51
|
Elahi S, Mashhouri S. Immunological consequences of extramedullary erythropoiesis: immunoregulatory functions of CD71 + erythroid cells. Haematologica 2020; 105:1478-1483. [PMID: 32354873 PMCID: PMC7271582 DOI: 10.3324/haematol.2019.243063] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/06/2020] [Indexed: 12/22/2022] Open
Affiliation(s)
- Shokrollah Elahi
- School of Dentistry, University of Alberta, Alberta .,Department of Medical Microbiology and Immunology, University of Alberta, Alberta.,Department of Medical Oncology, Faculty of Medicine and Dentistry, University of Alberta, Alberta.,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
| | | |
Collapse
|
52
|
Gotschlich EC, Colbert RA, Gill T. Methods in microbiome research: Past, present, and future. Best Pract Res Clin Rheumatol 2020; 33:101498. [PMID: 32340923 DOI: 10.1016/j.berh.2020.101498] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The human microbiome is impressively immense and participates in many aspects of our health and wellness, particularly involving the development and maintenance of a healthy immune system. Not only do our microbes teach the immune system to fight infection, they also teach immune tolerance and help maintain homeostasis. From this knowledge, we have learned that the loss of tolerance to microbiota in both innate and adaptive processes plays an important role in immune-mediated and autoimmune disease. In this chapter, we will be discussing about methods used to study the microbiome, both old and new methods, fundamental concepts that have taken hold within the field, and how these principles relate to rheumatology, including thoughts on how microbiome research may be focused in the next decade.
Collapse
Affiliation(s)
- Emily C Gotschlich
- NIH/NIAMS, Building 4 Room 228, 4 Memorial Drive, Bethesda, MD 20892, USA.
| | - Robert A Colbert
- Pediatric Translational Research Branch, 10 Center Drive, Bldg. 10, Rm 12N240E, Bethesda, MD 20892, USA.
| | - Tejpal Gill
- Oregon Health and Science University, 3215 SW Pavilion Loop, Lamfrom Biomedical Research Building 253E, Portland, OR 97239, USA.
| |
Collapse
|
53
|
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.
Collapse
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
| |
Collapse
|
54
|
Albarrak AA, Romana BS, Uraz S, Yousef MH, Juboori AA, Tahan V. Clostridium Difficile Infection in Inflammatory Bowel Disease Patients. Endocr Metab Immune Disord Drug Targets 2020; 19:929-935. [PMID: 30827274 DOI: 10.2174/1871530319666190301120558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 02/12/2019] [Accepted: 02/15/2019] [Indexed: 01/04/2023]
Abstract
BACKGROUND The rising incidence of Clostridium difficile infection (CDI) in the general population has been recognized by health care organizations worldwide. The emergence of hypervirulent strains has made CDI more challenging to understand and treat. Inflammatory bowel disease (IBD) patients are at higher risk of infection, including CDI. OBJECTIVE A diagnostic approach for recurrent CDI has yet to be validated, particularly for IBD patients. Enzyme immunoassay (EIA) for toxins A and B, as well as glutamate dehydrogenase EIA, are both rapid testing options for the identification of CDI. Without a high index of suspicion, it is challenging to initially differentiate CDI from an IBD flare based on clinical evaluation alone. METHODS Here, we provide an up-to-date review on CDI in IBD patients. When caring for an IBD patient with suspected CDI, it is appropriate to empirically treat the presumed infection while awaiting further test results. RESULTS Treatment with vancomycin or fidaxomicin, but not oral metronidazole, has been advocated by an expert review from the clinical practice update committee of the American Gastroenterology Association. Recurrent CDI is more common in IBD patients compared to non-IBD patients (32% versus 24%), thus more aggressive treatment is recommended for IBD patients along with early consideration of fecal microbiota transplant. CONCLUSION Although the use of infliximab during CDI has been debated, clinical experience exists supporting its use in an IBD flare, even with active CDI when needed.
Collapse
Affiliation(s)
- Abdulmajeed A Albarrak
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri, United States
| | - Bhupinder S Romana
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri, United States
| | - Suleyman Uraz
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri, United States
| | - Mohamad H Yousef
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri, United States
| | - Alhareth A Juboori
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri, United States
| | - Veysel Tahan
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri, United States
| |
Collapse
|
55
|
Site-Specific Profiling of the Dental Mycobiome Reveals Strong Taxonomic Shifts during Progression of Early-Childhood Caries. Appl Environ Microbiol 2020; 86:AEM.02825-19. [PMID: 31953340 DOI: 10.1128/aem.02825-19] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/15/2020] [Indexed: 02/02/2023] Open
Abstract
Dental caries is one of the most common diseases worldwide. Bacteria and fungi are both commensals in the oral cavity; however, most research regarding caries has focused on bacterial impacts. The oral fungal mycobiome associated with caries is not well characterized, and its role in disease is unclear. ITS1 amplicon sequencing was used to generate taxonomic profiles from site-specific supragingival plaque samples (n = 82) obtained from 33 children with different caries status. Children were either caries free (CF), caries active with enamel lesions (CAE), or caries active with dentin lesions (CA). Plaque samples were collected from caries-free surfaces (PF) and from enamel (PE) and dentin (PD) lesions. Taxonomic profiles representing the different categorizations (CF-PF, CAE-PF, CAE-PE, CA-PF, CA-PE, and CA-PD) were used to characterize the mycobiome and its change through disease progression. A total of 139 fungal species were identified. Candida albicans was the most abundant species, followed by Candida dubliniensis We found that severely progressed plaque communities (CA-PD) were significantly different from healthy plaque communities (CF-PF). A total of 32 taxa were differentially abundant across the plaque categories. C. albicans, C. dubliniensis, Nigrospora oryzae, and an unclassified Microdochium sp. were correlated with caries, whereas 12 other taxa were correlated with health. C. dubliniensis increased steadily as caries progressed, suggesting that C. dubliniensis may play an important role in caries pathogenicity. In contrast, four health-associated fungal taxa have the potential to antagonize the cariogen Streptococcus mutans via xylitol production, suggesting a possible fungal mechanism that could contribute to maintenance of dental health.IMPORTANCE Early-childhood caries is one of the most prevalent diseases in children worldwide and, while preventable, remains a global public health concern. Untreated cavities are painful and expensive and can lead to tooth loss and a lower quality of life. Caries are driven by acid production via microbial fermentation of dietary carbohydrates, resulting in enamel erosion. While caries is a well-studied disease, most research has focused on bacterial impacts, even though fungi are commensal organisms living within the plaque biofilm. There is very little known about how fungi impact caries pathogenicity. The elucidation of fungal taxa involved in caries disease progression is necessary for a more holistic view of the human oral microbiome. Data from this study will improve our understanding of how the fungal community changes as disease progresses and provide insight into the complex etiology of dental caries, which is necessary for the development of treatment plans and preventative measures.
Collapse
|
56
|
Yin J, Ren W, Wei B, Huang H, Li M, Wu X, Wang A, Xiao Z, Shen J, Zhao Y, Du F, Ji H, Kaboli PJ, Ma Y, Zhang Z, Cho CH, Wang S, Wu X, Wang Y. Characterization of chemical composition and prebiotic effect of a dietary medicinal plant Penthorum chinense Pursh. Food Chem 2020; 319:126568. [PMID: 32169768 DOI: 10.1016/j.foodchem.2020.126568] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/04/2020] [Accepted: 03/04/2020] [Indexed: 02/07/2023]
Abstract
Penthorum chinense Pursh is a dietary medicinal plant widely distributed in Asia-Pacific countries. The present study aims to profile the chemical constituents of P. chinense and investigate its prebiotic role in modulating gut microbiota. Fifty polyphenolic compounds were rapidly identified using UPLC-HR-MS. Total flavonoid and phenolic contents of P. chinense were 46.6% and 61.3% (w/w), respectively. Thirteen individual polyphenols were quantified, which accounted for 33.1% (w/w). P. chinense induced structural arrangement of microbial community in mice, showing increased microbiota diversity, elevated Bacteroidetes/Firmicutes ratio and enriched gut health-promoting bacteria. After a one-week drug-free wash, most of these changes were recovered, but the abundance of some beneficial bacteria was further increased. The altered composition of gut microbiota enriched several metabolic pathways. Moreover, P. chinense increased antioxidant capacity in vivo. The results suggest that polyphenol-enriched P. chinense modulates gut microbiota and enhances antioxidant capacity in mice toward a beneficial environment for host health.
Collapse
Affiliation(s)
- Jianhua Yin
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China; South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Wei Ren
- Drug Research Center of Integrated Traditional Chinese and Western Medicine, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, Sichuan, China
| | - Bin Wei
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou, China
| | - Huimin Huang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China; South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China; South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Xiaoxiao Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China; South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Anqi Wang
- PU-UM Innovative Institute of Chinese Medical Sciences, Guangdong-Macau Traditional Chinese Medicine Technology Industrial Park Development Co., Ltd, Hengqin New Area, Zhuhai, Guangdong, China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China; South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China; South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China; South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Fukuan Du
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China; South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Huijiao Ji
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China; South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Parham Jabbarzadeh Kaboli
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China; South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Yongshun Ma
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China; South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Zhuo Zhang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China; South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Chi Hin Cho
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China; South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China
| | - Shengpeng Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China.
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China; South Sichuan Institute of Translational Medicine, Luzhou, Sichuan, China.
| | - Yitao Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| |
Collapse
|
57
|
Protective effect of Saccharomyces boulardii on intestinal mucosal barrier of dextran sodium sulfate-induced colitis in mice. Chin Med J (Engl) 2020; 132:1951-1958. [PMID: 31335471 PMCID: PMC6708699 DOI: 10.1097/cm9.0000000000000364] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background: The effect and mechanism of Saccharomyces boulardii (Sb) in inflammatory bowel disease are unclear. The objective of the study was to evaluate the impact of Sb on intestinal mucosal barrier and intestinal flora in a colitis mouse model. Methods: Forty C57BL/6J male mice were randomly assigned to five groups: normal control group (A), pathologic control group (B), Sb treatment group (C), mesalazine treatment group (D), and Sb combined with mesalazine treatment group (E). Colitis was induced by the addition of 2.5% (wt/vol) dextran sodium sulfate (DSS) in the drinking water ad libitum for 7 days. The general condition, weight change, stool property, and bloody stool level of mice were observed to evaluate the disease activity index. The expression of zona occludens-1 (ZO-1) and occludin in intestinal tissue were measured by immunohistochemistry. The level of tumor necrosis factor-α (TNF-α) and interleukin (IL)-8 in plasma was measured by enzyme linked immunosorbent assay. Inter-cellular tight junctions were observed by transmission electron microscopy. The feces and intestinal contents were collected sterilely, and intestinal flora was analyzed by 16S rRNA sequencing. Results: Compared with group B, Sb reduced the disease activity index and histological score of group C (disease activity index: group B 2.708 ± 0.628, group C 1.542 ± 0.616, PBC = 0.005; histological score: group B 9.875 ± 3.271, group C 4.750 ± 1.832, PBC = 0.005) in DSS-induced colitis in mice. Sb exerted a protect effect on the expression of ZO-1 (group B 2.075 ± 1.176, group C 4.225 ± 1.316, PBC = 0.019) and occludin (group B 2.200 ± 0.968, group C 3.525 ± 1.047, PBC = 0.023). Compared with group B, Sb decreased the level of TNF-α and IL-8 of group C (TNF-α: group B 716.323 ± 44.691 ng/L, group C 521.740 ± 90.121 ng/L, PBC = 0.001; IL-8: group B 128.992 ± 11.475 pg/mL, group C 106.283 ± 15.906 pg/mL, PBC = 0.012). Treatment with Sb preserved the tight junctions and ameliorated microvilli and inter-cellular space. Treatment with Sb also showed its own characteristics: a higher percentage of Bacteroidetes and a lower percentage of Firmicutes, with significant differences or a significant trend. The proportion of the S24-7 family was increased significantly in the Sb treatment group. Conclusions: Sb shows an anti-inflammatory effect and has a protective effect on the intestinal mucosal mechanical barrier. Sb may up-regulate the abundance of family S24-7 specifically, and maybe a mechanism underlying its function.
Collapse
|
58
|
Song YF, Pei LX, Chen L, Geng H, Yuan MQ, Xu WL, Wu J, Zhou JY, Sun JH. Electroacupuncture Relieves Irritable Bowel Syndrome by Regulating IL-18 and Gut Microbial Dysbiosis in a Trinitrobenzene Sulfonic Acid-Induced Post-Inflammatory Animal Model. THE AMERICAN JOURNAL OF CHINESE MEDICINE 2020; 48:77-90. [PMID: 31918565 DOI: 10.1142/s0192415x20500044] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Post inflammatory irritable bowel syndrome (PI-IBS), a subset of IBS, is characterized by symptoms of visceral pain, bloating, and changed bowel habits that occur post initial episode of intestinal infection. Gut microbial dysbiosis or inflammation plays a key role in the pathogenesis of abdominal hypersensitivity of PI-IBS. Electroacupuncture (EA) stimulation results in an alleviated PI-IBS-associated symptom. This study investigated the effect of EA on IL-18 and gut microbial dysbiosis in one visceral hypersensitive rat models with PI-IBS. A trinitrobenzene sulfonic acid (TNBS)-induced visceral hypersensitivity rat model was developed. EA stimulation was applied to the ST25 and ST36 acupoints. Animals were assessed using abdominal withdrawal reflex (AWR) scores to determine the development of colonic visceral hypersensitivity. The 16S rRNA was used to correlate microbial diversity. IL-18 expression in colon was quantified by quantitative real-time PCR and western blotting. We identified that model rats had an increased visceral hypersensitivity to colorectal distention at different distention pressures compared with the normal group. Sensitivity to colorectal distention decreased after EA stimulation. The composition of the fecal microbiota was different between groups. Specifically, in the model group Empedobacter, Psychrobacter, Enterococcus, Butyricimonas, Vampirovibrio, Kurthia, Intestinimonas, Neisseria, Falsiporphyromonas, Bilophila, Fusobacterium, Alistipes, Veillonella, Flavonifractor, Clostridium XlVa were more abundant affected genera, whereas Lactobacillus was enriched in normal rats. EA stimulation was correlated with significant decrease in the phyla of Fusobacteria. The mRNA and protein levels of IL-18 were higher in the model group. Meanwhile, EA stimulation attenuated this response. In a word, our findings suggest that PI-IBS is associated with significant increase in IL-18 levels as well as an alteration in microbiome diversity. These changes can be reversed with EA treatment. EA stimulation has a positive effect in alleviating symptoms of visceral hypersensitivity and protecting the gastrointestinal tract.
Collapse
Affiliation(s)
- Ya-Fang Song
- Department of Acupuncture, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, P. R. China
| | - Li-Xia Pei
- Department of Acupuncture, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, P. R. China
| | - Lu Chen
- Department of Acupuncture, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, P. R. China
| | - Hao Geng
- Department of Acupuncture, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, P. R. China
| | - Meng-Qian Yuan
- Department of Acupuncture, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, P. R. China
| | - Wan-Li Xu
- Department of the First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, P. R. China
| | - Jian Wu
- Department of Central Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, P. R. China
| | - Jin-Yong Zhou
- Department of Central Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, P. R. China
| | - Jian-Hua Sun
- Department of Acupuncture, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, P. R. China
| |
Collapse
|
59
|
Abstract
Objective: The metabolites produced by the gut microbiota are of interest to scientists. The objective of this review was to provide an updated summary of progress regarding the microbiota and their metabolites and influences on the pathogenesis of inflammatory bowel disease (IBD). Data sources: The author retrieved information from the PubMed database up to January 2018, using various combinations of search terms, including IBD, microbiota, and metabolite. Study selection: Both clinical studies and animal studies of intestinal microbiota and metabolites in IBD were selected. The information explaining the possible pathogenesis of microbiota in IBD was organized. Results: In IBD patients, the biodiversity of feces/mucosa-associated microbiota is decreased, and the probiotic microbiota is also decreased, whereas the pathogenic microbiota are increased. The gut microbiota may be a target for diagnosis and treatment of IBD. Substantial amounts of data support the view that the microbiota and their metabolites play pivotal roles in IBD by affecting intestinal permeability and the immune response. Conclusions: This review highlights the advances in recent gut microbiota research and clarifies the importance of the gut microbiota in IBD pathogenesis. Future research is needed to study the function of altered bacterial community compositions and the roles of metabolites.
Collapse
|
60
|
Huidrom S, Beg M. Dysbiosis of gut microbiota and human diseases. JOURNAL OF MAHATMA GANDHI INSTITUTE OF MEDICAL SCIENCES 2020. [DOI: 10.4103/jmgims.jmgims_59_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
|
61
|
Kim S, Thapa I, Zhang L, Ali H. A novel graph theoretical approach for modeling microbiomes and inferring microbial ecological relationships. BMC Genomics 2019; 20:945. [PMID: 31856723 PMCID: PMC6923821 DOI: 10.1186/s12864-019-6288-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background Microbiomes play vital roles in shaping environments and stabilize them based on their compositions and inter-species relationships among its species. Variations in microbial properties have been reported to have significant impact on their host environment. For example, variants in gut microbiomes have been reported to be associated with several chronic conditions, such as inflammatory disease and irritable bowel syndrome. However, how microbial bacteria contribute to pathogenesis still remains unclear and major research questions in this domain remain unanswered. Methods We propose a split graph model to represent the composition and interactions of a given microbiome. We used metagenomes from Korean populations in this study. The dataset consists of three different types of samples, viz. mucosal tissue and stool from Crohn’s disease patients and stool from healthy individuals. We use the split graph model to analyze the impact of microbial compositions on various host phenotypes. Utilizing the graph model, we have developed a pipeline that integrates genomic information and pathway analysis to characterize both critical informative components of inter-bacterial correlations and associations between bacterial taxa and various metabolic pathways. Results The obtained results highlight the importance of the microbial communities and their inter-relationships and show how these microbial structures are correlated with Crohn’s disease. We show that there are significant positive associations between detected taxonomic biomarkers as well as multiple functional modules in the split graph of mucosal tissue samples from CD patients. Bacteria Moraxellaceae and Pseudomonadaceae were detected as taxonomic biomarkers in CD groups. Higher abundance of these bacteria have been reported in previous study and several metabolic pathways associated with these bacteria were characterized in CD samples. Conclusions The proposed pipeline provides a new way to approach the analysis of complex microbiomes. The results obtained from this study show great potential in unraveling mechansims in complex biological systems to understand how various components in such complex environments are associated with critical biological functions.
Collapse
Affiliation(s)
- Suyeon Kim
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, 68182, NE, USA
| | - Ishwor Thapa
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, 68182, NE, USA
| | - Ling Zhang
- School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, 68182, NE, USA
| | - Hesham Ali
- College of Information Science and Technology, University of Nebraska at Omaha, Omaha, 68182, NE, USA.
| |
Collapse
|
62
|
Li KJ, Chen ZL, Huang Y, Zhang R, Luan XQ, Lei TT, Chen L. Dysbiosis of lower respiratory tract microbiome are associated with inflammation and microbial function variety. Respir Res 2019; 20:272. [PMID: 31796027 PMCID: PMC6892239 DOI: 10.1186/s12931-019-1246-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 11/22/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Lower respiratory tract (LRT) microbiome has been reported to associate with pulmonary diseases. Unregulated inflammation is an underlying cause of variable lung diseases. The lung microbiome may play an important role in the smoking-induced inflammatory lung diseases. What's more, the function of microbiome may be more important for understanding how microbes interact with host. Our study aims to explore the effects of smoking on the lower respiratory tract microbiome, the association between variation of lower respiratory tract microbiome and inflammation and whether smoking exposure changes the function of lower respiratory tract microbime. METHODS Forty male mice were randomly divided into smoking group and non-smoking group, and the smoking group was exposed to cigarette smoke for 2 h per day for 90 days. After experiment, the blood samples were collected to measure the concentration of interleukin-6 (IL-6) and C reactive protein (CRP) by ELISA. Lung tissue samples were used to detect the community and diversity of lower respiratory tract microbiome through 16S rRNA gene quantification and sequencing technology. ANOSIM and STAMP were performed to analyze the differences of the microbial community structure between smoking group and non-smoking group. SPSS 24.0 software was used to analyze the correlations between microbiome and inflammation mediators through scatter plots and Spearman correlation coefficient. Microbial metabolic function was predicted by PICRUSt based on the 16 s rRNA gene quantification and sequencing results. PATRIC database was searched for the potential pathogenic bacteria in lower respiratory tract. RESULTS Our results suggested that smoking had markedly effects on the microbiota structure of lower respiratory tract based on Bray-Curtis distance (R2 = 0.084, p = 0.005) and on unweighted uniFrac distance (R2 = 0.131, p = 0.002). Smoking mainly affected the abundance of microbiome which belong to Proteobacteria phyla and Firmicutes phyla. Moreover, our results also found that smoking increased the abundance of Acinetobacter, Bacillus and Staphylococcus, which were defined as pathogenic bacteria. Inflammatory mediators were observed to associate with certain microbiome at every level. Most of microbiome which were associated with inflammation belonged to Proteobacteria phyla or Firmicutes phyla. Moreover, we found that the decreased microbiome in smoking group, including Oceanospirillales, Desulfuromonadales, Nesterenkonia, and Lactobacillaceae, all were negatively correlated with IL-6 or CRP. Based on the level of inflammation, the abundance of microbiome differs. At genus level, Lactobacillus, Pelagibacterium, Geobacter and Zoogloea were significantly higher in smoking group with lower IL-6 concentration. The abundance of microbiome was not observed any statistical difference in subgroups with different weight. Three dominant genus, defined as pathogen, were found higher in the smoking group. The microbial functional prediction analysis revealed that ABC-type transport systems, transcription factors, amino acide transport and metabolism, arginine and proline metabolism et al. were distinctively decreased in smoking group, while the proportions of replication, recombination and repair, ribosome, DNA repair and recombination proteins were increased in smoking group (q < 0.05). CONCLUSIONS Members of Proteobacteria phyla and Firmicutes phyla played an important role in the microbial community composition and keeping a relatively balanced homeostasis. Microbiome dysbiosis might break the balance of immune system to drive lung inflammation. There might exist potential probiotics in lower respiratory tract, such as Lactobacillaceae. The altered function of Lower respiratory tract microbiome under smoking exposure may affect the physiological homeostasis of host.
Collapse
Affiliation(s)
- Kang-jie Li
- School of Public Health and Management, Chongqing Medical University, Chongqing, 400016 China
| | - Zi-long Chen
- First Clinical College, Chongqing Medical University, Chongqing, 400016 China
| | - Yao Huang
- First Clinical College, Chongqing Medical University, Chongqing, 400016 China
| | - Rui Zhang
- School of Public Health and Management, Chongqing Medical University, Chongqing, 400016 China
| | - Xiao-qian Luan
- School of Public Health and Management, Chongqing Medical University, Chongqing, 400016 China
| | - Ting-ting Lei
- First Clinical College, Chongqing Medical University, Chongqing, 400016 China
| | - Ling Chen
- The Center of Experimental Teaching Management, Chongqing Medical University, Chongqing, 401331 China
| |
Collapse
|
63
|
Allez M, Auzolle C, Ngollo M, Bottois H, Chardiny V, Corraliza AM, Salas A, Perez K, Stefanescu C, Nancey S, Buisson A, Pariente B, Fumery M, Sokol H, Tréton X, Barnich N, Seksik P, Le Bourhis L. T cell clonal expansions in ileal Crohn's disease are associated with smoking behaviour and postoperative recurrence. Gut 2019; 68:1961-1970. [PMID: 30792246 DOI: 10.1136/gutjnl-2018-317878] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 12/14/2022]
Abstract
UNLABELLED T cell clonal expansions are present in the inflamed mucosa of patients with Crohn's disease (CD) and may be implicated in postoperative recurrence after ileocolonic resection. METHODS T cell receptor (TCR) analysis was performed in 57 patients included in a prospective multicentre cohort. Endoscopic recurrence was defined by a Rutgeerts score >i0. DNA and mRNA were extracted from biopsies collected from the surgical specimen and endoscopy, and analysed by high throughput sequencing and microarray, respectively. RESULTS TCR repertoire in the mucosa of patients with CD displayed diverse clonal expansions. Active smokers at time of surgery had a significantly increased proportion of clonal expansions as compared with non-smokers (25.9%vs17.9%, p=0.02). The percentage of high frequency clones in the surgical specimen was significantly higher in patients with recurrence and correlated with postoperative endoscopic recurrence (area under the curve (AUC) 0.69, 95% CI 0.54 to 0.83). All patients with clonality above 26.8% (18/57) had an endoscopic recurrence. These patients with a high clonality were more frequently smokers than patients with a low clonality (61% vs 23%, p=0.005). The persistence of a similar TCR repertoire at postoperative endoscopy was associated with smoking and disease recurrence. Patients with high clonality showed increased expression of genes associated with CD8 T cells and reduced expression of inflammation-related genes. Expanded clones were found predominantly in the CD8 T cell compartment. CONCLUSION Clonal T cell expansions are implicated in postoperative endoscopic recurrence. CD patients with increased proportion of clonal T cell expansions in the ileal mucosa represent a subgroup associated with smoking and where pathogenesis appears as T cell driven. TRIAL REGISTRATION NUMBER NCT03458195.
Collapse
Affiliation(s)
- Matthieu Allez
- Department of Gastroenterology, Hopital Saint Louis, Paris, France.,INSERM U1160, Hôpital Saint-Louis, Paris, France
| | - Claire Auzolle
- Department of Gastroenterology, Hopital Saint Louis, Paris, France
| | | | - Hugo Bottois
- INSERM U1160, Hôpital Saint-Louis, Paris, France
| | | | | | - Azucena Salas
- Hospital Clinic Barcelona, IDIBAPS, CIBERehd, Barcelona, Spain
| | - Kevin Perez
- INSERM U1160, Hôpital Saint-Louis, Paris, France
| | - Carmen Stefanescu
- Service de Gastroentérologie, MICI et Assistance Nutritive, Hôpital Beaujon, Clichy, France
| | - Stéphane Nancey
- Department of Gastroenterology, Lyon Sud Hospital, Hospices Civils de Lyon, Pierre Benite, Lyon, France
| | - Anthony Buisson
- Gastroenterology Department, University Hospital Estaing, Clermont-Ferrand, France
| | - Benjamin Pariente
- Department of Gastroenterology, Hopital Claude huriez, Lille, France
| | - Mathurin Fumery
- Hepato-Gastroenterology Department, CHU Amiens, Amiens, France
| | - Harry Sokol
- Department of Gastroenterology, Hopital Saint-Antoine, Paris, Île-de-France, France
| | - Xavier Tréton
- Service de Gastroentérologie, MICI et Assistance Nutritive, Hopital Beaujon, Clichy, France
| | - Nicolas Barnich
- M2iSH, UMR Inserm U1071, USC INRA 2018, Université d'Auvergne, Clermont Ferrand, France
| | - Philippe Seksik
- Department of Gastroenterology, Hopital Saint-Antoine, Paris, Île-de-France, France
| | | | | |
Collapse
|
64
|
Xu C, Zhu H, Qiu P. Aging progression of human gut microbiota. BMC Microbiol 2019; 19:236. [PMID: 31660868 PMCID: PMC6819604 DOI: 10.1186/s12866-019-1616-2] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 10/17/2019] [Indexed: 02/07/2023] Open
Abstract
Background Human gut microbiota are important for human health and have been regarded as a “forgotten organ”, whose variation is closely linked with various factors, such as host genetics, diet, pathological conditions and external environment. The diversity of human gut microbiota has been correlated with aging, which was characterized by different abundance of bacteria in various age groups. In the literature, most of the previous studies of age-related gut microbiota changes focused on individual species in the gut community with supervised methods. Here, we aimed to examine the underlying aging progression of the human gut microbial community from an unsupervised perspective. Results We obtained raw 16S rRNA sequencing data of subjects ranging from newborns to centenarians from a previous study, and summarized the data into a relative abundance matrix of genera in all the samples. Without using the age information of samples, we applied an unsupervised algorithm to recapitulate the underlying aging progression of microbial community from hosts in different age groups and identify genera associated to this progression. Literature review of these identified genera indicated that for individuals with advanced ages, some beneficial genera are lost while some genera related with inflammation and cancer increase. Conclusions The multivariate unsupervised analysis here revealed the existence of a continuous aging progression of human gut microbiota along with the host aging process. The identified genera associated to this aging process are meaningful for designing probiotics to maintain the gut microbiota to resemble a young age, which hopefully will lead to positive impact on human health, especially for individuals in advanced age groups.
Collapse
Affiliation(s)
- Congmin Xu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China.,Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, 30332, USA
| | - Huaiqiu Zhu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Peng Qiu
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, 30332, USA.
| |
Collapse
|
65
|
Gao Z, Chen KY, Mueller O, Zhang H, Rakhilin N, Chen J, Shen X. Microbiota of Inflammatory Bowel Disease Models. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2019; 2018:2374-2377. [PMID: 30440884 DOI: 10.1109/embc.2018.8512848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Gut microbiome plays an important role in inflammatory bowel disease (IBD), a group of intestinal chronic inflammation conditions that affect a large population. The animal models of IBD have long been established on basis of pathological features, but their ability to recapitulate patient gut microbiota is unknown. We investigated and compared the composition and biodiversity of bacterial population in the fecal samples from rat models of the two IBD subtypes, and compared them with patient samples. Our analyses revealed that inflammation reduces overall microbiome diversity and increased variation between individuals. We identified specific microbial signatures associated with the two IBD subtypes that were consistent between the animal models and human IBD patients, suggesting that the animal models can partially recapitulate the microbiota in human diseases. Furthermore, metagenome prediction analysis suggested microbial functions that were likely altered by host-microbiota interactions in IBD models.
Collapse
|
66
|
Palmer NP, Silvester JA, Lee JJ, Beam AL, Fried I, Valtchinov VI, Rahimov F, Kong SW, Ghodoussipour S, Hood HC, Bousvaros A, Grand RJ, Kunkel LM, Kohane IS. Concordance between gene expression in peripheral whole blood and colonic tissue in children with inflammatory bowel disease. PLoS One 2019; 14:e0222952. [PMID: 31618209 PMCID: PMC6795427 DOI: 10.1371/journal.pone.0222952] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/10/2019] [Indexed: 12/19/2022] Open
Abstract
Background Presenting features of inflammatory bowel disease (IBD) are non-specific. We hypothesized that mRNA profiles could (1) identify genes and pathways involved in disease pathogenesis; (2) identify a molecular signature that differentiates IBD from other conditions; (3) provide insight into systemic and colon-specific dysregulation through study of the concordance of the gene expression. Methods Children (8–18 years) were prospectively recruited at the time of diagnostic colonoscopy for possible IBD. We used transcriptome-wide mRNA profiling to study gene expression in colon biopsies and paired whole blood samples. Using blood mRNA measurements, we fit a regression model for disease state prediction that was validated in an independent test set of adult subjects (GSE3365). Results Ninety-eight children were recruited [39 Crohn’s disease, 18 ulcerative colitis, 2 IBDU, 39 non-IBD]. There were 1,118 significantly differentially (IBD vs non-IBD) expressed genes in colon tissue, and 880 in blood. The direction of relative change in expression was concordant for 106/112 genes differentially expressed in both tissue types. The regression model from the blood mRNA measurements distinguished IBD vs non-IBD disease status in the independent test set with 80% accuracy using only 6 genes. The overlap of 5 immune and metabolic pathways in the two tissue types was significant (p<0.001). Conclusions Blood and colon tissue from patients with IBD share a common transcriptional profile dominated by immune and metabolic pathways. Our results suggest that peripheral blood expression levels of as few as 6 genes (IL7R, UBB, TXNIP, S100A8, ALAS2, and SLC2A3) may distinguish patients with IBD from non-IBD.
Collapse
Affiliation(s)
- Nathan P. Palmer
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jocelyn A. Silvester
- Division of Gastroenterology and Nutrition, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
| | - Jessica J. Lee
- Division of Gastroenterology and Nutrition, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Andrew L. Beam
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Inbar Fried
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Vladimir I. Valtchinov
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Evidence Based Imaging, Brigham and Women’s Hospital, Harvard Medical School, Massachusetts, United States of America
| | - Fedik Rahimov
- Division of Genetics and Genomics, Boston Children’s Hospital, Departments of Genetics and Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Sek Won Kong
- Computational Health Informatics Program, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Saum Ghodoussipour
- Division of Gastroenterology and Nutrition, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Helen C. Hood
- Division of Gastroenterology and Nutrition, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Athos Bousvaros
- Division of Gastroenterology and Nutrition, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richard J. Grand
- Division of Gastroenterology and Nutrition, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Louis M. Kunkel
- Division of Genetics and Genomics, Boston Children’s Hospital, Departments of Genetics and Pediatrics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Isaac S. Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| |
Collapse
|
67
|
Abstract
Introduction: Inflammatory bowel diseases (IBD) are on the rise worldwide. This review covers the current concepts of the etiology of Crohn´s disease and ulcerative colitis by focusing on an unbalanced interaction between the intestinal microbiota and the mucosal barrier. Understanding these issues is of paramount importance for the development of targeted therapies aiming at the disease cause.Area covered: Gut microbiota alterations and a dysfunctional intestinal mucosa are associated with IBD. Here we focus on specific defense structures of the mucosal barrier, namely antimicrobial peptides and the mucus layer, which keep the gut microbiota at a distance under healthy conditions and are defective in IBD.Expert commentary: The microbiology of both forms of IBD is different but characterized by a reduced bacterial diversity and richness. Abundance of certain bacterial species is altered, and the compositional changes are related to disease activity. In IBD the mucus layer above the epithelium is contaminated by bacteria and the immune reaction is dominated by the antibacterial response. Human genetics suggest that many of the basic deficiencies in the mucosal response, due to Paneth cell, defensin and mucus defects, are primary. Nutrition may also be important but so far there is no therapy targeting the mucosal barrier.
Collapse
Affiliation(s)
- Eduard F Stange
- Innere Medizin I, Medizinische Universitätsklinik, Tübingen, Germany
| | - Bjoern O Schroeder
- Laboratory for Molecular Infection Medicine Sweden (MIMS) -The Nordic EMBL Partnership for Molecular Medicine, and Department of Molecular Biology, Umeå University, Umeå, Sweden
| |
Collapse
|
68
|
Garo LP, Ajay AK, Fujiwara M, Beynon V, Kuhn C, Gabriely G, Sadhukan S, Raheja R, Rubino S, Weiner HL, Murugaiyan G. Smad7 Controls Immunoregulatory PDL2/1-PD1 Signaling in Intestinal Inflammation and Autoimmunity. Cell Rep 2019; 28:3353-3366.e5. [PMID: 31553906 PMCID: PMC6925592 DOI: 10.1016/j.celrep.2019.07.065] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 06/09/2019] [Accepted: 07/18/2019] [Indexed: 02/08/2023] Open
Abstract
Smad7, a negative regulator of TGF-β signaling, has been implicated in the pathogenesis and treatment of inflammatory bowel diseases (IBDs), including Crohn's disease (CD) and ulcerative colitis (UC). Here, we found that Smad7 mediates intestinal inflammation by limiting the PDL2/1-PD1 axis in dendritic cells (DCs) and CD4+T cells. Smad7 deficiency in DCs promotes TGF-β responsiveness and the co-inhibitory molecules PDL2/1 on DCs, and it further imprints T cell-PD1 signaling to promote Treg differentiation. DC-specific Smad7 deletion mitigates DSS-induced colitis by inducing CD103+PDL2/1+DCs and Tregs. In addition, Smad7 deficiency in CD4+T cells promotes PD1 and PD1-induced Tregs in vitro. The transfer of Smad7-deficient CD4+T cells enhances Tregs in vivo and protects against T cell-mediated colitis. Furthermore, Smad7 antisense ameliorates DSS-induced UC, increasing TGF-β and PDL2/1-PD1 signaling. Enhancing PD1 signaling directly via Fc-fused PDL2/1 is also beneficial. Our results identify how Smad7 mediates intestinal inflammation and leverages these pathways therapeutically, providing additional strategies for IBD intervention.
Collapse
Affiliation(s)
- Lucien P Garo
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Amrendra K Ajay
- Renal Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Mai Fujiwara
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Vanessa Beynon
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Chantal Kuhn
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Galina Gabriely
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Supriya Sadhukan
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Radhika Raheja
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Stephen Rubino
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Howard L Weiner
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Gopal Murugaiyan
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
69
|
Thuy-Boun PS, Wolan DW. A glycal-based photoaffinity probe that enriches sialic acid binding proteins. Bioorg Med Chem Lett 2019; 29:2609-2612. [PMID: 31387789 DOI: 10.1016/j.bmcl.2019.07.054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/29/2019] [Accepted: 07/31/2019] [Indexed: 12/22/2022]
Abstract
To identify sialic acid binding proteins from complex proteomes, three photocrosslinking affinity-based probes were constructed using Neu5Ac (5 and 6) and Neu5Ac2en (7) scaffolds. Kinetic inhibition assays and Western blotting revealed the Neu5Ac2en-based 7 to be an effective probe for the labeling of a purified gut microbial sialidase (BDI_2946) and a purified human sialic acid binding protein (hCD33). Additionally, LC-MS/MS affinity-based protein profiling verified the ability of 7 to enrich a low-abundance sialic acid binding protein (complement factor H) from human serum thus validating the utility of this probe in a complex context.
Collapse
Affiliation(s)
- Peter S Thuy-Boun
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Dennis W Wolan
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
| |
Collapse
|
70
|
Abstract
Inflammatory bowel disease (IBD) defines a spectrum of complex disorders. Understanding how environmental risk factors, alterations of the intestinal microbiota, and polygenetic and epigenetic susceptibility impact on immune pathways is key for developing targeted therapies. Mechanistic understanding of polygenic IBD is complemented by Mendelian disorders that present with IBD, pharmacological interventions that cause colitis, autoimmunity, and multiple animal models. Collectively, this multifactorial pathogenesis supports a concept of immune checkpoints that control microbial-host interactions in the gut by modulating innate and adaptive immunity, as well as epithelial and mesenchymal cell responses. In addition to classical immunosuppressive strategies, we discuss how resetting the microbiota and restoring innate immune responses, in particular autophagy and epithelial barrier function, might be key for maintaining remission or preventing IBD. Targeting checkpoints in genetically stratified subgroups of patients with Mendelian disorder-associated IBD increasingly directs treatment strategies as part of personalized medicine.
Collapse
Affiliation(s)
- Holm H Uhlig
- Department of Pediatrics, University of Oxford, Oxford OX3 9DU, United Kingdom; .,Translational Gastroenterology Unit, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Fiona Powrie
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom; .,Translational Gastroenterology Unit, University of Oxford, Oxford OX3 9DU, United Kingdom
| |
Collapse
|
71
|
Valm AM. The Structure of Dental Plaque Microbial Communities in the Transition from Health to Dental Caries and Periodontal Disease. J Mol Biol 2019; 431:2957-2969. [PMID: 31103772 PMCID: PMC6646062 DOI: 10.1016/j.jmb.2019.05.016] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/27/2019] [Accepted: 05/09/2019] [Indexed: 01/01/2023]
Abstract
The human oral cavity harbors diverse communities of microbes that live as biofilms: highly ordered, surface-associated assemblages of microbes embedded in an extracellular matrix. Oral microbial communities contribute to human health by fine-tuning immune responses and reducing dietary nitrate. Dental caries and periodontal disease are together the most prevalent microbially mediated human diseases worldwide. Both of these oral diseases are known to be caused not by the introduction of exogenous pathogens to the oral environment, but rather by a homeostasis breakdown that leads to changes in the structure of the microbial communities present in states of health. Both dental caries and periodontal disease are mediated by synergistic interactions within communities, and both diseases are further driven by specific host inputs: diet and behavior in the case of dental caries and immune system interactions in the case of periodontal disease. Changes in community structure (taxonomic identity and abundance) are well documented during the transition from health to disease. In this review, changes in biofilm physical structure during the transition from oral health to disease and the concomitant relationship between structure and community function will be emphasized.
Collapse
Affiliation(s)
- Alex M Valm
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12210, USA.
| |
Collapse
|
72
|
Kök M, Çekin Y, Çekin AH, Uyar S, Harmandar F, Şahintürk Y. The role of Blastocystis hominis in the activation of ulcerative colitis. TURKISH JOURNAL OF GASTROENTEROLOGY 2019; 30:40-46. [PMID: 30644363 DOI: 10.5152/tjg.2018.18498] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
BACKGROUND/AIMS Several studies have shown that a change in microbiota plays an important role in the pathogenesis of inflammatory bowel disease (IBD). Furthermore, with the emergence in recent studies of differences according to the subtype of IBD and whether the disease is active or in remission, there has started to be research into the relationship between IBD and several microorganisms. Blastocystis hominis is primary among these organisms. The aim of the present study was to determine the role of B. hominis in the acute flare-up of ulcerative colitis (UC). MATERIALS AND METHODS A total of 114 patients with UC were included in the study, with 52 in the active phase. The Mayo scoring system was used for the activity index. Patients determined with a flare-up agent other than B. hominis were excluded from the study. Fecal samples of the patients were examined by the polymerase chain reaction method for the presence of B. hominis. RESULTS B. hominis positivity was determined in 37 (34%) patients with UC. Of the patients, 17 (32.6%) were in the acute flare-up phase, and 20 (32.2%) were in remission (p=0.961). In 11 (64.7%) of the B. hominis positive patients, the disease severity was determined as mild-moderate (p<0.001). CONCLUSION The results of the present study showed that while there was no difference between the active and remission phases in respect of B. hominis presence, there was milder involvement in those determined with B. hominis.
Collapse
Affiliation(s)
- Mehmet Kök
- Department of Internal Medicine, University of Health Sciences Antalya Training and Research Hospital, Antalya, Turkey
| | - Yeşim Çekin
- Department of Microbiology, University of Health Sciences Antalya Training and Research Hospital, Antalya, Turkey
| | - Ayhan Hilmi Çekin
- Department of Gastroenterology, University of Health Sciences Antalya Training and Research Hospital, Antalya, Turkey
| | - Seyit Uyar
- Department of Internal Medicine, University of Health Sciences Antalya Training and Research Hospital, Antalya, Turkey
| | - Ferda Harmandar
- Department of Gastroenterology, University of Health Sciences Antalya Training and Research Hospital, Antalya, Turkey
| | - Yasin Şahintürk
- Department of Internal Medicine, University of Health Sciences Antalya Training and Research Hospital, Antalya, Turkey
| |
Collapse
|
73
|
IgA Responses to Microbiota. Immunity 2019; 49:211-224. [PMID: 30134201 DOI: 10.1016/j.immuni.2018.08.011] [Citation(s) in RCA: 196] [Impact Index Per Article: 39.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/03/2018] [Accepted: 08/06/2018] [Indexed: 12/12/2022]
Abstract
Various immune mechanisms are deployed in the mucosa to confront the immense diversity of resident bacteria. A substantial fraction of the commensal microbiota is coated with immunoglobulin A (IgA) antibodies, and recent findings have established the identities of these bacteria under homeostatic and disease conditions. Here we review the current understanding of IgA biology, and present a framework wherein two distinct types of humoral immunity coexist in the gastrointestinal mucosa. Homeostatic IgA responses employ a polyreactive repertoire to bind a broad but taxonomically distinct subset of microbiota. In contrast, mucosal pathogens and vaccines elicit high-affinity, T cell-dependent antibody responses. This model raises fundamental questions including how polyreactive IgA specificities are generated, how these antibodies exert effector functions, and how they exist together with other immune responses during homeostasis and disease.
Collapse
|
74
|
Gajula P, Quigley EM. Overlapping irritable bowel syndrome and inflammatory bowel disease. MINERVA GASTROENTERO 2019; 65:107-115. [PMID: 30746927 DOI: 10.23736/s1121-421x.19.02559-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The pathogenesis of irritable bowel-type symptoms occurring in patients with inflammatory bowel disease who are in apparent remission continues to generate scientific controversy and the interpretation and management of these symptoms, so distressing to the sufferer, represent major challenges for the clinician. On the one hand, these symptoms often satisfy Rome IV criteria for IBS and their occurrence correlates highly with anxiety, a known trigger for IBS. On the other hand, recent studies have shown that many of these patients exhibit subtle inflammatory changes. These observations beg the question: are these symptoms "true" IBS superimposed on IBD, or an active but subclinical form of IBD? While it is certain that earlier studies failed to detect subclinical inflammation, it is also evident that even with the use of sensitive biomarkers for inflammation, such as calprotectin and lactoferrin backed up by pan-endoscopy and biopsy to exclude ongoing inflammatory activity in its most subtle form, the prevalence of IBS-type symptoms remains higher than expected in the IBD patient. Pending further definition of its etiology and pathology, we coined the term irritable inflammatory bowel syndrome (IIBS) to refer to this phenomenon. Here we explore the risk factors for this entity, sift through clues to its pathogenesis and attempt to provide, albeit bereft of a robust evidence base, an approach to its management.
Collapse
Affiliation(s)
- Prianka Gajula
- Department of Medicine, Houston Methodist Hospital and Weill Cornell Medical College, Houston, TX, USA
| | - Eamonn M Quigley
- Division of Gastroenterology and Hepatology, Lynda K. and David M. Underwood Center for Digestive Disorders, Houston Methodist Hospital and Weill Cornell Medical College, Houston, TX, USA -
| |
Collapse
|
75
|
Dunsmore G, Koleva P, Ghobakhloo N, Sutton R, Ambrosio L, Meng X, Hotte N, Nguyen V, Madsen KL, Dieleman LA, Huang V, Elahi S. Lower Abundance and Impaired Function of CD71+ Erythroid Cells in Inflammatory Bowel Disease Patients During Pregnancy. J Crohns Colitis 2019; 13:230-244. [PMID: 30272151 PMCID: PMC6357902 DOI: 10.1093/ecco-jcc/jjy147] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS CD71+ erythroid cells are enriched during pregnancy with immuno suppressive properties. We investigated the frequency and functionality of CD71+ erythroid cells in peripheral blood, cord blood, and placenta of inflammatory bowel disease [IBD] patients versus healthy controls [HCs]. We aimed to determine their role in IBD pathogenesis during pregnancy. METHODS Peripheral blood was collected at preconception, the first, second and third trimesters, and postpartum. Cord blood and placental tissues were collected at the time of birth. Cells from different specimens were subjected to immune-phenotyping and functional assays. CD71+ erythroid cells were purified for quantitative polymerase chain reaction [qPCR] analysis. Using an allogeneic mouse model of pregnancy, the effects of CD71+ erythroid cells depletion on intestinal homeostasis and dysbiosis was studied. RESULTS IBD patients had lower CD71+ erythroid cells during pregnancy compared with HCs. Placenta and cord blood CD71+ erythroid cells from IBD patients exhibited impaired functionality and expressed lower inhibitory molecules including VISTA, TGF-β, and reactive oxygen species [ROS]. Lower CD71+ erythroid cells were correlated with reduced regulatory T cells and increased immune-activation in IBD patients. Depletion of CD71+ erythroid cells in an allogeneic pregnancy model resulted in upregulation of TLRs, IL-6, and CXCL-1, and enhanced production of TNF-α, in intestinal tissues. In contrast, TGF-β gene expression was reduced. Excessive inflammatory response in the gut [e.g. TNF-α] affects intestinal integrity and CD71+ erythroid cells impact on the gut's bacterial composition. CONCLUSIONS Reduced frequency and/or impaired functionality of CD71+ erythroid cells during pregnancy may predispose IBD patients to a more pro-inflammatory milieu in their gastrointestinal tract, characterised by lower Tregs, higher IL-6, and TNF-α, and dysbiosis.
Collapse
Affiliation(s)
- Garett Dunsmore
- Department of Dentistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada,Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Petya Koleva
- Department of Dentistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Nafiseh Ghobakhloo
- Department of Dentistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada,Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Reed Sutton
- Division of Gastroenterology, University of Alberta, Edmonton, AB, Canada
| | - Lindsy Ambrosio
- Division of Gastroenterology, University of Alberta, Edmonton, AB, Canada
| | - Xuanyi Meng
- Department of Dentistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Naomi Hotte
- Division of Gastroenterology, University of Alberta, Edmonton, AB, Canada
| | - Vivian Nguyen
- Division of Gastroenterology, University of Alberta, Edmonton, AB, Canada
| | - Karen L Madsen
- Division of Gastroenterology, University of Alberta, Edmonton, AB, Canada
| | - Levinus A Dieleman
- Division of Gastroenterology, University of Alberta, Edmonton, AB, Canada
| | - Vivian Huang
- Division of Gastroenterology, University of Alberta, Edmonton, AB, Canada,Division of Gastroenterology, University of Toronto, Mount Sinai Hospital, Toronto, ON, Canada
| | - Shokrollah Elahi
- Department of Dentistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada,Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada,Corresponding author: Shokrollah Elahi, PhD, 7020L, Katz Group Centre for Pharmacology and Health Research, 11361-87th Ave NW, Edmonton, AB, T6G2E1, Canada. Tel.: 780-492-1336; fax: 780-492-7466;
| |
Collapse
|
76
|
Sprouse ML, Bates NA, Felix KM, Wu HJJ. Impact of gut microbiota on gut-distal autoimmunity: a focus on T cells. Immunology 2019; 156:305-318. [PMID: 30560993 DOI: 10.1111/imm.13037] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/07/2018] [Accepted: 11/25/2018] [Indexed: 12/14/2022] Open
Abstract
The immune system is essential for maintaining a delicate balance between eliminating pathogens and maintaining tolerance to self-tissues to avoid autoimmunity. An enormous and complex community of gut microbiota provides essential health benefits to the host, particularly by regulating immune homeostasis. Many of the metabolites derived from commensals can impact host health by directly regulating the immune system. Many autoimmune diseases arise from an imbalance between pathogenic effector T cells and regulatory T (Treg) cells. Recent interest has emerged in understanding how cross-talk between gut microbiota and the host immune system promotes autoimmune development by controlling the differentiation and plasticity of T helper and Treg cells. At the molecular level, our recent study, along with others, demonstrates that asymptomatic colonization by commensal bacteria in the gut is capable of triggering autoimmune disease by molecular mimicking self-antigen and skewing the expression of dual T-cell receptors on T cells. Dysbiosis, an imbalance of the gut microbiota, is involved in autoimmune development in both mice and humans. Although it is well known that dysbiosis can impact diseases occurring within the gut, growing literature suggests that dysbiosis also causes the development of gut-distal/non-gut autoimmunity. In this review, we discuss recent advances in understanding the potential molecular mechanisms whereby gut microbiota induces autoimmunity, and the evidence that the gut microbiota triggers gut-distal autoimmune diseases.
Collapse
Affiliation(s)
- Maran L Sprouse
- Department of Immunobiology, University of Arizona, Tucson, AZ, USA
| | - Nicholas A Bates
- Department of Immunobiology, University of Arizona, Tucson, AZ, USA
| | - Krysta M Felix
- Department of Immunobiology, University of Arizona, Tucson, AZ, USA
| | - Hsin-Jung Joyce Wu
- Department of Immunobiology, University of Arizona, Tucson, AZ, USA.,Arizona Arthritis Center, College of Medicine, University of Arizona, Tucson, AZ, USA
| |
Collapse
|
77
|
Hathaway-Schrader JD, Steinkamp HM, Chavez MB, Poulides NA, Kirkpatrick JE, Chew ME, Huang E, Alekseyenko AV, Aguirre JI, Novince CM. Antibiotic Perturbation of Gut Microbiota Dysregulates Osteoimmune Cross Talk in Postpubertal Skeletal Development. THE AMERICAN JOURNAL OF PATHOLOGY 2019; 189:370-390. [PMID: 30660331 DOI: 10.1016/j.ajpath.2018.10.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 09/01/2018] [Accepted: 10/16/2018] [Indexed: 12/17/2022]
Abstract
Commensal gut microbiota-host immune responses are experimentally delineated via gnotobiotic animal models or alternatively by antibiotic perturbation of gut microbiota. Osteoimmunology investigations in germ-free mice, revealing that gut microbiota immunomodulatory actions critically regulate physiologic skeletal development, highlight that antibiotic perturbation of gut microbiota may dysregulate normal osteoimmunological processes. We investigated the impact of antibiotic disruption of gut microbiota on osteoimmune response effects in postpubertal skeletal development. Sex-matched C57BL/6T mice were administered broad-spectrum antibiotics or vehicle-control from the age of 6 to 12 weeks. Antibiotic alterations in gut bacterial composition and skeletal morphology were sex dependent. Antibiotics did not influence osteoblastogenesis or endochondral bone formation, but notably enhanced osteoclastogenesis. Unchanged Tnf or Ccl3 expression in marrow and elevated tumor necrosis factor-α and chemokine (C-C motif) ligand 3 in serum indicated that the pro-osteoclastic effects of the antibiotics are driven by increased systemic inflammation. Antibiotic-induced broad changes in adaptive and innate immune cells in mesenteric lymph nodes and spleen demonstrated that the perturbation of gut microbiota drives a state of dysbiotic hyperimmune response at secondary lymphoid tissues draining local gut and systemic circulation. Antibiotics up-regulated the myeloid-derived suppressor cells, immature myeloid progenitor cells known for immunosuppressive properties in pathophysiologic inflammatory conditions. Myeloid-derived suppressor cell-mediated immunosuppression can be antigen specific. Therefore, antibiotic-induced broad suppression of major histocompatibility complex class II antigen presentation genes in bone marrow discerns that antibiotic perturbation of gut microbiota dysregulates critical osteoimmune cross talk.
Collapse
Affiliation(s)
- Jessica D Hathaway-Schrader
- Department of Oral Health Sciences, Medical University of South Carolina College of Dental Medicine, Charleston, South Carolina; Endocrinology Division, Department of Pediatrics, Medical University of South Carolina College of Medicine, Charleston, South Carolina
| | - Heidi M Steinkamp
- Department of Oral Health Sciences, Medical University of South Carolina College of Dental Medicine, Charleston, South Carolina; Division of Pediatric Dentistry, The Ohio State University College of Dentistry, Columbus, Ohio
| | - Michael B Chavez
- Department of Oral Health Sciences, Medical University of South Carolina College of Dental Medicine, Charleston, South Carolina; Division of Biosciences, The Ohio State University College of Dentistry, Columbus, Ohio
| | - Nicole A Poulides
- Department of Oral Health Sciences, Medical University of South Carolina College of Dental Medicine, Charleston, South Carolina; Endocrinology Division, Department of Pediatrics, Medical University of South Carolina College of Medicine, Charleston, South Carolina
| | - Joy E Kirkpatrick
- Department of Oral Health Sciences, Medical University of South Carolina College of Dental Medicine, Charleston, South Carolina
| | - Michael E Chew
- Department of Oral Health Sciences, Medical University of South Carolina College of Dental Medicine, Charleston, South Carolina
| | - Emily Huang
- Department of Oral Health Sciences, Medical University of South Carolina College of Dental Medicine, Charleston, South Carolina
| | - Alexander V Alekseyenko
- Department of Oral Health Sciences, Medical University of South Carolina College of Dental Medicine, Charleston, South Carolina; Department of Public Health Sciences, Medical University of South Carolina College of Medicine, Charleston, South Carolina
| | - Jose I Aguirre
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida
| | - Chad M Novince
- Department of Oral Health Sciences, Medical University of South Carolina College of Dental Medicine, Charleston, South Carolina; Endocrinology Division, Department of Pediatrics, Medical University of South Carolina College of Medicine, Charleston, South Carolina.
| |
Collapse
|
78
|
Abstract
Intestinal damage driven by unrestricted immune responses against the intestinal microbiota can lead to the development of inflammatory diseases including inflammatory bowel disease. How such breakdown in tolerance occurs alongside the mechanisms to reinforce homeostasis with the microbiota are a focus of many studies. Our recent work demonstrates coordinated interactions between intact microbiota and CX3CR1 expressing intestinal antigen presenting cells (APCs) that limits T helper 1 cell responses and promotes differentiation of regulatory T cells (Treg) against intestinal antigens including pathogens, soluble proteins and the microbiota itself. We find a microbial attachment to intestinal epithelial cells is necessary to support these anti-inflammatory immune functions. In this addendum, we discuss how our findings enhance understanding of microbiota-directed homeostatic functions of the intestinal immune system and implications of modulating this interaction in ameliorating inflammatory disease.
Collapse
Affiliation(s)
- Myunghoo Kim
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA,Department of Animal Science, Pusan National University, Busan, Republic of Korea
| | - Andrea A. Hill
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Wan-Jung Wu
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Gretchen E. Diehl
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA,Biology of Inflammation Center, Baylor College of Medicine, Houston, TX, USA,CONTACT Gretchen E. Diehl
| |
Collapse
|
79
|
SPG-56 from Sweet potato Zhongshu-1 delayed growth of tumor xenografts in nude mice by modulating gut microbiota. J Funct Foods 2019. [DOI: 10.1016/j.jff.2018.10.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
80
|
Abstract
The dynamic and polymicrobial oral microbiome is a direct precursor of diseases such as dental caries and periodontitis, two of the most prevalent microbially induced disorders worldwide. Distinct microenvironments at oral barriers harbour unique microbial communities, which are regulated through sophisticated signalling systems and by host and environmental factors. The collective function of microbial communities is a major driver of homeostasis or dysbiosis and ultimately health or disease. Despite different aetiologies, periodontitis and caries are each driven by a feedforward loop between the microbiota and host factors (inflammation and dietary sugars, respectively) that favours the emergence and persistence of dysbiosis. In this Review, we discuss current knowledge and emerging mechanisms governing oral polymicrobial synergy and dysbiosis that have both enhanced our understanding of pathogenic mechanisms and aided the design of innovative therapeutic approaches for oral diseases.
Collapse
Affiliation(s)
- Richard J Lamont
- Department of Oral Immunology and Infectious Diseases, School of Dentistry, University of Louisville, Louisville, KY, USA.
| | - Hyun Koo
- Department of Orthodontics and Divisions of Pediatric Dentistry and Community Oral Health, Penn Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - George Hajishengallis
- Department of Microbiology, Penn Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
81
|
Garcia-Montoya L, Gul H, Emery P. Recent advances in ankylosing spondylitis: understanding the disease and management. F1000Res 2018; 7. [PMID: 30345001 PMCID: PMC6173104 DOI: 10.12688/f1000research.14956.1] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/11/2018] [Indexed: 12/14/2022] Open
Abstract
The term spondyloarthritis refers to a group of immune-mediated diseases characterised by inflammation of the axial skeleton, peripheral joints, and entheses. Ankylosing spondylitis (AS) is the most common and characteristic of these entities and even though it was first described over two centuries ago, the understanding of the underlying disease mechanism remains incomplete. It is known that around 40% of patients with AS have subclinical bowel inflammation, suggesting that the origin of the disease could be in the gut. Also, more genes and new molecules have demonstrated a role in the pathogenesis of AS. In this review, we analyse the latest therapies for spondyloarthritis and the most relevant discoveries over the last three years, together with their implications for different aspects of the disease.
Collapse
Affiliation(s)
- Leticia Garcia-Montoya
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Chapel Allerton Hospital, Chapeltown Road, Leeds, LS7 4SA, UK.,NIHR Leeds Musculoskeletal Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Hanna Gul
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Chapel Allerton Hospital, Chapeltown Road, Leeds, LS7 4SA, UK.,NIHR Leeds Musculoskeletal Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Paul Emery
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Chapel Allerton Hospital, Chapeltown Road, Leeds, LS7 4SA, UK.,NIHR Leeds Musculoskeletal Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| |
Collapse
|
82
|
Abstract
Studies of the human intestinal microbiome in patients with inflammatory bowel disease (IBD) consistently show that there are differences (an abnormal or unbalanced microbiome, "dysbiosis") when compared to healthy subjects. We sought to describe changes in the microbiome in individual patients over time, and determine the clinical factors that are associated with significant alteration. Forty-two mucosal biopsies were collected from 20 patients that were spaced an average of 2.4 years apart. These were analysed using bacterial 16S rRNA gene high-throughput sequencing methods. Presence of active inflammation was determined endoscopically and histologically. Inferred metagenomics analysis was conducted using the PICRUSt package. We found that the differences in the microbiome over time in individual patients were greatest in the presence of ongoing intestinal inflammation, as determined by the Yue and Clayton theta distance between sample pairs (adjusted p = 0.00031). Samples from patients with previous abdominal surgery had lower alpha (within sample) diversity compared with those with no prior operations (mean Shannon index 2.083, 2.510 respectively, p = 0.017). There were no changes in the inferred bacterial metagenomic profile. The microbiome in IBD undergoes considerable fluctuation over time. These changes are greatest when there is histologically confirmed inflammation at both time-points.
Collapse
Affiliation(s)
- Christopher John Kiely
- IBD Research Laboratory, Medical School, College of Medicine, Biology and Environment, Australian National University, Canberra, ACT, Australia,CONTACT Dr. Christopher John Kiely, MBBS IBD Research Laboratory, Level 5, Building 10, ANU Medical School, Canberra Hospital Campus, Yamba Drive, Garran, ACT, Australia, 2605
| | - Paul Pavli
- IBD Research Laboratory, Medical School, College of Medicine, Biology and Environment, Australian National University, Canberra, ACT, Australia,Gastroenterology and Hepatology Unit, Canberra Hospital, ACT, Australia
| | - Claire Louise O'Brien
- IBD Research Laboratory, Medical School, College of Medicine, Biology and Environment, Australian National University, Canberra, ACT, Australia,Gastroenterology and Hepatology Unit, Canberra Hospital, ACT, Australia
| |
Collapse
|
83
|
Fucoidan alleviates dyslipidemia and modulates gut microbiota in high-fat diet-induced mice. J Funct Foods 2018. [DOI: 10.1016/j.jff.2018.07.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
|
84
|
Skowron KB, Shogan BD, Rubin DT, Hyman NH. The New Frontier: the Intestinal Microbiome and Surgery. J Gastrointest Surg 2018; 22:1277-1285. [PMID: 29633119 DOI: 10.1007/s11605-018-3744-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 03/12/2018] [Indexed: 01/31/2023]
Abstract
The microbiome exerts a remarkable effect on human physiology. The study of the human-microbiome relationship is a burgeoning field with great potential to improve our understanding of health and disease. In this review, we address common surgical problems influenced by the human microbiome and explore what is thus far known about this relationship. These include inflammatory bowel disease, colorectal neoplasms, and diverticular disease. We will also discuss the effect of the microbiome on surgical complications, specifically anastomotic leak. We hope that further research in this field will enlighten our management of these and other surgical problems.
Collapse
Affiliation(s)
- Kinga B Skowron
- Department of Surgery, University of Chicago Medicine, 5841 S. Maryland Avenue, MC 5095, Chicago, IL, 60637, USA
| | - Benjamin D Shogan
- Department of Surgery, University of Chicago Medicine, 5841 S. Maryland Avenue, MC 5095, Chicago, IL, 60637, USA.
| | - David T Rubin
- Department of Medicine, Section of Gastroenterology, Hepatology and Nutrition, University of Chicago Medicine, Chicago, IL, USA
| | - Neil H Hyman
- Department of Surgery, University of Chicago Medicine, 5841 S. Maryland Avenue, MC 5095, Chicago, IL, 60637, USA
| |
Collapse
|
85
|
Yoon H, Schaubeck M, Lagkouvardos I, Blesl A, Heinzlmeir S, Hahne H, Clavel T, Panda S, Ludwig C, Kuster B, Manichanh C, Kump P, Haller D, Hörmannsperger G. Increased Pancreatic Protease Activity in Response to Antibiotics Impairs Gut Barrier and Triggers Colitis. Cell Mol Gastroenterol Hepatol 2018; 6:370-388.e3. [PMID: 30182050 PMCID: PMC6121113 DOI: 10.1016/j.jcmgh.2018.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/15/2018] [Indexed: 12/19/2022]
Abstract
Background & Aims Antibiotic (ABx) therapy is associated with increased risk for Crohn's disease but underlying mechanisms are unknown. We observed high fecal serine protease activity (PA) to be a frequent side effect of ABx therapy. The aim of the present study was to unravel whether this rise in large intestinal PA may promote colitis development via detrimental effects on the large intestinal barrier. Methods Transwell experiments were used to assess the impact of high PA in ABx-treated patients or vancomycin/metronidazole-treated mice on the epithelial barrier. Serine protease profiling was performed using liquid chromatography-mass spectrometry/mass spectrometry analysis. The impact of high large intestinal PA on the intestinal barrier in wild-type and interleukin (IL)10-/- mice and on colitis development in IL10-/- mice was investigated using vancomycin/metronidazole with or without oral serine protease inhibitor (AEBSF) treatment. Results The ABx-induced, high large intestinal PA was caused by significantly increased levels of pancreatic proteases and impaired epithelial barrier integrity. In wild-type mice, the rise in PA caused a transient increase in intestinal permeability but did not affect susceptibility to chemically induced acute colitis. In IL10-/- mice, increased PA caused a consistent impairment of the intestinal barrier associated with inflammatory activation in the large intestinal tissue. In the long term, the vancomycin/metronidazole-induced lasting increase in PA aggravated colitis development in IL10-/- mice. Conclusions High large intestinal PA is a frequent adverse effect of ABx therapy, which is detrimental to the large intestinal barrier and may contribute to the development of chronic intestinal inflammation in susceptible individuals.
Collapse
Key Words
- ABx, antibiotics
- AEBSF, 4-(2-aminoethyl) benzenesulfonyl fluoride hydrochloride
- DSS, dextran sulfate sodium
- Epithelial Barrier
- GF, germ-free
- Gut Microbiota
- IBD, inflammatory bowel diseases
- IL, interleukin
- Inflammatory Bowel Diseases
- LC-MS/MS, liquid chromatography–mass spectrometry/mass spectrometry
- PA, protease activity
- PBS, phosphate-buffered saline
- PMSF, phenylmethane-sulfonylfluoride
- SPF, specific pathogen-free
- Serine Proteases
- TEER, transepithelial electrical resistance
- V/M, vancomycin/metronidazole
- WT, wild-type
- cecal-sup, cecal-supernatants
- ctr, control
- stool-sup, stool-supernatants
Collapse
Affiliation(s)
- Hongsup Yoon
- Technische Universität München, Chair of Nutrition and Immunology, Freising-Weihenstephan, Germany
| | - Monika Schaubeck
- Max Planck Institute of Neurobiology, Department of Neuroimmunology, Martinsried, Germany
| | - Ilias Lagkouvardos
- Technische Universität München, Junior Research Group Microbial Bioinformatics, ZIEL – Institute for Food and Health, Freising-Weihenstephan, Germany
- Technische Universität München, ZIEL – Institute for Food & Health, Freising-Weihenstephan, Germany
| | - Andreas Blesl
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Stephanie Heinzlmeir
- Technische Universität München, Chair of Proteomics and Bioanalytics, Freising-Weihenstephan, Germany
- Technische Universität München, Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Freising-Weihenstephan, Germany
| | - Hannes Hahne
- Technische Universität München, Chair of Proteomics and Bioanalytics, Freising-Weihenstephan, Germany
- OmicScouts GmbH, Freising, Germany
| | - Thomas Clavel
- Technische Universität München, ZIEL – Institute for Food & Health, Freising-Weihenstephan, Germany
- RWTH University Hospital, Institute of Medical Microbiology, Functional Microbiome Research Group, Aachen, Germany
| | - Suchita Panda
- Vall d'Hebron Research Institute, Digestive Research Unit, Barcelona, Spain
| | - Christina Ludwig
- Technische Universität München, Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Freising-Weihenstephan, Germany
| | - Bernhard Kuster
- Technische Universität München, Chair of Proteomics and Bioanalytics, Freising-Weihenstephan, Germany
- Technische Universität München, Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Freising-Weihenstephan, Germany
| | | | - Patrizia Kump
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Dirk Haller
- Technische Universität München, Chair of Nutrition and Immunology, Freising-Weihenstephan, Germany
- Technische Universität München, ZIEL – Institute for Food & Health, Freising-Weihenstephan, Germany
| | - Gabriele Hörmannsperger
- Technische Universität München, Chair of Nutrition and Immunology, Freising-Weihenstephan, Germany
| |
Collapse
|
86
|
Bajic JE, Johnston IN, Howarth GS, Hutchinson MR. From the Bottom-Up: Chemotherapy and Gut-Brain Axis Dysregulation. Front Behav Neurosci 2018; 12:104. [PMID: 29872383 PMCID: PMC5972222 DOI: 10.3389/fnbeh.2018.00104] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 04/30/2018] [Indexed: 12/12/2022] Open
Abstract
The central nervous system and gastrointestinal tract form the primary targets of chemotherapy-induced toxicities. Symptoms associated with damage to these regions have been clinically termed chemotherapy-induced cognitive impairment and mucositis. Whilst extensive literature outlines the complex etiology of each pathology, to date neither chemotherapy-induced side-effect has considered the potential impact of one on the pathogenesis of the other disorder. This is surprising considering the close bidirectional relationship shared between each organ; the gut-brain axis. There are complex multiple pathways linking the gut to the brain and vice versa in both normal physiological function and disease. For instance, psychological and social factors influence motility and digestive function, symptom perception, and behaviors associated with illness and pathological outcomes. On the other hand, visceral pain affects central nociception pathways, mood and behavior. Recent interest highlights the influence of functional gut disorders, such as inflammatory bowel diseases and irritable bowel syndrome in the development of central comorbidities. Gut-brain axis dysfunction and microbiota dysbiosis have served as key portals in understanding the potential mechanisms associated with these functional gut disorders and their effects on cognition. In this review we will present the role gut-brain axis dysregulation plays in the chemotherapy setting, highlighting peripheral-to-central immune signaling mechanisms and their contribution to neuroimmunological changes associated with chemotherapy exposure. Here, we hypothesize that dysregulation of the gut-brain axis plays a major role in the intestinal, psychological and neurological complications following chemotherapy. We pay particular attention to evidence surrounding microbiota dysbiosis, the role of intestinal permeability, damage to nerves of the enteric and peripheral nervous systems and vagal and humoral mediated changes.
Collapse
Affiliation(s)
- Juliana E Bajic
- Discipline of Physiology, School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Ian N Johnston
- School of Psychology, The University of Sydney, Sydney, NSW, Australia
| | - Gordon S Howarth
- School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA, Australia.,Department of Gastroenterology, Women's and Children's Hospital, North Adelaide, SA, Australia
| | - Mark R Hutchinson
- Discipline of Physiology, School of Medicine, Faculty of Health Sciences, University of Adelaide, Adelaide, SA, Australia.,Centre of Excellence for Nanoscale Biophotonics, The University of Adelaide, Adelaide, SA, Australia
| |
Collapse
|
87
|
Moon C, Stupp GS, Su AI, Wolan DW. Metaproteomics of Colonic Microbiota Unveils Discrete Protein Functions among Colitic Mice and Control Groups. Proteomics 2018; 18:10.1002/pmic.201700391. [PMID: 29319931 PMCID: PMC5921860 DOI: 10.1002/pmic.201700391] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/19/2017] [Indexed: 12/14/2022]
Abstract
Metaproteomics can greatly assist established high-throughput sequencing methodologies to provide systems biological insights into the alterations of microbial protein functionalities correlated with disease-associated dysbiosis of the intestinal microbiota. Here, the authors utilize the well-characterized murine T cell transfer model of colitis to find specific changes within the intestinal luminal proteome associated with inflammation. MS proteomic analysis of colonic samples permitted the identification of ≈10 000-12 000 unique peptides that corresponded to 5610 protein clusters identified across three groups, including the colitic Rag1-/- T cell recipients, isogenic Rag1-/- controls, and wild-type mice. The authors demonstrate that the colitic mice exhibited a significant increase in Proteobacteria and Verrucomicrobia and show that such alterations in the microbial communities contributed to the enrichment of specific proteins with transcription and translation gene ontology terms. In combination with 16S sequencing, the authors' metaproteomics-based microbiome studies provide a foundation for assessing alterations in intestinal luminal protein functionalities in a robust and well-characterized mouse model of colitis, and set the stage for future studies to further explore the functional mechanisms of altered protein functionalities associated with dysbiosis and inflammation.
Collapse
Affiliation(s)
- Clara Moon
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Gregory S Stupp
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew I Su
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Dennis W Wolan
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| |
Collapse
|
88
|
Li M, Gao J, Tang Y, Liu M, Wu S, Qu K, Long X, Li H, Liu M, Liu Y, Yuan J, Mao L, Liu Y, Zheng X, Wang E, Wang J, Yang Y. Traditional Herbal Medicine-Derived Sulforaphene LFS-01 Reverses Colitis in Mice by Selectively Altering the Gut Microbiota and Promoting Intestinal Gamma-Delta T Cells. Front Pharmacol 2018; 8:959. [PMID: 29375374 PMCID: PMC5767259 DOI: 10.3389/fphar.2017.00959] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 12/15/2017] [Indexed: 02/06/2023] Open
Abstract
Sulforaphene (LFS-01) is a natural compound derived from traditional herbal medicine. Here, we show that oral administration of LFS-01 is able to dramatically alter the skewed gut microbiota and reverse colitis in model mice associated with an increase of intestinal γδT cells. Through 16S rDNA sequencing, we showed that LFS-01 can selectively suppress enteric pathogens such as Escherichia–Shigella and Helicobacter whereas the protective strains including Lactobacillus and Lachnospiraceae were significantly expanded after LFS-01 treatment. Interestingly, we demonstrated that LFS-01 administration can significantly promote the IL-17+γδT cells in model mice in response to the expanded Lactobacillus. We verified that the intracellular components of Lactobacillus can stimulate the growth of IL-17+γδT cells upon preincubation. The increased IL-17A after LFS-01 treatment in turn recovers the disrupted occludin subcellular location and protects the epithelial barrier in the colon of model mice. Remarkably, LFS-01 does not show apparent toxicity to animals and we demonstrated that LFS-01 also exerts strong protective effects in TNBS-induced colitis rats. Therefore, LFS-01 holds great promise for the treatment of inflammatory bowel disease (IBD) and warrants translation for use in clinical trials. Our work provided a new avenue for the treatment of IBD based on the strategy of harnessing intestinal symbiosis.
Collapse
Affiliation(s)
- Ming Li
- Department of Microecology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Jiali Gao
- Center for Molecular Medicine, School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, China
| | - Yan Tang
- Department of Microecology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Meishuo Liu
- Center for Molecular Medicine, School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, China
| | - Sijin Wu
- Center for Molecular Medicine, School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, China
| | - Kunli Qu
- Center for Molecular Medicine, School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, China
| | - Xiangyu Long
- Center for Molecular Medicine, School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, China
| | - Huajun Li
- Department of Microecology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Min Liu
- Department of Microecology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Yinhui Liu
- Department of Microecology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Jieli Yuan
- Department of Microecology, College of Basic Medical Sciences, Dalian Medical University, Dalian, China
| | - Lei Mao
- DrivingForce Therapeutics, Venture Harbor, Dalian, China
| | - Yu Liu
- School of Software, Dalian University of Technology, Dalian, China
| | - Xiliang Zheng
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China.,Department of Chemistry and Physics, State University of New York, Stony Brook, NY, United States
| | - Yongliang Yang
- Center for Molecular Medicine, School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, China
| |
Collapse
|
89
|
Scotti E, Boué S, Sasso GL, Zanetti F, Belcastro V, Poussin C, Sierro N, Battey J, Gimalac A, Ivanov NV, Hoeng J. Exploring the microbiome in health and disease. TOXICOLOGY RESEARCH AND APPLICATION 2017. [DOI: 10.1177/2397847317741884] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The analysis of human microbiome is an exciting and rapidly expanding field of research. In the past decade, the biological relevance of the microbiome for human health has become evident. Microbiome comprises a complex collection of microorganisms, with their genes and metabolites, colonizing different body niches. It is now well known that the microbiome interacts with its host, assisting in the bioconversion of nutrients and detoxification, supporting immunity, protecting against pathogenic microbes, and maintaining health. Remarkable new findings showed that our microbiome not only primarily affects the health and function of the gastrointestinal tract but also has a strong influence on general body health through its close interaction with the nervous system and the lung. Therefore, a perfect and sensitive balanced interaction of microbes with the host is required for a healthy body. In fact, growing evidence suggests that the dynamics and function of the indigenous microbiota can be influenced by many factors, including genetics, diet, age, and toxicological agents like cigarette smoke, environmental contaminants, and drugs. The disruption of this balance, that is called dysbiosis, is associated with a plethora of diseases, including metabolic diseases, inflammatory bowel disease, chronic obstructive pulmonary disease, periodontitis, skin diseases, and neurological disorders. The importance of the host microbiome for the human health has also led to the emergence of novel therapeutic approaches focused on the intentional manipulation of the microbiota, either by restoring missing functions or eliminating harmful roles. In the present review, we outline recent studies devoted to elucidate not only the role of microbiome in health conditions and the possible link with various types of diseases but also the influence of various toxicological factors on the microbial composition and function.
Collapse
Affiliation(s)
- Elena Scotti
- PMI R&D, Philip Morris Products S.A., Neuchatel, Switzerland (Part of Philip Morris International group of companies)
| | - Stéphanie Boué
- PMI R&D, Philip Morris Products S.A., Neuchatel, Switzerland (Part of Philip Morris International group of companies)
| | - Giuseppe Lo Sasso
- PMI R&D, Philip Morris Products S.A., Neuchatel, Switzerland (Part of Philip Morris International group of companies)
| | - Filippo Zanetti
- PMI R&D, Philip Morris Products S.A., Neuchatel, Switzerland (Part of Philip Morris International group of companies)
| | - Vincenzo Belcastro
- PMI R&D, Philip Morris Products S.A., Neuchatel, Switzerland (Part of Philip Morris International group of companies)
| | - Carine Poussin
- PMI R&D, Philip Morris Products S.A., Neuchatel, Switzerland (Part of Philip Morris International group of companies)
| | - Nicolas Sierro
- PMI R&D, Philip Morris Products S.A., Neuchatel, Switzerland (Part of Philip Morris International group of companies)
| | - James Battey
- PMI R&D, Philip Morris Products S.A., Neuchatel, Switzerland (Part of Philip Morris International group of companies)
| | - Anne Gimalac
- PMI R&D, Philip Morris Products S.A., Neuchatel, Switzerland (Part of Philip Morris International group of companies)
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A., Neuchatel, Switzerland (Part of Philip Morris International group of companies)
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Neuchatel, Switzerland (Part of Philip Morris International group of companies)
| |
Collapse
|
90
|
Nakamoto N, Amiya T, Aoki R, Taniki N, Koda Y, Miyamoto K, Teratani T, Suzuki T, Chiba S, Chu PS, Hayashi A, Yamaguchi A, Shiba S, Miyake R, Katayama T, Suda W, Mikami Y, Kamada N, Ebinuma H, Saito H, Hattori M, Kanai T. Commensal Lactobacillus Controls Immune Tolerance during Acute Liver Injury in Mice. Cell Rep 2017; 21:1215-1226. [PMID: 29091761 DOI: 10.1016/j.celrep.2017.10.022] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 09/06/2017] [Accepted: 10/05/2017] [Indexed: 02/08/2023] Open
Abstract
Gut-derived microbial antigens trigger the innate immune system during acute liver injury. During recovery, regulatory immunity plays a role in suppressing inflammation; however, the precise mechanism underlying this process remains obscure. Here, we find that recruitment of immune-regulatory classical dendritic cells (cDCs) is crucial for liver tolerance in concanavalin A-induced acute liver injury. Acute liver injury resulted in enrichment of commensal Lactobacillus in the gut. Notably, Lactobacillus activated IL-22 production by gut innate lymphoid cells and raised systemic IL-22 levels. Gut-derived IL-22 enhanced mucosal barrier function and promoted the recruitment of regulatory cDCs to the liver. These cDCs produced IL-10 and TGF-β through TLR9 activation, preventing further liver inflammation. Collectively, our results indicate that beneficial gut microbes influence tolerogenic immune responses in the liver. Therefore, modulation of the gut microbiota might be a potential option to regulate liver tolerance.
Collapse
Affiliation(s)
- Nobuhiro Nakamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 1608582, Japan.
| | - Takeru Amiya
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 1608582, Japan; Research Unit/Frontier Therapeutic Sciences, Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Kanagawa 2270033, Japan
| | - Ryo Aoki
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 1608582, Japan; Institute of Health Science, Ezaki Glico Co., Ltd., Osaka 5558502, Japan
| | - Nobuhito Taniki
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Yuzo Koda
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 1608582, Japan; Research Unit/Frontier Therapeutic Sciences, Sohyaku, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, Kanagawa 2270033, Japan
| | - Kentaro Miyamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 1608582, Japan; Miyarisan Pharmaceutical Co., Ltd., Research Laboratory, Tokyo 1140016, Japan
| | - Toshiaki Teratani
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Takahiro Suzuki
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Sayako Chiba
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Po-Sung Chu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Atsushi Hayashi
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 1608582, Japan; Miyarisan Pharmaceutical Co., Ltd., Research Laboratory, Tokyo 1140016, Japan
| | - Akihiro Yamaguchi
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Shunsuke Shiba
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Rei Miyake
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Tadashi Katayama
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Wataru Suda
- Department of Microbiology, Keio University School of Medicine, Tokyo 1608582, Japan; Laboratory of Metagenomics, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 2778561, Japan
| | - Yohei Mikami
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Nobuhiko Kamada
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hirotoshi Ebinuma
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 1608582, Japan
| | - Hidetsugu Saito
- Division of Pharmacotherapeutics, Keio University School of Pharmacy, Tokyo 1058512, Japan
| | - Masahira Hattori
- Laboratory of Metagenomics, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 2778561, Japan; Cooperative Major in Advanced Health Science, Graduate School of Advanced Science and Engineering, Faculty of Science and Engineering, Waseda University, Tokyo 1698555, Japan
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo 1608582, Japan.
| |
Collapse
|
91
|
Sorrentino D. Microbial dysbiosis in spouses of ulcerative colitis patients: Any clues to disease pathogenesis? World J Gastroenterol 2017; 23:6747-6749. [PMID: 29085220 PMCID: PMC5645610 DOI: 10.3748/wjg.v23.i37.6747] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 07/30/2017] [Accepted: 08/25/2017] [Indexed: 02/06/2023] Open
Abstract
A number of alterations have been found within the gut microbial profile of patients with inflammatory bowel diseases when compared with the healthy population; however, it is unclear whether such dysbiosis is the cause or simply the consequence of the disease state. In ulcerative colitis, the environment seems to play a crucial role in disease etiology since monozygotic twins show a concordance rate of only 8%-10% - though it is unclear whether it does so by acting through the microbiome. In this study, the authors investigated the influence of cohabitation on the gut microbial community in healthy partners of ulcerative colitis patients - with the intent of clarifying some of these issues. As expected, ulcerative colitis patients had a significant dysbiosis and alterations in microbial metabolism. Interestingly, these abnormal fecal microbial communities were relatively similar amongst patients and their spouses. Thus, this study shows that the microbial profile might be partially transferred from ulcerative colitis patients to healthy individuals. Whether this finding impacts on disease development or has any implication for the role of the microbiome in inflammatory bowel disease etiology remains to be determined.
Collapse
Affiliation(s)
- Dario Sorrentino
- IBD Center, Division of Gastroenterology, Virginia Tech Carilion School of Medicine, Roanoke, VA 24016, United States
- Department of Clinical and Experimental Medical Sciences, University of Udine School of Medicine, 33100 Udine, Italy
| |
Collapse
|
92
|
Abstract
OBJECTIVE During the last decade, experimental and observational studies have shown that patients with inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) may have an altered intestinal microbial composition compared with healthy individuals. However, no uniform microbial signature has as yet been detected for either IBD or IBS. This review summarizes the current knowledge of microbial dysbiosis and its potential relationship to the pathophysiology in IBD and IBS. METHODS A selective review was conducted to summarize the current knowledge of gut microbiota in the pathophysiology of IBD and IBS. RESULTS Experimental and observational studies provide good evidence for intestinal microbial dysbiosis in subgroups of IBD and IBS. Still, no uniform disease pattern has been detected. This is most likely due to the heterogeneous nature of IBD and IBS, in combination with the effects of intrinsic and extrinsic factors. Such intrinsic factors include genetics, the gastrointestinal environment, and the host immune system, whereas extrinsic factors include early life diet, breastfeeding, and method of infant delivery. CONCLUSIONS Recent and ongoing work to define microbial dysbiosis in IBD and IBS shows promise, but future well-designed studies with well-characterized study individuals are needed. It is likely that the microbial dysbiosis in IBD and IBS is dependent on the natural disease course of IBD and symptom pattern in IBS. Therefore, assessment of the entire microbiota along the gastrointestinal tract, in relationship to confounding factors, symptom fluctuations, and other pathophysiological factors, is needed for further understanding of the etiology of these common diseases.
Collapse
|
93
|
Pitt JM, Vétizou M, Daillère R, Roberti MP, Yamazaki T, Routy B, Lepage P, Boneca IG, Chamaillard M, Kroemer G, Zitvogel L. Resistance Mechanisms to Immune-Checkpoint Blockade in Cancer: Tumor-Intrinsic and -Extrinsic Factors. Immunity 2017; 44:1255-69. [PMID: 27332730 DOI: 10.1016/j.immuni.2016.06.001] [Citation(s) in RCA: 719] [Impact Index Per Article: 102.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Indexed: 12/11/2022]
Abstract
Inhibition of immune regulatory checkpoints, such as CTLA-4 and the PD-1-PD-L1 axis, is at the forefront of immunotherapy for cancers of various histological types. However, such immunotherapies fail to control neoplasia in a significant proportion of patients. Here, we review how a range of cancer-cell-autonomous cues, tumor-microenvironmental factors, and host-related influences might account for the heterogeneous responses and failures often encountered during therapies using immune-checkpoint blockade. Furthermore, we describe the emerging evidence of how the strong interrelationship between the immune system and the host microbiota can determine responses to cancer therapies, and we introduce a concept by which prior or concomitant modulation of the gut microbiome could optimize therapeutic outcomes upon immune-checkpoint blockade.
Collapse
Affiliation(s)
- Jonathan M Pitt
- Institut de Cancérologie, Gustave Roussy Cancer Campus, 94800 Villejuif, France; INSERM U1015, 94800 Villejuif, France; Faculté de Médecine, Université Paris Sud, Université Paris-Saclay, 94276 Le Kremlin Bicêtre, France
| | - Marie Vétizou
- Institut de Cancérologie, Gustave Roussy Cancer Campus, 94800 Villejuif, France; INSERM U1015, 94800 Villejuif, France; Faculté de Médecine, Université Paris Sud, Université Paris-Saclay, 94276 Le Kremlin Bicêtre, France
| | - Romain Daillère
- Institut de Cancérologie, Gustave Roussy Cancer Campus, 94800 Villejuif, France; INSERM U1015, 94800 Villejuif, France; Faculté de Médecine, Université Paris Sud, Université Paris-Saclay, 94276 Le Kremlin Bicêtre, France
| | - María Paula Roberti
- Institut de Cancérologie, Gustave Roussy Cancer Campus, 94800 Villejuif, France; INSERM U1015, 94800 Villejuif, France
| | - Takahiro Yamazaki
- Institut de Cancérologie, Gustave Roussy Cancer Campus, 94800 Villejuif, France; INSERM U1015, 94800 Villejuif, France
| | - Bertrand Routy
- Institut de Cancérologie, Gustave Roussy Cancer Campus, 94800 Villejuif, France; INSERM U1015, 94800 Villejuif, France; Faculté de Médecine, Université Paris Sud, Université Paris-Saclay, 94276 Le Kremlin Bicêtre, France
| | - Patricia Lepage
- Micalis UMR 1319, Institut National de la Recherche Agronomique, 78360 Jouy-en-Josas, France
| | - Ivo Gomperts Boneca
- Unit of Biology and Genetics of the Bacterial Cell Wall, Institut Pasteur, 75015 Paris, France; Equipe Avenir, INSERM, 75015 Paris, France
| | - Mathias Chamaillard
- Université de Lille, Centre National de la Recherche Scientifique, INSERM, Centre Hospitalier Universitaire Lille, Institut Pasteur de Lille, U1019, UMR 8204, Centre d'Infection et d'Immunité de Lille, 59000 Lille, France
| | - Guido Kroemer
- INSERM U848, 94800 Villejuif, France; Metabolomics Platform, Gustave Roussy Cancer Campus, 94800 Villejuif, France; Equipe 11 Labellisée Ligue contre le Cancer, INSERM U1138, Centre de Recherche des Cordeliers, 75006 Paris, France; Pôle de Biologie, Hôpital Européen Georges Pompidou, Assistance Publique - Hôpitaux de Paris, 75015 Paris, France; Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France; Université Pierre et Marie Curie, 75005 Paris, France; Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Laurence Zitvogel
- Institut de Cancérologie, Gustave Roussy Cancer Campus, 94800 Villejuif, France; INSERM U1015, 94800 Villejuif, France; Faculté de Médecine, Université Paris Sud, Université Paris-Saclay, 94276 Le Kremlin Bicêtre, France; Center of Clinical Investigations CICBT1428, Gustave Roussy Cancer Campus, 94805 Villejuif Cedex 05, France.
| |
Collapse
|
94
|
Wellman AS, Metukuri MR, Kazgan N, Xu X, Xu Q, Ren NSX, Czopik A, Shanahan MT, Kang A, Chen W, Azcarate-Peril MA, Gulati AS, Fargo DC, Guarente L, Li X. Intestinal Epithelial Sirtuin 1 Regulates Intestinal Inflammation During Aging in Mice by Altering the Intestinal Microbiota. Gastroenterology 2017; 153:772-786. [PMID: 28552621 PMCID: PMC5581719 DOI: 10.1053/j.gastro.2017.05.022] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 05/05/2017] [Accepted: 05/19/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Intestinal epithelial homeostasis is maintained by complex interactions among epithelial cells, commensal gut microorganisms, and immune cells. Disruption of this homeostasis is associated with disorders such as inflammatory bowel disease (IBD), but the mechanisms of this process are not clear. We investigated how Sirtuin 1 (SIRT1), a conserved mammalian NAD+-dependent protein deacetylase, senses environmental stress to alter intestinal integrity. METHODS We performed studies of mice with disruption of Sirt1 specifically in the intestinal epithelium (SIRT1 iKO, villin-Cre+, Sirt1flox/flox mice) and control mice (villin-Cre-, Sirt1flox/flox) on a C57BL/6 background. Acute colitis was induced in some mice by addition of 2.5% dextran sodium sulfate to drinking water for 5-9 consecutive days. Some mice were given antibiotics via their drinking water for 4 weeks to deplete their microbiota. Some mice were fed with a cholestyramine-containing diet for 7 days to sequester their bile acids. Feces were collected and proportions of microbiota were analyzed by 16S rRNA amplicon sequencing and quantitative PCR. Intestines were collected from mice and gene expression profiles were compared by microarray and quantitative PCR analyses. We compared levels of specific mRNAs between colon tissues from age-matched patients with ulcerative colitis (n=10) vs without IBD (n=8, controls). RESULTS Mice with intestinal deletion of SIRT1 (SIRT1 iKO) had abnormal activation of Paneth cells starting at the age of 5-8 months, with increased activation of NF-κB, stress pathways, and spontaneous inflammation at 22-24 months of age, compared with control mice. SIRT1 iKO mice also had altered fecal microbiota starting at 4-6 months of age compared with control mice, in part because of altered bile acid metabolism. Moreover, SIRT1 iKO mice with defective gut microbiota developed more severe colitis than control mice. Intestinal tissues from patients with ulcerative colitis expressed significantly lower levels of SIRT1 mRNA than controls. Intestinal tissues from SIRT1 iKO mice given antibiotics, however, did not have signs of inflammation at 22-24 months of age, and did not develop more severe colitis than control mice at 4-6 months. CONCLUSIONS In analyses of intestinal tissues, colitis induction, and gut microbiota in mice with intestinal epithelial disruption of SIRT1, we found this protein to prevent intestinal inflammation by regulating the gut microbiota. SIRT1 might therefore be an important mediator of host-microbiome interactions. Agents designed to activate SIRT1 might be developed as treatments for IBDs.
Collapse
Affiliation(s)
- Alicia S Wellman
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Mallikarjuna R Metukuri
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Nevzat Kazgan
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Xiaojiang Xu
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Qing Xu
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Natalie S X Ren
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Agnieszka Czopik
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Michael T Shanahan
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Ashley Kang
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina; NIEHS Scholars Connect Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Willa Chen
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - M Andrea Azcarate-Peril
- Department of Medicine, Division of Gastroenterology and Hepatology and Microbiome Core Facility, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Ajay S Gulati
- Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - David C Fargo
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Leonard Guarente
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Xiaoling Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina.
| |
Collapse
|
95
|
Chassaing B, De Bodt J, Marzorati M, Van de Wiele T, Gewirtz AT. Dietary emulsifiers directly alter human microbiota composition and gene expression ex vivo potentiating intestinal inflammation. Gut 2017; 66:1414-1427. [PMID: 28325746 PMCID: PMC5940336 DOI: 10.1136/gutjnl-2016-313099] [Citation(s) in RCA: 310] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 02/13/2017] [Accepted: 02/28/2017] [Indexed: 02/07/2023]
Abstract
OBJECTIVE The intestinal microbiota plays a central role in the development of many chronic inflammatory diseases including IBD and metabolic syndrome. Administration of substances that alter microbiota composition, including the synthetic dietary emulsifiers polysorbate 80 (P80) and carboxymethylcellulose (CMC), can promote such inflammatory disorders. However, that inflammation itself impacts microbiota composition has obfuscated defining the extent to which these compounds or other substances act directly upon the microbiota versus acting on host parameters that promote inflammation, which subsequently reshapes the microbiota. DESIGN We examined the direct impact of CMC and P80 on the microbiota using the mucosal simulator of the human intestinal microbial ecosystem (M-SHIME) model that maintains a complex stable human microbiota in the absence of a live host. RESULTS This approach revealed that both P80 and CMC acted directly upon human microbiota to increase its proinflammatory potential, as revealed by increased levels of bioactive flagellin. The CMC-induced increase in flagellin was rapid (1 day) and driven by altered microbiota gene expression. In contrast, the P80-induced flagellin increase occurred more slowly and was closely associated with altered species composition. Transfer of both emulsifier-treated M-SHIME microbiotas to germ-free recipient mice recapitulated many of the host and microbial alterations observed in mice directly treated with emulsifiers. CONCLUSIONS These results demonstrate a novel paradigm of deconstructing host-microbiota interactions and indicate that the microbiota can be directly impacted by these commonly used food additives, in a manner that subsequently drives intestinal inflammation.
Collapse
Affiliation(s)
- Benoit Chassaing
- Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA
| | - Jana De Bodt
- Center of Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, B-9000, Belgium
| | - Massimo Marzorati
- Center of Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, B-9000, Belgium
| | - Tom Van de Wiele
- Center of Microbial Ecology and Technology (CMET), Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, Ghent, B-9000, Belgium
| | - Andrew T. Gewirtz
- Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA
| |
Collapse
|
96
|
Davis SC, Yadav JS, Barrow SD, Robertson BK. Gut microbiome diversity influenced more by the Westernized dietary regime than the body mass index as assessed using effect size statistic. Microbiologyopen 2017; 6. [PMID: 28677210 PMCID: PMC5552927 DOI: 10.1002/mbo3.476] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 02/13/2017] [Accepted: 02/22/2017] [Indexed: 12/19/2022] Open
Abstract
Human gut microbiome dysbiosis has been associated with the onset of metabolic diseases and disorders. However, the critical factors leading to dysbiosis are poorly understood. In this study, we provide increasing evidence of the association of diet type and body mass index (BMI) and how they relatively influence the taxonomic structure of the gut microbiota with respect to the causation of gut microbiome dysbiosis. The study included randomly selected Alabama residents (n = 81), including females (n = 45) and males (n = 36). The demographics data included age (33 ± 13.3 years), height (1.7 ± 0.11 meters), and weight (82.3 ± 20.6 kg). The mean BMI was 28.3 ± 7.01, equating to an overweight BMI category. A cross-sectional case-control design encompassing the newly recognized effect size approach to bioinformatics analysis was used to analyze data from donated stool samples and accompanying nutrition surveys. We investigated the microbiome variations in the Bacteroidetes-Firmicutes ratio relative to BMI, food categories, and dietary groups at stratified abundance percentages of <20%, 20%, 30%, 40%, 50%, 60%, and ≥70%. We further investigated variation in the Firmicutes and Bacteroidetes phyla composition (at the genus and species level) in relation to BMI, food categories, and dietary groups (Westernized or healthy). The Pearson Correlation coefficient as an indication of effect size across Alpha diversity indices was used to test the hypothesis (H0 ): increased BMI has greater effect on taxonomic diversity than Westernized diet type, (Ha ): increased BMI does not have a greater effect on taxonomic diversity than Westernized diet type. In conclusion, we rejected the (H0 ) as our results demonstrated that Westernized diet type had an effect size of 0.22 posing a greater impact upon the gut microbiota diversity than an increased BMI with an effect size of 0.16. This implied Westernized diet as a critical factor in causing dysbiosis as compared to an overweight or obese body mass index.
Collapse
Affiliation(s)
- Shannon C Davis
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL, USA
| | - Jagjit S Yadav
- Microbial Pathogenesis and Immunotoxicology Laboratory, Department of Environmental Health, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Stephanie D Barrow
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL, USA
| | - Boakai K Robertson
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL, USA
| |
Collapse
|
97
|
Shankar J. Insights into study design and statistical analyses in translational microbiome studies. ANNALS OF TRANSLATIONAL MEDICINE 2017; 5:249. [PMID: 28706917 DOI: 10.21037/atm.2017.01.13] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Research questions in translational microbiome studies are substantially more complex than their counterparts in basic science. Robust study designs with appropriate statistical analysis frameworks are pivotal to the success of these translational studies. This review considers how study designs can account for heterogeneous phenotypes by adopting representative sampling schemes for recruiting the study population and making careful choices about the control population. Advantages and limitations of 16S profiling and whole-genome sequencing, the two primary techniques for measuring the microbiome, are discussed followed by an overview of bioinformatic processing of high-throughput sequencing data from these measurements. Practical insights into the downstream statistical analyses including data processing and integration, variable transformations, and data exploration are provided. The merits of regularization and ensemble modeling for analyzing microbiome data are discussed along with a recommendation for selecting modeling approaches based on data-driven simulations and objective evaluation. The review builds on several recent discussions of study design issues in microbiome research but with a stronger emphasis on the downstream and often-ignored aspects of statistical analyses that are crucial for bridging the gap between basic science and translation.
Collapse
|
98
|
Dietary Supplementation With Nonfermentable Fiber Alters the Gut Microbiota and Confers Protection in Murine Models of Sepsis. Crit Care Med 2017; 45:e516-e523. [PMID: 28252538 DOI: 10.1097/ccm.0000000000002291] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
OBJECTIVES Links between microbial alterations and systemic inflammation have been demonstrated in chronic disease, but little is known about these interactions during acute inflammation. This study investigates the effect of dietary supplementation with cellulose, a nonfermentable fiber, on the gut microbiota, inflammatory markers, and survival in two murine models of sepsis. DESIGN Prospective experimental study. SETTING University laboratory. SUBJECTS Six-week-old male C57BL/6 wild-type mice. INTERVENTIONS Mice were assigned to low-fiber, normal-fiber, or high-fiber diets with or without antibiotics for 2 weeks and then subjected to sepsis by cecal ligation and puncture or endotoxin injection. Fecal samples were collected for microbiota analyses before and after dietary interventions. MEASUREMENTS AND MAIN RESULTS Mice that received a high-fiber diet demonstrated increased survival after cecal ligation and puncture relative to mice receiving low-fiber or normal-fiber diets. The survival benefit was associated with decreased serum concentration of pro-inflammatory cytokines, reduced neutrophil infiltration in the lungs, and diminished hepatic inflammation. The high-fiber diet also increased survival after endotoxin injection. Bacterial 16S ribosomal RNA gene sequences from each sample were amplified, sequenced, and analyzed. Fiber supplementation yielded an increase in relative abundance of the genera Akkermansia and Lachnospiraceae, taxa commonly associated with metabolic health. Administration of antibiotics to mice on the high-fiber diet negated the enrichment of Akkermansia species and the survival benefit after cecal ligation and puncture. CONCLUSION Dietary supplementation with cellulose offers a microbe-mediated survival advantage in murine models of sepsis. Improved understanding of the link between diet, the microbiota, and systemic illness may yield new therapeutic strategies for patients with sepsis.
Collapse
|
99
|
Kang M, Martin A. Microbiome and colorectal cancer: Unraveling host-microbiota interactions in colitis-associated colorectal cancer development. Semin Immunol 2017; 32:3-13. [PMID: 28465070 DOI: 10.1016/j.smim.2017.04.003] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/19/2017] [Indexed: 02/07/2023]
Abstract
Dysbiosis of gut microbiota occurs in many human chronic immune-mediated diseases, such as inflammatory bowel disease (IBD) and colitis-associated colorectal cancer (CAC). Reciprocally, uncontrolled immune responses, that may or may not be induced by dysbiosis, are central to the development of IBD and CAC. There has been a surge of interest in investigating the relationship between microbiota, inflammation and CAC. In this review, we discuss recent findings related to gut microbiota and chronic immune-mediated diseases, such as IBD and CAC. Moreover, the molecular mechanisms underlying the roles of chronic inflammation in CAC are examined. Finally, we discuss the development of novel microbiota-based therapeutics for IBD and colorectal cancer.
Collapse
Affiliation(s)
- Mingsong Kang
- University of Toronto, Department of Immunology, Toronto, Ontario, Canada
| | - Alberto Martin
- University of Toronto, Department of Immunology, Toronto, Ontario, Canada.
| |
Collapse
|
100
|
Gut microbiome as a clinical tool in gastrointestinal disease management: are we there yet? Nat Rev Gastroenterol Hepatol 2017; 14:315-320. [PMID: 28356581 DOI: 10.1038/nrgastro.2017.29] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Spurred on by ever-evolving developments in analytical methodology, the microbiome, and the gut microbiome in particular, has become the hot topic in biomedical research. Ingenious experiments in animal models have revealed the extent to which the gut microbiota sustains health and how its disruption might contribute to disease pathogenesis. Not surprisingly, associations between the microbiota and disease states in humans have been the subject of considerable interest and many links proposed. However, with rare exceptions, the incrimination of an altered microbiota in disease pathogenesis seems premature at this time given our incomplete understanding of the composition of the gut microbiota in health and the effect of many confounding factors in the interpretation of supposedly abnormal microbial signatures. Future studies must account for these variables and the bidirectionality of host-microorganism interactions in health and disease. In this Perspectives, the status of microbiota signatures in the clinical arena (for facilitating diagnosis or refining prognosis) will be critically assessed and guidance toward future progress provided.
Collapse
|