1
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Vasquez Ayala A, Hsu CY, Oles RE, Matsuo K, Loomis LR, Buzun E, Carrillo Terrazas M, Gerner RR, Lu HH, Kim S, Zhang Z, Park JH, Rivaud P, Thomson M, Lu LF, Min B, Chu H. Commensal bacteria promote type I interferon signaling to maintain immune tolerance in mice. J Exp Med 2024; 221:e20230063. [PMID: 38085267 PMCID: PMC10716256 DOI: 10.1084/jem.20230063] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 10/05/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
Type I interferons (IFNs) exert a broad range of biological effects important in coordinating immune responses, which have classically been studied in the context of pathogen clearance. Yet, whether immunomodulatory bacteria operate through IFN pathways to support intestinal immune tolerance remains elusive. Here, we reveal that the commensal bacterium, Bacteroides fragilis, utilizes canonical antiviral pathways to modulate intestinal dendritic cells (DCs) and regulatory T cell (Treg) responses. Specifically, IFN signaling is required for commensal-induced tolerance as IFNAR1-deficient DCs display blunted IL-10 and IL-27 production in response to B. fragilis. We further establish that IFN-driven IL-27 in DCs is critical in shaping the ensuing Foxp3+ Treg via IL-27Rα signaling. Consistent with these findings, single-cell RNA sequencing of gut Tregs demonstrated that colonization with B. fragilis promotes a distinct IFN gene signature in Foxp3+ Tregs during intestinal inflammation. Altogether, our findings demonstrate a critical role of commensal-mediated immune tolerance via tonic type I IFN signaling.
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Affiliation(s)
| | - Chia-Yun Hsu
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Renee E. Oles
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Kazuhiko Matsuo
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
- Division of Chemotherapy, Kindai University Faculty of Pharmacy, Higashi-osaka, Japan
| | - Luke R. Loomis
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Ekaterina Buzun
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | | | - Romana R. Gerner
- TUM School of Life Sciences Weihenstephan, ZIEL Institute for Food & Health, Freising-Weihenstephan, Germany
| | - Hsueh-Han Lu
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Sohee Kim
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ziyue Zhang
- School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Jong Hwee Park
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Paul Rivaud
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Matt Thomson
- Division of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Li-Fan Lu
- School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Booki Min
- Department of Microbiology and Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Hiutung Chu
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines, University of California, San Diego, La Jolla, CA, USA
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Canada
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2
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Nakandalage R, Guan LL, Malmuthuge N. Microbial Interventions to Improve Neonatal Gut Health. Microorganisms 2023; 11:1328. [PMID: 37317302 DOI: 10.3390/microorganisms11051328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/04/2023] [Accepted: 05/16/2023] [Indexed: 06/16/2023] Open
Abstract
The diverse pioneer microbial community colonizing the mammalian gastrointestinal tract is critical for the developing immune system. Gut microbial communities of neonates can be affected by various internal and external factors, resulting in microbial dysbiosis. Microbial dysbiosis during early life affects gut homeostasis by changing metabolic, physiological, and immunological status, which increases susceptibility to neonatal infections and long-term pathologies. Early life is crucial for the establishment of microbiota and the development of the host immune system. Therefore, it provides a window of opportunity to reverse microbial dysbiosis with a positive impact on host health. Recent attempts to use microbial interventions during early life have successfully reversed dysbiotic gut microbial communities in neonates. However, interventions with persistent effects on microbiota and host health are still limited. This review will critically discuss microbial interventions, modulatory mechanisms, their limitations, and gaps in knowledge to understand their roles in improving neonatal gut health.
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Affiliation(s)
- Ranga Nakandalage
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
- Lethbridge Research and Development Center, Agriculture Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Nilusha Malmuthuge
- Lethbridge Research and Development Center, Agriculture Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
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3
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Li XB, Huang XX, Li Q, Li XY, Li JH, Li C, He LJ, Jing HX, Yang KL. Effects of different grains on bacterial diversity and enzyme activity associated with digestion of starch in the foal stomach. BMC Vet Res 2022; 18:407. [PMCID: PMC9670411 DOI: 10.1186/s12917-022-03510-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022] Open
Abstract
Abstract
Background
Compared with the stomach of ruminant cattle, the stomach of horse is small and mainly for chemical digestion, but the microorganisms in the stomach play an important role in maintaining the homeostasis of the internal environment. Due to the complexity of the microbes in the stomach, little is known about the diversity and structure of bacteria in the equine stomach. Grains are the main energy source for plant-eating livestock and energy is derived through enzymatic hydrolysis of grains into glucose or their microbial fermentation into Volatile fatty acids (VFA). However, the mechanism through which these ingested grains are chemically digested as well as the effect of these grains on the stomach remains elusive. This study explored the effects of feeding different grains (corn, oats, and barley) on bacterial diversity, structure, and composition in the foal’s stomach content. Furthermore, the effects of different grains on the vitality of starch digestion-related stomach enzymes were investigated.
Results
No significant differences were observed (P > 0.05) in the bacterial rarefaction curves of Operational Taxonomic Units (OTUs) and diversity of the stomach microbiota in all foals. This study also revealed the statistical differences for Firmicutes, Cyanobacteria, Actinobacteria, Fibrobacteres, Lactobacillaceae, Streptococcaceae, Unidentified_Clostridiales, Prevotellaceae, Lactobacillus, Streptococcus, Unidentified_Cyanobacteria, Unidentified_Clostridiales, Lactococcus, Sphingomonas, Lactobacillus_hayakitensis, Lactobacillus_equigenerosi, and Clostridium_perfringens. The linear discriminant analysis effect size analysis revealed 9 bacteria at each classification level. The functional analysis of species information by using FAPROTAX software was able to predict 35 functions, and the top 5 functions were chemoheterotrophy, fermentation, animal_parasites_or_symbionts, nitrate_reduction, and aerobic_chemoheterotrophy. The study also revealed statistical differences for pH, glucose concentration, β-amylase, maltase, and amylase.
Conclusions
The different grains had no significant effect on the microbial diversity of the stomach content of the foal. However, the relative bacterial abundances differed significantly in response to different diets. Particularly, oats fed to the foals significantly increased the relative abundance of Firmicutes, Lactobacillaceae, Lactobacillus, and Lactobacillus_hayakitensis. The grain had no significant effect on the pH of the stomach content, glucose concentration, and enzyme viability in the foal.
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4
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Wymore Brand M, Proctor AL, Hostetter JM, Zhou N, Friedberg I, Jergens AE, Phillips GJ, Wannemuehler MJ. Vertical transmission of attaching and invasive E. coli from the dam to neonatal mice predisposes to more severe colitis following exposure to a colitic insult later in life. PLoS One 2022; 17:e0266005. [PMID: 35381031 PMCID: PMC8982877 DOI: 10.1371/journal.pone.0266005] [Citation(s) in RCA: 2] [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: 11/16/2021] [Accepted: 03/14/2022] [Indexed: 11/18/2022] Open
Abstract
The gastrointestinal microbiota begins to be acquired at birth and continually matures through early adolescence. Despite the relevance for gut health, few studies have evaluated the impact of pathobiont colonization of neonates on the severity of colitis later in life. LF82 is an adherent invasive E. coli strain associated with ileal Crohn’s disease. The aim of this study was to evaluate the severity of dextran sodium sulfate (DSS)-induced colitis in mice following E. coli LF82 colonization. Gnotobiotic mice harboring the altered Schaedler flora (ASF) were used as the model. While E. coli LF82 is neither adherent nor invasive, it was been demonstrated that adult ASF mice colonized with E. coli LF82 develop more severe DSS-induced colitis compared to control ASF mice treated with DSS. Therefore, we hypothesized that E. coli LF82 colonization of neonatal ASF mice would reduce the severity of DSS-induced inflammation compared to adult ASF mice colonized with E. coli LF82. To test this hypothesis, adult ASF mice were colonized with E. coli LF82 and bred to produce offspring (LF82N) that were vertically colonized with LF82. LF82N and adult-colonized (LF82A) mice were given 2.0% DSS in drinking water for seven days to trigger colitis. More severe inflammatory lesions were observed in the LF82N + DSS mice when compared to LF82A + DSS mice, and were characterized as transmural in most of the LF82N + DSS mice. Colitis was accompanied by secretion of proinflammatory cytokines (IFNγ, IL-17) and specific mRNA transcripts within the colonic mucosa. Using 16S rRNA gene amplicon sequencing, LF82 colonization did not induce significant changes in the ASF community; however, minimal changes in spatial redistribution by fluorescent in situ hybridization were observed. These results suggest that the age at which mice were colonized with E. coli LF82 pathobiont differentially impacted severity of subsequent colitic events.
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Affiliation(s)
- Meghan Wymore Brand
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States of America
| | - Alexandra L. Proctor
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States of America
| | - Jesse M. Hostetter
- Department of Veterinary Pathology, College of Veterinary Medicine, Iowa State University, Ames, IA, United States of America
| | - Naihui Zhou
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States of America
| | - Iddo Friedberg
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States of America
| | - Albert E. Jergens
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Iowa State University, Ames, IA, United States of America
| | - Gregory J. Phillips
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States of America
| | - Michael J. Wannemuehler
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA, United States of America
- * E-mail:
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5
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Liang W, Enée E, Andre-Vallee C, Falcone M, Sun J, Diana J. Intestinal Cathelicidin Antimicrobial Peptide Shapes a Protective Neonatal Gut Microbiota Against Pancreatic Autoimmunity. Gastroenterology 2022; 162:1288-1302.e16. [PMID: 34973295 DOI: 10.1053/j.gastro.2021.12.272] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 12/08/2021] [Accepted: 12/21/2021] [Indexed: 01/13/2023]
Abstract
BACKGROUND & AIMS Alteration of the gut microbiota is implicated in the development of autoimmune type 1 diabetes (T1D), as shown in humans and the nonobese diabetic (NOD) mouse model. However, how gut dysbiosis arises and promotes the autoimmune response remains an open question. We investigated whether early events affecting the intestinal homeostasis in newborn NOD mice may explain the development of the autoimmune response in the adult pancreas. METHODS We profiled the transcriptome and the microbiota in the colon between newborn NOD mice and nonautoimmune strains. We identified a seminal defect in the intestinal homeostasis of newborn NOD mice and deciphered the mechanism linking this defect to the diabetogenic response in the adult. RESULTS We determined that the cathelicidin-related antimicrobial peptide (CRAMP) expression was defective in the colon of newborn NOD mice, allowing inducing dysbiosis. Dysbiosis stimulated the colonic epithelial cells to produce type I interferons that pathologically imprinted the local neonatal immune system. This pathological immune imprinting later promoted the pancreatic autoimmune response in the adult and the development of diabetes. Increasing colonic CRAMP expression in newborn NOD mice by means of local CRAMP treatment or CRAMP-expressing probiotic restored colonic homeostasis and halted the diabetogenic response, preventing autoimmune diabetes. CONCLUSIONS We identified whether a defective colonic expression in the CRAMP antimicrobial peptide induces dysbiosis, contributing to autoimmunity in the pancreas. Hence, the manipulation of intestinal antimicrobial peptides may be considered a relevant therapeutic approach to prevent autoimmune diabetes in at-risk children.
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Affiliation(s)
- Wenjie Liang
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Université de Paris, Paris, France
| | - Emmanuelle Enée
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Université de Paris, Paris, France
| | - Cédric Andre-Vallee
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Université de Paris, Paris, France
| | - Marika Falcone
- Experimental Diabetes Unit, Division of Immunology, Transplantation and Infectious Diseases, Istituto di Ricovero e Cura a Carattere Scientifico, San Raffaele Scientific Institute, Milan, Italy
| | - Jia Sun
- Nutritional Immunology and Translational Medicine Laboratory, State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.
| | - Julien Diana
- Institut Necker-Enfants Malades, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Université de Paris, Paris, France.
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6
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Development of epithelial cholinergic chemosensory cells of the urethra and trachea of mice. Cell Tissue Res 2021; 385:21-35. [PMID: 33616728 PMCID: PMC8270884 DOI: 10.1007/s00441-021-03424-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 01/24/2021] [Indexed: 12/24/2022]
Abstract
Cholinergic chemosensory cells (CCC) are infrequent epithelial cells with immunosensor function, positioned in mucosal epithelia preferentially near body entry sites in mammals including man. Given their adaptive capacity in response to infection and their role in combatting pathogens, we here addressed the time points of their initial emergence as well as their postnatal development from first exposure to environmental microbiota (i.e., birth) to adulthood in urethra and trachea, utilizing choline acetyltransferase (ChAT)-eGFP reporter mice, mice with genetic deletion of MyD88, toll-like receptor-2 (TLR2), TLR4, TLR2/TLR4, and germ-free mice. Appearance of CCC differs between the investigated organs. CCC of the trachea emerge during embryonic development at E18 and expand further after birth. Urethral CCC show gender diversity and appear first at P6-P10 in male and at P11-P20 in female mice. Urethrae and tracheae of MyD88- and TLR-deficient mice showed significantly fewer CCC in all four investigated deficient strains, with the effect being most prominent in the urethra. In germ-free mice, however, CCC numbers were not reduced, indicating that TLR2/4-MyD88 signaling, but not vita-PAMPs, governs CCC development. Collectively, our data show a marked postnatal expansion of CCC populations with distinct organ-specific features, including the relative impact of TLR2/4-MyD88 signaling. Strong dependency on this pathway (urethra) correlates with absence of CCC at birth and gender-specific initial development and expansion dynamics, whereas moderate dependency (trachea) coincides with presence of first CCC at E18 and sex-independent further development.
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7
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Laouar A. Maternal Leukocytes and Infant Immune Programming during Breastfeeding. Trends Immunol 2020; 41:225-239. [PMID: 32057705 DOI: 10.1016/j.it.2020.01.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 01/10/2020] [Accepted: 01/12/2020] [Indexed: 12/11/2022]
Abstract
The fetal immune system develops in a rather sterile environment relative to the outside world and, therefore, lacks antigenic education. Soon after birth, the newborn is exposed to the hostile environment of pathogens. Recently, animal- and limited human-based studies have indicated that help from the mother, upon transfer of leukocytes and their products via breast milk feeding, greatly assists the newborn's immune system. Here, I discuss the newest advances on how milk leukocytes impact early life immunity, with an emphasis on the development of the infant T cell repertoire and early immune responses in the periphery and gut-associated lymphoid tissue. A deeper understanding of these novel mechanistic insights may inform potential translational approaches to improving immunity in infants.
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Affiliation(s)
- Amale Laouar
- Surgery Department and the Child Health Institute of New Jersey, Robert Wood Johnson Medical School-Rutgers University, 89 French Street, New Brunswick, NJ 08901, USA.
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8
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Davoodi S, Foley E. Host-Microbe-Pathogen Interactions: A Review of Vibrio cholerae Pathogenesis in Drosophila. Front Immunol 2020; 10:3128. [PMID: 32038640 PMCID: PMC6993214 DOI: 10.3389/fimmu.2019.03128] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/23/2019] [Indexed: 12/14/2022] Open
Abstract
Most animals maintain mutually beneficial symbiotic relationships with their intestinal microbiota. Resident microbes in the gastrointestinal tract breakdown indigestible food, provide essential nutrients, and, act as a barrier against invading microbes, such as the enteric pathogen Vibrio cholerae. Over the last decades, our knowledge of V. cholerae pathogenesis, colonization, and transmission has increased tremendously. A number of animal models have been used to study how V. cholerae interacts with host-derived resources to support gastrointestinal colonization. Here, we review studies on host-microbe interactions and how infection with V. cholerae disrupts these interactions, with a focus on contributions from the Drosophila melanogaster model. We will discuss studies that highlight the connections between symbiont, host, and V. cholerae metabolism; crosstalk between V. cholerae and host microbes; and the impact of the host immune system on the lethality of V. cholerae infection. These studies suggest that V. cholerae modulates host immune-metabolic responses in the fly and improves Vibrio fitness through competition with intestinal microbes.
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Affiliation(s)
| | - Edan Foley
- Department of Medical Microbiology and Immunology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
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9
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Ortigão R, Pimentel-Nunes P, Dinis-Ribeiro M, Libânio D. Gastrointestinal Microbiome - What We Need to Know in Clinical Practice. GE-PORTUGUESE JOURNAL OF GASTROENTEROLOGY 2020; 27:336-351. [PMID: 32999906 DOI: 10.1159/000505036] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 11/14/2019] [Indexed: 12/12/2022]
Abstract
Human gut microbiota plays an important role in individual health. When the balance between host and gut microbiota is disrupted, changes in microbiota composition and function occur, which is referred as dysbiosis. Environmental factors as diet, proton pump inhibitors, and antibiotics can lead to a permanent dysbiotic disruption. Clarification of these imbalances was made possible by recent advances in genome sequencing methods that supported acknowledgment of the interplay between microbiome and intestinal and extraintestinal disorders. This review focuses on the microbiota impact in inflammatory bowel disease, gastric cancer, colorectal cancer, nonalcoholic fatty liver disease (NAFLD), irritable bowel syndrome (IBS), and Clostridium difficile infection (CDI). Furthermore, novel therapies are summarized. Fecal microbiota transplant (FMT) is a successful and established therapy in recurrent CDI, and its application in other dysbiosis-related diseases is attracting enormous interest. Pre- and probiotics target microbial rebalance and have positive effects mainly in NAFLD, ulcerative colitis, IBS, and CDI patients. Promising anticarcinogenic effects have also been demonstrated in animal models. The literature increasingly describes microbial changes in many dysbiotic disorders and shows what needs to be treated. However, probiotics and FMT application in clinical practice suffers from a shortage of randomized controlled trials with standardized therapy regimens to support their recommendation.
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Affiliation(s)
- Raquel Ortigão
- Department of Gastroenterology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Pedro Pimentel-Nunes
- Department of Gastroenterology, Portuguese Oncology Institute of Porto, Porto, Portugal.,MEDCIDS - Department of Community Medicine, Information and Decision in Health, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Mário Dinis-Ribeiro
- Department of Gastroenterology, Portuguese Oncology Institute of Porto, Porto, Portugal.,MEDCIDS - Department of Community Medicine, Information and Decision in Health, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Diogo Libânio
- Department of Gastroenterology, Portuguese Oncology Institute of Porto, Porto, Portugal.,MEDCIDS - Department of Community Medicine, Information and Decision in Health, Faculty of Medicine, University of Porto, Porto, Portugal
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10
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Lindenberg F, Krych L, Kot W, Fielden J, Frøkiær H, van Galen G, Nielsen DS, Hansen AK. Development of the equine gut microbiota. Sci Rep 2019; 9:14427. [PMID: 31594971 PMCID: PMC6783416 DOI: 10.1038/s41598-019-50563-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 09/09/2019] [Indexed: 02/06/2023] Open
Abstract
Shortly after birth the mammalian gut is colonized, by a transient microbiota, highly susceptible to environment and diet, that eventually stabilizes and becomes the resident gut microbiota. In a window of opportunity during the colonization, oral tolerance is established towards resident bacteria. In this study, the development of the equine gut microbiota was investigated in ten foals from parturition until post weaning. We found great differences in the core species of the gut microbiota composition between time-matched samples on Day 7 and 20 post-partum. Between day 20 and Day 50 post-partum, we saw the gut microbiota became increasingly dominated by fiber fermenting species. After Day 50, no significant changes in species abundance were observed. Gene expression analysis of pro- and anti-inflammatory cytokines in the blood revealed no significant changes before and after weaning. In summary, relative stability of the gut microbiota was reached within 50 days post-partum and, weaning did not have a major impact on the microbial composition.
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Affiliation(s)
- F Lindenberg
- Brogaarden Aps, Copenhagen, Denmark. .,Faculty of Health and Medical Sciences, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - L Krych
- Faculty of Sciences, Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - W Kot
- Department of Environmental Sciences, Aarhus University, København, Denmark
| | | | - H Frøkiær
- Faculty of Health and Medical Sciences, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - G van Galen
- Faculty of Health and Medical Sciences, Department of Veterinary Clinical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - D S Nielsen
- Faculty of Sciences, Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - A K Hansen
- Faculty of Health and Medical Sciences, Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
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11
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Schwartz DJ, Rebeck ON, Dantas G. Complex interactions between the microbiome and cancer immune therapy. Crit Rev Clin Lab Sci 2019; 56:567-585. [PMID: 31526274 DOI: 10.1080/10408363.2019.1660303] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Immuno-oncology has rapidly grown in the last thirty years, and immunotherapeutic agents are now approved to treat many disparate cancers. Immune checkpoint inhibitors (ICIs) are employed to augment cytotoxic anti-cancer activity by inhibiting negative regulatory elements of the immune system. Modulating the immune system to target neoplasms has improved survivability of numerous cancers in many individuals, but forecasting outcomes post therapy is difficult due to insufficient predictive biomarkers. Recently, the tumor and gastrointestinal microbiome and immune milieu have been investigated as predictors and influencers of cancer immune therapy. In this review, we discuss: (1) ways to measure the microbiome including relevant bioinformatic analyses, (2) recent developments in animal studies and human clinical trials utilizing gut microbial composition and function as biomarkers of cancer immune therapy response and toxicity, and (3) using prebiotics, probiotics, postbiotics, antibiotics, and fecal microbiota transplant (FMT) to modulate immune therapy. We discuss the respective benefits of 16S ribosomal RNA (rRNA) gene and shotgun metagenomic sequencing including important considerations in obtaining samples and in designing and interpreting human and animal microbiome studies. We then focus on studies discussing the differences in response to ICIs in relation to the microbiome and inflammatory mediators. ICIs cause colitis in up to 25% of individuals, and colitis is often refractory to common immunosuppressive medications. Researchers have measured microbiota composition prior to ICI therapy and correlated baseline microbiota composition with efficacy and colitis. Certain bacterial taxa that appear to enhance therapeutic benefit are also implicated in increased susceptibility to colitis, alluding to a delicate balance between pro-inflammatory tumor killing and anti-inflammatory protection from colitis. Pre-clinical and clinical models have trialed probiotic administration, e.g. Bifidobacterium spp. or FMT, to treat colitis when immune suppressive agents fail. We are excited about the future of modulating the microbiome to predict and influence cancer outcomes. Furthermore, novel therapies employed for other illnesses including bacteriophage and genetically-engineered microbes can be adapted in the future to promote increased advancements in cancer treatment and side effect management.
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Affiliation(s)
- Drew J Schwartz
- Department of Pediatrics, Division of Infectious Diseases, Washington University School of Medicine , St. Louis , MO , USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine , St. Louis , MO , USA
| | - Olivia N Rebeck
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine , St. Louis , MO , USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine , St. Louis , MO , USA.,Department of Molecular Microbiology and Microbial Pathogenesis, Washington University School of Medicine in St. Louis , MO , USA.,Department of Pathology and Immunology, Washington University School of Medicine in St. Louis , MO , USA.,Department of Biomedical Engineering, Washington University in St. Louis , St. Louis , MO , USA
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12
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Zhao ZH, Lai JKL, Qiao L, Fan JG. Role of gut microbial metabolites in nonalcoholic fatty liver disease. J Dig Dis 2019; 20:181-188. [PMID: 30706694 DOI: 10.1111/1751-2980.12709] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 01/08/2019] [Accepted: 01/30/2019] [Indexed: 12/11/2022]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a common, multifactorial liver disease that has emerged as a global challenge due to its increasing prevalence and lack of sustainable treatment options. Gut microbiota possess vital functions in fermenting dietary nutrients and synthesizing bioactive molecules. This function is of great importance in maintaining health because these microbial metabolites are essential in regulating energy metabolism, immune response, and other vital physiological processes. Altered gut flora can result in a change in gut microbial metabolites, affecting the onset and progression of multiple diseases. In this review we summarize the metabolites that may have beneficial or harmful effects on the development and progression of NAFLD. This will help us better understand the possible mechanisms underlying the pathogenesis of NAFLD and facilitate the identification of potential therapeutic approaches for NAFLD.
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Affiliation(s)
- Ze Hua Zhao
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jonathan King-Lam Lai
- Storr Liver Centre, Westmead Institute for Medical Research, University of Sydney and Westmead Hospital, Sydney, New South Wales, Australia
| | - Liang Qiao
- Storr Liver Centre, Westmead Institute for Medical Research, University of Sydney and Westmead Hospital, Sydney, New South Wales, Australia
| | - Jian Gao Fan
- Center for Fatty Liver, Department of Gastroenterology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Janeckova L, Kostovcikova K, Svec J, Stastna M, Strnad H, Kolar M, Hudcovic T, Stancikova J, Tureckova J, Baloghova N, Sloncova E, Galuskova K, Tlaskalova-Hogenova H, Korinek V. Unique Gene Expression Signatures in the Intestinal Mucosa and Organoids Derived from Germ-Free and Monoassociated Mice. Int J Mol Sci 2019; 20:ijms20071581. [PMID: 30934845 PMCID: PMC6480644 DOI: 10.3390/ijms20071581] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/18/2019] [Accepted: 03/26/2019] [Indexed: 12/19/2022] Open
Abstract
Commensal microbiota contribute to gut homeostasis by inducing transcription of mucosal genes. Analysis of the impact of various microbiota on intestinal tissue provides an important insight into the function of this organ. We used cDNA microarrays to determine the gene expression signature of mucosa isolated from the small intestine and colon of germ-free (GF) mice and animals monoassociated with two E. coli strains. The results were compared to the expression data obtained in conventionally reared (CR) mice. In addition, we analyzed gene expression in colon organoids derived from CR, GF, and monoassociated animals. The analysis revealed that the complete absence of intestinal microbiota mainly affected the mucosal immune system, which was not restored upon monoassociation. The most important expression changes observed in the colon mucosa indicated alterations in adipose tissue and lipid metabolism. In the comparison of differentially expressed genes in the mucosa or organoids obtained from GF and CR mice, only six genes were common for both types of samples. The results show that the increased expression of the angiopoietin-like 4 (Angptl4) gene encoding a secreted regulator of lipid metabolism indicates the GF status.
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Affiliation(s)
- Lucie Janeckova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Klara Kostovcikova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Jiri Svec
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
- Department of Radiotherapy and Oncology, Third Faculty of Medicine, Charles University, Prague, Srobarova 50, 100 34 Prague 10, Czech Republic.
| | - Monika Stastna
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Hynek Strnad
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Michal Kolar
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Tomas Hudcovic
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Jitka Stancikova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Jolana Tureckova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Nikol Baloghova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Eva Sloncova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Katerina Galuskova
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Helena Tlaskalova-Hogenova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
| | - Vladimir Korinek
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague 4, Czech Republic.
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Abstract
The lung and gut microbiome are factors in asthma risk or protection. Relevant elements of the microbiome within both niches include the importance of the early life window for microbiome establishment, the diversity of bacteria, richness of bacteria, and effect of those bacteria on the local epithelium and immune system. Mechanisms of protection include direct anti-inflammatory action or induction of non-type 2 inflammation by certain bacterial colonies. The gut microbiome further impacts asthma risk through the contribution of metabolic products. This article reviews the mechanisms that connect the lung and gut microbiota to asthma development and severity.
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Affiliation(s)
- Tara F Carr
- Department of Medicine, University of Arizona, 1501 North Campbell Avenue, Tucson, AZ 85724-5030, USA.
| | - Rhonda Alkatib
- Department of Medicine, University of Arizona, 1501 North Campbell Avenue, Tucson, AZ 85724-5030, USA
| | - Monica Kraft
- Department of Medicine, University of Arizona, 1501 North Campbell Avenue, Tucson, AZ 85724-5030, USA
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15
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Immunomodulatory effects of probiotics: Can they be used to treat allergies and autoimmune diseases? Maturitas 2018; 119:25-38. [PMID: 30502748 DOI: 10.1016/j.maturitas.2018.11.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 11/06/2018] [Accepted: 11/08/2018] [Indexed: 12/12/2022]
Abstract
As a person ages, physiological, immunological and gut microbiome changes collectively result in an array of chronic conditions. According to the 'hygiene hypothesis' the increasing prevalence of immune-mediated disorders may be related to intestinal dysbiosis, leading to immune dysfunction and associated conditions such as eczema, asthma, allergies and autoimmune diseases. Beneficial probiotic bacteria can be utilized by increasing their abundance within the gastrointestinal lumen, which in turn will modulate immune cells, such as, T helper (Th)-1, Th2, Th17, regulatory T (Treg) cells and B cells, which have direct relevance to human health and the pathogenesis of immune disorders. Here, we describe the cross-talk between probiotics and the gastrointestinal immune system, and their effects in relation to inflammatory bowel disease, multiple sclerosis, allergies and atopic dermatitis.
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16
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Diet, gut microbiota composition and feeding behavior. Physiol Behav 2018; 192:177-181. [DOI: 10.1016/j.physbeh.2018.03.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/23/2018] [Accepted: 03/23/2018] [Indexed: 02/07/2023]
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17
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Sun J, Zhong H, Du L, Li X, Ding Y, Cao H, Liu Z, Ge L. Gene expression profiles of germ-free and conventional piglets from the same litter. Sci Rep 2018; 8:10745. [PMID: 30013139 PMCID: PMC6048018 DOI: 10.1038/s41598-018-29093-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 07/02/2018] [Indexed: 11/24/2022] Open
Abstract
Germ-free (GF) pigs have clear microbiological backgrounds, and are extensively used as large animal models in the biomedical sciences. However, investigations of the transcriptomic differences between GF and cesarean-derived conventional (CV) piglets are limited. To improve our understanding of GF pigs, and to increase the utility of pigs as an alternative non-rodent model, we used RNA sequencing to profile gene expression in five tissues (the oral mucosae, jejunum, colon, liver, and spleen) of four male GF piglets and four male CV piglets from the same litter. We identified 14 genes that were differentially expressed in all five tissues. Seven of these common differentially expressed genes (DEGs) were interferon-inducible genes, and all 14 were consistently downregulated in the GF piglets as compared to the CV piglets. Compared to the other tissues tested, the expression of transcription factors (TFs) in the colon was most affected by the absence of a microbiota. The expression patterns of immune-related genes were downregulated in the GF piglets as compared to the CV piglets, indicating that the intestinal microbiota influenced gene expression in other tissues besides the gut. Gene Ontology (GO) analysis indicated that, in pigs, the intestinal microbiota affected the expression of genes related to immune system function and development.
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Affiliation(s)
- Jing Sun
- Chongqing Academy of Animal Sciences, Chongqing, 402460, China
- Key Laboratory of Pig Industry Sciences, Ministry of Agriculture, Chongqing, 402460, China
- Chongqing Key Laboratory of Pig Industry Sciences, Chongqing, 402460, China
| | - Hang Zhong
- Chongqing Academy of Animal Sciences, Chongqing, 402460, China
| | - Lei Du
- Chongqing Academy of Animal Sciences, Chongqing, 402460, China
| | - Xiaolei Li
- Chongqing Academy of Animal Sciences, Chongqing, 402460, China
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuchun Ding
- Chongqing Academy of Animal Sciences, Chongqing, 402460, China
- Key Laboratory of Pig Industry Sciences, Ministry of Agriculture, Chongqing, 402460, China
- Chongqing Key Laboratory of Pig Industry Sciences, Chongqing, 402460, China
| | - Haoran Cao
- Chongqing Academy of Animal Sciences, Chongqing, 402460, China
- Key Laboratory of Pig Industry Sciences, Ministry of Agriculture, Chongqing, 402460, China
- Chongqing Key Laboratory of Pig Industry Sciences, Chongqing, 402460, China
| | - Zuohua Liu
- Chongqing Academy of Animal Sciences, Chongqing, 402460, China.
- Key Laboratory of Pig Industry Sciences, Ministry of Agriculture, Chongqing, 402460, China.
- Chongqing Key Laboratory of Pig Industry Sciences, Chongqing, 402460, China.
| | - Liangpeng Ge
- Chongqing Academy of Animal Sciences, Chongqing, 402460, China.
- Key Laboratory of Pig Industry Sciences, Ministry of Agriculture, Chongqing, 402460, China.
- Chongqing Key Laboratory of Pig Industry Sciences, Chongqing, 402460, China.
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18
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Harbeson D, Ben-Othman R, Amenyogbe N, Kollmann TR. Outgrowing the Immaturity Myth: The Cost of Defending From Neonatal Infectious Disease. Front Immunol 2018; 9:1077. [PMID: 29896192 PMCID: PMC5986917 DOI: 10.3389/fimmu.2018.01077] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 04/30/2018] [Indexed: 12/28/2022] Open
Abstract
Newborns suffer high rates of mortality due to infectious disease-this has been generally regarded to be the result of an "immature" immune system with a diminished disease-fighting capacity. However, the immaturity dogma fails to explain (i) greater pro-inflammatory responses than adults in vivo and (ii) the ability of neonates to survive a significantly higher blood pathogen burden than of adults. To reconcile the apparent contradiction of clinical susceptibility to disease and the host immune response findings when contrasting newborn to adult, it will be essential to capture the entirety of available host-defense strategies at the newborn's disposal. Adults focus heavily on the disease resistance approach: pathogen reduction and elimination. Newborn hyperactive innate immunity, sensitivity to immunopathology, and the energetic requirements of growth and development (immune and energy costs), however, preclude them from having an adult-like resistance response. Instead, newborns also may avail themselves of disease tolerance (minimizing immunopathology without reducing pathogen load), as a disease tolerance approach provides a counterbalance to the dangers of a heightened innate immunity and has lower-associated immune costs. Further, disease tolerance allows for the establishment of a commensal bacterial community without mounting an unnecessarily dangerous immune resistance response. Since disease tolerance has its own associated costs (immune suppression leading to unchecked pathogen proliferation), it is the maintenance of homeostasis between disease tolerance and disease resistance that is critical to safe and effective defense against infections in early life. This paradigm is consistent with nearly all of the existing evidence.
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Affiliation(s)
- Danny Harbeson
- Department of Experimental Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Rym Ben-Othman
- Department of Pediatrics, Division of Infectious Diseases, University of British Columbia, Vancouver, BC, Canada
| | - Nelly Amenyogbe
- Department of Experimental Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Tobias R. Kollmann
- Department of Experimental Medicine, University of British Columbia, Vancouver, BC, Canada
- Department of Pediatrics, Division of Infectious Diseases, University of British Columbia, Vancouver, BC, Canada
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19
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Wu YY, Westwater C, Xiao E, Dias Corrêa J, Xiao WM, Graves DT. Establishment of oral bacterial communities in germ-free mice and the influence of recipient age. Mol Oral Microbiol 2018; 33:38-46. [PMID: 28776953 PMCID: PMC6525632 DOI: 10.1111/omi.12194] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2017] [Indexed: 02/05/2023]
Abstract
The acquisition of the oral microbiome is a complex process. We examined how the timing of microbial exposure alters bacterial colonization of the tooth surface. Germ-free mice were conventionalized by exposure to specific pathogen-free (SPF) mice to acquire a commensal microbiome over three distinct 4-week periods, 0-4 weeks of age (Conv0-4w), 4-8 weeks (Conv4-8w), or 8-12 weeks (Conv8-12w). Bacterial DNA was extracted from the tooth surface and analyzed by 16S rDNA sequencing. Total bacteria and inflammatory cytokine expression in gingiva were determined by quantitative real-time polymerase chain reaction. After co-housing with SPF mice, Conv0-4w and Conv4-8w mice had low bacterial diversity, whereas Conv8-12w mice had high bacterial diversity that was similar to that of SPF donor mice, as determined by both operational taxonomic units and the Shannon Index. Cluster analysis with unweighted Unifrac distance also supported these trends. This was surprising as the amount of maturation time, 4 weeks, was equal in all conventionalized mice and tooth eruption was largely completed by 4 weeks. This suggests that host factors that occur after tooth eruption have a significant effect on the microbial tooth colonization.
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Affiliation(s)
- Y Y Wu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - C Westwater
- Department of Oral Health Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - E Xiao
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology, Beijing, China
| | - J Dias Corrêa
- Dentistry school, Department of Oral Surgery and Pathology, Federal University of Minas Gerais, Minas Gerais, Brazil
| | - W M Xiao
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Periodontology, Peking University School and Hospital of Stomatology, Beijing, China
| | - D T Graves
- Department of Periodontics, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
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20
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Cawthon CR, de La Serre CB. Gut bacteria interaction with vagal afferents. Brain Res 2018; 1693:134-139. [PMID: 29360469 DOI: 10.1016/j.brainres.2018.01.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/03/2018] [Accepted: 01/08/2018] [Indexed: 12/25/2022]
Abstract
Contemporary techniques including the use of germ-free models and next generation sequencing have deepened our understanding of the gut microbiota dynamics and its influence on host physiology. There is accumulating evidence that the gut microbiota can communicate to the CNS and is involved in the development of metabolic and behavioral disorders. Vagal afferent terminals are positioned beneath the gut epithelium where they can receive, directly or indirectly, signals produced by the gut microbiota, to affect host behavior, including feeding behavior. Supplementation with L. Rhamnosus in mice notably causes a decrease in anxiety and these effects are abolished by vagotomy. Additionally, chronic treatment with bacterial byproduct lipopolysaccharide (LPS) blunts vagally-mediated post-ingestive feedback and is associated with increased food intake. Inflammation in the nodose ganglion (NG), the location of vagal afferent neurons' cell bodies, may be a key triggering factor of microbiota-driven vagal alteration. Interestingly, several models show that vagal damage leads to an increase in immune cell (microglia) activation in the NG and remodeling of the vagal pathway. Similarly, diet-driven microbiota dysbiosis is associated with NG microglia activation and decreased vagal outputs to the CNS. Crucially, preventing dysbiosis and microglia activation in high-fat diet fed rodents normalizes vagal innervation and energy intake, highlighting the importance of microbiota/vagal communication in controlling feeding behavior. As of today, new consideration of potential roles for glial influence on vagal communication and new methods of vagal afferent ablation open opportunities to increase our understanding of how the gut microbiota influence its host's health and behavior.
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Affiliation(s)
- Carolina R Cawthon
- Department of Foods and Nutrition, University of Georgia, 372 Dawson Hall, 305 Sanford Drive, Athens, GA 30602 USA.
| | - Claire B de La Serre
- Department of Foods and Nutrition, University of Georgia, 372 Dawson Hall, 305 Sanford Drive, Athens, GA 30602 USA.
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21
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Clavel T, Neto JCG, Lagkouvardos I, Ramer-Tait AE. Deciphering interactions between the gut microbiota and the immune system via microbial cultivation and minimal microbiomes. Immunol Rev 2017; 279:8-22. [PMID: 28856739 PMCID: PMC5657458 DOI: 10.1111/imr.12578] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The community of microorganisms in the mammalian gastrointestinal tract, referred to as the gut microbiota, influences host physiology and immunity. The last decade of microbiome research has provided significant advancements for the field and highlighted the importance of gut microbes to states of both health and disease. Novel molecular techniques have unraveled the tremendous diversity of intestinal symbionts that potentially influence the host, many proof-of-concept studies have demonstrated causative roles of gut microbial communities in various pathologies, and microbiome-based approaches are beginning to be implemented in the clinic for diagnostic purposes or for personalized treatments. However, several challenges for the field remain: purely descriptive reports outnumbering mechanistic studies and slow translation of experimental results obtained in animal models into the clinics. Moreover, there is a dearth of knowledge regarding how gut microbes, including novel species that have yet to be identified, impact host immune responses. The sheer complexity of the gut microbial ecosystem makes it difficult, in part, to fully understand the microbiota-host networks that regulate immunity. In the present manuscript, we review key findings on the interactions between gut microbiota members and the immune system. Because culturing microbes allows performing functional studies, we have emphasized the impact of specific taxa or communities thereof. We also highlight underlying molecular mechanisms and discuss opportunities to implement minimal microbiome-based strategies.
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Affiliation(s)
- Thomas Clavel
- Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - João Carlos Gomes Neto
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Ilias Lagkouvardos
- ZIEL Institute for Food and Health, Core Facility Microbiome/NGS, Technical University of Munich, Germany
| | - Amanda E. Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
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22
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Food contact materials and gut health: Implications for toxicity assessment and relevance of high molecular weight migrants. Food Chem Toxicol 2017; 109:1-18. [PMID: 28830834 DOI: 10.1016/j.fct.2017.08.023] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/17/2017] [Accepted: 08/19/2017] [Indexed: 02/08/2023]
Abstract
Gut health is determined by an intact epithelial barrier and balanced gut microbiota, both involved in the regulation of immune responses in the gut. Disruption of this system contributes to the etiology of various non-communicable diseases, including intestinal, metabolic, and autoimmune disorders. Studies suggest that some direct food additives, but also some food contaminants, such as pesticide residues and substances migrating from food contact materials (FCMs), may adversely affect the gut barrier or gut microbiota. Here, we focus on gut-related effects of FCM-relevant substances (e.g. surfactants, N-ring containing substances, nanoparticles, and antimicrobials) and show that gut health is an underappreciated target in the toxicity assessment of FCMs. Understanding FCMs' impact on gut health requires more attention to ensure safety and prevent gut-related chronic diseases. Our review further points to the existence of large population subgroups with an increased intestinal permeability; this may lead to higher uptake of compounds of not only low (<1000 Da) but also high (>1000 Da) molecular weight. We discuss the potential toxicological relevance of high molecular weight compounds in the gut and suggest that the scientific justification for the application of a molecular weight-based cut-off in risk assessment of FCMs should be reevaluated.
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Kotredes KP, Thomas B, Gamero AM. The Protective Role of Type I Interferons in the Gastrointestinal Tract. Front Immunol 2017; 8:410. [PMID: 28428788 PMCID: PMC5382159 DOI: 10.3389/fimmu.2017.00410] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/22/2017] [Indexed: 12/18/2022] Open
Abstract
The immune system of the gastrointestinal (GI) tract manages the significant task of recognizing and eliminating pathogens while maintaining tolerance of commensal bacteria. Dysregulation of this delicate balance can be detrimental, resulting in severe inflammation, intestinal injury, and cancer. Therefore, mechanisms to relay important signals regulating cell growth and immune reactivity must be in place to support GI homeostasis. Type I interferons (IFN-I) are a family of pleiotropic cytokines, which exert a wide range of biological effects including promotion of both pro- and anti-inflammatory activities. Using animal models of colitis, investigations into the regulation of intestinal epithelium inflammation highlight the role of IFN-I signaling during fine modulation of the immune system. The intestinal epithelium of the gut guides the immune system to differentiate between commensal and pathogenic microbiota, which relies on intimate links with the IFN-I signal-transduction pathway. The current paradigm depicts an IFN-I-induced antiproliferative state in the intestinal epithelium enabling cell differentiation, cell maturation, and proper intestinal barrier function, strongly supporting its role in maintaining baseline immune activity and clearance of damaged epithelia or pathogens. In this review, we will highlight the importance of IFN-I in intestinal homeostasis by discussing its function in inflammation, immunity, and cancer.
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Affiliation(s)
- Kevin P Kotredes
- Department of Medical Genetics and Molecular Biochemistry, Temple University School of Medicine, Philadelphia, PA, USA
| | - Brianna Thomas
- Department of Medical Genetics and Molecular Biochemistry, Temple University School of Medicine, Philadelphia, PA, USA
| | - Ana M Gamero
- Department of Medical Genetics and Molecular Biochemistry, Temple University School of Medicine, Philadelphia, PA, USA
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Abstract
The human gut is in constant complex interaction with the external environment. Although much is understood about the composition and function of the microbiota, much remains to be learnt about the mechanisms by which these organisms interact with the immune system in health and disease. Type 1 interferon (T1IFN), a ubiquitous and pleiotropic family of cytokines, is a critical mediator of the response to viral, bacterial, and other antigens sampled in the intestine. Although inflammation is enhanced in mouse model of colitis when T1IFN signaling is lost, the action of T1IFN is context specific and can be pro- or anti-inflammatory. In humans, T1IFN has been used to treat inflammatory diseases, including multiple sclerosis and inflammatory bowel disease but intestinal inflammation can also develop after the administration of T1IFN. Recent findings indicate that "tonic" or "endogenous" T1IFN, induced by signals from the commensal microbiota, modulates the local signaling environment to prime the intestinal mucosal immune system to determine later responses to pathogens and commensal organisms. This review will summarize the complex immunological effects of T1IFN and recent the role of T1IFN as a mediator between the microbiota and the mucosal immune system, highlighting human data wherever possible. It will discuss what we can learn from clinical experiences with T1IFN and how the T1IFN pathway may be manipulated in the future to maintain mucosal homeostasis.
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25
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The microbiome-immune-host defense barrier complex (microimmunosome) and developmental programming of noncommunicable diseases. Reprod Toxicol 2017; 68:49-58. [DOI: 10.1016/j.reprotox.2016.04.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/15/2016] [Accepted: 04/29/2016] [Indexed: 12/29/2022]
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26
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Bashiardes S, Shapiro H, Rozin S, Shibolet O, Elinav E. Non-alcoholic fatty liver and the gut microbiota. Mol Metab 2016; 5:782-94. [PMID: 27617201 PMCID: PMC5004228 DOI: 10.1016/j.molmet.2016.06.003] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 06/04/2016] [Accepted: 06/08/2016] [Indexed: 02/06/2023] Open
Abstract
Background Non-alcoholic fatty liver (NAFLD) is a common, multi-factorial, and poorly understood liver disease whose incidence is globally rising. NAFLD is generally asymptomatic and associated with other manifestations of the metabolic syndrome. Yet, up to 25% of NAFLD patients develop a progressive inflammatory liver disease termed non-alcoholic steatohepatitis (NASH) that may progress towards cirrhosis, hepatocellular carcinoma, and the need for liver transplantation. In recent years, several lines of evidence suggest that the gut microbiome represents a significant environmental factor contributing to NAFLD development and its progression into NASH. Suggested microbiome-associated mechanisms contributing to NAFLD and NASH include dysbiosis-induced deregulation of the gut endothelial barrier function, which facilitates systemic bacterial translocation, and intestinal and hepatic inflammation. Furthermore, increased microbiome-modulated metabolites such as lipopolysaccharides, short chain fatty acids (SCFAs), bile acids, and ethanol, may affect liver pathology through multiple direct and indirect mechanisms. Scope of review Herein, we discuss the associations, mechanisms, and clinical implications of the microbiome's contribution to NAFLD and NASH. Understanding these contributions to the development of fatty liver pathogenesis and its clinical course may serve as a basis for development of therapeutic microbiome-targeting approaches for treatment and prevention of NAFLD and NASH. Major conclusions Intestinal host–microbiome interactions play diverse roles in the pathogenesis and progression of NAFLD and NASH. Elucidation of the mechanisms driving these microbial effects on the pathogenesis of NAFLD and NASH may enable to identify new diagnostic and therapeutic targets of these common metabolic liver diseases. This article is part of a special issue on microbiota.
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Affiliation(s)
- Stavros Bashiardes
- Immunology Department, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Hagit Shapiro
- Immunology Department, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Shachar Rozin
- Immunology Department, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Oren Shibolet
- Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel; Department of Gastroenterology, Tel Aviv Medical Center, Tel Aviv 6423906, Israel
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, 76100 Rehovot, Israel
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27
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Bashiardes S, Zilberman-Schapira G, Elinav E. Use of Metatranscriptomics in Microbiome Research. Bioinform Biol Insights 2016; 10:19-25. [PMID: 27127406 PMCID: PMC4839964 DOI: 10.4137/bbi.s34610] [Citation(s) in RCA: 226] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 03/02/2016] [Accepted: 03/07/2016] [Indexed: 12/21/2022] Open
Abstract
The human intestinal microbiome is a microbial ecosystem that expresses as many as 100 times more genes than the human host, thereby constituting an important component of the human holobiome, which contributes to multiple health and disease processes. As most commensal species are difficult or impossible to culture, genomic characterization of microbiome composition and function, under various environmental conditions, comprises a central tool in understanding its roles in health and disease. The first decade of microbiome research was mainly characterized by usage of DNA sequencing-based 16S rDNA and shotgun metagenome sequencing, allowing for the elucidation of microbial composition and genome structure. Technological advances in RNA-seq have recently provided us with an ability to gain insight into the genes that are actively expressed in complex bacterial communities, enabling the elucidation of the functional changes that dictate the microbiome functions at given contexts, its interactions with the host, and functional alterations that accompany the conversion of a healthy microbiome toward a disease-driving configuration. Here, we highlight some of the key metatranscriptomics strategies that are implemented to determine microbiota gene expression and its regulation and discuss the advantages and potential challenges associated with these approaches.
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Affiliation(s)
- Stavros Bashiardes
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Eran Elinav
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
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West CE, Jenmalm MC, Kozyrskyj AL, Prescott SL. Probiotics for treatment and primary prevention of allergic diseases and asthma: looking back and moving forward. Expert Rev Clin Immunol 2016; 12:625-39. [PMID: 26821735 DOI: 10.1586/1744666x.2016.1147955] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Microbial ecosystems cover the surface of the human body and it is becoming increasingly clear that our modern environment has profound effects on microbial composition and diversity. A dysbiotic gut microbiota has been associated with allergic diseases and asthma in cross-sectional and observational studies. In an attempt to restore this dysbiosis, probiotics have been evaluated in randomized controlled trials. Here, we review treatment and primary prevention studies, recent meta-analyses, and discuss the current understanding of the role of probiotics in this context. Many meta-analyses have shown a moderate benefit of probiotics for eczema prevention, whereas there is less evidence of a benefit for other allergic manifestations. Because of very low quality evidence and heterogeneity between studies, specific advice on the most effective regimens cannot yet be given - not even for eczema prevention. To be able to adopt results into specific recommendations, international expert organizations stress the need for well-designed studies.
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Affiliation(s)
- Christina E West
- a International Inflammation (in-FLAME) network of the World Universities Network.,b Department of Clinical Sciences, Pediatrics , Umeå University , Umeå , Sweden
| | - Maria C Jenmalm
- a International Inflammation (in-FLAME) network of the World Universities Network.,c Department of Clinical and Experimental Medicine , Linköping University , Linköping , Sweden
| | - Anita L Kozyrskyj
- a International Inflammation (in-FLAME) network of the World Universities Network.,d Department of Pediatrics, Faculty of Medicine & Dentistry , University of Alberta , Edmonton , Canada
| | - Susan L Prescott
- a International Inflammation (in-FLAME) network of the World Universities Network.,e School of Paediatrics and Child Health , University of Western Australia, Princess Margaret Hospital , Perth , WA , Australia
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Keely S, Walker MM, Marks E, Talley NJ. Immune dysregulation in the functional gastrointestinal disorders. Eur J Clin Invest 2015; 45:1350-9. [PMID: 26444549 DOI: 10.1111/eci.12548] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/03/2015] [Indexed: 12/14/2022]
Abstract
Gastrointestinal conditions may be broadly classified into two: organic and functional disease, with functional disorders accounting for the majority of patients with chronic gastrointestinal symptoms. Functional gastrointestinal disorders (FGIDs) present with no obvious pathology or well-accepted biochemical mechanism and, as such, treatment strategies are limited and focus on symptoms rather than cure. Irritable bowel syndrome and functional dyspepsia are the most widely recognised FGIDs, and there is a growing body of evidence to suggest an underlying inflammatory phenotype in subsets with these conditions. Here, we discuss the current knowledge of immune involvement in FGIDs and the commonalities between the different manifestations of FGIDs and propose a new hypothesis, potentially defining an underlying immunopathological basis of these conditions.
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Affiliation(s)
- Simon Keely
- School of Biomedical Sciences & Pharmacy, University of Newcastle & Vaccine and Asthma (VIVA) Program, Hunter Medical Research Institute, Callaghan, NSW, Australia
| | - Marjorie M Walker
- School of Medicine & Public Health, University of Newcastle, Callaghan, NSW, Australia
| | - Ellen Marks
- School of Biomedical Sciences & Pharmacy, University of Newcastle & Vaccine and Asthma (VIVA) Program, Hunter Medical Research Institute, Callaghan, NSW, Australia
| | - Nicholas J Talley
- School of Medicine & Public Health, University of Newcastle, Callaghan, NSW, Australia
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30
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Selwyn FP, Cheng SL, Klaassen CD, Cui JY. Regulation of Hepatic Drug-Metabolizing Enzymes in Germ-Free Mice by Conventionalization and Probiotics. ACTA ACUST UNITED AC 2015; 44:262-74. [PMID: 26586378 DOI: 10.1124/dmd.115.067504] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 11/18/2015] [Indexed: 01/26/2023]
Abstract
Little is known regarding the effect of intestinal microbiota modifiers, such as probiotics and conventionalization with exogenous bacteria, on host hepatic drug metabolism. Therefore, the goal of this study was to determine the effect of these modifiers on the expression of various drug-metabolizing enzymes of the host liver. VSL3 is a probiotic that contains eight live strains of bacteria. Five groups of mice were used: 1) conventional mice (CV), 2) conventional mice treated with VSL3 in drinking water, 3) germ-free (GF) mice, 4) GF mice treated with VSL3, and 5) GF mice exposed to the conventional environment for 2 months. All mice were 3 months old at tissue collection. GF conditions markedly downregulated the cytochrome P450 (P450) 3a gene cluster, but upregulated the Cyp4a cluster, whereas conventionalization normalized their expression to conventional levels [reverse-transcription quantitative polymerase chain reaction (qPCR) and western blot]. Changes in the Cyp3a and 4a gene expression correlated with alterations in the pregnane X receptor and peroxisome proliferator-activated receptor α-DNA binding, respectively (chromatin immunoprecipitation-qPCR). VSL3 increased each bacterial component in the large intestinal content of the CV mice, and increased these bacteria even more in GF mice, likely due to less competition for growth in the GF environment. VSL3 given to conventional mice increased the mRNAs of Cyp4v3, alcohol dehydrogenase 1, and carboxyesterase 2a, but decreased the mRNAs of multiple phase II glutathione-S-transferases. VSL3 given to germ-free mice decreased the mRNAs of UDP-glucuronosyltransferases 1a9 and 2a3. In conclusion, conventionalization and VSL3 alter the expression of many drug-metabolizing enzyme s in the liver, suggesting the importance of considering "bacteria-drug" interactions for various adverse drug reactions in patients.
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Affiliation(s)
- Felcy Pavithra Selwyn
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington
| | - Sunny Lihua Cheng
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington
| | - Curtis D Klaassen
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington
| | - Julia Yue Cui
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington
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Liang L, Ai L, Qian J, Fang JY, Xu J. Long noncoding RNA expression profiles in gut tissues constitute molecular signatures that reflect the types of microbes. Sci Rep 2015; 5:11763. [PMID: 26123364 PMCID: PMC4485256 DOI: 10.1038/srep11763] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 06/03/2015] [Indexed: 12/26/2022] Open
Abstract
The gut microbiota is commonly referred to as a hidden organ due to its pivotal effects on host physiology, metabolism, nutrition and immunity. The gut microbes may be shaped by environmental and host genetic factors, and previous studies have focused on the roles of protein-coding genes. Here we show a link between long non-coding RNA (lncRNA) expression and gut microbes. By repurposing exon microarrays and comparing the lncRNA expression profiles between germ-free, conventional and different gnotobiotic mice, we revealed subgroups of lncRNAs that were specifically enriched in each condition. A nearest shrunken centroid methodology was applied to obtain lncRNA-based signatures to identify mice in different conditions. The lncRNA-based prediction model successfully identified different gnotobiotic mice from conventional and germ-free mice, and also discriminated mice harboring transplanted microbes from fecal samples of mice or zebra fishes. To achieve optimal prediction accuracy, fewer lncRNAs were required in the prediction model than protein-coding genes. Taken together, our study demonstrated the effecacy of lncRNA expression profiles in discriminating the types of microbes in the gut. These results also provide a resource of gut microbe-associated lncRNAs for the development of lncRNA biomarkers and the identification of functional lncRNAs in host-microbes interactions.
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Affiliation(s)
- Lunxi Liang
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, China
- Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, 145 Middle Shandong Rd, Shanghai 200001, China
| | - Luoyan Ai
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, China
- Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, 145 Middle Shandong Rd, Shanghai 200001, China
| | - Jin Qian
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, China
- Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, 145 Middle Shandong Rd, Shanghai 200001, China
| | - Jing-Yuan Fang
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, China
- Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, 145 Middle Shandong Rd, Shanghai 200001, China
| | - Jie Xu
- State Key Laboratory for Oncogenes and Related Genes; Key Laboratory of Gastroenterology & Hepatology, Ministry of Health; Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, China
- Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, 145 Middle Shandong Rd, Shanghai 200001, China
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Rakoff-Nahoum S, Kong Y, Kleinstein SH, Subramanian S, Ahern PP, Gordon JI, Medzhitov R. Analysis of gene-environment interactions in postnatal development of the mammalian intestine. Proc Natl Acad Sci U S A 2015; 112:1929-36. [PMID: 25691701 PMCID: PMC4343130 DOI: 10.1073/pnas.1424886112] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Unlike mammalian embryogenesis, which takes place in the relatively predictable and stable environment of the uterus, postnatal development can be affected by a multitude of highly variable environmental factors, including diet, exposure to noxious substances, and microorganisms. Microbial colonization of the intestine is thought to play a particularly important role in postnatal development of the gastrointestinal, metabolic, and immune systems. Major changes in environmental exposure occur right after birth, upon weaning, and during pubertal maturation into adulthood. These transitions include dramatic changes in intestinal contents and require appropriate adaptations to meet changes in functional demands. Here, we attempt to both characterize and provide mechanistic insights into postnatal intestinal ontogeny. We investigated changes in global intestinal gene expression through postnatal developmental transitions. We report profound alterations in small and large intestinal transcriptional programs that accompany both weaning and puberty in WT mice. Using myeloid differentiation factor 88 (MyD88)/TIR-domain-containing adapter-inducing interferon-β (TRIF) double knockout littermates, we define the role of toll-like receptors (TLRs) and interleukin (IL)-1 receptor family member signaling in postnatal gene expression programs and select ontogeny-specific phenotypes, such as vascular and smooth muscle development and neonatal epithelial and mast cell homeostasis. Metaanalysis of the effect of the microbiota on intestinal gene expression allowed for mechanistic classification of developmentally regulated genes by TLR/IL-1R (TIR) signaling and/or indigenous microbes. We find that practically every aspect of intestinal physiology is affected by postnatal transitions. Developmental timing, microbial colonization, and TIR signaling seem to play distinct and specific roles in regulation of gene-expression programs throughout postnatal development.
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Affiliation(s)
- Seth Rakoff-Nahoum
- Howard Hughes Medical Institute, Department of Immunobiology, Division of Infectious Diseases, Department of Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115
| | - Yong Kong
- Department of Molecular Biophysics and Biochemistry, W. M. Keck Foundation Biotechnology Resource Laboratory, and
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics and Department of Pathology, Yale University School of Medicine, New Haven, CT 06510
| | - Sathish Subramanian
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108; and
| | - Philip P Ahern
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108; and
| | - Jeffrey I Gordon
- Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108; and
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Cho H, Kelsall BL. The role of type I interferons in intestinal infection, homeostasis, and inflammation. Immunol Rev 2015; 260:145-67. [PMID: 24942688 DOI: 10.1111/imr.12195] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Type I interferons are a widely expressed family of effector cytokines that promote innate antiviral and antibacterial immunity. Paradoxically, they can also suppress immune responses by driving production of anti-inflammatory cytokines, and dysregulation of these cytokines can contribute to host-mediated immunopathology and disease progression. Recent studies describe their anti-inflammatory role in intestinal inflammation and the locus containing IFNAR, a heterodimeric receptor for the type I interferons has been identified as a susceptibility region for human inflammatory bowel disease. This review focuses on the role of type I IFNs in the intestine in health and disease and their emerging role as immune modulators. Clear understanding of type I IFN-mediated immune responses may provide avenues for fine-tuning existing IFN treatment for infection and intestinal inflammation.
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Affiliation(s)
- Hyeseon Cho
- Mucosal Immunobiology Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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Appropriate development of the liver Treg compartment is modulated by the microbiota and requires TGF-β and MyD88. J Immunol Res 2014; 2014:279736. [PMID: 25177709 PMCID: PMC4142300 DOI: 10.1155/2014/279736] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Accepted: 06/30/2014] [Indexed: 01/22/2023] Open
Abstract
Neither the early postnatal development of the liver Treg compartment nor the factors that regulate its development has been characterized. We compared the early developmental patterns of Treg cell accumulation in murine liver, thymus, and spleen. A FoxP3EGFP reporter mouse was employed to identify Treg cells. Mononuclear cells were isolated from organs postnatally, stained for CD4, and examined by flow cytometry to enumerate FoxP3+CD4hi cells. To assess roles for TGF-β1, MyD88, and TLR2, gene-specific knockout pups were generated from heterozygous breeders. To test the role of commensal bacteria, pregnant dams were administered antibiotics during gestation and after parturition. The pattern of appearance of Treg cells differed in liver, spleen, and thymus. Notably, at 1-2 weeks, the frequency of CD4hi FoxP3+ T cells in liver exceeded that in spleen by 1.5- to 2-fold. The relative increase in liver Treg frequency was transient and was dependent upon TGF-β1 and MyD88, but not TLR2, and was abrogated by antibiotic treatment. A relative increase in liver Treg frequency occurs approximately 1-2 weeks after parturition that appears to be driven by colonization of the intestine with commensal bacteria and is mediated by a pathway that requires TGF-β1 and MyD88, but not TLR2.
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Abstract
The colon serves as the habitat for trillions of microbes, which it must maintain, regulate, and sequester. This is managed by what is termed the mucosal barrier. The mucosal barrier separates the gut flora from the host tissues; regulates the absorption of water, electrolytes, minerals, and vitamins; and facilitates host-flora interactions. Colonic homeostasis depends on a complex interaction between the microflora and the mucosal epithelium, immune system, vasculature, stroma, and nervous system. Disruptions in the colonic microenvironment such as changes in microbial composition, epithelial cell function/proliferation/differentiation, mucus production/makeup, immune function, diet, motility, or blood flow may have substantial local and systemic consequences. Understanding the complex activities of the colon in health and disease is important in drug development, as xenobiotics can impact all segments of the colon. Direct and indirect effects of pharmaceuticals on intestinal function can produce adverse findings in laboratory animals and humans and can negatively impact drug development. This review will discuss normal colon homeostasis with examples, where applicable, of xenobiotics that disrupt normal function.
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Affiliation(s)
- Rani S Sellers
- 1Albert Einstein College of Medicine, Bronx, New York, USA
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36
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Abstract
PURPOSE OF REVIEW It has been hypothesized that increased cleanliness, reduced family size, and subsequent decreased microbial exposure could explain the increases in global asthma prevalence. This review considers the recent evidence for and against the 'hygiene hypothesis'. RECENT FINDINGS Recent evidence does not provide unequivocal support for the hygiene hypothesis: the hygiene hypothesis specifically relates to atopic asthma, but some of the protective effects (e.g. farm exposures) appear to apply to both atopic and nonatopic asthma; asthma prevalence has begun to decline in some western countries, but there is little evidence that they have become less clean; Latin American countries with high infection rates have high asthma prevalence and the hygiene hypothesis relates to early-life exposures, but exposures throughout life may be important. SUMMARY There is a considerable body of evidence which warrants scepticism about the hygiene hypothesis. However, these anomalies contradict the 'narrow' version of it in which microbial pressure early in life protects against atopic asthma by suppressing T-helper 2 immune responses. It is possible that a more general version of the hygiene hypothesis is still valid, but the aetiologic mechanisms involved are currently unclear.
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Probiotics, prebiotics and immunomodulation of gut mucosal defences: homeostasis and immunopathology. Nutrients 2013; 5:1869-912. [PMID: 23760057 PMCID: PMC3725482 DOI: 10.3390/nu5061869] [Citation(s) in RCA: 290] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 05/08/2013] [Accepted: 05/09/2013] [Indexed: 12/13/2022] Open
Abstract
Probiotics are beneficial microbes that confer a realistic health benefit on the host, which in combination with prebiotics, (indigestible dietary fibre/carbohydrate), also confer a health benefit on the host via products resulting from anaerobic fermentation. There is a growing body of evidence documenting the immune-modulatory ability of probiotic bacteria, it is therefore reasonable to suggest that this is potentiated via a combination of prebiotics and probiotics as a symbiotic mix. The need for probiotic formulations has been appreciated for the health benefits in "topping up your good bacteria" or indeed in an attempt to normalise the dysbiotic microbiota associated with immunopathology. This review will focus on the immunomodulatory role of probiotics and prebiotics on the cells, molecules and immune responses in the gut mucosae, from epithelial barrier to priming of adaptive responses by antigen presenting cells: immune fate decision-tolerance or activation? Modulation of normal homeostatic mechanisms, coupled with findings from probiotic and prebiotic delivery in pathological studies, will highlight the role for these xenobiotics in dysbiosis associated with immunopathology in the context of inflammatory bowel disease, colorectal cancer and hypersensitivity.
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Hansen CH, Metzdorff SB, Hansen AK. Customizing laboratory mice by modifying gut microbiota and host immunity in an early "window of opportunity". Gut Microbes 2013; 4:241-5. [PMID: 23549457 PMCID: PMC3669170 DOI: 10.4161/gmic.23999] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We recently investigated how post-natal microbial gut colonization is important for the development of the immune system, especially in the systemic compartments. This addendum presents additional data which in accordance with our previous findings show that early life microbial colonization is critical for a fine-tuned immune homeostasis to develop also in the intestinal environment. A generalized reduction in the expression of immune signaling related genes in the small intestine may explain previously shown increased systemic adaptive immune reactivity, if the regulatory cross-talk between intra- and extra-intestinal immune cells is immature following a neonatal germ-free period. These findings are furthermore discussed in the context of recently published results on how lack of microbial exposure in the neonatal life modifies disease expression in rodents used as models mimicking human inflammatory diseases. In particular, with a focus on how these interesting findings could be used to optimize the use of rodent models.
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Abstract
The animal and bacterial kingdoms have coevolved and coadapted in response to environmental selective pressures over hundreds of millions of years. The meta'omics revolution in both sequencing and its analytic pipelines is fostering an explosion of interest in how the gut microbiome impacts physiology and propensity to disease. Gut microbiome studies are inherently interdisciplinary, drawing on approaches and technical skill sets from the biomedical sciences, ecology, and computational biology. Central to unraveling the complex biology of environment, genetics, and microbiome interaction in human health and disease is a deeper understanding of the symbiosis between animals and bacteria. Experimental model systems, including mice, fish, insects, and the Hawaiian bobtail squid, continue to provide critical insight into how host-microbiota homeostasis is constructed and maintained. Here we consider how model systems are influencing current understanding of host-microbiota interactions and explore recent human microbiome studies.
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Affiliation(s)
- Aleksandar D. Kostic
- Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- The Broad Institute of Harvard and Massachusetts Institute of Technology, Boston, Massachusetts 02141, USA
| | - Michael R. Howitt
- Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Wendy S. Garrett
- Harvard School of Public Health, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- The Broad Institute of Harvard and Massachusetts Institute of Technology, Boston, Massachusetts 02141, USA
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