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Zhao Y, Liu Y, Jia L. Gut microbial dysbiosis and inflammation: Impact on periodontal health. J Periodontal Res 2024. [PMID: 38991951 DOI: 10.1111/jre.13324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024]
Abstract
Periodontitis is widely acknowledged as the most prevalent type of oral inflammation, arising from the dynamic interplay between oral pathogens and the host's immune responses. It is also recognized as a contributing factor to various systemic diseases. Dysbiosis of the oral microbiota can significantly alter the composition and diversity of the gut microbiota. Researchers have delved into the links between periodontitis and systemic diseases through the "oral-gut" axis. However, whether the associations between periodontitis and the gut microbiota are simply correlative or driven by causative mechanistic interactions remains uncertain. This review investigates how dysbiosis of the gut microbiota impacts periodontitis, drawing on existing preclinical and clinical data. This study highlights potential mechanisms of this interaction, including alterations in subgingival microbiota, oral mucosal barrier function, neutrophil activity, and abnormal T-cell recycling, and offers new perspectives for managing periodontitis, especially in cases linked to systemic diseases.
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Affiliation(s)
- Yifan Zhao
- Laboratory of Tissue Regeneration and Immunology and Department of Periodontics, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, China
| | - Yi Liu
- Laboratory of Tissue Regeneration and Immunology and Department of Periodontics, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, China
| | - Lu Jia
- Laboratory of Tissue Regeneration and Immunology and Department of Periodontics, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, School of Stomatology, Capital Medical University, Beijing, China
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Sheikh IA, Bianchi-Smak J, Laubitz D, Schiro G, Midura-Kiela MT, Besselsen DG, Vedantam G, Jarmakiewicz S, Filip R, Ghishan FK, Gao N, Kiela PR. Transplant of microbiota from Crohn's disease patients to germ-free mice results in colitis. Gut Microbes 2024; 16:2333483. [PMID: 38532703 PMCID: PMC10978031 DOI: 10.1080/19490976.2024.2333483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 03/18/2024] [Indexed: 03/28/2024] Open
Abstract
Although the role of the intestinal microbiota in the pathogenesis of inflammatory bowel disease (IBD) is beyond debate, attempts to verify the causative role of IBD-associated dysbiosis have been limited to reports of promoting the disease in genetically susceptible mice or in chemically induced colitis. We aimed to further test the host response to fecal microbiome transplantation (FMT) from Crohn's disease patients on mucosal homeostasis in ex-germ-free (xGF) mice. We characterized and transferred fecal microbiota from healthy patients and patients with defined Crohn's ileocolitis (CD_L3) to germ-free mice and analyzed the resulting microbial and mucosal homeostasis by 16S profiling, shotgun metagenomics, histology, immunofluorescence (IF) and RNAseq analysis. We observed a markedly reduced engraftment of CD_L3 microbiome compared to healthy control microbiota. FMT from CD_L3 patients did not lead to ileitis but resulted in colitis with features consistent with CD: a discontinued pattern of colitis, more proximal colonic localization, enlarged isolated lymphoid follicles and/or tertiary lymphoid organ neogenesis, and a transcriptomic pattern consistent with epithelial reprograming and promotion of the Paneth cell-like signature in the proximal colon and immune dysregulation characteristic of CD. The observed inflammatory response was associated with persistently increased abundance of Ruminococcus gnavus, Erysipelatoclostridium ramosum, Faecalimonas umbilicate, Blautia hominis, Clostridium butyricum, and C. paraputrificum and unexpected growth of toxigenic C. difficile, which was below the detection level in the community used for inoculation. Our study provides the first evidence that the transfer of a dysbiotic community from CD patients can lead to spontaneous inflammatory changes in the colon of xGF mice and identifies a signature microbial community capable of promoting colonization of pathogenic and conditionally pathogenic bacteria.
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Affiliation(s)
- Irshad Ali Sheikh
- Daniel Cracchiolo Institute for Pediatric Autoimmune Disease Research, Steele Children’s Research Center, Department of Pediatrics, University of Arizona, Tucson, AZ, USA
| | | | - Daniel Laubitz
- Daniel Cracchiolo Institute for Pediatric Autoimmune Disease Research, Steele Children’s Research Center, Department of Pediatrics, University of Arizona, Tucson, AZ, USA
| | - Gabriele Schiro
- Daniel Cracchiolo Institute for Pediatric Autoimmune Disease Research, Steele Children’s Research Center, Department of Pediatrics, University of Arizona, Tucson, AZ, USA
| | - Monica T. Midura-Kiela
- Daniel Cracchiolo Institute for Pediatric Autoimmune Disease Research, Steele Children’s Research Center, Department of Pediatrics, University of Arizona, Tucson, AZ, USA
| | - David G. Besselsen
- Pediatrics, University Animal Care, University of Arizona, Tucson, AZ, USA
| | - Gayatri Vedantam
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ, USA
| | - Sara Jarmakiewicz
- Institute of Health Sciences, Medical College of Rzeszow, Rzeszow University, Rzeszow, Poland
| | - Rafał Filip
- Institute of Medicine, Medical College of Rzeszow University, Rzeszow, Poland
- Department of Gastroenterology with IBD Unit, Clinical Hospital, Rzeszow, Poland
| | - Fayez K. Ghishan
- Daniel Cracchiolo Institute for Pediatric Autoimmune Disease Research, Steele Children’s Research Center, Department of Pediatrics, University of Arizona, Tucson, AZ, USA
| | - Nan Gao
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA
| | - Pawel R. Kiela
- Daniel Cracchiolo Institute for Pediatric Autoimmune Disease Research, Steele Children’s Research Center, Department of Pediatrics, University of Arizona, Tucson, AZ, USA
- Department of Immunobiology, University of Arizona, Tucson, AZ, USA
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Kriaa A, Mariaule V, De Rudder C, Jablaoui A, Sokol H, Wilmes P, Maguin E, Rhimi M. From animal models to gut-on-chip: the challenging journey to capture inter-individual variability in chronic digestive disorders. Gut Microbes 2024; 16:2333434. [PMID: 38536705 PMCID: PMC10978023 DOI: 10.1080/19490976.2024.2333434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/10/2024] Open
Abstract
Chronic digestive disorders are of increasing incidence worldwide with expensive treatments and no available cure. Available therapeutic schemes mainly rely on symptom relief, with large degrees of variability in patients' response to such treatments, underlining the need for new therapeutic strategies. There are strong indications that the gut microbiota's contribution seems to be a key modulator of disease activity and patients' treatment responses. Hence, efforts have been devoted to understanding host-microbe interactions and the mechanisms underpinning such variability. Animal models, being the gold standard, provide valuable mechanistic insights into host-microbe interactions. However, they are not exempt from limitations prompting the development of alternative methods. Emerging microfluidic technologies and gut-on-chip models were shown to mirror the main features of gut physiology and disease state, reflect microbiota modification, and include functional readouts for studying host responses. In this commentary, we discuss the relevance of animal models in understanding host-microbe interactions and how gut-on-chip technology holds promises for addressing patient variability in responses to chronic digestive disease treatment.
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Affiliation(s)
- Aicha Kriaa
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Vincent Mariaule
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Charlotte De Rudder
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Amin Jablaoui
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Harry Sokol
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- INSERM UMRS-938, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Sorbonne Université, Paris, France
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Emmanuelle Maguin
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Moez Rhimi
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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Štofilová J, Kvaková M, Kamlárová A, Hijová E, Bertková I, Guľašová Z. Probiotic-Based Intervention in the Treatment of Ulcerative Colitis: Conventional and New Approaches. Biomedicines 2022; 10:2236. [PMID: 36140337 PMCID: PMC9496552 DOI: 10.3390/biomedicines10092236] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 12/02/2022] Open
Abstract
Although there are number of available therapies for ulcerative colitis (UC), many patients are unresponsive to these treatments or experience secondary failure during treatment. Thus, the development of new therapies or alternative strategies with minimal side effects is inevitable. Strategies targeting dysbiosis of gut microbiota have been tested in the management of UC due to the unquestionable role of gut microbiota in the etiology of UC. Advanced molecular analyses of gut microbiomes revealed evident dysbiosis in UC patients, characterized by a reduced biodiversity of commensal microbiota. Administration of conventional probiotic strains is a commonly applied approach in the management of the disease to modify the gut microbiome, improve intestinal barrier integrity and function, and maintain a balanced immune response. However, conventional probiotics do not always provide the expected health benefits to a patient. Their benefits vary significantly, depending on the type and stage of the disease and the strain and dose of the probiotics administered. Their mechanism of action is also strain-dependent. Recently, new candidates for potential next-generation probiotics have been discovered. This could bring to light new approaches in the restoration of microbiome homeostasis and in UC treatment in a targeted manner. The aim of this paper is to provide an updated review on the current options of probiotic-based therapies, highlight the effective conventional probiotic strains, and outline the future possibilities of next-generation probiotic and postbiotic supplementation and fecal microbiota transplantation in the management of UC.
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Affiliation(s)
- Jana Štofilová
- Center of Clinical and Preclinical Research MEDIPARK, Faculty of Medicine, Pavol Jozef Safarik University in Kosice, Trieda SNP 1, 040 11 Kosice, Slovakia
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Zhang Y, Si X, Yang L, Wang H, Sun Y, Liu N. Association between intestinal microbiota and inflammatory bowel disease. Animal Model Exp Med 2022; 5:311-322. [PMID: 35808814 PMCID: PMC9434590 DOI: 10.1002/ame2.12255] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 05/21/2022] [Indexed: 12/15/2022] Open
Abstract
Inflammatory bowel disease (IBD), which includes Crohn's disease (CD) and ulcerative colitis (UC), has emerged as a global disease with high incidence, long duration, devastating clinical symptoms, and low curability (relapsing immune response and barrier function defects). Mounting studies have been performed to investigate its pathogenesis to provide an ever‐expanding arsenal of therapeutic options, while the precise etiology of IBD is not completely understood yet. Recent advances in high‐throughput sequencing methods and animal models have provided new insights into the association between intestinal microbiota and IBD. In general, dysbiosis characterized by an imbalanced microbiota has been widely recognized as a pathology of IBD. However, intestinal microbiota alterations represent the cause or result of IBD process remains unclear. Therefore, more evidences are needed to identify the precise role of intestinal microbiota in the pathogenesis of IBD. Herein, this review aims to outline the current knowledge of commonly used, chemically induced, and infectious mouse models, gut microbiota alteration and how it contributes to IBD, and dysregulated metabolite production links to IBD pathogenesis.
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Affiliation(s)
- Yunchang Zhang
- Ministry of Agriculture and Rural Affairs, Institute of Feed Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuemeng Si
- State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, China Agricultural University, Beijing, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Nutrition and Health, China Agricultural University, Beijing, China
| | - Ling Yang
- Department of Food and Bioengineering, Beijing Vocational College of Agriculture, Beijing, China
| | - Hui Wang
- Department of Food and Bioengineering, Beijing Vocational College of Agriculture, Beijing, China
| | - Ye Sun
- Institute of Medical Laboratory Animal Science, Chinese Academy of Medical Sciences & Comparative Medical Center, Peking Union Medical College, Beijing, China
| | - Ning Liu
- State Key Laboratory of Animal Nutrition, Department of Animal Nutrition and Feed Science, China Agricultural University, Beijing, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Nutrition and Health, China Agricultural University, Beijing, China
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Li M, Wang Z, Wang L, Xue B, Hu R, Zou H, Liu S, Shah AM, Peng Q. Comparison of changes in fecal microbiota of calves with and without dam. PeerJ 2022; 10:e12826. [PMID: 35386429 PMCID: PMC8978885 DOI: 10.7717/peerj.12826] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 01/03/2022] [Indexed: 01/10/2023] Open
Abstract
In pastoral areas and semi-agricultural and semi-pastoral areas of Sichuan, beef cattle breeding mode is mainly dependent on nature to raise livestock. On the one hand, owing to the shortage of forage grass in spring, cows suffer from malnutrition. On the other hand, competition for milk between human and livestock further deepens the malnutrition of newborn calves, and the mortality rate even exceeds 40%, resulting in serious waste of beef cattle source resources. The objective of this study was to investigate the effect of different cultivation methods (calves with and without dam) and age on calves hindgut microbiome. Sixteen healthy calves (Yak ♂ × Pian cattle ♀, with similar birthday 0 ± 2 d and body weight 13.1 ± 1.13 kg), were selected and randomly divided into two groups. The control group was cultivated with heifers, whereas the treatment group was cultivated without heifers and was fed milk replacer during the whole 95 days formal experimental period. Fecal samples were collected on 35, 65 and 95 days of age for high-throughput sequencing. The α-diversity was different between the two groups on day 35; however, the bacterial species richness and diversity was almost not different on day 95. Principal coordinates analysis revealed significant difference between the two groups on all the three time points, and the timepoints of day 65 and 95 were closer and separated from the timepoints of day 35 in calves with dam, whereas the timepoints of day 35 and 65 were closer and separated from day 95 in calves without dam. As time passed, the abundance of Firmicutes increased, while Proteobacteria and Actinobacteria decreased in calves with dam. But in calves without dam, the abundance of Bacteroidetes and Proteobacteria increased on day 65 and then decreased on day 95. In genus level, the relative abundance of Bacteroides decreased in calf with dam while its abundance increased first and then decreased in calf without dam but both resulted in the range of 3.5~4.5%. The relative abundance of Lactobacillus decreased, whereas Ruminococcaceae UCG-005 increased in both groups as the calf grew up. It was concluded that the richness and evenness of the microbial communities was higher in calves with dam than without dam, and a stable gut microbiome in calve with dam is established earlier than calf without dam.
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Aldhafiri FK. COVID-19 and gut dysbiosis, understanding the role of probiotic supplements in reversing gut dysbiosis and immunity. NUTR CLIN METAB 2022. [PMCID: PMC8825305 DOI: 10.1016/j.nupar.2022.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In December 2019, an outbreak of novel beta-coronavirus started in Wuhan, China, spread globally as coronavirus disease 2019 (COVID-19) pandemic and is still underway. The causative agent for COVID-19 identified as a novel strain of beta coronavirus named nSARS-CoV-2. The nSARS-CoV-2 primarily targets the respiratory tract and results in severe acute respiratory distress (ARDS), leading to the collapse of the respiratory tract. The virus internalizes primarily via ACEII receptor, and many tissues reported a significant level of expression of ACEII receptor including lungs, hearts, kidneys, and gastrointestinal tract. The clinical manifestations of COVID-19 are diverse, but growing evidence suggests that gut dysbiosis is one of them and poses a threat to native immunity. The human microbial ecology plays a vital role in human physiology, including building immunity. The gastrointestinal tract (GIT) habitats trillions of beneficial microbes’ precisely bacterial species synchronize with human physiology and remain symbiotic. On the contrary, harmful microbiota seeks an opportunity to break the equilibrium failure of balance between beneficial and detrimental human gut microbiota results in impaired physiology and immunity. The grown research evidence demonstrated that infection caused by the nSARS-CoV-2 result in moderate to severe diarrheal outcomes. The diarrheal conditions in COVID-19 patients are due to alteration of gut microbial ecology. The management of COVID-19 requires specialized therapeutics along with a series of nutraceuticals. Probiotics remain vital nutrient supplements in COVID-19 management, offer relief in diarrhea and improve/restore immunity. This study uses available data/findings to emphasize an association between COVID-19 and gut dysbiosis. The study also provides a scientific basis of impaired immunity during gut dysbiosis in COVID-19 and how probiotics help restore and improve impaired immunity and diarrhea.
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Zou J, Liu C, Jiang S, Qian D, Duan J. Cross Talk between Gut Microbiota and Intestinal Mucosal Immunity in the Development of Ulcerative Colitis. Infect Immun 2021; 89:e0001421. [PMID: 33526559 PMCID: PMC8370674 DOI: 10.1128/iai.00014-21] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ulcerative colitis (UC), a nonspecific inflammatory disease, is characterized by inflammation and mucosal damage in the colon, and its prevalence in the world is increasing. Nevertheless, the exact pathogenesis of UC is still unclear. Accumulating data have suggested that its pathogenesis is multifactorial, involving genetic predisposition, environmental factors, microbial dysbiosis, and dysregulated immune responses. Generally, UC is aroused by inappropriate immune activation based on the interaction of host and intestinal microbiota. The relationship between microbiota and host immune system in the pathogenesis of UC is complicated. However, increasing evidence indicates that the shift of microbiota composition can substantially influence intestinal immunity. In this review, we primarily focus on the delicate balance between microbiota and gut mucosal immunity during UC progression.
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Affiliation(s)
- Junfeng Zou
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Chen Liu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Shu Jiang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Dawei Qian
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Jinao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
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Johnson SD, Olwenyi OA, Bhyravbhatla N, Thurman M, Pandey K, Klug EA, Johnston M, Dyavar SR, Acharya A, Podany AT, Fletcher CV, Mohan M, Singh K, Byrareddy SN. Therapeutic implications of SARS-CoV-2 dysregulation of the gut-brain-lung axis. World J Gastroenterol 2021; 27:4763-4783. [PMID: 34447225 PMCID: PMC8371510 DOI: 10.3748/wjg.v27.i29.4763] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/10/2021] [Accepted: 07/20/2021] [Indexed: 02/06/2023] Open
Abstract
The emergence and rapid spread of novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused over 180 million confirmed cases resulting in over 4 million deaths worldwide with no clear end in sight for the coronavirus disease 19 (COVID-19) pandemic. Most SARS-CoV-2 exposed individuals experience mild to moderate symptoms, including fever, cough, fatigue, and loss of smell and taste. However, many individuals develop pneumonia, acute respiratory distress syndrome, septic shock, and multiorgan dysfunction. In addition to these primarily respiratory symptoms, SARS-CoV-2 can also infiltrate the central nervous system, which may damage the blood-brain barrier and the neuron's synapses. Resultant inflammation and neurodegeneration in the brain stem can further prevent efferent signaling to cranial nerves, leading to the loss of anti-inflammatory signaling and normal respiratory and gastrointestinal functions. Additionally, SARS-CoV-2 can infect enterocytes resulting in gut damage followed by microbial dysbiosis and translocation of bacteria and their byproducts across the damaged epithelial barrier. As a result, this exacerbates pro-inflammatory responses both locally and systemically, resulting in impaired clinical outcomes. Recent evidence has highlighted the complex interactions that mutually modulate respiratory, neurological, and gastrointestinal function. In this review, we discuss the ways SARS-CoV-2 potentially disrupts the gut-brain-lung axis. We further highlight targeting specific responses to SARS-CoV-2 for the development of novel, urgently needed therapeutic interventions. Finally, we propose a prospective related to the individuals from Low- and Middle-Income countries. Here, the underlying propensity for heightened gut damage/microbial translocation is likely to result in worse clinical outcomes during this COVID-19 pandemic.
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Affiliation(s)
- Samuel D Johnson
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, United States
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Omalla A Olwenyi
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, United States
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Namita Bhyravbhatla
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Michellie Thurman
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Kabita Pandey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, United States
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Elizabeth A Klug
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, United States
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Morgan Johnston
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Shetty Ravi Dyavar
- Antiviral Pharmacology Laboratory, University of Nebraska Medical Center (UNMC) Center for Drug Discovery, Omaha, NE 68198, United States
| | - Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Anthony T Podany
- Antiviral Pharmacology Laboratory, University of Nebraska Medical Center (UNMC) Center for Drug Discovery, Omaha, NE 68198, United States
| | - Courtney V Fletcher
- Antiviral Pharmacology Laboratory, University of Nebraska Medical Center (UNMC) Center for Drug Discovery, Omaha, NE 68198, United States
| | - Mahesh Mohan
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX 78227, United States
| | - Kamal Singh
- Department of Molecular Microbiology and Immunology and Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, United States
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, United States
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, United States
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, United States
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Katz-Agranov N, Zandman-Goddard G. Autoimmunity and COVID-19 - The microbiotal connection. Autoimmun Rev 2021; 20:102865. [PMID: 34118455 PMCID: PMC8189735 DOI: 10.1016/j.autrev.2021.102865] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 03/28/2021] [Indexed: 02/07/2023]
Abstract
Background and aims The novel SARS-CoV-2 has been rattling the world since its outbreak in December 2019, leading to the COVID-19 pandemic. The learning curve of this new virus has been steep, with a global scientific community desperate to learn how the virus is transmitted, how it replicates, why it causes such a wide spectrum of disease manifestations, resulting in none or few symptoms in some. Others are burdened by an intense immune response that resembles the cytokine storm syndrome (CSS), which leads to severe disease manifestations, often complicated by fatal acute respiratory distress syndrome and death. Research efforts have been focusing on finding effective cures and vaccinations for this virus. The presence of SARS-CoV-2 in the gastrointestinal (GI) tract, represented by several GI manifestations, has led to its investigation as a target for the virus and as an indicator of disease severity. The response of the microbiome (which is heavily linked to immunity) to the novel SARS-CoV-2 virus, and its role in igniting the exaggerated immune response has therefore become a focus of interest. The objective of our study was to gather the data connecting between the microbiome, the GI tract and COVID-19 and to investigate whether these reported alterations in the gut microbiome bear any resemblance to those seen in lupus, the prototypical autoimmune disease. Confirming such changes may become the steppingstone to potential therapies that may prevent transmission, progression and immune related manifestations of COVID-19, via manipulation of the gut microbiota. Methods We performed an extensive literature review, utilizing the Pubmed search engine and Google Scholar for studies evaluating the microbiome in COVID-19 patients and compared results with studies evaluating the microbiome in lupus. We searched for the terms: microbiome, dysbiosis, COVID-19, SARS-CoV-2, gastrointestinal as well as lupus and autoimmune. While there were hundreds of articles which referred to gastrointestinal manifestations in COVID-19, to date only 4 studies investigated the gastrointestinal microbiome in this setting. We compared the similarities between microbiome of COVID-19 patients and lupus patients. Results We found that there are several similar processes of immune dysregulation in patients with COVID-19 and in those with lupus, with several other alterations seen in other pathological states. Some of these similarities include loss of microbiota biodiversity, increased representation of pathobionts, which are microbes associated with inflammation and disease (i.e Proteobacteria) and a relative decrease of symbionts, which are protective microbes, associated with anti-inflammatory properties (i.e Lactobacillus). Compromise to the intestinal barrier has also been reported in both. Conclusions We conclude that the gastrointestinal tract contributes to the disease manifestations in COVID-19. Whether gastrointestinal dysbiosis is the cause or effect of gastrointestinal manifestations and several severe systemic manifestations, which may be the response to an increased pro-inflammatory environment, is still debatable and warrants further investigation. Given the resemblance of the microbiome in COVID-19 patients to that seen in lupus patients, it becomes clearer why several therapies used in autoimmune conditions are currently under investigation for the treatment of COVID-19 patients. Moreover, these findings should promote further investigating the utility of manipulation of the microbiome, via nutritional supplementation or even fecal transplantations, interventions that may alter the course of the disease, and potentially prevent disease transmission at low cost and low risk.
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Affiliation(s)
- Nurit Katz-Agranov
- Department of Medicine, Saint Elizabeth's Medical Center, Boston, MA, USA; Tufts University School of Medicine, Boston, MA, USA.
| | - Gisele Zandman-Goddard
- Department of Medicine C, Wolfson Medical Center, Holon, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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Mohamed SS, Abdeltawab NF, Wadie W, Ahmed LA, Ammar RM, Rabini S, Abdel-Aziz H, Khayyal MT. Effect of the standard herbal preparation, STW5, treatment on dysbiosis induced by dextran sodium sulfate in experimental colitis. BMC Complement Med Ther 2021; 21:168. [PMID: 34103031 PMCID: PMC8188707 DOI: 10.1186/s12906-021-03337-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/05/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The standardized herbal preparation, STW 5, is effective clinically in functional gastrointestinal disorders and experimentally in ulcerative colitis (UC). The present study explores whether the beneficial effect of STW 5 involves influencing the intestinal microbiota. METHODS UC was induced in Wistar rats by feeding them 5% dextran sodium sulfate (DSS) in drinking water for 7 days. Rats were treated concurrently with STW 5 and sacrificed 24 h after last drug administration. Fecal samples were used to determine changes in the abundance of selected microbial phyla and genera using real-time PCR. RESULTS Induction of UC led to dysbiosis and changes in the gut microbiota. The changes included an increase in some genera of the Firmicutes, namely Enterococcus, and a decrease in others, namely Blautia, Clostridium, and Lactobacillus. DSS further induced a marked increase in the abundance of Bacteroidetes and Proteobacteria as well as in the relative abundance of Actinobacteria and its genus Bifidobacterium. Methanobrevibacter levels (phylum Euryarchaeota) were also increased. Microbial dysbiosis was associated with changes in various parameters of colonic inflammation. STW 5 effectively guarded against those changes and significantly affected the indices of edema and inflammation in the UC model. Changes in colon length, colon mass index, inflammatory and apoptotic markers, and histological changes induced by DSS were also prevented. CONCLUSIONS Dysbiosis plays a contributing role in the development of DSS-induced UC. Derangements in the microbial flora and associated inflammatory processes were largely prevented by STW 5, suggesting that this effect might contribute towards its beneficial usefulness in this condition.
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Affiliation(s)
- Sarah S Mohamed
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, 11562, Egypt
| | - Nourtan F Abdeltawab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Walaa Wadie
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, 11562, Egypt
| | - Lamiaa A Ahmed
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, 11562, Egypt
| | - Ramy M Ammar
- Bayer Consumer Health, Steigerwald Arzneimittelwerk GmbH, Darmstadt, Germany
- Pharmacology Department, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Sabine Rabini
- Bayer Consumer Health, Steigerwald Arzneimittelwerk GmbH, Darmstadt, Germany
| | - Heba Abdel-Aziz
- Bayer Consumer Health, Steigerwald Arzneimittelwerk GmbH, Darmstadt, Germany
| | - Mohamed T Khayyal
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, 11562, Egypt.
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12
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The CD200 Regulates Inflammation in Mice Independently of TNF-α Production. Int J Mol Sci 2021; 22:ijms22105358. [PMID: 34069671 PMCID: PMC8161250 DOI: 10.3390/ijms22105358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/06/2021] [Accepted: 05/14/2021] [Indexed: 11/16/2022] Open
Abstract
Inflammatory bowel disease is characterized by the infiltration of immune cells and chronic inflammation. The immune inhibitory receptor, CD200R, is involved in the downregulation of the activation of immune cells to prevent excessive inflammation. We aimed to define the role of CD200R ligand-CD200 in the experimental model of intestinal inflammation in conventionally-reared mice. Mice were given a dextran sodium sulfate solution in drinking water. Bodyweight loss was monitored daily and the disease activity index was calculated, and a histological evaluation of the colon was performed. TNF-α production was measured in the culture of small fragments of the distal colon or bone marrow-derived macrophages (BMDMs) cocultured with CD200+ cells. We found that Cd200-/- mice displayed diminished severity of colitis when compared to WT mice. Inflammation significantly diminished CD200 expression in WT mice, particularly on vascular endothelial cells and immune cells. The co-culture of BMDMs with CD200+ cells inhibited TNF-α secretion. In vivo, acute colitis induced by DSS significantly increased TNF-α secretion in colon tissue in comparison to untreated controls. However, Cd200-/- mice secreted a similar level of TNF-α to WT mice in vivo. CD200 regulates the severity of DSS-induced colitis in conventionally-reared mice. The presence of CD200+ cells decreases TNF-α production by macrophages in vitro. However, during DDS-induced intestinal inflammation secretion of TNF-α is independent of CD200 expression.
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13
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Park H, Yeo S, Kang S, Huh CS. Longitudinal Microbiome Analysis in a Dextran Sulfate Sodium-Induced Colitis Mouse Model. Microorganisms 2021; 9:370. [PMID: 33673349 PMCID: PMC7917662 DOI: 10.3390/microorganisms9020370] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
The role of the gut microbiota in the pathogenesis of inflammatory bowel disease (IBD) has been in focus for decades. Although metagenomic observations in patients/animal colitis models have been attempted, the microbiome results were still indefinite and broad taxonomic presumptions were made due to the cross-sectional studies. Herein, we conducted a longitudinal microbiome analysis in a dextran sulfate sodium (DSS)-induced colitis mouse model with a two-factor design based on serial DSS dose (0, 1, 2, and 3%) and duration for 12 days, and four mice from each group were sacrificed at two-day intervals. During the colitis development, a transition of the cecal microbial diversity from the normal state to dysbiosis and dynamic changes of the populations were observed. We identified genera that significantly induced or depleted depending on DSS exposure, and confirmed the correlations of the individual taxa to the colitis severity indicated by inflammatory biomarkers (intestinal bleeding and neutrophil-derived indicators). Of note, each taxonomic population showed its own susceptibility to the changing colitis status. Our findings suggest that an understanding of the individual susceptibility to colitis conditions may contribute to identifying the role of the gut microbes in the pathogenesis of IBD.
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Affiliation(s)
- Hyunjoon Park
- Research Institute of Eco-Friendly Livestock Science, Institute of Green-Bio Science and Technology, Seoul National University, Pyeongchang, Gangwon 25354, Korea;
- Advanced Green Energy and Environment Institute, Handong Global University, Pohang 37554, Korea
| | - Soyoung Yeo
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea;
| | - Seokwon Kang
- Department of Life Sciences, Handong Global University, Pohang 37554, Korea;
| | - Chul Sung Huh
- Research Institute of Eco-Friendly Livestock Science, Institute of Green-Bio Science and Technology, Seoul National University, Pyeongchang, Gangwon 25354, Korea;
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang, Gangwon 25354, Korea
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14
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Din AU, Mazhar M, Waseem M, Ahmad W, Bibi A, Hassan A, Ali N, Gang W, Qian G, Ullah R, Shah T, Ullah M, Khan I, Nisar MF, Wu J. SARS-CoV-2 microbiome dysbiosis linked disorders and possible probiotics role. Biomed Pharmacother 2021; 133:110947. [PMID: 33197765 PMCID: PMC7657099 DOI: 10.1016/j.biopha.2020.110947] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/21/2020] [Accepted: 10/25/2020] [Indexed: 01/07/2023] Open
Abstract
In December 2019, a pneumonia outbreak of unknown etiology was reported which caused panic in Wuhan city of central China, which was later identified as Coronavirus disease (COVID-19) caused by a novel coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by the Chinese Centre for Disease Control and Prevention (CDC) and WHO. To date, the SARS-CoV-2 spread has already become a global pandemic with a considerable death toll. The associated symptoms of the COVID-19 infection varied with increased inflammation as an everyday pathological basis. Among various other symptoms such as fever, cough, lethargy, gastrointestinal (GI) symptoms included diarrhea and IBD with colitis, have been reported. Currently, there is no sole cure for COVID-19, and researchers are actively engaged to search out appropriate treatment and develop a vaccine for its prevention. Antiviral for controlling viral load and corticosteroid therapy for reducing inflammation seems to be inadequate to control the fatality rate. Based on the available related literature, which documented GI symptoms with diarrhea, inflammatory bowel diseases (IBD) with colitis, and increased deaths in the intensive care unit (ICU), conclude that dysbiosis occurs during SARS-COV-2 infection as the gut-lung axis cannot be ignored. As probiotics play a therapeutic role for GI, IBD, colitis, and even in viral infection. So, we assume that the inclusion of studies to investigate gut microbiome and subsequent therapies such as probiotics might help decrease the inflammatory response of viral pathogenesis and respiratory symptoms by strengthening the host immune system, amelioration of gut microbiome, and improvement of gut barrier function.
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Affiliation(s)
- Ahmad Ud Din
- Drug Discovery Research Center, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Maryam Mazhar
- Research Center of Integrated Traditional Chinese and Western Medicine, Affiliated Traditional Medicine Hospital, Southwest Medical University, Luzhou, China
| | - Muhammed Waseem
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Waqar Ahmad
- Drug Discovery Research Center, Southwest Medical University, Luzhou, 646000, Sichuan, China; College of Marine Life Sciences and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Asma Bibi
- Institute of Zoonosis Anhui Medical University, Hefei Anhui, 230032, China
| | - Adil Hassan
- Key Laboratory for Bio-rheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants Bioengineering College of Chongqing University, Chongqing, 400030, China
| | - Niaz Ali
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bio-resources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, Guangxi, China
| | - Wang Gang
- Drug Discovery Research Center, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Gao Qian
- Drug Discovery Research Center, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Razi Ullah
- Key Laboratory for Bio-rheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants Bioengineering College of Chongqing University, Chongqing, 400030, China
| | - Tariq Shah
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Mehraj Ullah
- Department of Biotechnology School of Fermentation Engineering Tianjin University of Science and Technology China, China
| | - Israr Khan
- School of Life Sciences, Lanzhou University, China
| | - Muhammad Farrukh Nisar
- Department of Physiology and Biochemistry, Cholistan University of Veterinary and Animal Sciences (CUVAS), Bahawalpur, 63100, Pakistan
| | - Jianbo Wu
- Drug Discovery Research Center, Southwest Medical University, Luzhou, 646000, Sichuan, China.
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15
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Swanson GR, Kochman N, Amin J, Chouhan V, Yim W, Engen PA, Shaikh M, Naqib A, Tran L, Voigt RM, Forsyth CB, Green SJ, Keshavarzian A. Disrupted Circadian Rest-Activity Cycles in Inflammatory Bowel Disease Are Associated With Aggressive Disease Phenotype, Subclinical Inflammation, and Dysbiosis. Front Med (Lausanne) 2021; 8:770491. [PMID: 35265631 PMCID: PMC8900134 DOI: 10.3389/fmed.2021.770491] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/08/2021] [Indexed: 12/11/2022] Open
Abstract
Patients with inflammatory bowel disease (IBD)-Crohn's disease (CD), and ulcerative colitis (UC), have poor sleep quality. Sleep and multiple immunologic and gastrointestinal processes in the body are orchestrated by the circadian clock, and we recently reported that a later category or chronotype of the circadian clock was associated with worse IBD specific outcomes. The goal of this study was to determine if circadian misalignment by rest-activity cycles is associated with markers of aggressive disease, subclinical inflammation, and dysbiosis in IBD. A total of 42 patients with inactive but biopsy-proven CD or UC and 10 healthy controls participated in this prospective cohort study. Subjects were defined as having an aggressive IBD disease history (steroid dependence, use of biologic or immunomodulator, and/or surgery) or non-aggressive history. All participants did two weeks of wrist actigraphy, followed by measurement of intestinal permeability and stool microbiota. Wrist actigraphy was used to calculate circadian markers of rest-activity- interdaily stability (IS), intradaily variability (IV), and relative amplitude (RA). Aggressive IBD history was associated with decrease rest-activity stability (IS) and increased fragmentation compared to non-aggressive IBD and health controls at 0.39 ±.15 vs. 0.51 ± 0.10 vs. 0.55 ± 0.09 (P < 0.05) and 0.83 ± 0.20 vs. 0.72 ± 0.14 (P < 0.05) but not HC at 0.72 ± 0.14 (P = 0.08); respectively. There was not a significant difference in RA by IBD disease history. Increased intestinal permeability and increased TNF-α levels correlated with an increased rest activity fragmentation (IV) at R = 0.35, P < 0.05 and R = 0.37, P < 0.05, respectively; and decreased rest-activity amplitude (RA) was associated with increased stool calprotectin at R = 0.40, P < 0.05. Analysis of intestinal microbiota showed a significant decrease in commensal butyrate producing taxa and increased pro-inflammatory bacteria with disrupted rest-activity cycles. In this study, different components of circadian misalignment by rest-activity cycles were associated with a more aggressive IBD disease history, increased intestinal permeability, stool calprotectin, increased pro-inflammatory cytokines, and dysbiosis. Wrist activity allows for an easy non-invasive assessment of circadian activity which may be an important biomarker of inflammation in IB.
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Affiliation(s)
- Garth R. Swanson
- Division of Digestive Diseases and Nutrition, Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
- Rush Medical College, Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
- *Correspondence: Garth R. Swanson
| | - Nicole Kochman
- Division of Digestive Diseases and Nutrition, Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Jaimin Amin
- Division of Digestive Diseases and Nutrition, Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Vijit Chouhan
- Division of Digestive Diseases and Nutrition, Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Wesley Yim
- Division of Digestive Diseases and Nutrition, Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Phillip A. Engen
- Rush Medical College, Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Maliha Shaikh
- Rush Medical College, Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Ankur Naqib
- Rush Medical College, Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Laura Tran
- Rush Medical College, Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Robin M. Voigt
- Rush Medical College, Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Christopher B. Forsyth
- Rush Medical College, Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
| | - Stefan J. Green
- Genomics and Microbiome Core Facility, Rush University, Chicago, IL, United States
| | - Ali Keshavarzian
- Division of Digestive Diseases and Nutrition, Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
- Rush Medical College, Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, IL, United States
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16
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El Aidy S, Bolsius YG, Raven F, Havekes R. A brief period of sleep deprivation leads to subtle changes in mouse gut microbiota. J Sleep Res 2020; 29:e12920. [PMID: 31515894 PMCID: PMC7757181 DOI: 10.1111/jsr.12920] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 08/08/2019] [Accepted: 08/20/2019] [Indexed: 12/14/2022]
Abstract
Not getting enough sleep is a common problem in our society and contributes to numerous health problems, including high blood pressure, diabetes and obesity. Related to these observations, a wealth of studies has underscored the negative impact of both acute and chronic sleep deprivation on cognitive function. More recently it has become apparent that the gut microbiota composition can be rapidly altered, modulates brain function and is affected by the aforementioned health problems. As such, changes in the microbiota composition may contribute to the behavioural and physiological phenotypes associated with sleep deprivation. It is unclear, however, whether a brief period of sleep deprivation can also negatively impact the gut microbiota. Here, we examined the impact of 5 hr of sleep deprivation on gut microbiota composition of male C57Bl6/J mice. Despite the fact that the overall microbial composition did not change between the control- and sleep-deprived groups, the relative abundance of the Clostridiaceae and Lachnospiraceae were slightly altered in sleep-deprived animals compared to controls. Together, these data suggest that depriving mice of sleep for 5 hr leads to subtle changes in the gut microbiota composition.
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Affiliation(s)
- Sahar El Aidy
- Department of Molecular Immunology and MicrobiologyGroningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenGroningenThe Netherlands
| | - Youri G. Bolsius
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
| | - Frank Raven
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
| | - Robbert Havekes
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
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17
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Jun X, Ning C, Yang S, Zhe W, Na W, Yifan Z, Xinhua R, Yulan L. Alteration of Fungal Microbiota After 5-ASA Treatment in UC Patients. Inflamm Bowel Dis 2020; 26:380-390. [PMID: 31750918 DOI: 10.1093/ibd/izz207] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Indexed: 12/13/2022]
Abstract
The effect of treatment regimens on fungal microbiota is unclear in ulcerative colitis (UC) patients. Here, we aimed to clarify the effect of 5-aminosalicylic acid (5-ASA) treatment on gut fungal microbiota in UC patients. Fifty-seven UC patients, including 20 treatment-naïve and 37 5-ASA-treated, were recruited into an exploration study. We compared the gut fungal profiles of these 2 groups of patients using ITS1-2 rDNA sequencing. Ten out of 20 treatment-naïve UC patients were followed up and enrolled for a validation study and underwent a 5-ASA treatment. We assessed the longitudinal differences of fungal microbiota in these patients before and after 5-ASA treatment. Results acquired from the validation study were accordant to those from the exploration study. Ascomycota was the dominant phylum in both noninflamed and inflamed mucosae. At the phylum level, Ascomycota decreased in inflamed mucosae before 5-ASA treatment. At the genus level, pathogens such as Scytalidium, Morchella, and Paecilomyces increased, and Humicola and Wickerhamomyces decreased in inflamed mucosae. After 5-ASA treatment, Ascomycota and Wickerhamomyces increased and Scytalidium, Fusarium, Morchella, and Paecilomyces decreased in both noninflamed and inflamed mucosae. Additionally, the balanced bacteria-fungi correlation was interrupted in inflamed mucosae, and 5-ASA treatment altered group-specific fungal microbiota and restored bacteria-fungi correlation in UC patients. Our results demonstrated that fungal diversity and composition were altered and the bacteria-fungi correlation was restored in inflamed mucosae after 5-ASA treatment.
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Affiliation(s)
- Xu Jun
- Department of Gastroenterology, Peking University People's Hospital, Xicheng District, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Xicheng District, Beijing, China.,Institute of Clinical Molecular Biology & Central Laboratory, Peking University People's Hospital, Xicheng District, Beijing, China
| | - Chen Ning
- Department of Gastroenterology, Peking University People's Hospital, Xicheng District, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Xicheng District, Beijing, China
| | - Song Yang
- Department of Gastroenterology, Peking University People's Hospital, Xicheng District, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Xicheng District, Beijing, China
| | - Wu Zhe
- Department of Gastroenterology, Peking University People's Hospital, Xicheng District, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Xicheng District, Beijing, China
| | - Wu Na
- Institute of Clinical Molecular Biology & Central Laboratory, Peking University People's Hospital, Xicheng District, Beijing, China
| | - Zhang Yifan
- Department of Gastroenterology, Peking University People's Hospital, Xicheng District, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Xicheng District, Beijing, China
| | - Ren Xinhua
- Department of Gastroenterology, Peking University People's Hospital, Xicheng District, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Xicheng District, Beijing, China
| | - Liu Yulan
- Department of Gastroenterology, Peking University People's Hospital, Xicheng District, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Xicheng District, Beijing, China
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18
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Lertnimitphun P, Jiang Y, Kim N, Fu W, Zheng C, Tan H, Zhou H, Zhang X, Pei W, Lu Y, Xu H. Safranal Alleviates Dextran Sulfate Sodium-Induced Colitis and Suppresses Macrophage-Mediated Inflammation. Front Pharmacol 2019; 10:1281. [PMID: 31736758 PMCID: PMC6838343 DOI: 10.3389/fphar.2019.01281] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/07/2019] [Indexed: 12/15/2022] Open
Abstract
Introduction:Crocus sativus (saffron) is widely used in China, Iran, and India for dyeing and as a food additive and medicinal plant. Safranal, as one of the main constituents of saffron, is responsible for its aroma and has been reported to have anticancer, antioxidant, and anti-inflammation properties. Objective: In this study, we investigated the anti-inflammatory effects of Safranal in RAW264.7 cells, bone marrow-derived macrophages (BMDMs), and dextran sulfate sodium (DSS)-induced colitis mice. Methods: Safranal toxicity was determined using an MTT assay. We evaluated the inhibitory effect of nitric oxide (NO) and levels of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) in RAW264.7 cells and BMDMs. We assessed the inhibitory effect of pro-inflammatory cytokines, and the mRNA expressions of interleukin-6 (IL-6), tumor necrosis factor alpha (TNF-α), classical inflammatory pathways (MAPK and NF-κB), and the nuclear translocation factors AP-1 and NF-κB p65 were investigated. The in vivo anti-inflammatory effects of Safranal were assessed in a DSS-induced colitis model. DSS3.5% was used to induce colitis in mice with or without Safranal for 7 days; weight and disease activity index (DAI) were recorded daily. At the end of the experiment, the colon, mesenteric lymph nodes (MLNs), and spleen were collected for flow cytometry, ELISA, and Western blot analysis. Results: Safranal suppressed NO production, iNOS, and COX-2 in lipopolysaccharide (LPS)-stimulated RAW264.7 cells and BMDMs. Safranal decreased the production and mRNA expression of IL-6 and TNF-α in the RAW264.7 cell line and inhibited the phosphorylation and nuclear translocation of components of the MAPK and NF-κB pathways. Safranal alleviated clinical symptoms in the DSS-induced colitis model, and colon histology showed decreased severity of inflammation, depth of inflammatory involvement, and crypt damage. Immunohistochemical staining and flow cytometry showed reduced macrophage infiltration in colonic tissues and macrophage numbers in MLNs and the spleen. The levels of colonic IL-6 and TNF-α also decreased in Safranal-treated colitis mice. This study elucidates the anti-inflammation activity of Safranal, which may be a candidate for inflammatory bowel syndrome (IBD) therapy.
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Affiliation(s)
| | - Yiwen Jiang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Nami Kim
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wenwei Fu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Changwu Zheng
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hongsheng Tan
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hua Zhou
- Institute of Cardiovascular Disease of Integrated Traditional Chinese and Western Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xue Zhang
- Shanghai Traditional Chinese medicine Co., Ltd., Shanghai, China
| | - Weizhong Pei
- Shanghai Traditional Chinese medicine Co., Ltd., Shanghai, China
| | - Yue Lu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hongxi Xu
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Cardiovascular Disease of Integrated Traditional Chinese and Western Medicine, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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19
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Coufal S, Galanova N, Bajer L, Gajdarova Z, Schierova D, Jiraskova Zakostelska Z, Kostovcikova K, Jackova Z, Stehlikova Z, Drastich P, Tlaskalova-Hogenova H, Kverka M. Inflammatory Bowel Disease Types Differ in Markers of Inflammation, Gut Barrier and in Specific Anti-Bacterial Response. Cells 2019; 8:cells8070719. [PMID: 31337064 PMCID: PMC6678638 DOI: 10.3390/cells8070719] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/06/2019] [Accepted: 07/11/2019] [Indexed: 12/12/2022] Open
Abstract
Crohn’s disease (CD), ulcerative colitis (UC) and inflammatory bowel disease (IBD) associated with primary sclerosing cholangitis (PSC-IBD), share three major pathogenetic mechanisms of inflammatory bowel disease (IBD)-gut dysbiosis, gut barrier failure and immune system dysregulation. While clinical differences among them are well known, the underlying mechanisms are less explored. To gain an insight into the IBD pathogenesis and to find a specific biomarker pattern for each of them, we used protein array, ELISA and flow cytometry to analyze serum biomarkers and specific anti-microbial B and T cell responses to the gut commensals. We found that decrease in matrix metalloproteinase (MMP)-9 and increase in MMP-14 are the strongest factors discriminating IBD patients from healthy subjects and that PSC-IBD patients have higher levels of Mannan-binding lectin, tissue inhibitor of metalloproteinases 1 (TIMP-1), CD14 and osteoprotegerin than patients with UC. Moreover, we found that low transforming growth factor-β1 (TGF-β1) is associated with disease relapse and low osteoprotegerin with anti-tumor necrosis factor-alpha (TNF-α) therapy. Patients with CD have significantly decreased antibody and increased T cell response mainly to genera Eubacterium, Faecalibacterium and Bacteroides. These results stress the importance of the gut barrier function and immune response to commensal bacteria and point at the specific differences in pathogenesis of PSC-IBD, UC and CD.
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Affiliation(s)
- Stepan Coufal
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Natalie Galanova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Lukas Bajer
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
- Institute for Clinical and Experimental Medicine, Videnska 1958/9, 140 21 Prague, Czech Republic
| | - Zuzana Gajdarova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Dagmar Schierova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | | | - Klara Kostovcikova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Zuzana Jackova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Zuzana Stehlikova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Pavel Drastich
- Institute for Clinical and Experimental Medicine, Videnska 1958/9, 140 21 Prague, Czech Republic
| | - Helena Tlaskalova-Hogenova
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Miloslav Kverka
- Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic.
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic.
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20
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Yilmaz B, Juillerat P, Øyås O, Ramon C, Bravo FD, Franc Y, Fournier N, Michetti P, Mueller C, Geuking M, Pittet VEH, Maillard MH, Rogler G, Wiest R, Stelling J, Macpherson AJ. Microbial network disturbances in relapsing refractory Crohn's disease. Nat Med 2019; 25:323-336. [PMID: 30664783 DOI: 10.1038/s41591-018-0308-z] [Citation(s) in RCA: 243] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 11/19/2018] [Indexed: 02/06/2023]
Abstract
Inflammatory bowel diseases (IBD) can be broadly divided into Crohn's disease (CD) and ulcerative colitis (UC) from their clinical phenotypes. Over 150 host susceptibility genes have been described, although most overlap between CD, UC and their subtypes, and they do not adequately account for the overall incidence or the highly variable severity of disease. Replicating key findings between two long-term IBD cohorts, we have defined distinct networks of taxa associations within intestinal biopsies of CD and UC patients. Disturbances in an association network containing taxa of the Lachnospiraceae and Ruminococcaceae families, typically producing short chain fatty acids, characterize frequently relapsing disease and poor responses to treatment with anti-TNF-α therapeutic antibodies. Alterations of taxa within this network also characterize risk of later disease recurrence of patients in remission after the active inflamed segment of CD has been surgically removed.
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Affiliation(s)
- Bahtiyar Yilmaz
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland.,Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Pascal Juillerat
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland.,Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Ove Øyås
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Basel, Switzerland
| | - Charlotte Ramon
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Basel, Switzerland
| | - Francisco Damian Bravo
- Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Yannick Franc
- Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne, Switzerland
| | - Nicolas Fournier
- Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne, Switzerland
| | - Pierre Michetti
- Gastroenterology La Source-Beaulieu, Lausanne, Switzerland.,Service of Gastroenterology and Hepatology, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Christoph Mueller
- Division of Experimental Pathology, Institute of Pathology, University of Bern, Bern, Switzerland
| | - Markus Geuking
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland
| | - Valerie E H Pittet
- Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne, Switzerland
| | - Michel H Maillard
- Gastroenterology La Source-Beaulieu, Lausanne, Switzerland.,Service of Gastroenterology and Hepatology, Department of Medicine, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | | | - Reiner Wiest
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland.,Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Jörg Stelling
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, ETH Zurich, Basel, Switzerland
| | - Andrew J Macpherson
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, Bern, Switzerland. .,Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Bern, Switzerland.
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21
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Britton GJ, Contijoch EJ, Mogno I, Vennaro OH, Llewellyn SR, Ng R, Li Z, Mortha A, Merad M, Das A, Gevers D, McGovern DPB, Singh N, Braun J, Jacobs JP, Clemente JC, Grinspan A, Sands BE, Colombel JF, Dubinsky MC, Faith JJ. Microbiotas from Humans with Inflammatory Bowel Disease Alter the Balance of Gut Th17 and RORγt + Regulatory T Cells and Exacerbate Colitis in Mice. Immunity 2019; 50:212-224.e4. [PMID: 30650377 PMCID: PMC6512335 DOI: 10.1016/j.immuni.2018.12.015] [Citation(s) in RCA: 318] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 10/03/2018] [Accepted: 12/13/2018] [Indexed: 12/13/2022]
Abstract
Microbiota are thought to influence the development and progression of inflammatory bowel disease (IBD), but determining generalizable effects of microbiota on IBD etiology requires larger-scale functional analyses. We colonized germ-free mice with intestinal microbiotas from 30 healthy and IBD donors and determined the homeostatic intestinal T cell response to each microbiota. Compared to microbiotas from healthy donors, transfer of IBD microbiotas into germ-free mice increased numbers of intestinal Th17 cells and Th2 cells and decreased numbers of RORγt+ Treg cells. Colonization with IBD microbiotas exacerbated disease in a model where colitis is induced upon transfer of naive T cells into Rag1-/- mice. The proportions of Th17 and RORγt+ Treg cells induced by each microbiota were predictive of human disease status and accounted for disease severity in the Rag1-/- colitis model. Thus, an impact on intestinal Th17 and RORγt+ Treg cell compartments emerges as a unifying feature of IBD microbiotas, suggesting a general mechanism for microbial contribution to IBD pathogenesis.
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Affiliation(s)
- Graham J Britton
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eduardo J Contijoch
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ilaria Mogno
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olivia H Vennaro
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sean R Llewellyn
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruby Ng
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhihua Li
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arthur Mortha
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Miriam Merad
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anuk Das
- Janssen Human Microbiome Institute, Janssen Research and Development, LLC, Spring House, PA, USA
| | - Dirk Gevers
- Janssen Human Microbiome Institute, Janssen Research and Development, LLC, Spring House, PA, USA
| | - Dermot P B McGovern
- Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Namita Singh
- Pediatric Gastroenterology and Inflammatory Bowel Disease, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jonathan Braun
- UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Jonathan P Jacobs
- Division of Digestive Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jose C Clemente
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ari Grinspan
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce E Sands
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jean-Frederic Colombel
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marla C Dubinsky
- Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Pediatric Gastroenterology and Hepatology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeremiah J Faith
- Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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22
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An Early Life Mucosal Insult Temporarily Decreases Acute Oxazolone-Induced Inflammation in Mice. Inflammation 2018; 41:1437-1447. [PMID: 29666981 DOI: 10.1007/s10753-018-0790-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Inflammatory priming of immune cells in early life may optimize the response to a subsequent inflammatory challenge later in life. To prime the immune cells in the gut in vivo through a short inflammatory insult, we administered a low dose of dextran sulfate sodium (DSS) to 5-weeks-old BALB/c mice in the drinking water. We hypothesized that DSS-primed mice would show decreased inflammation and difference in immunological profiling, when subjected to presensitizing and oxazolone-induced colitis by rectal instillation at 9 weeks compared to non-DSS-primed control mice. In fact, this low-dose DSS priming apparently decreased the acute inflammation, as colitis scores along with IFNγ, IL-1ß, and IL-4 were significantly decreased with the same tendency for IL-5, TNFα, and IL-2 on day 3 post-induction compared to control mice. On day 7, both DSS-primed and control mice had significantly higher numbers of FoxP3+CD8+ regulatory T cells, while they did not differ in any inflammation parameters. No significant differences were found for intraepithelial lymphocytes or mesenteric lymphocytes at any time point after colitis induction. In conclusion, the priming did decrease local acute tissue inflammation of the colon in this commonly applied mouse model of T helper cell type 2-dominated model of inflammatory bowel disease.
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23
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Arias-Jayo N, Abecia L, Alonso-Sáez L, Ramirez-Garcia A, Rodriguez A, Pardo MA. High-Fat Diet Consumption Induces Microbiota Dysbiosis and Intestinal Inflammation in Zebrafish. MICROBIAL ECOLOGY 2018; 76:1089-1101. [PMID: 29736898 DOI: 10.1007/s00248-018-1198-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 04/27/2018] [Indexed: 05/26/2023]
Abstract
Energy-dense foods and overnutrition represent major starting points altering lipid metabolism, systemic inflammation and gut microbiota. The aim of this work was to investigate the effects of a high-fat diet (HFD) over a period of 25 days on intestinal microbiota and inflammation in zebrafish. Microbial composition of HFD-fed animals was analysed and compared to controls by 16S rRNA sequencing and quantitative PCR. The expression level on several genes related to inflammation was tested. Furthermore, microscopic assessment of the intestine was performed in both conditions. The consumption of the HFD resulted in microbial dysbiosis, characterised by an increase in the relative abundance of the phylum Bacteroidetes. Moreover, an emerging intestinal inflammation via NF-κβ activation was confirmed by the overexpression of several genes related to signalling receptors, antimicrobial metabolism and the inflammatory cascade. The intestinal barrier was also damaged, with an increase of goblet cell mucin production. This is the first study performed in zebrafish which suggests that the consumption of a diet enriched with 10% fat changes the intestinal microbial community composition, which was correlated with low-grade inflammation.
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Affiliation(s)
- Nerea Arias-Jayo
- Food research, Azti, Parque tecnológico de Bizkaia, Astondo Bidea 609, 48160, Derio, Spain.
| | - Leticia Abecia
- CIC bioGUNE, Parque Tecnológico de Bizkaia, Edificio 801A, 48160, Derio, Spain
| | - Laura Alonso-Sáez
- Marine research, Azti, Txatxarramendi ugartea z/g, 48395, Txatxarramendi, Spain
| | - Andoni Ramirez-Garcia
- Departmento de Immunología, Microbiología y Parasitología, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), 48940, Leioa, Spain
| | - Alfonso Rodriguez
- St Luke's General Hospital, Freshford Road, Friarsinch, Kilkenny, R95 FY71, Ireland
| | - Miguel A Pardo
- Food research, Azti, Parque tecnológico de Bizkaia, Astondo Bidea 609, 48160, Derio, Spain
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24
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Harrison CA, Laubitz D, Ohland CL, Midura-Kiela MT, Patil K, Besselsen DG, Jamwal DR, Jobin C, Ghishan FK, Kiela PR. Microbial dysbiosis associated with impaired intestinal Na +/H + exchange accelerates and exacerbates colitis in ex-germ free mice. Mucosal Immunol 2018; 11:1329-1341. [PMID: 29875400 PMCID: PMC6162102 DOI: 10.1038/s41385-018-0035-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 03/29/2018] [Accepted: 04/15/2018] [Indexed: 02/04/2023]
Abstract
Intestinal epithelial Na+/H+ exchange facilitated by the apical NHE3 (Slc9a3) is a highly regulated process inhibited by intestinal pathogens and in inflammatory bowel diseases. NHE3-/- mice develop spontaneous, bacterially mediated colitis, and IBD-like dysbiosis. Disruption of epithelial Na+/H+ exchange in IBD may thus represent a host response contributing to the altered gut microbial ecology, and may play a pivotal role in modulating the severity of inflammation in a microbiome-dependent manner. To test whether microbiome fostered in an NHE3-deficient environment is able to drive mucosal immune responses affecting the onset or severity of colitis, we performed a series of cohousing experiments and fecal microbiome transplants into germ-free Rag-deficient or IL-10-/- mice. We determined that in the settings where the microbiome of NHE3-deficient mice was stably engrafted in the recipient host, it was able accelerate the onset and amplify severity of experimental colitis. NHE3-deficiency was characterized by the reduction in pH-sensitive butyrate-producing Firmicutes families Lachnospiraceae and Ruminococcaceae (Clostridia clusters IV and XIVa), with an expansion of inflammation-associated Bacteroidaceae. We conclude that the microbiome fostered by impaired epithelial Na+/H+ exchange enhances the onset and severity of colitis through disruption of the gut microbial ecology.
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Affiliation(s)
- Christy A Harrison
- Department of Pediatrics, Steele Children's Research Center, Tucson, AZ, USA
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Daniel Laubitz
- Department of Pediatrics, Steele Children's Research Center, Tucson, AZ, USA
| | | | | | - Karuna Patil
- University Animal Care, University of Arizona, Tucson, AZ, USA
| | | | - Deepa R Jamwal
- Department of Pediatrics, Steele Children's Research Center, Tucson, AZ, USA
| | - Christian Jobin
- Division of Gastroenterology, Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Fayez K Ghishan
- Department of Pediatrics, Steele Children's Research Center, Tucson, AZ, USA
| | - Pawel R Kiela
- Department of Pediatrics, Steele Children's Research Center, Tucson, AZ, USA.
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, AZ, USA.
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25
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Li X, Naser SA, Khaled A, Hu H, Li X. When old metagenomic data meet newly sequenced genomes, a case study. PLoS One 2018; 13:e0198773. [PMID: 29902201 PMCID: PMC6002052 DOI: 10.1371/journal.pone.0198773] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/24/2018] [Indexed: 01/30/2023] Open
Abstract
Dozens of computational methods are developed to identify species present in a metagenomic dataset. Many of these computational methods depend on available sequenced microbial species, which are still far from being representative. To see how newly sequenced genomes affect the analysis results, we re-analyzed a shotgun metagenomic dataset composed of twelve colitis free metagenomic samples and ten colitis-related metagenomic samples. Unexpectedly, we identified at least two new phyla that may relate to colitis development in patients, together with the phylum identified previously. Compared with the previously identified phylum that differed between the two types of samples, the differences associated with the two new phyla are statistically more significant. Moreover, the abundance of the two new phyla correlates more with the severity of colitis. Surprisingly, even by repeating the analyses implemented in the previous study, we found that at least one main conclusion in the previous study is not supported. Our study indicates the importance of re-analysis of the generated metagenomic datasets and the necessity of considering multiple updated tools in metagenomic studies. It also sheds light on the limitations of the popular tools used currently and the importance to infer the presence of taxa without relying upon available sequenced genomes.
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Affiliation(s)
- Xin Li
- Department of Computer Science, University of Central Florida, Orlando, Florida, United States of America
| | - Saleh A. Naser
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Annette Khaled
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Haiyan Hu
- Department of Computer Science, University of Central Florida, Orlando, Florida, United States of America
| | - Xiaoman Li
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
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26
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Xu J, Chen N, Wu Z, Song Y, Zhang Y, Wu N, Zhang F, Ren X, Liu Y. 5-Aminosalicylic Acid Alters the Gut Bacterial Microbiota in Patients With Ulcerative Colitis. Front Microbiol 2018; 9:1274. [PMID: 29951050 PMCID: PMC6008376 DOI: 10.3389/fmicb.2018.01274] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/24/2018] [Indexed: 12/15/2022] Open
Abstract
Background: The aim of this study was to clarify the effect of 5-aminosalicylic acid (5-ASA) treatment on gut bacterial microbiota in patients with ulcerative colitis (UC). Methods: A total of 57 UC patients, including 20 untreated and 37 5-ASA-treated, were recruited into an exploration cohort. We endoscopically collected both non-inflamed and inflamed mucosal samples from all patients, and compared the gut bacterial profiles using 16S rDNA sequencing. Ten untreated UC patients were then treated with 5-ASA and subsequently recruited for an independent validation study to confirm the acquired data. Results: In untreated UC patients, compared with those in non-inflamed mucosae, Firmicutes (such as Enterococcus) were decreased and Proteobacteria (e.g., Escherichia–Shigella) were increased in the inflamed mucosae. Compared with the inflamed mucosae of untreated UC patients, there was a higher abundance of Firmicutes (e.g., Enterococcus) and lower Proteobacteria (Escherichia–Shigella) in the inflamed mucosae of 5-ASA treated UC patients. In the validation cohort, after administration of 5-ASA, bacterial alteration was consistent with these data. Furthermore, there was a skewed negative correlation between Escherichia–Shigella and bacterial genera of Firmicutes in the inflamed mucosae. 5-ASA treatment decreased the strength of bacterial correlation and weakened the skewed negative correlation pattern. Conclusion: The microbial dysbiosis (mainly characterized by an increased abundance in the Escherichia–Shigella genus) and the skewed negative correlation between Escherichia–Shigella and bacterial genera of Firmicutes are two characteristics of the inflamed mucosae of UC patients. 5-ASA treatment decreases Escherichia–Shigella and weakens the skewed correlations, which may be related to its treatment efficiency.
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Affiliation(s)
- Jun Xu
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Ning Chen
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Zhe Wu
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Yang Song
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Yifan Zhang
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Na Wu
- Institute of Clinical Molecular Biology and Central Laboratory, Peking University People's Hospital, Beijing, China
| | - Feng Zhang
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Xinhua Ren
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Yulan Liu
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
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27
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Interleukin 1α-Deficient Mice Have an Altered Gut Microbiota Leading to Protection from Dextran Sodium Sulfate-Induced Colitis. mSystems 2018; 3:mSystems00213-17. [PMID: 29766049 PMCID: PMC5940968 DOI: 10.1128/msystems.00213-17] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/13/2018] [Indexed: 01/08/2023] Open
Abstract
Here, we show a connection between IL-1α expression, microbiota composition, and clinical outcomes of DSS-induced colitis. Specifically, we show that the mild colitis symptoms seen in IL-1α-deficient mice following administration of DSS are correlated with the unique gut microbiota compositions of the mice. However, when these mice are exposed to WT microbiota by cohousing, their gut microbiota composition returns to resemble that of WT mice, and their disease severity increases significantly. As inflammatory bowel diseases are such common diseases, with limited effective treatments to date, there is a great need to better understand the interactions between microbiota composition, the immune system, and colitis. This study shows correlation between microbiota composition and DSS resistance; it may potentially lead to the development of improved probiotics for IBD treatment. Inflammatory bowel diseases (IBD) are a group of chronic inflammatory disorders of the intestine, with as-yet-unclear etiologies, affecting over a million people in the United States alone. With the emergence of microbiome research, numerous studies have shown a connection between shifts in the gut microbiota composition (dysbiosis) and patterns of IBD development. In a previous study, we showed that interleukin 1α (IL-1α) deficiency in IL-1α knockout (KO) mice results in moderate dextran sodium sulfate (DSS)-induced colitis compared to that of wild-type (WT) mice, characterized by reduced inflammation and complete healing, as shown by parameters of weight loss, disease activity index (DAI) score, histology, and cytokine expression. In this study, we tested whether the protective effects of IL-1α deficiency on DSS-induced colitis correlate with changes in the gut microbiota and whether manipulation of the microbiota by cohousing can alter patterns of colon inflammation. We analyzed the gut microbiota composition in both control (WT) and IL-1α KO mice under steady-state homeostasis, during acute DSS-induced colitis, and after recovery using 16S rRNA next-generation sequencing. Additionally, we performed cohousing of both mouse groups and tested the effects on the microbiota and clinical outcomes. We demonstrate that host-derived IL-1α has a clear influence on gut microbiota composition, as well as on severity of DSS-induced acute colon inflammation. Cohousing both successfully changed the gut microbiota composition and increased the disease severity of IL-1α-deficient mice to levels similar to those of WT mice. This study shows a strong and novel correlation between IL-1α expression, microbiota composition, and clinical outcomes of DSS-induced colitis. IMPORTANCE Here, we show a connection between IL-1α expression, microbiota composition, and clinical outcomes of DSS-induced colitis. Specifically, we show that the mild colitis symptoms seen in IL-1α-deficient mice following administration of DSS are correlated with the unique gut microbiota compositions of the mice. However, when these mice are exposed to WT microbiota by cohousing, their gut microbiota composition returns to resemble that of WT mice, and their disease severity increases significantly. As inflammatory bowel diseases are such common diseases, with limited effective treatments to date, there is a great need to better understand the interactions between microbiota composition, the immune system, and colitis. This study shows correlation between microbiota composition and DSS resistance; it may potentially lead to the development of improved probiotics for IBD treatment.
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28
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Liu B, Li S, Sui X, Guo L, Liu X, Li H, Gao L, Cai S, Li Y, Wang T, Piao X. Root Extract of Polygonum cuspidatum Siebold & Zucc. Ameliorates DSS-Induced Ulcerative Colitis by Affecting NF-kappaB Signaling Pathway in a Mouse Model via Synergistic Effects of Polydatin, Resveratrol, and Emodin. Front Pharmacol 2018; 9:347. [PMID: 29695964 PMCID: PMC5904535 DOI: 10.3389/fphar.2018.00347] [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: 12/11/2017] [Accepted: 03/26/2018] [Indexed: 01/07/2023] Open
Abstract
Background:Polygonum cuspidatum Siebold & Zucc. (PCS) has antibacterial properties and may prevent Ulcerative colitis (UC) but related molecular mechanism remains unknown. NF-κB signaling pathway is associated with inflammatory responses and its inactivation may be critical for effective therapy of UC. Methods: UC mouse (C57BL/6J) model was established by using dextran sulfate sodium (DSS). The extract of PCS (PCSE) was prepared by using ethanol and its main ingredients were measured by HPLC. Thirty-two UC mice were evenly assigned into DG (received vehicle control), LG (0.1 g/kg PCSE daily), MG (0.2 g/kg PCSE daily) and HG (0.4 g/kg PCSE daily) groups. Meanwhile, 8 healthy mice were assigned as a control group (CG). Serum pharmacokinetics of PCS was measured by using HPLC. After 8-day treatment, weight, colon length and disease activity index (DAI) were measured. Inflammatory cytokines and oxidant biomarkers were measured by ELISA kits. The levels of cytokines, and key molecules in NF-κB pathway, were measured by using Western Blot. The effects of main ingredients of PCSE on cytokines and NF-κB signaling pathway were explored by using intestinal cells of a mouse UC model. The normality criterion was evaluated using the Saphiro–Wilk test. The quantitative variables were compared using the paired Student’s-t test. Results: The main ingredients of PCSE were polydatin, resveratrol and emodin. Polydatin may be transformed into resveratrol in the intestine of the mice. PCSE prevented DSS-caused weight loss and colon length reduction, and improved histopathology of UC mice (P < 0.05). PCSE treatment increased the serum levels of IL-10 and reduced the levels of IL-1 beta, IL-6 and TNF-α (P < 0.05). PCSE increased the activities of SOD, CAT, GPX and reduced the level of MDA, BCL-2, beta-arrestin, NF-κB p65 and the activity of MPO (P < 0.05). The combination of polydatin, resveratrol or emodin, and or PCSE exhibited higher inhibitory activities for cytokines and NF-κB signaling related molecules than any one of the three ingredients with same concentration treatment. Conclusion: Oral administration of PCSE suppressed NF-κB signaling pathway and exerts its anti-colitis effects via synergistic effects of polydatin, resveratrol or emodin.
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Affiliation(s)
- Baohai Liu
- Department of Gastroenterology, The First Affiliated Hospital, Jinzhou Medical University, Jinzhou, China
| | - Shuangdi Li
- Heart Disease Center, The Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, China
| | - Xiaodan Sui
- Department of Hepatology, The Affiliated Hospital of Changchun University of Traditional Chinese Medicine, Changchun, China
| | - Lianyi Guo
- Department of Gastroenterology, The First Affiliated Hospital, Jinzhou Medical University, Jinzhou, China
| | - Xingmei Liu
- Department of Gastroenterology, The First Affiliated Hospital, Jinzhou Medical University, Jinzhou, China
| | - Hongmei Li
- Department of Gastroenterology, The First Affiliated Hospital, Jinzhou Medical University, Jinzhou, China
| | - Leming Gao
- The Second Dental Center, School of Stomatology, Peking University, Beijing, China
| | - Shusheng Cai
- Department of Gastroenterology, The First Affiliated Hospital, Jinzhou Medical University, Jinzhou, China
| | - Yanrong Li
- Department of Gastroenterology, The First Affiliated Hospital, Jinzhou Medical University, Jinzhou, China
| | - Tingting Wang
- Department of Gastroenterology, The First Affiliated Hospital, Jinzhou Medical University, Jinzhou, China
| | - Xuehua Piao
- Department of Traditional Chinese Medicine, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
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Jeong JJ, Lee HJ, Jang SE, Han MJ, Kim DH. Lactobacillus plantarum C29 alleviates NF-κB activation and Th17/Treg imbalance in mice with TNBS-induced colitis. FOOD AGR IMMUNOL 2018. [DOI: 10.1080/09540105.2017.1418841] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Jin-Ju Jeong
- Department of Life and Nanopharmaceutical Sciences, College of Pharmacy, Kyung Hee University, Seoul, Korea
| | - Hae-Ji Lee
- Department of Life and Nanopharmaceutical Sciences, College of Pharmacy, Kyung Hee University, Seoul, Korea
| | - Se-Eun Jang
- Department of Life and Nanopharmaceutical Sciences, College of Pharmacy, Kyung Hee University, Seoul, Korea
- Department of Food and Nutrition, Kyung Hee University, Seoul, Korea
| | - Myung Joo Han
- Department of Food and Nutrition, Kyung Hee University, Seoul, Korea
| | - Dong-Hyun Kim
- Department of Life and Nanopharmaceutical Sciences, College of Pharmacy, Kyung Hee University, Seoul, Korea
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30
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Arias-Jayo N, Alonso-Saez L, Ramirez-Garcia A, Pardo MA. Zebrafish Axenic Larvae Colonization with Human Intestinal Microbiota. Zebrafish 2017; 15:96-106. [PMID: 29261035 DOI: 10.1089/zeb.2017.1460] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The human intestine hosts a vast and complex microbial community that is vital for maintaining several functions related with host health. The processes that determine the gut microbiome composition are poorly understood, being the interaction between species, the external environment, and the relationship with the host the most feasible. Animal models offer the opportunity to understand the interactions between the host and the microbiota. There are different gnotobiotic mice or rat models colonized with the human microbiota, however, to our knowledge, there are no reports on the colonization of germ-free zebrafish with a complex human intestinal microbiota. In the present study, we have successfully colonized 5 days postfertilization germ-free zebrafish larvae with the human intestinal microbiota previously extracted from a donor and analyzed by high-throughput sequencing the composition of the transferred microbial communities that established inside the zebrafish gut. Thus, we describe for first time which human bacteria phylotypes are able to colonize the zebrafish digestive tract. Species with relevant interest because of their linkage to dysbiosis in different human diseases, such as Akkermansia muciniphila, Eubacterium rectale, Faecalibacterium prausnitzii, Prevotella spp., or Roseburia spp. have been successfully transferred inside the zebrafish digestive tract.
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Affiliation(s)
- Nerea Arias-Jayo
- 1 Azti, Food Quality, Safety and Identity Department, Derio, Spain
| | | | - Andoni Ramirez-Garcia
- 3 Fungal and Bacterial Biomics Research Group, Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU) , Leioa, Spain
| | - Miguel A Pardo
- 1 Azti, Food Quality, Safety and Identity Department, Derio, Spain
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Chiu CC, Ching YH, Li YP, Liu JY, Huang YT, Huang YW, Yang SS, Huang WC, Chuang HL. Nonalcoholic Fatty Liver Disease Is Exacerbated in High-Fat Diet-Fed Gnotobiotic Mice by Colonization with the Gut Microbiota from Patients with Nonalcoholic Steatohepatitis. Nutrients 2017; 9:nu9111220. [PMID: 29113135 PMCID: PMC5707692 DOI: 10.3390/nu9111220] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/24/2017] [Accepted: 11/02/2017] [Indexed: 12/20/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a serious liver disorder associated with the accumulation of fat and inflammation. The objective of this study was to determine the gut microbiota composition that might influence the progression of NAFLD. Germ-free mice were inoculated with feces from patients with nonalcoholic steatohepatitis (NASH) or from healthy persons (HL) and then fed a standard diet (STD) or high-fat diet (HFD). We found that the epididymal fat weight, hepatic steatosis, multifocal necrosis, and inflammatory cell infiltration significantly increased in the NASH-HFD group. These findings were consistent with markedly elevated serum levels of alanine transaminase, aspartate transaminase, endotoxin, interleukin 6 (IL-6), monocyte chemotactic protein 1 (Mcp1), and hepatic triglycerides. In addition, the mRNA expression levels of Toll-like receptor 2 (Tlr2), Toll-like receptor 4 (Tlr4), tumor necrosis factor alpha (Tnf-α), Mcp1, and peroxisome proliferator-activated receptor gamma (Ppar-γ) significantly increased. Only abundant lipid accumulation and a few inflammatory reactions were observed in group HL-HFD. Relative abundance of Bacteroidetes and Firmicutes shifted in the HFD-fed mice. Furthermore, the relative abundance of Streptococcaceae was the highest in group NASH-HFD. Nevertheless, obesity-related Lactobacillaceae were significantly upregulated in HL-HFD mice. Our results revealed that the gut microbiota from NASH Patients aggravated hepatic steatosis and inflammation. These findings might partially explain the NAFLD progress distinctly was related to different compositions of gut microbiota.
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Affiliation(s)
- Chien-Chao Chiu
- Animal Technology Laboratories, Agricultural Technology Research Institute, Miaoli 350, Taiwan.
| | - Yung-Hao Ching
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Hualien 970, Taiwan.
| | - Yen-Peng Li
- Graduate Institute of Veterinary Pathobiology, National Chung Hsing University, Taichung 402, Taiwan.
| | - Ju-Yun Liu
- National Laboratory Animal Center, National Applied Research Laboratories, Taipei 115, Taiwan.
| | - Yen-Te Huang
- National Laboratory Animal Center, National Applied Research Laboratories, Taipei 115, Taiwan.
| | - Yi-Wen Huang
- Liver Center, Cathay General Hospital Medical Center, Taipei 106, Taiwan.
- School of Medicine, Taipei Medical University College of Medicine, Taipei 110, Taiwan.
| | - Sien-Sing Yang
- Liver Center, Cathay General Hospital Medical Center, Taipei 106, Taiwan.
| | - Wen-Ching Huang
- Department of Exercise and Health Science, National Taipei University of Nursing and Health Sciences, Taipei 112, Taiwan.
| | - Hsiao-Li Chuang
- National Laboratory Animal Center, National Applied Research Laboratories, Taipei 115, Taiwan.
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Selber-Hnatiw S, Rukundo B, Ahmadi M, Akoubi H, Al-Bizri H, Aliu AF, Ambeaghen TU, Avetisyan L, Bahar I, Baird A, Begum F, Ben Soussan H, Blondeau-Éthier V, Bordaries R, Bramwell H, Briggs A, Bui R, Carnevale M, Chancharoen M, Chevassus T, Choi JH, Coulombe K, Couvrette F, D'Abreau S, Davies M, Desbiens MP, Di Maulo T, Di Paolo SA, Do Ponte S, Dos Santos Ribeiro P, Dubuc-Kanary LA, Duncan PK, Dupuis F, El-Nounou S, Eyangos CN, Ferguson NK, Flores-Chinchilla NR, Fotakis T, Gado Oumarou H D M, Georgiev M, Ghiassy S, Glibetic N, Grégoire Bouchard J, Hassan T, Huseen I, Ibuna Quilatan MF, Iozzo T, Islam S, Jaunky DB, Jeyasegaram A, Johnston MA, Kahler MR, Kaler K, Kamani C, Karimian Rad H, Konidis E, Konieczny F, Kurianowicz S, Lamothe P, Legros K, Leroux S, Li J, Lozano Rodriguez ME, Luponio-Yoffe S, Maalouf Y, Mantha J, McCormick M, Mondragon P, Narayana T, Neretin E, Nguyen TTT, Niu I, Nkemazem RB, O'Donovan M, Oueis M, Paquette S, Patel N, Pecsi E, Peters J, Pettorelli A, Poirier C, Pompa VR, Rajen H, Ralph RO, Rosales-Vasquez J, Rubinshtein D, Sakr S, Sebai MS, Serravalle L, Sidibe F, Sinnathurai A, Soho D, Sundarakrishnan A, Svistkova V, Ugbeye TE, Vasconcelos MS, Vincelli M, Voitovich O, Vrabel P, Wang L, Wasfi M, Zha CY, Gamberi C. Human Gut Microbiota: Toward an Ecology of Disease. Front Microbiol 2017; 8:1265. [PMID: 28769880 PMCID: PMC5511848 DOI: 10.3389/fmicb.2017.01265] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 06/23/2017] [Indexed: 12/17/2022] Open
Abstract
Composed of trillions of individual microbes, the human gut microbiota has adapted to the uniquely diverse environments found in the human intestine. Quickly responding to the variances in the ingested food, the microbiota interacts with the host via reciprocal biochemical signaling to coordinate the exchange of nutrients and proper immune function. Host and microbiota function as a unit which guards its balance against invasion by potential pathogens and which undergoes natural selection. Disturbance of the microbiota composition, or dysbiosis, is often associated with human disease, indicating that, while there seems to be no unique optimal composition of the gut microbiota, a balanced community is crucial for human health. Emerging knowledge of the ecology of the microbiota-host synergy will have an impact on how we implement antibiotic treatment in therapeutics and prophylaxis and how we will consider alternative strategies of global remodeling of the microbiota such as fecal transplants. Here we examine the microbiota-human host relationship from the perspective of the microbial community dynamics.
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Affiliation(s)
| | - Belise Rukundo
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Masoumeh Ahmadi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Hayfa Akoubi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Hend Al-Bizri
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Adelekan F Aliu
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Lilit Avetisyan
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Irmak Bahar
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Alexandra Baird
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Fatema Begum
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | - Helene Bramwell
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Alicia Briggs
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Richard Bui
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Talia Chevassus
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Jin H Choi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Karyne Coulombe
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Meghan Davies
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Tamara Di Maulo
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | | | - Paola K Duncan
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Sara El-Nounou
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | - Tanya Fotakis
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Metodi Georgiev
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | - Tazkia Hassan
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Iman Huseen
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Tania Iozzo
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Safina Islam
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Dilan B Jaunky
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | | | - Cedric Kamani
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Filip Konieczny
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Karina Legros
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Jun Li
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Yara Maalouf
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Jessica Mantha
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | | | - Thi T T Nguyen
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Ian Niu
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Matthew Oueis
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Nehal Patel
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Emily Pecsi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Jackie Peters
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | | | | | | | | | - Surya Sakr
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Lisa Serravalle
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Fily Sidibe
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Dominique Soho
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | | | | | - Olga Voitovich
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Pamela Vrabel
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Lu Wang
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Maryse Wasfi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Cong Y Zha
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Chiara Gamberi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
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Buttó LF, Haller D. Functional relevance of microbiome signatures: The correlation era requires tools for consolidation. J Allergy Clin Immunol 2017; 139:1092-1098. [DOI: 10.1016/j.jaci.2017.02.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 02/17/2017] [Accepted: 02/22/2017] [Indexed: 12/16/2022]
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Schwarzer M, Srutkova D, Hermanova P, Leulier F, Kozakova H, Schabussova I. Diet Matters: Endotoxin in the Diet Impacts the Level of Allergic Sensitization in Germ-Free Mice. PLoS One 2017; 12:e0167786. [PMID: 28052076 PMCID: PMC5215724 DOI: 10.1371/journal.pone.0167786] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 11/21/2016] [Indexed: 01/17/2023] Open
Abstract
Germ-free animals have been used to define the vital role of commensal bacteria on the maturation of the host immune system. However, the role of bacterial residues in diet in this setting is poorly understood. Here we investigated the effect of bacterial contamination in sterile diet on the level of allergic sensitization in germ-free mice. Sterile grain-based diets ST1 and R03 were tested for the level of bacterial contamination. ST1 contained higher amount of bacterial DNA, approximately ten times more endotoxin, and induced higher, TLR4-dependent, cytokine production in dendritic cells compared to R03. In a germ-free mouse model of sensitization to the major birch pollen allergen Bet v 1, feeding on ST1 for at least two generations was associated with decreased production of allergen-specific IgE and IgG1 antibodies in sera in comparison to R03. Furthermore, reduced levels of allergen-specific and ConA-induced cytokines IL-4, IL-5 and IL-13 accompanied by increased levels of IFN-γ were detected in splenocytes cultures of these mice. Our results show that contamination of experimental diet with bacterial residues, such as endotoxin, significantly affects the development of allergic sensitization in germ-free mice. Therefore, careful selection of sterile food is critical for the outcomes of germ-free or gnotobiotic experimental models of immune-deviated diseases.
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Affiliation(s)
- Martin Schwarzer
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, v. v. i., Novy Hradek, Czech Republic
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Iniversité Claude Bernard Lyon 1, Lyon, France
| | - Dagmar Srutkova
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, v. v. i., Novy Hradek, Czech Republic
| | - Petra Hermanova
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, v. v. i., Novy Hradek, Czech Republic
| | - Francois Leulier
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Iniversité Claude Bernard Lyon 1, Lyon, France
| | - Hana Kozakova
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, v. v. i., Novy Hradek, Czech Republic
| | - Irma Schabussova
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Vienna, Austria
- * E-mail:
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Abstract
Several members of the SLC9A family of Na+/H+ exchangers are expressed in the gut, with varying expression patterns and cellular localization. Not only do they participate in the regulation of basic epithelial cell functions, including control of transepithelial Na+ absorption, intracellular pH (pH i ), cell volume, and nutrient absorption, but also in cellular proliferation, migration, and apoptosis. Additionally, they modulate the extracellular milieu in order to facilitate other nutrient absorption and to regulate the intestinal microbial microenvironment. Na+/H+ exchangers are frequent targets of inhibition in gastrointestinal pathologies, either by intrinsic factors (e.g. bile acids, inflammatory mediators) or infectious agents and associated microbial toxins. Based on emerging evidence, disruption of NHE activity via impaired expression or function of respective isoforms may contribute not only to local and systemic electrolyte imbalance, but also to the disease severity via multiple mechanisms. Here, we review the current state of knowledge about the roles Na+/H+ exchangers play in the pathogenesis of disorders of diverse origin and affecting a range of GI tissues.
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Affiliation(s)
- Michael A. Gurney
- Department of Pediatrics, Steele Children’s Research Center, University of Arizona, Tucson, Arizona
| | - Daniel Laubitz
- Department of Pediatrics, Steele Children’s Research Center, University of Arizona, Tucson, Arizona
| | - Fayez K. Ghishan
- Department of Pediatrics, Steele Children’s Research Center, University of Arizona, Tucson, Arizona
| | - Pawel R. Kiela
- Department of Pediatrics, Steele Children’s Research Center, University of Arizona, Tucson, Arizona,Department of Immunobiology, University of Arizona, Tucson, Arizona,Correspondence Address correspondence to: Pawel R. Kiela, DVM, PhD, Department of Pediatrics, University of Arizona, 1501 North Campbell Avenue, Tucson, Arizona 85724. fax: (520) 626-4141.Department of Pediatrics, University of Arizona1501 North Campbell AvenueTucsonArizona 85724
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The Rhizome Mixture of Anemarrhena asphodeloides and Coptis chinensis Attenuates Mesalazine-Resistant Colitis in Mice. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2016; 2016:5895184. [PMID: 27761147 PMCID: PMC5059552 DOI: 10.1155/2016/5895184] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/18/2016] [Accepted: 08/18/2016] [Indexed: 12/17/2022]
Abstract
We investigated the effect of DWac on the gut microbiota composition in mice with 2,3,6-trinitrobenzenesulfonic acid- (TNBS-) induced colitis. Treatment with DWac restored TNBS-disturbed gut microbiota composition and attenuated TNBS-induced colitis. Moreover, we examined the effect of DWac in mice with mesalazine-resistant colitis (MRC). Intrarectal injection of TNBS in MRC mice caused severe colitis, as well as colon shortening, edema, and increased myeloperoxidase activity. Treatment with mesalazine (30 mg/kg) did not attenuate TNBS-induced colitis in MRC mice, whereas treatment with DWac (30 mg/kg) significantly attenuated TNBS-induced colitis. Moreover, treatment with the mixture of mesalazine (15 mg/kg) and DWac (15 mg/kg) additively attenuated colitis in MRC mice. Treatment with DWac and its mixture with mesalazine inhibited TNBS-induced activation of NF-κB and expression of M1 macrophage markers but increased TNBS-suppressed expression of M2 macrophage markers. Furthermore, these inhibited TNBS-induced T-bet, RORγt, TNF-α, and IL-17 expression but increased TNBS-suppressed Foxp3 and IL-10 expression. However, Th2 cell differentiation and GATA3 and IL-5 expression were not affected. These findings suggest that DWac can ameliorate MRC by increasing the polarization of M2 macrophage and correcting the disturbance of gut microbiota and Th1/Th17/Treg, as well as additively attenuating MRC along with mesalazine.
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37
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Kang GD, Kim DH. Poncirin and its metabolite ponciretin attenuate colitis in mice by inhibiting LPS binding on TLR4 of macrophages and correcting Th17/Treg imbalance. JOURNAL OF ETHNOPHARMACOLOGY 2016; 189:175-185. [PMID: 27224242 DOI: 10.1016/j.jep.2016.05.044] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/10/2016] [Accepted: 05/16/2016] [Indexed: 06/05/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The fruit of Poncirus trifoliate, which contains poncirin as a main constituent, is frequently used in the traditional Chinese medicine for inflammation, asthma, and infection diseases. AIM OF THE STUDY To examine anti-colitic effects of poncirin and ponciretin, a metabolite of poncirin by gut microbiota. MATERIALS AND METHODS Colitis was induced in mice by the intrarectal injection of 2,4,6-trinitrobenzenesulfonic acid (TNBS). Inflammatory markers were analyzed by enzyme-linked immunosorbent assay, immunoblotting, quantitative polymerase chain reaction, confocal microscopy, and flow cytometry. Peritoneal macrophages were isolated from mice stimulated with 4% thioglycolate. RESULTS Poncirin was metabolized to ponciretin in vitro and in vivo by gut microbiota of mice. Orally administered poncirin and ponciretin suppressed TNBS-induced colitis in mice: these inhibited colon shortening, myeloperoxidase activity, NF-κB activation, and Th17 cell differentiation, but increased occludin, claudin-1, and ZO-1 expressions and Treg cell differentiation. Poncirin and ponciretin suppressed the differentiation of splenocytes into Th17 cells and expression of IL-17 and Foxp3 in vitro, as well as the activation of macrophages stimulated with lipopolysaccharide (LPS) by inhibiting the binding of LPS on TLR4 of macrophages. These increased the differentiation of splenocytes into Treg cells. The ant-inflammatory effect of ponciretin was superior to that of poncirin. CONCLUSION Orally administered poncirin is metabolized to ponciretin by gut microbiota and poncirin and ponciretin attenuates colitis by suppressing NF-κB activation through the inhibition of LPS binding on macrophages and correcting Th17/Treg cell imbalance.
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MESH Headings
- Administration, Oral
- Animals
- Anti-Inflammatory Agents/administration & dosage
- Anti-Inflammatory Agents/metabolism
- Anti-Inflammatory Agents/pharmacology
- Bacteria/metabolism
- Biotransformation
- Cells, Cultured
- Colitis/chemically induced
- Colitis/immunology
- Colitis/metabolism
- Colitis/prevention & control
- Colon/drug effects
- Colon/immunology
- Colon/metabolism
- Disease Models, Animal
- Dose-Response Relationship, Drug
- Drugs, Chinese Herbal/administration & dosage
- Drugs, Chinese Herbal/metabolism
- Drugs, Chinese Herbal/pharmacology
- Flavonoids/administration & dosage
- Flavonoids/metabolism
- Flavonoids/pharmacology
- Gastrointestinal Agents/administration & dosage
- Gastrointestinal Agents/metabolism
- Gastrointestinal Agents/pharmacology
- Gastrointestinal Microbiome
- Inflammation Mediators/metabolism
- Lipopolysaccharides/metabolism
- Lipopolysaccharides/pharmacology
- Macrophage Activation/drug effects
- Macrophages, Peritoneal/drug effects
- Macrophages, Peritoneal/immunology
- Macrophages, Peritoneal/metabolism
- Macrophages, Peritoneal/pathology
- Male
- Mice, Inbred C57BL
- NF-kappa B/metabolism
- Signal Transduction/drug effects
- Spleen/drug effects
- Spleen/immunology
- Spleen/metabolism
- T-Lymphocytes, Regulatory/drug effects
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- Th17 Cells/drug effects
- Th17 Cells/immunology
- Th17 Cells/metabolism
- Time Factors
- Toll-Like Receptor 4/drug effects
- Toll-Like Receptor 4/metabolism
- Trinitrobenzenesulfonic Acid
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Affiliation(s)
- Geum-Dan Kang
- Department of Life and Nanopharmaceutical Sciences, College of Pharmacy, Kyung Hee University, 1, Hoegi, Dongdaemun-gu, Seoul 130-701, South Korea
| | - Dong-Hyun Kim
- Department of Life and Nanopharmaceutical Sciences, College of Pharmacy, Kyung Hee University, 1, Hoegi, Dongdaemun-gu, Seoul 130-701, South Korea.
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38
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Chen EZ, Bushman FD, Li H. A Model-Based Approach For Species Abundance Quantification Based On Shotgun Metagenomic Data. STATISTICS IN BIOSCIENCES 2016; 9:13-27. [PMID: 28959368 DOI: 10.1007/s12561-016-9148-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The human microbiome, which includes the collective microbes residing in or on the human body, has a profound influence on the human health. DNA sequencing technology has made the large-scale human microbiome studies possible by using shotgun metagenomic sequencing. One important aspect of data analysis of such metagenomic data is to quantify the bacterial abundances based on the metagenomic sequencing data. Existing methods almost always quantify such abundances one sample at a time, which ignore certain systematic differences in read coverage along the genomes due to GC contents, copy number variation and the bacterial origin of replication. In order to account for such differences in read counts, we propose a multi-sample Poisson model to quantify microbial abundances based on read counts that are assigned to species-specific taxonomic markers. Our model takes into account the marker-specific effects when normalizing the sequencing count data in order to obtain more accurate quantification of the species abundances. Compared to currently available methods on simulated data and real data sets, our method has demonstrated an improved accuracy in bacterial abundance quantification, which leads to more biologically interesting results from downstream data analysis.
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Affiliation(s)
- Eric Z Chen
- Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Hongzhe Li
- Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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39
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Laubitz D, Harrison CA, Midura-Kiela MT, Ramalingam R, Larmonier CB, Chase JH, Caporaso JG, Besselsen DG, Ghishan FK, Kiela PR. Reduced Epithelial Na+/H+ Exchange Drives Gut Microbial Dysbiosis and Promotes Inflammatory Response in T Cell-Mediated Murine Colitis. PLoS One 2016; 11:e0152044. [PMID: 27050757 PMCID: PMC4822813 DOI: 10.1371/journal.pone.0152044] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 02/16/2016] [Indexed: 12/26/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are associated with functional inhibition of epithelial Na+/H+ exchange. In mice, a selective disruption of NHE3 (Slc9a3), a major apical Na+/H+ exchanger, also promotes IBD-like symptoms and gut microbial dysbiosis. We hypothesized that disruption of Na+/H+ exchange is necessary for the development of dysbiosis, which promotes an exacerbated mucosal inflammatory response. Therefore, we performed a temporal analysis of gut microbiota composition, and mucosal immune response to adoptive T cell transfer was evaluated in Rag2-/- and NHE3-/-/Rag2-/- (DKO) mice with and without broad-spectrum antibiotics. Microbiome (16S profiling), colonic histology, T cell and neutrophil infiltration, mucosal inflammatory tone, and epithelial permeability were analyzed. In adoptive T cell transfer colitis model, Slc9a3 status was the most significant determinant of gut microbial community. In DKO mice, NHE3-deficiency and dysbiosis were associated with dramatically accelerated and exacerbated disease, with rapid body weight loss, increased mucosal T cell and neutrophil influx, increased mucosal cytokine expression, increased permeability, and expansion of CD25-FoxP3+ Tregs; this enhanced susceptibility was alleviated by oral broad-spectrum antibiotics. Based on these results and our previous work, we postulate that epithelial electrolyte homeostasis is an important modulator in the progression of colitis, acting through remodeling of the gut microbial community.
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Affiliation(s)
- Daniel Laubitz
- Department of Pediatrics—Steele Children’s Research Center, University of Arizona, Tucson, Arizona, United States of America
| | - Christy A. Harrison
- Department of Pediatrics—Steele Children’s Research Center, University of Arizona, Tucson, Arizona, United States of America
| | - Monica T. Midura-Kiela
- Department of Pediatrics—Steele Children’s Research Center, University of Arizona, Tucson, Arizona, United States of America
| | - Rajalakshmy Ramalingam
- Department of Pediatrics—Steele Children’s Research Center, University of Arizona, Tucson, Arizona, United States of America
| | - Claire B. Larmonier
- Department of Pediatrics—Steele Children’s Research Center, University of Arizona, Tucson, Arizona, United States of America
| | - John H. Chase
- Department of Biological Sciences, Center for Microbial Genetics and Genomics at Northern Arizona University, Flagstaff, Arizona, United States of America
| | - J. Gregory Caporaso
- Department of Biological Sciences, Center for Microbial Genetics and Genomics at Northern Arizona University, Flagstaff, Arizona, United States of America
| | - David G. Besselsen
- University Animal Care, University of Arizona, Tucson, Arizona, United States of America
| | - Fayez K. Ghishan
- Department of Pediatrics—Steele Children’s Research Center, University of Arizona, Tucson, Arizona, United States of America
| | - Pawel R. Kiela
- Department of Pediatrics—Steele Children’s Research Center, University of Arizona, Tucson, Arizona, United States of America
- Department of Immunobiology, University of Arizona, Tucson, Arizona, United States of America
- * E-mail:
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40
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Dysbiosis in intestinal inflammation: Cause or consequence. Int J Med Microbiol 2016; 306:302-309. [PMID: 27012594 DOI: 10.1016/j.ijmm.2016.02.010] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 02/26/2016] [Accepted: 02/29/2016] [Indexed: 02/07/2023] Open
Abstract
The intestinal microbiota encompasses hundreds of bacterial species that constitute a relatively stable ecosystem. Alteration in the microbiota composition may arise from infections, immune defects, metabolic alterations, diet or antibiotic treatment. Dysbiosis is considered as an alteration in microbiota community structure and/or function, capable of causing/driving a detrimental distortion of microbe-host homeostasis. A variety of pathologies are associated with changes in the community structure and function of the gut microbiota, suggesting a link between dysbiosis and disease etiology. With an emphasis in this review on inflammatory bowel diseases (IBD), the non-trivial question is whether dysbiosis is the cause or consequence of inflammation. It is important to understand whether changes in microbial ecosystems are causally linked to the pathology and to what extend disease risk is predicable based on characteristic changes in community structure and/or function. Local changes in tissue integrity associated with focal areas of inflammation may result in the selection of a dysbiotic bacterial community associated with the propagation of a disease phenotype. This review outlines the role of dysbiosis in intestinal inflammation with particular focus on IBD-relevant gnotobiotic mouse models, the factors implicated in the development of dysbiosis and the means available to investigate dysbiosis in the context of human diseases.
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