and late antibiotic groups, whereas other groups showed distinct gut microbial profiles. There was a positive correlation between number of tumors and number of operational taxonomic units. Colonic tumorigenesis was attenuated by antibiotic administration, except for that only prior to DSS administration, suggesting that gut microbial changes should be maintained throughout the entire period of inflammation to suppress tumorigenesis.
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180
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Czaja AJ. Examining pathogenic concepts of autoimmune hepatitis for cues to future investigations and interventions. World J Gastroenterol 2019; 25:6579-6606. [PMID: 31832000 PMCID: PMC6906207 DOI: 10.3748/wjg.v25.i45.6579] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/25/2019] [Accepted: 11/29/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Multiple pathogenic mechanisms have been implicated in autoimmune hepatitis, but they have not fully explained susceptibility, triggering events, and maintenance or escalation of the disease. Furthermore, they have not identified a critical defect that can be targeted. The goals of this review are to examine the diverse pathogenic mechanisms that have been considered in autoimmune hepatitis, indicate investigational opportunities to validate their contribution, and suggest interventions that might evolve to modify their impact. English abstracts were identified in PubMed by multiple search terms. Full length articles were selected for review, and secondary and tertiary bibliographies were developed. Genetic and epigenetic factors can affect susceptibility by influencing the expression of immune regulatory genes. Thymic dysfunction, possibly related to deficient production of programmed cell death protein-1, can allow autoreactive T cells to escape deletion, and alterations in the intestinal microbiome may help overcome immune tolerance and affect gender bias. Environmental factors may trigger the disease or induce epigenetic changes in gene function. Molecular mimicry, epitope spread, bystander activation, neo-antigen production, lymphocytic polyspecificity, and disturbances in immune inhibitory mechanisms may maintain or escalate the disease. Interventions that modify epigenetic effects on gene expression, alter intestinal dysbiosis, eliminate deleterious environmental factors, and target critical pathogenic mechanisms are therapeutic possibilities that might reduce risk, individualize management, and improve outcome. In conclusion, diverse pathogenic mechanisms have been implicated in autoimmune hepatitis, and they may identify a critical factor or sequence that can be validated and used to direct future management and preventive strategies.
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Affiliation(s)
- Albert J Czaja
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, United States
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181
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Gut Microbiome of Chinese Forest Musk Deer Examined across Gender and Age. BIOMED RESEARCH INTERNATIONAL 2019; 2019:9291216. [PMID: 31886268 PMCID: PMC6925676 DOI: 10.1155/2019/9291216] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/28/2019] [Indexed: 12/23/2022]
Abstract
Animal gut microbiota begins to colonize after birth and is functionally indispensable for maintaining the health of the host. It has been reported that gender and age influence the composition of the intestinal microbiome. However, the effects of gender and age on the intestinal microorganism of forest musk deer (FMD) remain unclear. The aim of this study was to establish the relationship between the structure and composition of fecal microbiota of male and female forest musk deer with age. Here, Illumina Miseq 300PE sequencing platform targeting 16S rRNA V3–V4 hypervariable region applied to define the fecal microbiota of male and female FMD with two age groups, juvenile (age 1–2 years) and adult (age 4–10 years). Alpha diversity index did not show significant difference in bacterial diversity between the males and females or among age groups. The intestinal microbiota of FMD was dominated by three phyla, the Firmicutes, Proteobacteria and Bacteroidetes regardless of gender and different ages. Higher proportions of Proteobacteria were found in adult male and juvenile female individuals. The composition of Bacteroidetes was stable with the gender and age of FMD. Interestingly, the relative abundance of genera Clostridiales and Bacteroidales were higher in the juvenile FMD. Conversely, proportions of Pseudomonas and Lachnospiraceae were abundant in the adult FMD. Higher proportions of Ruminococcaceae, Dore, and 5-7N15 were found in the juvenile male groups. They may reflect the different immune resistance of male and female individuals at different stages of development. This study explored the fecal microbiota composition of forest musk deer in relation to gender and age, which may provide an effective strategy for developing intestinal microecological preparations and potential musk deer breeding.
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182
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Zhao H, Cheng N, Zhou W, Chen S, Wang Q, Gao H, Xue X, Wu L, Cao W. Honey Polyphenols Ameliorate DSS‐Induced Ulcerative Colitis via Modulating Gut Microbiota in Rats. Mol Nutr Food Res 2019; 63:e1900638. [DOI: 10.1002/mnfr.201900638] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 09/08/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Haoan Zhao
- Collage of Food Science and TechnologyNorthwest University 229 North TaiBai Road Xi'an 710069 China
- School of Chemical EngineeringNorthwest University 229 North TaiBai Road Xi'an 710069 China
| | - Ni Cheng
- Collage of Food Science and TechnologyNorthwest University 229 North TaiBai Road Xi'an 710069 China
| | - Wenqi Zhou
- Collage of Food Science and TechnologyNorthwest University 229 North TaiBai Road Xi'an 710069 China
| | - Sinan Chen
- Collage of Food Science and TechnologyNorthwest University 229 North TaiBai Road Xi'an 710069 China
| | - Qian Wang
- School of Chemical EngineeringNorthwest University 229 North TaiBai Road Xi'an 710069 China
| | - Hui Gao
- Collage of Food Science and TechnologyNorthwest University 229 North TaiBai Road Xi'an 710069 China
| | - Xiaofeng Xue
- Institute of Apicultural ResearchChinese Academy of Agricultural Sciences Beijing 100093 China
| | - Liming Wu
- Institute of Apicultural ResearchChinese Academy of Agricultural Sciences Beijing 100093 China
| | - Wei Cao
- Collage of Food Science and TechnologyNorthwest University 229 North TaiBai Road Xi'an 710069 China
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183
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Tiffany CR, Bäumler AJ. Dysbiosis: from fiction to function. Am J Physiol Gastrointest Liver Physiol 2019; 317:G602-G608. [PMID: 31509433 PMCID: PMC6879887 DOI: 10.1152/ajpgi.00230.2019] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 08/28/2019] [Accepted: 09/06/2019] [Indexed: 01/31/2023]
Abstract
Advances in data collection technologies reveal that an imbalance (dysbiosis) in the composition of host-associated microbial communities (microbiota) is linked to many human illnesses. This association makes dysbiosis a central concept for understanding how the human microbiota contributes to health and disease. However, it remains problematic to define the term dysbiosis by cataloguing microbial species names. Here, we discuss how incorporating the germ-organ concept, ecological assumptions, and immunological principles into a theoretical framework for microbiota research provides a functional definition for dysbiosis. The generation of such a framework suggests that the next logical step in microbiota research will be to illuminate the mechanistic underpinnings of dysbiosis, which often involves a weakening of immune mechanisms that balance our microbial communities.
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Affiliation(s)
- Connor R Tiffany
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis California
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California at Davis, Davis California
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184
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Induction of Inflammatory Macrophages in the Gut and Extra-Gut Tissues by Colitis-Mediated Escherichia coli. iScience 2019; 21:474-489. [PMID: 31707260 PMCID: PMC6849333 DOI: 10.1016/j.isci.2019.10.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 09/13/2019] [Accepted: 10/23/2019] [Indexed: 12/02/2022] Open
Abstract
Inflammatory macrophages play a critical role in gut and extra-gut inflammatory disorders, which may be promoted through the dysbiosis of gut microbiota. However, it is poorly understood how gut microbiota affect inflammatory macrophages. Here, we found that increased Escherichia coli (E. coli) in inflamed colon may induce inflammatory macrophages in gut and extra-gut tissues. These E. coli are different from other commensal and pathogenic E. coli in genomic components and also in ability to induce inflammatory responses. Dominant E. coli from colitic tissues induce gut inflammatory macrophages through a regulating network consisted of IL-18, IFN-γ, IL-12, and IL-22 in gut tissues. These E. coli also directly activate macrophages. Cytosolic inflammasome components PCKδ, NLRC4, caspase8, and caspase1/11 are involved in E. coli-mediated activation in both gut epithelial cells and macrophages. These disclose a novel mechanism for how dysbiosis of gut microbiota in colitis cause inflammatory macrophages related to multiple diseases. Increased commensal E. coli in colitis induce inflammatory macrophages Colitic E. coli are different from other commensal and pathogenic E. coli Gut inflammatory macrophages by E. coli need IL-18, IFN-γ, IL-12, and IL-22 PCKδ, NLRC4, caspase8, and caspase1/11 are required for E. coli-mediated activation
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185
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Introducing Murine Microbiome Database (MMDB): A Curated Database with Taxonomic Profiling of the Healthy Mouse Gastrointestinal Microbiome. Microorganisms 2019; 7:microorganisms7110480. [PMID: 31652812 PMCID: PMC6920994 DOI: 10.3390/microorganisms7110480] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/17/2019] [Accepted: 10/21/2019] [Indexed: 12/15/2022] Open
Abstract
The gut microbiota modulates overall metabolism, the immune system and brain development of the host. The majority of mammalian gut microbiota consists of bacteria. Among various model animals, the mouse has been most widely used in pre-clinical biological experiments. The significant compositional differences in taxonomic profiles among different mouse strains due to gastrointestinal locations, genotypes and vendors have been well documented. However, details of such variations are yet to be elucidated. This study compiled and analyzed 16S rRNA gene-based taxonomic profiles of 554 healthy mouse samples from 14 different projects to construct a comprehensive database of the microbiome of a healthy mouse gastrointestinal tract. The database, named Murine Microbiome Database, should provide researchers with useful taxonomic information and better biological insight about how each taxon, such as genus and species, is associated with locations in the gastrointestinal tract, genotypes and vendors. The database is freely accessible over the Internet.
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186
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Chu C, Murdock MH, Jing D, Won TH, Chung H, Kressel AM, Tsaava T, Addorisio ME, Putzel GG, Zhou L, Bessman NJ, Yang R, Moriyama S, Parkhurst CN, Li A, Meyer HC, Teng F, Chavan SS, Tracey KJ, Regev A, Schroeder FC, Lee FS, Liston C, Artis D. The microbiota regulate neuronal function and fear extinction learning. Nature 2019; 574:543-548. [PMID: 31645720 PMCID: PMC6818753 DOI: 10.1038/s41586-019-1644-y] [Citation(s) in RCA: 255] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 09/05/2019] [Indexed: 12/13/2022]
Abstract
Multicellular organisms have co-evolved with complex consortia of viruses, bacteria, fungi and parasites, collectively referred to as the microbiota1. In mammals, changes in the composition of the microbiota can influence many physiologic processes (including development, metabolism and immune cell function) and are associated with susceptibility to multiple diseases2. Alterations in the microbiota can also modulate host behaviours-such as social activity, stress, and anxiety-related responses-that are linked to diverse neuropsychiatric disorders3. However, the mechanisms by which the microbiota influence neuronal activity and host behaviour remain poorly defined. Here we show that manipulation of the microbiota in antibiotic-treated or germ-free adult mice results in significant deficits in fear extinction learning. Single-nucleus RNA sequencing of the medial prefrontal cortex of the brain revealed significant alterations in gene expression in excitatory neurons, glia and other cell types. Transcranial two-photon imaging showed that deficits in extinction learning after manipulation of the microbiota in adult mice were associated with defective learning-related remodelling of postsynaptic dendritic spines and reduced activity in cue-encoding neurons in the medial prefrontal cortex. In addition, selective re-establishment of the microbiota revealed a limited neonatal developmental window in which microbiota-derived signals can restore normal extinction learning in adulthood. Finally, unbiased metabolomic analysis identified four metabolites that were significantly downregulated in germ-free mice and have been reported to be related to neuropsychiatric disorders in humans and mouse models, suggesting that microbiota-derived compounds may directly affect brain function and behaviour. Together, these data indicate that fear extinction learning requires microbiota-derived signals both during early postnatal neurodevelopment and in adult mice, with implications for our understanding of how diet, infection, and lifestyle influence brain health and subsequent susceptibility to neuropsychiatric disorders.
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Affiliation(s)
- Coco Chu
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Mitchell H Murdock
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Psychiatry, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Deqiang Jing
- Department of Psychiatry, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Tae Hyung Won
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Hattie Chung
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Adam M Kressel
- Center for Biomedical Science and Bioelectronic Medicine, Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA
- Elmezzi Graduate School, Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA
- Department of Surgery, Northshore University Hospital, Northwell Health, Manhasset, NY, USA
| | - Tea Tsaava
- Center for Biomedical Science and Bioelectronic Medicine, Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Meghan E Addorisio
- Center for Biomedical Science and Bioelectronic Medicine, Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Gregory G Putzel
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Lei Zhou
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Nicholas J Bessman
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ruirong Yang
- Department of Psychiatry, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Saya Moriyama
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Christopher N Parkhurst
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Anfei Li
- Department of Psychiatry, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Heidi C Meyer
- Department of Psychiatry, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Fei Teng
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Sangeeta S Chavan
- Center for Biomedical Science and Bioelectronic Medicine, Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA
- Elmezzi Graduate School, Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Kevin J Tracey
- Center for Biomedical Science and Bioelectronic Medicine, Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA
- Elmezzi Graduate School, Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, USA
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Koch Institute of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Francis S Lee
- Department of Psychiatry, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Conor Liston
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, NY, USA.
- Department of Psychiatry, Weill Cornell Medicine, Cornell University, New York, NY, USA.
- Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, Cornell University, New York, NY, USA.
| | - David Artis
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA.
- Friedman Center for Nutrition and Inflammation, Joan and Sanford I. Weill Department of Medicine, Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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187
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Shivaji S. Connect between gut microbiome and diseases of the human eye. J Biosci 2019; 44:110. [PMID: 31719219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Implicating dysbiosis of gut microbiome in digestive tract diseases/diet-related diseases (obesity, inflammatory bowel disease, enterocolitis, diabetes, etc.) may be expected. However, when gut microbiome dysbiosis is implicated in extraintestinal diseases like cancers, muscular dystrophy, mental disorders, vaginosis, etc., it is all the more challenging. An additional challenge would be to ascertain the role of gut microbiome in ocular diseases, which are as remote as the brain. The present review highlights studies that establish the connect between gut microbiome dysbiosis and inflammatory ocular diseases such as uveitis, bacterial keratitis, fungal keratitis, etc.
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Affiliation(s)
- S Shivaji
- Brien Holden Eye Research Centre, LV Prasad Eye Institute, Hyderabad 500 034, India,
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188
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Recent Advances in Our Understanding of the Link between the Intestinal Microbiota and Systemic Lupus Erythematosus. Int J Mol Sci 2019; 20:ijms20194871. [PMID: 31575045 PMCID: PMC6801612 DOI: 10.3390/ijms20194871] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 09/13/2019] [Accepted: 09/29/2019] [Indexed: 12/12/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease featuring enhanced expression of type I interferon (IFN) and autoantibody production triggering inflammation of, and damage to, multiple organs. Continuing research efforts focus on how gut microbes trigger systemic autoimmunity and SLE. The gut microbial communities of mice and humans with lupus have been investigated via high-throughput sequencing. The Firmicutes-to-Bacteroidetes ratio is consistently reduced in SLE patients, regardless of ethnicity. The relative abundance of Lactobacillus differs from the animal model used (MRL/lpr mice or NZB/W F1 mice). This may indicate that interactions between gut microbes and the host, rather than the enrichment of certain gut microbes, are especially significant in terms of SLE development. Enterococcus gallinarum and Lactobacillus reuteri, both of which are possible gut pathobionts, become translocated into systemic tissue if the gut epithelial barrier is impaired. The microbes then interact with the host immune systems, activating the type I IFN pathway and inducing autoantibody production. In addition, molecular mimicry may critically link the gut microbiome to SLE. Gut commensals of SLE patients share protein epitopes with the Ro60 autoantigen. Ruminococcus gnavus strain cross-reacted with native DNA, triggering an anti-double-stranded DNA antibody response. Expansion of R. gnavus in SLE patients paralleled an increase in disease activity and lupus nephritis. Such insights into the link between the gut microbiota and SLE enhance our understanding of SLE pathogenesis and will identify biomarkers predicting active disease.
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189
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Ungaro F, Massimino L, D'Alessio S, Danese S. The gut virome in inflammatory bowel disease pathogenesis: From metagenomics to novel therapeutic approaches. United European Gastroenterol J 2019; 7:999-1007. [PMID: 31662858 DOI: 10.1177/2050640619876787] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/16/2019] [Indexed: 12/24/2022] Open
Abstract
The association of intestinal dysbiosis with the pathogenesis of inflammatory bowel disease has been well established. Besides bacteria, microbiota comprises yeasts, archaea, protists and viruses, neglected actors in inflammatory bowel disease-associated microbiota. In the past, a great limitation in studying microbiota composition was the low sensitivity of sequencing technologies and that few computational approaches were sufficient to thoroughly analyse the whole microbiome. However, new cutting-edge technologies in nucleic acid sequencing, -omics analysis and the innovative statistics and bioinformatics pipelines made possible more sensitive and accurate metagenomics, ultimately identifying novel players in intestinal inflammation, including prokaryotic and eukaryotic viruses, that together form the gut virome. The discovery of peculiar inflammatory bowel disease-associated microbial strains will not only shed new light on inflammatory bowel disease aetiogenesis, they may also support the development of novel therapeutic strategies not merely treating symptoms, but precisely counteracting the primary cause of chronic intestinal inflammation.
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Affiliation(s)
- Federica Ungaro
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center, Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Luca Massimino
- Division of Neuroscience, San Raffaele Scientific Institute, Milan, Italy
| | - Silvia D'Alessio
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center, Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Silvio Danese
- IBD Center, Laboratory of Gastrointestinal Immunopathology, Humanitas Clinical and Research Center, Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Milan, Italy
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191
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Yi J, Bergstrom K, Fu J, Shan X, McDaniel JM, McGee S, Qu D, Houchen CW, Liu X, Xia L. Dclk1 in tuft cells promotes inflammation-driven epithelial restitution and mitigates chronic colitis. Cell Death Differ 2019; 26:1656-1669. [PMID: 30478383 PMCID: PMC6748088 DOI: 10.1038/s41418-018-0237-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 09/28/2018] [Accepted: 10/22/2018] [Indexed: 12/16/2022] Open
Abstract
Ulcerative colitis (UC) is a chronic inflammatory bowel disease characterized by defective intestinal barrier integrity toward the microbiota and epithelial damage. Double cortin-like kinase 1 (Dclk1), a marker of intestinal tuft cells, can regulate tissue regenerative responses, but its role in epithelial repair during bacterial-dependent chronic colitis is unclear. We addressed this question using our recently developed mouse model of spontaneous microbiota-dependent colitis induced by mucin-type O-glycan deficiency (DKO), which recapitulates most features of human UC. We generated DKO mice lacking intestinal epithelial Dclk1 (DKO;Dclk1ΔIEC) and analyzed colitis onset and severity using clinical and histologic indices, immune responses by qPCR and immunostaining, and epithelial responses using proliferation markers and organoid culture. We found 3-4-week-old DKO;Dclk1ΔIEC mice developed worsened spontaneous colitis characterized by reduced body weight, loose stool, severe colon thickening, epithelial lesions, and inflammatory cell infiltrates compared with DKO mice. The primary defect was an impaired epithelial proliferative response during inflammation. Dclk1 deficiency also reduced inflammation-induced proliferation and growth of colon organoids ex vivo. Mechanistically, Dclk1 expression was important for inflammation-induced Cox2 expression and prostaglandin E2 (PGE2) production in vivo, and PGE2 rescued proliferative defects in Dclk1-deficient colonic organoids. Although tuft cells were expanded in both DKO and DKO;Dclk1ΔIEC relative to WT mice, loss of Dclk1 was associated with reduced tuft cell activation (i.e., proliferation) during inflammation. Similar results were found in DKO vs. DKO;Dclk1ΔIEC mice at 3-6 months of age. Our results support that tuft cells, via Dclk1, are important responders to bacterial-induced colitis by enhancing epithelial repair responses, which in turn limits bacterial infiltration into the mucosa.
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Affiliation(s)
- Jun Yi
- Department of Gastroenterology, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, China
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Kirk Bergstrom
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Jianxin Fu
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Xindi Shan
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - J Michael McDaniel
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Samuel McGee
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Dongfeng Qu
- Department of Internal Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Courtney W Houchen
- Department of Internal Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Xiaowei Liu
- Department of Gastroenterology, Xiangya Hospital of Central South University, Changsha, Hunan, 410008, China.
| | - Lijun Xia
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA.
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.
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192
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Snider EJ, Compres G, Freedberg DE, Khiabanian H, Nobel YR, Stump S, Uhlemann AC, Lightdale CJ, Abrams JA. Alterations to the Esophageal Microbiome Associated with Progression from Barrett's Esophagus to Esophageal Adenocarcinoma. Cancer Epidemiol Biomarkers Prev 2019; 28:1687-1693. [PMID: 31466948 DOI: 10.1158/1055-9965.epi-19-0008] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 04/17/2019] [Accepted: 07/10/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The incidence of esophageal adenocarcinoma has risen dramatically over the past half century, and the underlying reasons are incompletely understood. Broad shifts to the upper gastrointestinal microbiome may be partly responsible. The goal of this study was to describe alterations in the esophageal microbiome that occur with progression from Barrett's esophagus to esophageal adenocarcinoma. METHODS A case-control study was performed of patients with and without Barrett's esophagus who were scheduled to undergo upper endoscopy. Demographic, clinical, and dietary intake data were collected, and esophageal brushings were collected during the endoscopy. 16S rRNA gene sequencing was performed to characterize the microbiome. RESULTS A total of 45 patients were enrolled and included in the analyses [16 controls; 14 Barrett's esophagus without dysplasia (NDBE); 6 low-grade dysplasia (LGD); 5 high-grade dysplasia (HGD); and 4 esophageal adenocarcinoma]. There was no difference in alpha diversity between non-Barrett's esophagus and Barrett's esophagus, but there was evidence of decreased diversity in patients with esophageal adenocarcinoma as assessed by Simpson index. There was an apparent shift in composition at the transition from LGD to HGD, and patients with HGD and esophageal adenocarcinoma had decreased Firmicutes and increased Proteobacteria. In addition, patients with HGD or esophageal adenocarcinoma had increased Enterobacteriaceae and Akkermansia muciniphila and reduced Veillonella. In the study population, patients taking proton pump inhibitors had increased Streptococcus and decreased Gram-negative bacteria overall. CONCLUSIONS Shifts in the Barrett's esophagus-associated microbiome were observed in patients with HGD and esophageal adenocarcinoma, with increases in certain potentially pathogenic bacteria. IMPACT The microbiome may play a role in esophageal carcinogenesis.
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Affiliation(s)
- Erik J Snider
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington
| | - Griselda Compres
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Daniel E Freedberg
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Hossein Khiabanian
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey
| | - Yael R Nobel
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Stephania Stump
- Department of Medicine, Columbia University Irving Medical Center, New York, New York.,Microbiome Core Facility, Columbia University Irving Medical Center, New York, New York
| | - Anne-Catrin Uhlemann
- Department of Medicine, Columbia University Irving Medical Center, New York, New York.,Microbiome Core Facility, Columbia University Irving Medical Center, New York, New York
| | - Charles J Lightdale
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Julian A Abrams
- Department of Medicine, Columbia University Irving Medical Center, New York, New York.
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193
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Goto Y. Epithelial Cells as a Transmitter of Signals From Commensal Bacteria and Host Immune Cells. Front Immunol 2019; 10:2057. [PMID: 31555282 PMCID: PMC6724641 DOI: 10.3389/fimmu.2019.02057] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/14/2019] [Indexed: 12/20/2022] Open
Abstract
Intestinal epithelial cells (IECs) are non-hematopoietic cells that form a physical barrier against external antigens. Recent studies indicate that IECs have pleiotropic functions in the regulation of luminal microbiota and the host immune system. IECs produce various immune modulatory cytokines and chemokines in response to commensal bacteria and contribute to developing the intestinal immune system. In contrast, IECs receive cytokine signals from immune cells and produce various immunological factors against luminal bacteria. This bidirectional function of IECs is critical to regulate homeostasis of microbiota and the host immune system. Disruption of the epithelial barrier leads to detrimental host diseases such as inflammatory bowel disease, colonic cancer, and pathogenic infection. This review provides an overview of the functions and physiology of IECs and highlights their bidirectional functions against luminal bacteria and immune cells, which contribute to maintaining gut homeostasis.
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Affiliation(s)
- Yoshiyuki Goto
- Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba, Japan.,Division of Mucosal Symbiosis, International Research and Development Center for Mucosal Vaccines, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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194
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Moderate Traumatic Brain Injury Alters the Gastrointestinal Microbiome in a Time-Dependent Manner. Shock 2019; 52:240-248. [DOI: 10.1097/shk.0000000000001211] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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195
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Litvak Y, Bäumler AJ. Microbiota-Nourishing Immunity: A Guide to Understanding Our Microbial Self. Immunity 2019; 51:214-224. [DOI: 10.1016/j.immuni.2019.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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196
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Zhu W, Miyata N, Winter MG, Arenales A, Hughes ER, Spiga L, Kim J, Sifuentes-Dominguez L, Starokadomskyy P, Gopal P, Byndloss MX, Santos RL, Burstein E, Winter SE. Editing of the gut microbiota reduces carcinogenesis in mouse models of colitis-associated colorectal cancer. J Exp Med 2019; 216:2378-2393. [PMID: 31358565 PMCID: PMC6781011 DOI: 10.1084/jem.20181939] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 05/28/2019] [Accepted: 07/09/2019] [Indexed: 12/13/2022] Open
Abstract
Enterobacteriaceae family members such as E. coli exacerbate development of intestinal malignancy. Zhu et al. report that targeting the metabolism of protumoral Enterobacteriaceae by tungstate prevents tumor development in murine models of colitis-associated colorectal cancer. Chronic inflammation and gut microbiota dysbiosis, in particular the bloom of genotoxin-producing E. coli strains, are risk factors for the development of colorectal cancer. Here, we sought to determine whether precision editing of gut microbiota metabolism and composition could decrease the risk for tumor development in mouse models of colitis-associated colorectal cancer (CAC). Expansion of experimentally introduced E. coli strains in the azoxymethane/dextran sulfate sodium colitis model was driven by molybdoenzyme-dependent metabolic pathways. Oral administration of sodium tungstate inhibited E. coli molybdoenzymes and selectively decreased gut colonization with genotoxin-producing E. coli and other Enterobacteriaceae. Restricting the bloom of Enterobacteriaceae decreased intestinal inflammation and reduced the incidence of colonic tumors in two models of CAC, the azoxymethane/dextran sulfate sodium colitis model and azoxymethane-treated, Il10-deficient mice. We conclude that metabolic targeting of protumoral Enterobacteriaceae during chronic inflammation is a suitable strategy to prevent the development of malignancies arising from gut microbiota dysbiosis.
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Affiliation(s)
- Wenhan Zhu
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Naoteru Miyata
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX.,Digestive Disease Center, International University of Health and Welfare, Mita Hospital, Japan
| | - Maria G Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Alexandre Arenales
- Departamento de Clinica e Cirurgia Veterinarias, Escola de Veterinaria, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Elizabeth R Hughes
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Luisella Spiga
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jiwoong Kim
- Department of Clinical Science, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX
| | | | - Petro Starokadomskyy
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX
| | - Purva Gopal
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Mariana X Byndloss
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN
| | - Renato L Santos
- Departamento de Clinica e Cirurgia Veterinarias, Escola de Veterinaria, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ezra Burstein
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX .,Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Sebastian E Winter
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX
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197
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Gut Microbiota: A New Strategy to Study the Mechanism of Electroacupuncture and Moxibustion in Treating Ulcerative Colitis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2019; 2019:9730176. [PMID: 31354859 PMCID: PMC6632505 DOI: 10.1155/2019/9730176] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/21/2019] [Accepted: 05/30/2019] [Indexed: 02/07/2023]
Abstract
Previous studies have confirmed that acupuncture and moxibustion is an effective way for treating ulcerative colitis (UC). However, the exact mechanism is unclear yet. In this study, DSS-induced UC mice were treated by electroacupuncture and moxibustion, and the genome of intestinal flora was subsequently detected by high-throughput sequencing in order to explore the detailed mechanism in terms of intestinal flora. The results indicated that the alpha diversity indices and beta diversity of intestinal flora were improved by electroacupuncture and moxibustion treatments, especially by the moxibustion treatment. These treatments inhibited Streptococcus, Odoribacter, and Allobaculum whereas it facilitated Lactobacillus on genus level. Further correlation analysis showed that the alpha diversity indices were positively correlated with the percentage of Treg cells in CD4+ cells but negatively correlated with the percentage of Th17 in CD4+ cells. These data indicated that both electroacupuncture and moxibustion can promote the intestinal flora diversity, providing a new view to understand the relationship between host and microbiome when using some external therapies.
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198
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Study Insights into Gastrointestinal Cancer through the Gut Microbiota. BIOMED RESEARCH INTERNATIONAL 2019; 2019:8721503. [PMID: 31341907 PMCID: PMC6612970 DOI: 10.1155/2019/8721503] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 05/28/2019] [Indexed: 12/16/2022]
Abstract
The gut microbiome in human is recognized as a “microbial organ” for its roles and contributions in regulating the human homeostasis and metabolism. Gastrointestinal (GI) cancers, especially colorectal cancer (CRC), rank as the most common cancer-related deaths worldwide. Evidences have suggested that the disorder of gut microbiota, also named as “dysbiosis,” is related to the development of a variety of diseases such as inflammatory bowel disease (IBD) and the CRC. However, detailed mechanisms between disease and gut microbiota remain largely unknown. This review introduced the correlation between gastrointestinal diseases and the microbiota in human gut from the recent studies, as well as the roles of microbiota in manipulating the CRC and IBDs development, in order to facilitate future studies and to develop novel methods for the precaution, diagnosis, or even cure of gastrointestinal diseases. Additionally, we also elucidated the possibility of probiotics in treatment against CRC.
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199
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Lengfelder I, Sava IG, Hansen JJ, Kleigrewe K, Herzog J, Neuhaus K, Hofmann T, Sartor RB, Haller D. Complex Bacterial Consortia Reprogram the Colitogenic Activity of Enterococcus faecalis in a Gnotobiotic Mouse Model of Chronic, Immune-Mediated Colitis. Front Immunol 2019; 10:1420. [PMID: 31281321 PMCID: PMC6596359 DOI: 10.3389/fimmu.2019.01420] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/05/2019] [Indexed: 12/17/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are associated with compositional and functional changes of the intestinal microbiota, but specific contributions of individual bacteria to chronic intestinal inflammation remain unclear. Enterococcus faecalis is a resident member of the human intestinal core microbiota that has been linked to the pathogenesis of IBD and induces chronic colitis in susceptible monoassociated IL-10-deficient (IL-10−/−) mice. In this study, we characterized the colitogenic activity of E. faecalis as part of a simplified human microbial consortium based on seven enteric bacterial strains (SIHUMI). RNA sequencing analysis of E. faecalis isolated from monoassociated wild type and IL-10−/− mice identified 408 genes including 14 genes of the ethanolamine utilization (eut) locus that were significantly up-regulated in response to inflammation. Despite considerable up-regulation of eut genes, deletion of ethanolamine utilization (ΔeutVW) had no impact on E. faecalis colitogenic activity in monoassociated IL-10−/− mice. However, replacement of the E. faecalis wild type bacteria by a ΔeutVW mutant in SIHUMI-colonized IL-10−/− mice resulted in exacerbated colitis, suggesting protective functions of E. faecalis ethanolamine utilization in complex bacterial communities. To better understand E. faecalis gene response in the presence of other microbes, we purified wild type E. faecalis cells from the colon content of SIHUMI-colonized wild type and IL-10−/− mice using immuno-magnetic separation and performed RNA sequencing. Transcriptional profiling revealed that the bacterial environment reprograms E. faecalis gene expression in response to inflammation, with the majority of differentially expressed genes not being shared between monocolonized and SIHUMI conditions. While in E. faecalis monoassociation a general bacterial stress response could be observed, expression of E. faecalis genes in SIHUMI-colonized mice was characterized by up-regulation of genes involved in growth and replication. Interestingly, in mice colonized with SIHUMI lacking E. faecalis enhanced inflammation was observed in comparison to SIHUMI-colonized mice, supporting the hypothesis that E. faecalis ethanolamine metabolism protects against colitis in complex consortia. In conclusion, this study demonstrates that complex bacterial consortia interactions reprogram the gene expression profile and colitogenic activity of the opportunistic pathogen E. faecalis toward a protective function.
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Affiliation(s)
- Isabella Lengfelder
- Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany
| | - Irina G Sava
- Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany
| | - Jonathan J Hansen
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC, United States
| | - Karin Kleigrewe
- Bavarian Center for Biomolecular Mass Spectrometry, Technische Universität München, Freising, Germany
| | - Jeremy Herzog
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC, United States
| | - Klaus Neuhaus
- ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany.,ZIEL Core Facility Microbiome, Technische Universität München, Freising, Germany
| | - Thomas Hofmann
- Bavarian Center for Biomolecular Mass Spectrometry, Technische Universität München, Freising, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
| | - R Balfour Sartor
- Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, NC, United States
| | - Dirk Haller
- Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany.,ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
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200
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Wortelboer K, Nieuwdorp M, Herrema H. Fecal microbiota transplantation beyond Clostridioides difficile infections. EBioMedicine 2019; 44:716-729. [PMID: 31201141 PMCID: PMC6606746 DOI: 10.1016/j.ebiom.2019.05.066] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/31/2019] [Accepted: 05/31/2019] [Indexed: 10/28/2022] Open
Abstract
The importance of the commensal microbiota to human health and well-being has become increasingly evident over the past decades. From a therapeutic perspective, the popularity of fecal microbiota transplantation (FMT) to restore a disrupted microbiota and amend imbalances has increased. To date, most clinical experience with FMT originates from the treatment of recurrent or refractory Clostridioides difficile infections (rCDI), with resolution rates up to 90%. In addition to CDI, a role for the intestinal microbiome has been implicated in several disorders. FMT has been tested in several randomized controlled trials for the treatment of inflammatory bowel disease, irritable bowel disease and constipation with mixed results. FMT has also been explored for extra-gastrointestinal disorders such as metabolic syndrome, hepatic encephalopathy and graft-versus-host disease. With the exception of recurrent CDI, FMT is currently used in experimental settings only and should not yet be offered as standard care. In addition, it is critical to further standardize and optimize procedures for FMT preparation. This includes determination of active components of FMT to develop (personalized) approaches to treat disease.
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Affiliation(s)
- Koen Wortelboer
- Department of Experimental Vascular Medicine, Amsterdam University Medical Center, Location Academic Medical Center, Amsterdam, the Netherlands.
| | - Max Nieuwdorp
- Department of Vascular Medicine, Amsterdam University Medical Center, Location Academic Medical Center, Amsterdam, the Netherlands; Department of Internal Medicine, Amsterdam University Medical Center, Location Academic Medical Center, Amsterdam, the Netherlands; Amsterdam Diabetes Center, Department of Internal Medicine, Amsterdam University Medical Center, Location VU University Medical Center, Amsterdam, the Netherlands
| | - Hilde Herrema
- Department of Experimental Vascular Medicine, Amsterdam University Medical Center, Location Academic Medical Center, Amsterdam, the Netherlands
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