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Peer A, Samuelson DR. The Role of the Microbiome in Allergy, Asthma, and Occupational Lung Disease. Curr Allergy Asthma Rep 2024:10.1007/s11882-024-01156-8. [PMID: 38904934 DOI: 10.1007/s11882-024-01156-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2024] [Indexed: 06/22/2024]
Abstract
PURPOSE OF REVIEW The human commensal microbiota is now widely accepted as a key regulator of human health and disease. The composition of the mucosal associated microbiota has been shown to play a critical role in the lung health. The role of the mucosal microbiota in the development and severity of allergy, asthma, and occupational lung disease is only beginning to take shape. However, advances in our understanding of these links have tremendous potential to led to new clinical interventions to reduce allergy, asthma, and occupational lung disease morbidity. RECENT FINDINGS We review recent work describing the relationship and role of the commensal microbiota in the development of allergy, asthma, and occupational lung disease. Our review primarily focuses on occupational exposures and the effects of the microbiome, both in composition and function. Data generated from these studies may lead to the development of interventions targeted at establishing and maintaining a healthy microbiota. We also highlight the role of environmental exposures and the effects on the commensal microbial community and their potential association with occupational lung disease. This review explores the current research describing the role of the human microbiome in the regulation of pulmonary health and disease, with a specific focus on the role of the mucosal microbiota in the development of allergy, asthma, and occupational lung disease.
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Affiliation(s)
- Ashley Peer
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep, University of Nebraska Medical Center, Omaha, NE, USA
| | - Derrick R Samuelson
- Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep, University of Nebraska Medical Center, Omaha, NE, USA.
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA.
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Yoon YM, Hrusch CL, Fei N, Barrón GM, Mills KAM, Hollinger MK, Velez TE, Leone VA, Chang EB, Sperling AI. Gut microbiota modulates bleomycin-induced acute lung injury response in mice. Respir Res 2022; 23:337. [PMID: 36496380 PMCID: PMC9741526 DOI: 10.1186/s12931-022-02264-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Airway instillation of bleomycin (BLM) in mice is a widely used, yet challenging, model for acute lung injury (ALI) with high variability in treatment scheme and animal outcomes among investigators. Whether the gut microbiota plays any role in the outcome of BLM-induced lung injury is currently unknown. METHODS Intratracheal instillation of BLM into C57BL/6 mice was performed. Fecal microbiomes were analyzed by 16s rRNA amplicon and metagenomic sequencing. Germ-free mice conventionalization and fecal microbiota transfer between SPF mice were performed to determine dominant commensal species that are associated with more severe BLM response. Further, lungs and gut draining lymph nodes of the mice were analyzed by flow cytometry to define immunophenotypes associated with the BLM-sensitive microbiome. RESULTS Mice from two SPF barrier facilities at the University of Chicago exhibited significantly different mortality and weight loss during BLM-induced lung injury. Conventionalizing germ-free mice with SPF microbiota from two different housing facilities recapitulated the respective donors' response to BLM. Fecal microbiota transfer from the facility where the mice had worse mortality into the mice in the facility with more survival rendered recipient mice more susceptible to BLM-induced weight loss in a dominant negative manner. BLM-sensitive phenotype was associated with the presence of Helicobacter and Desulfovibrio in the gut, decreased Th17-neutrophil axis during steady state, and augmented lung neutrophil accumulation during the acute phase of the injury response. CONCLUSION The composition of gut microbiota has significant impact on BLM-induced wasting and death suggesting a role of the lung-gut axis in lung injury.
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Affiliation(s)
- Young Me Yoon
- Committee on Immunology, University of Chicago, Chicago, IL, USA
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Cara L Hrusch
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Na Fei
- Section of Gastroenterology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Gabriel M Barrón
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Kathleen A M Mills
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Maile K Hollinger
- Committee on Immunology, University of Chicago, Chicago, IL, USA
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Tania E Velez
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Box 800546, Charlottesville, VA, 22908-0546, USA
| | - Vanessa A Leone
- Section of Gastroenterology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Eugene B Chang
- Section of Gastroenterology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Anne I Sperling
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Box 800546, Charlottesville, VA, 22908-0546, USA.
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Costantino A, Aversano GM, Lasagni G, Smania V, Doneda L, Vecchi M, Roncoroni L, Pastorello EA, Elli L. Diagnostic management of patients reporting symptoms after wheat ingestion. Front Nutr 2022; 9:1007007. [PMID: 36276818 PMCID: PMC9582535 DOI: 10.3389/fnut.2022.1007007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/12/2022] [Indexed: 12/11/2022] Open
Abstract
Many patients report symptoms after wheat ingestion experiencing a wide spectrum of clinical manifestations. Three possible diagnoses have been recognized: celiac disease (CD), wheat allergy (WA), and non-celiac (gluten) wheat sensitivity (NCGS/NCWS). CD is a chronic immune-mediated disease of the small bowel caused by exposure to dietary gluten in genetically predisposed individuals, with a prevalence of approximately 1%. It is characterized by mucosal inflammation and atrophy following exposure to gluten and improvement after gluten withdrawal. Food allergies are immunological responses to a food antigen. WA is the expression of an immunologically mediated process that can be immunoglobulin E (IgE) or non-IgE mediated; its many symptoms include urticaria/angioedema, asthma, rhinitis, and anaphylaxis. NCGS/NCWS is characterized by gastrointestinal and/or extra-intestinal symptoms after ingestion of gluten-containing food in subjects not affected by CD or WA. The aim of this review is to help physicians and nutritionists diagnose the cause of symptoms reported after wheat ingestion, thus avoiding patient frustration, inappropriate testing, and incorrect or missed diagnoses. An algorithm for the diagnostic approach in these patients is provided, to help to diagnose CD, WA, NCGS/NCWS or to identify possible functional disorders as the wheat-sensitive irritable bowel syndrome. A personalized approach, regular follow-up, and the help of a skilled healthcare professional are mandatory for patients with symptoms following wheat ingestion is provided. A gluten-free-diet is often recommended for patients with self-reported gluten/wheat-dependent symptoms; for patients with symptoms similar to those of functional diseases while there is evidence that a low-FODMAP diet could be the first option.
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Affiliation(s)
- Andrea Costantino
- Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Gloria Maria Aversano
- Department of Internal Medicine, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Giovanni Lasagni
- Department of Allergology and Immunology, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Veronica Smania
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Luisa Doneda
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - Maurizio Vecchi
- Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Leda Roncoroni
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | | | - Luca Elli
- Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy,*Correspondence: Luca Elli,
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Treatment with Distinct Antibiotic Classes Causes Different Pulmonary Outcomes on Allergic Airway Inflammation Associated with Modulation of Symbiotic Microbiota. J Immunol Res 2022; 2022:1466011. [PMID: 35785028 PMCID: PMC9242750 DOI: 10.1155/2022/1466011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/29/2022] [Accepted: 05/16/2022] [Indexed: 11/18/2022] Open
Abstract
Background Asthma is a chronic pulmonary disease that affects about 300 million people worldwide. Previous studies have associated antimicrobial use with allergies, but the real impact of antibiotics on asthma is still elusive. We investigated the potential impact of amoxicillin (Amox), trimethoprim/sulfamethoxazole (TMP/SMX), and metronidazole (Metro) in a murine model of OVA-induced allergic airway inflammation. Methods BALB/c mice received three cycles of 7 days of antibiotics in drinking water followed by 7 days washout and were sensitized i.p. with OVA/Alum at days 0 and 14. After the end of the last antibiotic washout, the mice were challenged with aerosolized OVA. Pulmonary parameters were evaluated, and serum, BAL, and feces were collected for analysis. Results Amox- and TMP/SMX-treated animals displayed more severe allergic airway inflammation parameters with increased airway hyperresponsiveness, reduced lung alveolar volume, and increased levels in BAL of IL-4 and IL-6. In contrast, Metro-treated mice showed preserved FEV-50, decreased lung inflammation, and higher levels of butyrate and propionate in their feces. Metro treatment was associated with increased OVA-specific IgA in serum. BAL microbiota was abundant in allergic groups but not in nonallergic controls with the Amox-treated group displaying the increased frequency of Proteobacteria, while Metro and TMP/SMX showed increased levels of Firmicutes. In the gut, we observed the enrichment of Akkermansia muciniphila associated with reduced airway inflammation phenotype in the Metro group, even after the recovery period. Conclusion Our data suggest that different antibiotic treatments may impact the course of experimental allergic airway inflammation in diverse ways by several mechanisms, including modulation of short-chain fat acids production by intestinal microbiota.
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Ke S, Weiss ST, Liu YY. Rejuvenating the human gut microbiome. Trends Mol Med 2022; 28:619-630. [PMID: 35781423 PMCID: PMC9339459 DOI: 10.1016/j.molmed.2022.05.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/23/2022] [Accepted: 05/03/2022] [Indexed: 12/13/2022]
Abstract
Industrial advances have caused significant loss of diversity in our gut microbiome, potentially increasing our susceptibility to many diseases. Recently, rewilding the human gut microbiome - that is, bringing it back to an ancestral or preindustrial state (e.g., by transplanting stool material from donors in nonindustrial societies) - has been hotly debated from medical, ethical, and evolutionary perspectives. Here we propose an alternative solution: rejuvenating the human gut microbiome by stool banking and autologous fecal microbiota transplantation, that is, collecting the hosts' stool samples at a younger age when they are at optimal health, and cryopreserving the samples in a stool bank for the hosts' own future use. In this article we discuss the motivation, applications, feasibility, and challenges of this solution.
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Lazebnik LB, Sarsenbaeva AS, Avalueva EB, Oreshko LS, Sitkin SI, Golovanova EV, Turkina SV, Khlynova OV, Sagalova OI, Mironchev OV. Clinical guidelines “Chronic diarrhea in adults”. EXPERIMENTAL AND CLINICAL GASTROENTEROLOGY 2021:7-67. [DOI: 10.31146/1682-8658-ecg-188-4-7-67] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Affiliation(s)
- L. B. Lazebnik
- Federal State Budgetary Educational Institution of Higher Education “A. I. Yevdokimov Moscow State University of Medicine and Dentistry” of the Ministry of Healthcare of the Russion Federation
| | | | - E. B. Avalueva
- North-Western state medical University named after I. I. Mechnikov, Ministry of health of the Russian Federation
| | - L. S. Oreshko
- North-Western state medical University named after I. I. Mechnikov, Ministry of health of the Russian Federation
| | - S. I. Sitkin
- North- Western state medical University named after I. I. Mechnikov, Ministry of health of the Russian Federation;
Federal State Budgetary Institution “Almazov National Medical Research Centre” of the Ministry of Health of the Russian Federation
| | - E. V. Golovanova
- Federal State Budgetary Educational Institution of Higher Education “A. I. Yevdokimov Moscow State University of Medicine and Dentistry” of the Ministry of Healthcare of the Russion Federation
| | - S. V. Turkina
- State-funded Educational Establishment of Higher Professional Education “Volgograd State Medical University of the Ministry of Public Health of the Russian Federation”
| | - O. V. Khlynova
- Perm State Medical University named after academician E. A. Vagner Ministry of Health care of Russia
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Niemeier-Walsh C, Ryan PH, Meller J, Ollberding NJ, Adhikari A, Reponen T. Exposure to traffic-related air pollution and bacterial diversity in the lower respiratory tract of children. PLoS One 2021; 16:e0244341. [PMID: 34166366 PMCID: PMC8224880 DOI: 10.1371/journal.pone.0244341] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 05/26/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Exposure to particulate matter has been shown to increase the adhesion of bacteria to human airway epithelial cells. However, the impact of traffic-related air pollution (TRAP) on the respiratory microbiome is unknown. METHODS Forty children were recruited through the Cincinnati Childhood Allergy and Air Pollution Study, a longitudinal cohort followed from birth through early adolescence. Saliva and induced sputum were collected at age 14 years. Exposure to TRAP was characterized from birth through the time of sample collection using a previously validated land-use regression model. Sequencing of the bacterial 16S and ITS fungal rRNA genes was performed on sputum and saliva samples. The relative abundance of bacterial taxa and diversity indices were compared in children with exposure to high and low TRAP. We also used multiple linear regression to assess the effect of TRAP exposure, gender, asthma status, and socioeconomic status on the alpha diversity of bacteria in sputum. RESULTS We observed higher bacterial alpha diversity indices in sputum than in saliva. The diversity indices for bacteria were greater in the high TRAP exposure group than the low exposure group. These differences remained after adjusting for asthma status, gender, and mother's education. No differences were observed in the fungal microbiome between TRAP exposure groups. CONCLUSION Our findings indicate that exposure to TRAP in early childhood and adolescence may be associated with greater bacterial diversity in the lower respiratory tract. Asthma status does not appear to confound the observed differences in diversity. These results demonstrate that there may be a TRAP-exposure related change in the lower respiratory microbiota that is independent of asthma status.
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Affiliation(s)
- Christine Niemeier-Walsh
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, United States of America
| | - Patrick H. Ryan
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, United States of America
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, United States of America
- Division of Biostatistics and Epidemiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States of America
| | - Jaroslaw Meller
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, United States of America
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, United States of America
| | - Nicholas J. Ollberding
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, United States of America
- Division of Biostatistics and Epidemiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, United States of America
| | - Atin Adhikari
- Jiann-Ping Hsu College of Public Health, Georgia Southern University, Statesboro, Georgia, United States of America
| | - Tiina Reponen
- Department of Environmental Health, University of Cincinnati, Cincinnati, OH, United States of America
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Investigation of Commensal Escherichia coli Populations of Cormorant Hatchlings in the Absence of Anthropogenic Impacts in Remote Areas of West Mongolia. Microorganisms 2021; 9:microorganisms9020372. [PMID: 33673351 PMCID: PMC7917637 DOI: 10.3390/microorganisms9020372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 11/17/2022] Open
Abstract
To increase our understanding of bacterial intestinal colonization in animal populations lacking substantial anthropogenic influence we studied the diversity of E. coli in cormorants from the pristine West-Mongolian steppe. E. coli were isolated from individual birds of two cormorant colonies located on small islands in lakes at least 100 km away from human settlements. Diversity of the isolates was studied using pulsed-field gel electrophoresis (PFGE). 137 isolates of cormorant colony-1 and 75 isolates of cormorant colony-2 resulted in 60 and 33 PFGE types, respectively. Representative strains of each PFGE type were analyzed via PCR in terms of phylogroups and extraintestinal virulence-associated genes (exVAGs). Bacterial adhesion to the chicken intestinal cell line CHIC-8E11 and antimicrobial resistance was also determined. Most isolates belonged to phylogroup B1 (68.3%) followed by B2 and E with B2 harboring the highest total number of exVAGs per isolate. Unexpectedly, a PFGE type with relatively few exVAGs displayed the highest isolation frequency, also showing a high adhesion rate. Comparative analysis of exVAGs to other E. coli populations of wildlife origin revealed that the secreted autotransporter toxin encoding sat gene was only present in cormorants. Overall, E. coli in cormorants maintained a high diversity under minimal anthropogenic influences, which likely enables intestinal colonization.
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Pires ES, Hardoim CCP, Miranda KR, Secco DA, Lobo LA, de Carvalho DP, Han J, Borchers CH, Ferreira RBR, Salles JF, Domingues RMCP, Antunes LCM. The Gut Microbiome and Metabolome of Two Riparian Communities in the Amazon. Front Microbiol 2019; 10:2003. [PMID: 31555238 PMCID: PMC6737013 DOI: 10.3389/fmicb.2019.02003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/15/2019] [Indexed: 01/15/2023] Open
Abstract
During the last decades it has become increasingly clear that the microbes that live on and in humans are critical for health. The communities they form, termed microbiomes, are involved in fundamental processes such as the maturation and constant regulation of the immune system. Additionally, they constitute a strong defense barrier to invading pathogens, and are also intricately linked to nutrition. The parameters that affect the establishment and maintenance of these microbial communities are diverse, and include the genetic background, mode of birth, nutrition, hygiene, and host lifestyle in general. Here, we describe the characterization of the gut microbiome of individuals living in the Amazon, and the comparison of these microbial communities to those found in individuals from an urban, industrialized setting. Our results showed striking differences in microbial communities from these two types of populations. Additionally, we used high-throughput metabolomics to study the chemical ecology of the gut environment and found significant metabolic changes between the two populations. Although we cannot point out a single cause for the microbial and metabolic changes observed between Amazonian and urban individuals, they are likely to include dietary differences as well as diverse patterns of environmental exposure. To our knowledge, this is the first description of gut microbial and metabolic profiles in Amazonian populations, and it provides a starting point for thorough characterizations of the impact of individual environmental conditions on the human microbiome and metabolome.
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Affiliation(s)
- Eder Soares Pires
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto Tecnológico Vale - Desenvolvimento Sustentável, Belém, Brazil
| | | | - Karla Rodrigues Miranda
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Danielle Angst Secco
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Leandro Araújo Lobo
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Denise Pires de Carvalho
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, aRio de Janeiro, Brazil
| | - Jun Han
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, Canada
| | - Christoph H Borchers
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.,Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Rosana B R Ferreira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Joana Falcão Salles
- Microbial Ecology Cluster, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | | | - Luis Caetano Martha Antunes
- Escola Nacional de Saúde Pública Sergio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas, Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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Summers KL, Frey JF, Ramsay TG, Arfken AM. The piglet mycobiome during the weaning transition: a pilot study1. J Anim Sci 2019; 97:2889-2900. [PMID: 31136650 DOI: 10.1093/jas/skz182] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/24/2019] [Indexed: 12/12/2022] Open
Abstract
The importance of the microbiota in the gastrointestinal tract of animals is recognized as a critical player in host health. Recently, the significance of the mycobiome has been recognized, but culture-independent studies are limited, especially in swine. Weaning is a time of stress, dietary changes, and a predisposition to infections, making it a time point of interest to industry. In this pilot study, we sought to assess and characterize the mycobiome in the feces of swine from birth through the critical weaning transition to investigate the mycobiome population and its temporal dynamics in piglet feces. Cultured fecal samples demonstrate a significant increase in fungal burden following weaning that does not differ from adult levels, suggesting stable colonization. Culturable fungi were not found in any environmental samples tested, including water, food, sow milk or colostrum. To determine the fungal diversity present and to address the problem of unculturable fungi, we performed a pilot study utilizing ITS and 16S rRNA focused primers for high-throughput sequencing of fungal and bacterial species, respectively. Bacterial populations increase in diversity over the experimental timeline (days 1 to 35 postbirth), but the fungal populations do not demonstrate the same temporal trend. Following weaning, there is a dynamic shift in the feces to a Saccharomycetaceae-dominated population. The shift in fungal population was because of the dominance of Kazachstania slooffiae, a poorly characterized colonizer of animal gastrointestinal tracts. This study provides insights into the early colonization and subsequent establishment of fungi during the weaning transition in piglets. Future studies will investigate the effect of the mycobiome on piglet growth and health during the weaning transition.
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Affiliation(s)
- Katie L Summers
- Animal Biosciences and Biotechnology Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD
| | - Juli Foster Frey
- Animal Biosciences and Biotechnology Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD
| | - Timothy G Ramsay
- Animal Biosciences and Biotechnology Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD
| | - Ann M Arfken
- Animal Biosciences and Biotechnology Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD
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Ali Mubaraki M, Ahmad M, Hafiz TA, Marie MA. The therapeutic prospect of crosstalk between prokaryotic and eukaryotic organisms in the human gut. FEMS Microbiol Ecol 2019; 94:4966977. [PMID: 29796663 DOI: 10.1093/femsec/fiy065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/09/2018] [Indexed: 12/19/2022] Open
Abstract
The peaceful phenomenon of the co-evolution between the prokaryotes (microbiota) and the eukaryotes (parasites including protozoa and helminths) in the animal gut has drawn the researchers' attention. Importantly, exploring the potential of helminths for therapeutic uses was one of the reasons behind understanding the physiological and immunological crosstalk existing between them. Here we discuss the interactive immunological associations of helminths and microbial responses individually and in combination with their hosts. Considering that there is probably crosstalk between eukaryotic organisms like helminths and protozoa with their host's gut microbiota, in this review we searched the literature identifying the privileged and favourable relationship generated between them in the host. Understanding the possibilities of the role of helminths along with gut microbiota as a black box would certainly help decode the therapeutic intrusion with helminths in experimental clinical trials, and a successful trial could be used to consider possible future and safe treatments for various immune-inflammatory diseases in humans.
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Affiliation(s)
- Murad Ali Mubaraki
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, Saudi Arabia
| | - Mohammad Ahmad
- Medical Surgical Nursing Department, College of Nursing, King Saud University, Saudi Arabia
| | - Taghreed A Hafiz
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, Saudi Arabia
| | - Mohammed A Marie
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, Saudi Arabia
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12
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Association between extrauterine growth restriction and changes of intestinal flora in Chinese preterm infants. J Dev Orig Health Dis 2019; 10:513-521. [PMID: 30834847 DOI: 10.1017/s2040174419000084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The aim of the study was to investigate any association between extrauterine growth restriction (EUGR) and intestinal flora of <30-week-old preterm infants. A total of 59 preterm infants were assigned to EUGR (n=23) and non-EUGR (n=36) groups. Intestinal bacteria were compared by using high-throughput sequencing of bacterial rRNA. The total abundance of bacteria in 344 genera (7568 v. 13,760; P<0.0001) and 456 species (10,032 v. 18,240; P<0.0001) was significantly decreased in the EUGR group compared with the non-EUGR group. After application of a multivariate logistic model and adjusting for potential confounding factors, as well as false-discovery rate corrections, we found four bacterial genera with higher and one bacterial genus with lower abundance in the EUGR group compared with the control group. In addition, the EUGR group showed significantly increased abundances of six species (Streptococcus parasanguinis, Bacterium RB5FF6, two Klebsiella species and Microbacterium), but decreased frequencies of three species (one Acinetobacter species, Endosymbiont_of_Sphenophorus_lev and one Enterobacter_species) compared with the non-EUGR group. Taken together, there were significant changes in the intestinal microflora of preterm infants with EUGR compared to preterm infants without EUGR.
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Mendez R, Banerjee S, Bhattacharya SK, Banerjee S. Lung inflammation and disease: A perspective on microbial homeostasis and metabolism. IUBMB Life 2019; 71:152-165. [PMID: 30466159 PMCID: PMC6352907 DOI: 10.1002/iub.1969] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/05/2018] [Accepted: 10/17/2018] [Indexed: 12/20/2022]
Abstract
It is now well appreciated that the human microbiome plays a significant role in a number of processes in the body, significantly affecting its metabolic, inflammatory, and immune homeostasis. Recent research has revealed that almost every mucosal surface in the human body is associated with a resident commensal microbiome of its own. While the gut microbiome and its role in regulation of host metabolism along with its alteration in a disease state has been well studied, there is a lacuna in understanding the resident microbiota of other mucosal surfaces. Among these, the scientific information on the role of lung microbiota in pulmonary diseases is currently severely limited. Historically, lungs have been considered to be sterile and lung diseases have only been studied in the context of bacterial pathogenesis. Recently however, studies have revealed a resilient microbiome in the upper and lower respiratory tracts and there is increased evidence on its central role in respiratory diseases. Knowledge of lung microbiome and its metabolic fallout (local and systemic) is still in its nascent stages and attracting immense interest in recent times. In this review, we will provide a perspective on lung-associated metabolic disorders defined for lung diseases (e.g., chronic obstructive pulmonary disease, asthma, and respiratory depression due to infection) and correlate it with lung microbial perturbation. Such perturbations may be due to altered biochemical or metabolic stress as well. Finally, we will draw evidence from microbiome and classical microbiology literature to demonstrate how specific lung morbidities associate with specific metabolic characteristics of the disease, and with the role of microbiome in this context. © 2018 IUBMB Life, 71(1):152-165, 2019.
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Affiliation(s)
- Roberto Mendez
- Surgery, Miller School of Medicine, University of Miami, Florida, USA
| | - Sulagna Banerjee
- Surgery, Miller School of Medicine, University of Miami, Florida, USA
- Miami Integrative Metabolomics Research Center, University of Miami, Florida, USA
| | - Sanjoy K. Bhattacharya
- Bascom Palmer Eye Institute, University of Miami, Florida, USA
- Miami Integrative Metabolomics Research Center, University of Miami, Florida, USA
| | - Santanu Banerjee
- Surgery, Miller School of Medicine, University of Miami, Florida, USA
- Miami Integrative Metabolomics Research Center, University of Miami, Florida, USA
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14
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Response to Fungal Dysbiosis by Gut-Resident CX3CR1 + Mononuclear Phagocytes Aggravates Allergic Airway Disease. Cell Host Microbe 2018; 24:847-856.e4. [PMID: 30503509 DOI: 10.1016/j.chom.2018.11.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 09/19/2018] [Accepted: 10/24/2018] [Indexed: 12/12/2022]
Abstract
Sensing of the gut microbiota, including fungi, regulates mucosal immunity. Whether fungal sensing in the gut can influence immunity at other body sites is unknown. Here we show that fluconazole-induced gut fungal dysbiosis has persistent effects on allergic airway disease in a house dust mite challenge model. Mice with a defined community of bacteria, but lacking intestinal fungi were not susceptible to fluconazole-induced dysbiosis, while colonization with a fungal mixture recapitulated the detrimental effects. Gut-resident mononuclear phagocytes (MNPs) expressing the fractalkine receptor CX3CR1 were essential for the effect of gut fungal dysbiosis on peripheral immunity. Depletion of CX3CR1+ MNPs or selective inhibition of Syk signaling downstream of fungal sensing in these cells ameliorated lung allergy. These results indicate that disruption of intestinal fungal communities can have persistent effects on peripheral immunity and aggravate disease severity through fungal sensing by gut-resident CX3CR1+ MNPs.
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15
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Exposure to heat-stress environment affects the physiology, circulation levels of cytokines, and microbiome in dairy cows. Sci Rep 2018; 8:14606. [PMID: 30279428 PMCID: PMC6168502 DOI: 10.1038/s41598-018-32886-1] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/13/2018] [Indexed: 12/13/2022] Open
Abstract
The microbiome has emerged as a new player on behavior, physiology and stress because of its significant effects on the brain-gut axis. The aim of this study was to increase our understanding of brain-gut function in dairy cows. We investigated the effects of a heat-stress (HS) environment and individual differences of heat sensitivity (IH) on bovine physiological characteristics and microbial composition. Results indicate that both HS and IH increased rectal temperature (RT) (P < 0.05). An HS environment increased plasma, as well as milk cortisol and cytokines in plasma; however, it decreased plasma, and milk oxytocin, triiodothyronine, and thyroxine (P < 0.05) levels. Exposure to an HS environment reduced the diversity of the fecal microbial population, and resulted in a higher expression of diseases, the environmental adaptation pathway, and the immune related pathway, whereas it lowered the expression of metabolic pathways (P < 0.05). High heat sensitive cows have upregulated metabolisms, environmental adaptation and cellular process pathways, and a downregulated neurodegenerative disease pathway (P < 0.05). Thus, we conclude that exposure to an HS environment modulates physiological characteristics, which may interplay with microbial activity, and in turn, alter the circulation levels of cytokines, implicating the role of the brain-gut axis in dairy cows. The HS environment affected physiological characteristics, cytokine levels, and microbial composition, but IH influenced RT and fecal microbial functions.
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16
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Lai GC, Tan TG, Pavelka N. The mammalian mycobiome: A complex system in a dynamic relationship with the host. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2018; 11:e1438. [PMID: 30255552 PMCID: PMC6586165 DOI: 10.1002/wsbm.1438] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 08/26/2018] [Accepted: 08/28/2018] [Indexed: 12/21/2022]
Abstract
Mammalian barrier surfaces are densely populated by symbiont fungi in much the same way the former are colonized by symbiont bacteria. The fungal microbiota, otherwise known as the mycobiota, is increasingly recognized as a critical player in the maintenance of health and homeostasis of the host. Here we discuss the impact of the mycobiota on host physiology and disease, the factors influencing mycobiota composition, and the current technologies used for identifying symbiont fungal species. Understanding the tripartite interactions among the host, mycobiota, and other members of the microbiota, will help to guide the development of novel prevention and therapeutic strategies for a variety of human diseases. This article is categorized under:
Physiology > Mammalian Physiology in Health and Disease Laboratory Methods and Technologies > Genetic/Genomic Methods Models of Systems Properties and Processes > Organismal Models
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17
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Chiabai A, Quiroga S, Martinez-Juarez P, Higgins S, Taylor T. The nexus between climate change, ecosystem services and human health: Towards a conceptual framework. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 635:1191-1204. [PMID: 29710574 DOI: 10.1016/j.scitotenv.2018.03.323] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 03/26/2018] [Accepted: 03/26/2018] [Indexed: 05/11/2023]
Abstract
This paper addresses the impact that changes in natural ecosystems can have on health and wellbeing focusing on the potential co-benefits that green spaces could provide when introduced as climate change adaptation measures. Ignoring such benefits could lead to sub-optimal planning and decision-making. A conceptual framework, building on the ecosystem-enriched Driver, Pressure, State, Exposure, Effect, Action model (eDPSEEA), is presented to aid in clarifying the relational structure between green spaces and human health, taking climate change as the key driver. The study has the double intention of (i) summarising the literature with a special emphasis on the ecosystem and health perspectives, as well as the main theories behind these impacts, and (ii) modelling these findings into a framework that allows for multidisciplinary approaches to the underlying relations between human health and green spaces. The paper shows that while the literature based on the ecosystem perspective presents a well-documented association between climate, health and green spaces, the literature using a health-based perspective presents mixed evidence in some cases. The role of contextual factors and the exposure mechanism are rarely addressed. The proposed framework could serve as a multidisciplinary knowledge platform for multi-perspecitve analysis and discussion among experts and stakeholders, as well as to support the operationalization of quantitative assessment and modelling exercises.
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Affiliation(s)
- Aline Chiabai
- BC3-Basque Centre for Climate Change, Bilbao, Spain.
| | - Sonia Quiroga
- Department of Economics, Universidad de Alcalá, Spain.
| | | | - Sahran Higgins
- European Centre for the Environment and Human Health, University of Exeter Medical School, United Kingdom
| | - Tim Taylor
- European Centre for the Environment and Human Health, University of Exeter Medical School, United Kingdom.
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18
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Elbehery AHA, Feichtmayer J, Singh D, Griebler C, Deng L. The Human Virome Protein Cluster Database (HVPC): A Human Viral Metagenomic Database for Diversity and Function Annotation. Front Microbiol 2018; 9:1110. [PMID: 29896176 PMCID: PMC5987705 DOI: 10.3389/fmicb.2018.01110] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 05/09/2018] [Indexed: 12/19/2022] Open
Abstract
Human virome, including those of bacteria (bacteriophages) have received an increasing attention recently, owing to the rapid developments in human microbiome research and the awareness of the far-reaching influence of microbiomes on health and disease. Nevertheless, human viromes are still underrepresented in literature making viruses a virtually untapped resource of diversity, functional and physiological information. Here we present the human virome protein cluster database as an effort to improve functional annotation and characterization of human viromes. The database was built out of hundreds of virome datasets from six different body sites. We also show the utility of this database through its use for the characterization of three bronchoalveolar lavage (BAL) viromes from one healthy control in addition to one moderate and one severe chronic obstructive pulmonary disease (COPD) patients. The use of the database allowed for a better functional annotation, which were otherwise poorly characterized when limited to annotation using sequences from full-length viral genomes. In addition, our BAL samples gave a first insight into viral communities of COPD patients and confirm a state of dysbiosis for viruses that increases with disease progression. Moreover, they shed light on the potential role of phages in the horizontal gene transfer of bacterial virulence factors, a phenomenon that highlights a possible contribution of phages to etiopathology.
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Affiliation(s)
- Ali H A Elbehery
- Institute of Virology, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Oberschleißheim, Germany
| | - Judith Feichtmayer
- Institute of Groundwater Ecology, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Oberschleißheim, Germany
| | - Dave Singh
- EvA Consortium, Manchester, United Kingdom.,Medicines Evaluation Unit, University Hospital of South Manchester Foundation Trust, University of Manchester, Manchester, United Kingdom
| | - Christian Griebler
- Institute of Groundwater Ecology, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Oberschleißheim, Germany
| | - Li Deng
- Institute of Virology, Helmholtz Zentrum München - Deutsches Forschungszentrum für Gesundheit und Umwelt, Oberschleißheim, Germany
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19
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Grieneisen LE, Livermore J, Alberts S, Tung J, Archie EA. Group Living and Male Dispersal Predict the Core Gut Microbiome in Wild Baboons. Integr Comp Biol 2018; 57:770-785. [PMID: 29048537 DOI: 10.1093/icb/icx046] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The mammalian gut microbiome plays a profound role in the physiology, metabolism, and overall health of its host. However, biologists have only a nascent understanding of the forces that drive inter-individual heterogeneity in gut microbial composition, especially the role of host social environment. Here we used 178 samples from 78 wild yellow baboons (Papio cynocephalus) living in two social groups to test how host social context, including group living, social interactions within groups, and transfer between social groups (e.g., dispersal) predict inter-individual variation in gut microbial alpha and beta diversity. We also tested whether social effects differed for prevalent "core" gut microbial taxa, which are thought to provide primary functions to hosts, versus rare "non-core" microbes, which may represent relatively transient environmental acquisitions. Confirming prior studies, we found that each social group harbored a distinct gut microbial community. These differences included both non-core and core gut microbial taxa, suggesting that these effects are not solely driven by recent gut microbial exposures. Within social groups, close grooming partners had more similar core microbiomes, but not non-core microbiomes, than individuals who rarely groomed each other, even controlling for kinship and diet similarity between grooming partners. Finally, in support of the idea that the gut microbiome can be altered by current social context, we found that the longer an immigrant male had lived in a given social group, the more closely his gut microbiome resembled the gut microbiomes of the group's long-term residents. Together, these results reveal the importance of a host's social context in shaping the gut microbiome and shed new light onto the microbiome-related consequences of male dispersal.
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Affiliation(s)
- Laura E Grieneisen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Josh Livermore
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Susan Alberts
- Department of Biology, Duke University, Durham, NC 27708, USA.,Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC 27708, USA.,Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.,Duke Population Research Institute, Duke University, Durham, NC 27708, USA
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
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20
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McKenzie C, Tan J, Macia L, Mackay CR. The nutrition-gut microbiome-physiology axis and allergic diseases. Immunol Rev 2018; 278:277-295. [PMID: 28658542 DOI: 10.1111/imr.12556] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Indexed: 02/06/2023]
Abstract
Dietary and bacterial metabolites influence immune responses. This raises the question whether the increased incidence of allergies, asthma, some autoimmune diseases, cardiovascular disease, and others might relate to intake of unhealthy foods, and the decreased intake of dietary fiber. In recent years, new knowledge on the molecular mechanisms underpinning a 'diet-gut microbiota-physiology axis' has emerged to substantiate this idea. Fiber is fermented to short chain fatty acids (SCFAs), particularly acetate, butyrate, and propionate. These metabolites bind 'metabolite-sensing' G-protein-coupled receptors such as GPR43, GPR41, and GPR109A. These receptors play fundamental roles in the promotion of gut homeostasis and the regulation of inflammatory responses. For instance, these receptors and their metabolites influence Treg biology, epithelial integrity, gut homeostasis, DC biology, and IgA antibody responses. The SCFAs also influence gene transcription in many cells and tissues, through their inhibition of histone deacetylase expression or function. Contained in this mix is the gut microbiome, as commensal bacteria in the gut have the necessary enzymes to digest dietary fiber to SCFAs, and dysbiosis in the gut may affect the production of SCFAs and their distribution to tissues throughout the body. SCFAs can epigenetically modify DNA, and so may be one mechanism to account for diseases with a 'developmental origin', whereby in utero or post-natal exposure to environmental factors (such as nutrition of the mother) may account for disease later in life. If the nutrition-gut microbiome-physiology axis does underpin at least some of the Western lifestyle influence on asthma and allergies, then there is tremendous scope to correct this with healthy foodstuffs, probiotics, and prebiotics.
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Affiliation(s)
- Craig McKenzie
- Infection and Immunity Program, Department of Biochemistry, Biomedicine Discovery Institute, Monash University, Clayton, Vic., Australia
| | - Jian Tan
- Infection and Immunity Program, Department of Biochemistry, Biomedicine Discovery Institute, Monash University, Clayton, Vic., Australia
| | - Laurence Macia
- Nutritional Immunometabolism Node Laboratory, Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia.,School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | - Charles R Mackay
- Infection and Immunity Program, Department of Biochemistry, Biomedicine Discovery Institute, Monash University, Clayton, Vic., Australia
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21
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Moossavi S, Miliku K, Sepehri S, Khafipour E, Azad MB. The Prebiotic and Probiotic Properties of Human Milk: Implications for Infant Immune Development and Pediatric Asthma. Front Pediatr 2018; 6:197. [PMID: 30140664 PMCID: PMC6095009 DOI: 10.3389/fped.2018.00197] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 06/19/2018] [Indexed: 12/22/2022] Open
Abstract
The incidence of pediatric asthma has increased substantially in recent decades, reaching a worldwide prevalence of 14%. This rapid increase may be attributed to the loss of "Old Friend" microbes from the human microbiota resulting in a less diverse and "dysbiotic" gut microbiota, which fails to optimally stimulate immune development during infancy. This hypothesis is supported by observations that the gut microbiota is different in infants who develop asthma later in life compared to those who remain healthy. Thus, early life exposures that influence gut microbiota play a crucial role in asthma development. Breastfeeding is one such exposure; it is generally considered protective against pediatric asthma, although conflicting results have been reported, potentially due to variations in milk composition between individuals and across populations. Human milk oligosaccharides (HMOs) and milk microbiota are two major milk components that influence the infant gut microbiota and hence, development of the immune system. Among their many immunomodulatory functions, HMOs exert a selective pressure within the infant gut microbial niche, preferentially promoting the proliferation of specific bacteria including Bifidobacteria. Milk is also a source of viable bacteria originating from the maternal gut and infant oral cavity. As such, breastmilk has prebiotic and probiotic properties that can modulate two of the main forces controlling the gut microbial community assembly, i.e., dispersal and selection. Here, we review the latest evidence, mechanisms and hypotheses for the synergistic and/or additive effects of milk microbiota and HMOs in protecting against pediatric asthma.
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Affiliation(s)
- Shirin Moossavi
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.,Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada.,Developmental Origins of Chronic Diseases in Children Network (DEVOTION), Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada.,Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Kozeta Miliku
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada.,Developmental Origins of Chronic Diseases in Children Network (DEVOTION), Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada.,Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
| | - Shadi Sepehri
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| | - Ehsan Khafipour
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.,Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada.,Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada
| | - Meghan B Azad
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada.,Developmental Origins of Chronic Diseases in Children Network (DEVOTION), Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada.,Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
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22
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Zhang I, Pletcher SD, Goldberg AN, Barker BM, Cope EK. Fungal Microbiota in Chronic Airway Inflammatory Disease and Emerging Relationships with the Host Immune Response. Front Microbiol 2017; 8:2477. [PMID: 29312187 PMCID: PMC5733051 DOI: 10.3389/fmicb.2017.02477] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 11/29/2017] [Indexed: 12/22/2022] Open
Abstract
The respiratory tract is a complex system that is inhabited by niche-specific communities of microbes including bacteria, fungi, and viruses. These complex microbial assemblages are in constant contact with the mucosal immune system and play a critical role in airway health and immune homeostasis. Changes in the composition and diversity of airway microbiota are frequently observed in patients with chronic inflammatory diseases including chronic rhinosinusitis (CRS), cystic fibrosis, allergy, and asthma. While the bacterial microbiome of the upper and lower airways has been the focus of many recent studies, the contribution of fungal microbiota to inflammation is an emerging research interest. Within the context of allergic airway disease, fungal products are important allergens and fungi are potent inducers of inflammation. In addition, murine models have provided experimental evidence that fungal microbiota in peripheral organs, notably the gastrointestinal (GI) tract, influence pulmonary health. In this review, we explore the role of the respiratory and GI microbial communities in chronic airway inflammatory disease development with a specific focus on fungal microbiome interactions with the airway immune system and fungal-bacterial interactions that likely contribute to inflammatory disease. These findings are discussed in the context of clinical and immunological features of fungal-mediated disease in CRS, allergy, and asthmatic patients. While this field is still nascent, emerging evidence suggests that dysbiotic fungal and bacterial microbiota interact to drive or exacerbate chronic airway inflammatory disease.
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Affiliation(s)
- Irene Zhang
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Steven D. Pletcher
- Department of Otolaryngology Head and Neck Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Andrew N. Goldberg
- Department of Otolaryngology Head and Neck Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Bridget M. Barker
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Emily K. Cope
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
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23
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Abstract
Fungi are an underappreciated component of the human gut microbiota. In this issue of Cell Host & Microbe, Wheeler et al. (2016) demonstrate that fungal dysbiosis induced by antifungal treatment or inoculation with typically rare fungi results in exaggerated immune responses, suggesting that fungal colonizers play key roles in immune homeostasis.
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Affiliation(s)
- Carol A Kumamoto
- Department of Molecular Biology and Microbiology, Tufts University, 150 Harrison Avenue, Boston, MA 02111, USA.
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24
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Tan J, McKenzie C, Vuillermin PJ, Goverse G, Vinuesa CG, Mebius RE, Macia L, Mackay CR. Dietary Fiber and Bacterial SCFA Enhance Oral Tolerance and Protect against Food Allergy through Diverse Cellular Pathways. Cell Rep 2017; 15:2809-24. [PMID: 27332875 DOI: 10.1016/j.celrep.2016.05.047] [Citation(s) in RCA: 407] [Impact Index Per Article: 58.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/02/2016] [Accepted: 05/10/2016] [Indexed: 02/07/2023] Open
Abstract
The incidence of food allergies in western countries has increased dramatically in recent decades. Tolerance to food antigens relies on mucosal CD103(+) dendritic cells (DCs), which promote differentiation of regulatory T (Treg) cells. We show that high-fiber feeding in mice improved oral tolerance and protected from food allergy. High-fiber feeding reshaped gut microbial ecology and increased the release of short-chain fatty acids (SCFAs), particularly acetate and butyrate. High-fiber feeding enhanced oral tolerance and protected against food allergy by enhancing retinal dehydrogenase activity in CD103(+) DC. This protection depended on vitamin A in the diet. This feeding regimen also boosted IgA production and enhanced T follicular helper and mucosal germinal center responses. Mice lacking GPR43 or GPR109A, receptors for SCFAs, showed exacerbated food allergy and fewer CD103(+) DCs. Dietary elements, including fiber and vitamin A, therefore regulate numerous protective pathways in the gastrointestinal tract, necessary for immune non-responsiveness to food antigens.
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Affiliation(s)
- Jian Tan
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Craig McKenzie
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | | | - Gera Goverse
- Department of Molecular Cell Biology and Immunology, VU University Medical Center, 1081 HZ Amsterdam, the Netherlands
| | - Carola G Vinuesa
- Department of Pathogens and Immunity, John Curtin School of Medical Research, Australian National University, Building 131, Garran Road, Canberra, ACT 0200, Australia
| | - Reina E Mebius
- Department of Molecular Cell Biology and Immunology, VU University Medical Center, 1081 HZ Amsterdam, the Netherlands
| | - Laurence Macia
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia; Department of Physiology, Faculty of Medicine, The University of Sydney, Sydney, NSW 2006, Australia.
| | - Charles R Mackay
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia; Department of Physiology, Faculty of Medicine, The University of Sydney, Sydney, NSW 2006, Australia.
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25
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Desired Turbulence? Gut-Lung Axis, Immunity, and Lung Cancer. JOURNAL OF ONCOLOGY 2017; 2017:5035371. [PMID: 29075294 PMCID: PMC5623803 DOI: 10.1155/2017/5035371] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/30/2017] [Accepted: 08/03/2017] [Indexed: 02/08/2023]
Abstract
The microbiota includes different microorganisms consisting of bacteria, fungi, viruses, and protozoa distributed over many human body surfaces including the skin, vagina, gut, and airways, with the highest density found in the intestine. The gut microbiota strongly influences our metabolic, endocrine, and immune systems, as well as both the peripheral and central nervous systems. Recently, a dialogue between the gut and lung microbiota has been discovered, suggesting that changes in one compartment could impact the other compartment, whether in relation to microbial composition or function. Further, this bidirectional axis is evidenced in an, either beneficial or malignant, altered immune response in one compartment following changes in the other compartment. Stimulation of the immune system arises from the microbial cells themselves, but also from their metabolites. It can be either direct or mediated by stimulated immune cells in one site impacting the other site. Additionally, this interaction may lead to immunological boost, assisting the innate immune system in its antitumour response. Thus, this review offers an insight into the composition of these sites, the gut and the lung, their role in shaping the immune system, and, finally, their role in the response to lung cancer.
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26
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Ng BF, Xiong JW, Wan MP. Application of acoustic agglomeration to enhance air filtration efficiency in air-conditioning and mechanical ventilation (ACMV) systems. PLoS One 2017; 12:e0178851. [PMID: 28594862 PMCID: PMC5464643 DOI: 10.1371/journal.pone.0178851] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Accepted: 05/21/2017] [Indexed: 12/01/2022] Open
Abstract
The recent episodes of haze in Southeast Asia have caused some of the worst regional atmospheric pollution ever recorded in history. In order to control the levels of airborne fine particulate matters (PM) indoors, filtration systems providing high PM capturing efficiency are often sought, which inadvertently also results in high airflow resistance (or pressure drop) that increases the energy consumption for air distribution. A pre-conditioning mechanism promoting the formation of particle clusters to enhance PM capturing efficiency without adding flow resistance in the air distribution ductwork could provide an energy-efficient solution. This pre-conditioning mechanism can be fulfilled by acoustic agglomeration, which is a phenomenon that promotes the coagulation of suspended particles by acoustic waves propagating in the fluid medium. This paper discusses the basic mechanisms of acoustic agglomeration along with influencing factors that could affect the agglomeration efficiency. The feasibility to apply acoustic agglomeration to improve filtration in air-conditioning and mechanical ventilation (ACMV) systems is investigated experimentally in a small-scale wind tunnel. Experimental results indicate that this novel application of acoustic pre-conditioning improves the PM2.5 filtration efficiency of the test filters by up to 10% without introducing additional pressure drop. The fan energy savings from not having to switch to a high capturing efficiency filter largely outstrip the additional energy consumed by the acoustics system. This, as a whole, demonstrates potential energy savings from the combined acoustic-enhanced filtration system without compromising on PM capturing efficiency.
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Affiliation(s)
- Bing Feng Ng
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore, Singapore
| | - Jin Wen Xiong
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore, Singapore
| | - Man Pun Wan
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore, Singapore
- * E-mail:
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Martin Manuel P, Elena B, Carolina MG, Gabriela P. Oral probiotics supplementation can stimulate the immune system in a stress process. JOURNAL OF NUTRITION & INTERMEDIARY METABOLISM 2017. [DOI: 10.1016/j.jnim.2017.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Barfod KK, Roggenbuck M, Al-Shuweli S, Fakih D, Sørensen SJ, Sørensen GL. Alterations of the murine gut microbiome in allergic airway disease are independent of surfactant protein D. Heliyon 2017; 3:e00262. [PMID: 28367508 PMCID: PMC5361934 DOI: 10.1016/j.heliyon.2017.e00262] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 02/09/2017] [Accepted: 03/08/2017] [Indexed: 02/07/2023] Open
Abstract
Background SP-D is an important host defense lectin in innate immunity and SP-D deficient mice show several abnormal immune effects and are susceptible to allergen-induced airway disease. At the same time, host microbiome interactions play an important role in the development of allergic airway disease, and alterations to gut microbiota have been linked to airway disease through the gut-lung axis. Currently, it is unknown if the genotype (Sftpd-/- or Sftpd+/+) of the standard SP-D mouse model can affect the host microbiota to such an degree that it would overcome the cohousing effect on microbiota and interfere with the interpretation of immunological data from the model. Generally, little is known about the effect of the SP-D protein in itself and in combination with airway disease on the microbiota. In this study, we tested the hypothesis that microbiome composition would change with the lack of SP-D protein and presence of allergic airway disease in the widely used SP-D-deficient mouse model. Results We describe here for the first time the lung and gut microbiota of the SP-D mouse model with OVA induced allergic airway disease. After the challenge animals were killed and fecal samples were taken from the caecum and lungs were subjected to bronchoalveolar lavage for comparison of gut and lung microbiota by Illumina 16S rRNA gene sequencing. A significant community shift was observed in gut microbiota after challenge with OVA. However, the microbial communities were not significantly different between SP-D deficient and wild type mice from the same cages in either naïve or OVA treated animals. Wild type animals did however show the largest variation between mice. Conclusions Our results show that the composition of the microbiota is not influenced by the SP-D deficient genotype under naïve or OVA induced airway disease. However, OVA sensitization and pulmonary challenge did alter the gut microbiota, supporting a bidirectional lung-gut crosstalk. Future mechanistic investigations of the influence of induced allergic airway disease on gut microbiota are warranted.
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Affiliation(s)
- Kenneth K Barfod
- National Research Centre for the Working Environment, Lersø Parkallé 105, 2100 Copenhagen O, Denmark
| | - Michael Roggenbuck
- University of Copenhagen, Department of Biology, Microbiology, Universitetsparken 15, 2100 Copenhagen O, Denmark
| | - Suzan Al-Shuweli
- National Research Centre for the Working Environment, Lersø Parkallé 105, 2100 Copenhagen O, Denmark
| | - Dalia Fakih
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark; Laboratory of Immunology, Faculty of public health, Lebanese University, Fanar, Lebanon
| | - Søren J Sørensen
- University of Copenhagen, Department of Biology, Microbiology, Universitetsparken 15, 2100 Copenhagen O, Denmark
| | - Grith L Sørensen
- Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
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Huang H, Krishnan HB, Pham Q, Yu LL, Wang TTY. Soy and Gut Microbiota: Interaction and Implication for Human Health. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:8695-8709. [PMID: 27798832 DOI: 10.1021/acs.jafc.6b03725] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Soy (Glycine max) is a major commodity in the United States, and soy foods are gaining popularity due to their reported health-promoting effects. In the past two decades, soy and soy bioactive components have been studied for their health-promoting/disease-preventing activities and potential mechanisms of action. Recent studies have identified gut microbiota as an important component in the human body ecosystem and possibly a critical modulator of human health. Soy foods' interaction with the gut microbiota may critically influence many aspects of human development, physiology, immunity, and nutrition at different stages of life. This review summarizes current knowledge on the effects of soy foods and soy components on gut microbiota population and composition. It was found, although results vary in different studies, in general, both animal and human studies have shown that consumption of soy foods can increase the levels of bifidobacteria and lactobacilli and alter the ratio between Firmicutes and Bacteroidetes. These changes in microbiota are consistent with reported reductions in pathogenic bacteria populations in the gut, thereby lowering the risk of diseases and leading to beneficial effects on human health.
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Affiliation(s)
- Haiqiu Huang
- Diet, Genomics and Immunology Laboratory, U.S. Department of Agriculture-Agricultural Research Service , Beltsville, Maryland 20705, United States
| | - Hari B Krishnan
- Plant Genetics Research Unit, U.S. Department of Agriculture-Agricultural Research Service, University of Missouri , Columbia, Missouri 65211, United States
| | - Quynhchi Pham
- Diet, Genomics and Immunology Laboratory, U.S. Department of Agriculture-Agricultural Research Service , Beltsville, Maryland 20705, United States
| | - Liangli Lucy Yu
- Department of Nutrition and Food Science, University of Maryland , College Park, Maryland 20742, United States
| | - Thomas T Y Wang
- Diet, Genomics and Immunology Laboratory, U.S. Department of Agriculture-Agricultural Research Service , Beltsville, Maryland 20705, United States
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Poroyko VA, Carreras A, Khalyfa A, Khalyfa AA, Leone V, Peris E, Almendros I, Gileles-Hillel A, Qiao Z, Hubert N, Farré R, Chang EB, Gozal D. Chronic Sleep Disruption Alters Gut Microbiota, Induces Systemic and Adipose Tissue Inflammation and Insulin Resistance in Mice. Sci Rep 2016; 6:35405. [PMID: 27739530 PMCID: PMC5064361 DOI: 10.1038/srep35405] [Citation(s) in RCA: 279] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/28/2016] [Indexed: 02/08/2023] Open
Abstract
Chronic sleep fragmentation (SF) commonly occurs in human populations, and although it does not involve circadian shifts or sleep deprivation, it markedly alters feeding behaviors ultimately promoting obesity and insulin resistance. These symptoms are known to be related to the host gut microbiota. Mice were exposed to SF for 4 weeks and then allowed to recover for 2 weeks. Taxonomic profiles of fecal microbiota were obtained prospectively, and conventionalization experiments were performed in germ-free mice. Adipose tissue insulin sensitivity and inflammation, as well as circulating measures of inflammation, were assayed. Effect of fecal water on colonic epithelial permeability was also examined. Chronic SF-induced increased food intake and reversible gut microbiota changes characterized by the preferential growth of highly fermentative members of Lachnospiraceae and Ruminococcaceae and a decrease of Lactobacillaceae families. These lead to systemic and visceral white adipose tissue inflammation in addition to altered insulin sensitivity in mice, most likely via enhanced colonic epithelium barrier disruption. Conventionalization of germ-free mice with SF-derived microbiota confirmed these findings. Thus, SF-induced metabolic alterations may be mediated, in part, by concurrent changes in gut microbiota, thereby opening the way for gut microbiome-targeted therapeutics aimed at reducing the major end-organ morbidities of chronic SF.
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Affiliation(s)
- Valeriy A Poroyko
- Section of Pediatric Sleep Medicine, Department of Pediatrics, Pritzker School of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL 60637, USA.,Department of Medical Oncology, City of Hope, Duarte, CA, 91010, USA
| | - Alba Carreras
- Section of Pediatric Sleep Medicine, Department of Pediatrics, Pritzker School of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL 60637, USA
| | - Abdelnaby Khalyfa
- Section of Pediatric Sleep Medicine, Department of Pediatrics, Pritzker School of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL 60637, USA
| | - Ahamed A Khalyfa
- Section of Pediatric Sleep Medicine, Department of Pediatrics, Pritzker School of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL 60637, USA
| | - Vanessa Leone
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Eduard Peris
- Section of Pediatric Sleep Medicine, Department of Pediatrics, Pritzker School of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL 60637, USA
| | - Isaac Almendros
- Section of Pediatric Sleep Medicine, Department of Pediatrics, Pritzker School of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL 60637, USA
| | - Alex Gileles-Hillel
- Section of Pediatric Sleep Medicine, Department of Pediatrics, Pritzker School of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL 60637, USA
| | - Zhuanhong Qiao
- Section of Pediatric Sleep Medicine, Department of Pediatrics, Pritzker School of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL 60637, USA
| | - Nathaniel Hubert
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - Ramon Farré
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, CIBER, Madrid, Spain.,Institut Investigacions Biomediques August Pi Sunyer, Barcelona, Spain.,Unitat de Biofísica i Bioenginyeria, Facultat de Medicina, Universitat de Barcelona-IDIBAPS, Barcelona, Spain
| | - Eugene B Chang
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | - David Gozal
- Section of Pediatric Sleep Medicine, Department of Pediatrics, Pritzker School of Medicine, Biological Sciences Division, The University of Chicago, Chicago, IL 60637, USA
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Wheeler ML, Limon JJ, Bar AS, Leal CA, Gargus M, Tang J, Brown J, Funari VA, Wang HL, Crother TR, Arditi M, Underhill DM, Iliev ID. Immunological Consequences of Intestinal Fungal Dysbiosis. Cell Host Microbe 2016; 19:865-73. [PMID: 27237365 DOI: 10.1016/j.chom.2016.05.003] [Citation(s) in RCA: 278] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/11/2016] [Accepted: 05/04/2016] [Indexed: 12/17/2022]
Abstract
Compared to bacteria, the role of fungi within the intestinal microbiota is poorly understood. In this study we investigated whether the presence of a "healthy" fungal community in the gut is important for modulating immune function. Prolonged oral treatment of mice with antifungal drugs resulted in increased disease severity in acute and chronic models of colitis, and also exacerbated the development of allergic airway disease. Microbiota profiling revealed restructuring of fungal and bacterial communities. Specifically, representation of Candida spp. was reduced, while Aspergillus, Wallemia, and Epicoccum spp. were increased. Oral supplementation with a mixture of three fungi found to expand during antifungal treatment (Aspergillus amstelodami, Epicoccum nigrum, and Wallemia sebi) was sufficient to recapitulate the exacerbating effects of antifungal drugs on allergic airway disease. Taken together, these results indicate that disruption of commensal fungal populations can influence local and peripheral immune responses and enhance relevant disease states.
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Affiliation(s)
- Matthew L Wheeler
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and the Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jose J Limon
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and the Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Agnieszka S Bar
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and the Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Christian A Leal
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and the Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Matthew Gargus
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and the Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jie Tang
- Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jordan Brown
- Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Vincent A Funari
- Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Hanlin L Wang
- Department of Pathology and Laboratory Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Timothy R Crother
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Moshe Arditi
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - David M Underhill
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and the Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA; Department of Pathology and Laboratory Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
| | - Iliyan D Iliev
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, and the Division of Immunology, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
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Beck JM, Schloss PD, Venkataraman A, Twigg H, Jablonski KA, Bushman FD, Campbell TB, Charlson ES, Collman RG, Crothers K, Curtis JL, Drews KL, Flores SC, Fontenot AP, Foulkes MA, Frank I, Ghedin E, Huang L, Lynch SV, Morris A, Palmer BE, Schmidt TM, Sodergren E, Weinstock GM, Young VB. Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals. Am J Respir Crit Care Med 2016; 192:1335-44. [PMID: 26247840 DOI: 10.1164/rccm.201501-0128oc] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
RATIONALE Improved understanding of the lung microbiome in HIV-infected individuals could lead to better strategies for diagnosis, therapy, and prophylaxis of HIV-associated pneumonias. Differences in the oral and lung microbiomes in HIV-infected and HIV-uninfected individuals are not well defined. Whether highly active antiretroviral therapy influences these microbiomes is unclear. OBJECTIVES We determined whether oral and lung microbiomes differed in clinically healthy groups of HIV-infected and HIV-uninfected subjects. METHODS Participating sites in the Lung HIV Microbiome Project contributed bacterial 16S rRNA sequencing data from oral washes and bronchoalveolar lavages (BALs) obtained from HIV-uninfected individuals (n = 86), HIV-infected individuals who were treatment naive (n = 18), and HIV-infected individuals receiving antiretroviral therapy (n = 38). MEASUREMENTS AND MAIN RESULTS Microbial populations differed in the oral washes among the subject groups (Streptococcus, Actinomyces, Rothia, and Atopobium), but there were no individual taxa that differed among the BALs. Comparison of oral washes and BALs demonstrated similar patterns from HIV-uninfected individuals and HIV-infected individuals receiving antiretroviral therapy, with multiple taxa differing in abundance. The pattern observed from HIV-infected individuals who were treatment naive differed from the other two groups, with differences limited to Veillonella, Rothia, and Granulicatella. CD4 cell counts did not influence the oral or BAL microbiome in these relatively healthy, HIV-infected subjects. CONCLUSIONS The overall similarity of the microbiomes in participants with and without HIV infection was unexpected, because HIV-infected individuals with relatively preserved CD4 cell counts are at higher risk for lower respiratory tract infections, indicating impaired local immune function.
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Affiliation(s)
- James M Beck
- 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado.,2 Veterans Affairs Eastern Colorado Health Care System, Denver, Colorado
| | - Patrick D Schloss
- 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Arvind Venkataraman
- 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Homer Twigg
- 4 Department of Medicine, Indiana University, Indianapolis, Indiana
| | - Kathleen A Jablonski
- 5 Department of Epidemiology and Biostatistics, George Washington University, Washington, District of Columbia
| | | | - Thomas B Campbell
- 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado
| | - Emily S Charlson
- 7 Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ronald G Collman
- 7 Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kristina Crothers
- 8 Department of Medicine, University of Washington, Seattle, Washington
| | - Jeffrey L Curtis
- 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.,9 Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan
| | - Kimberly L Drews
- 5 Department of Epidemiology and Biostatistics, George Washington University, Washington, District of Columbia
| | - Sonia C Flores
- 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado
| | - Andrew P Fontenot
- 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado
| | - Mary A Foulkes
- 5 Department of Epidemiology and Biostatistics, George Washington University, Washington, District of Columbia
| | - Ian Frank
- 7 Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Elodie Ghedin
- 10 Department of Computational and Systems Biology and
| | - Laurence Huang
- 11 Department of Medicine, University of California San Francisco, San Francisco, California; and
| | - Susan V Lynch
- 11 Department of Medicine, University of California San Francisco, San Francisco, California; and
| | - Alison Morris
- 12 Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Brent E Palmer
- 1 Department of Medicine, University of Colorado Denver, Aurora, Colorado
| | - Thomas M Schmidt
- 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Erica Sodergren
- 13 The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | | | - Vincent B Young
- 3 Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
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O'Doherty KC, Virani A, Wilcox ES. The Human Microbiome and Public Health: Social and Ethical Considerations. Am J Public Health 2016; 106:414-20. [PMID: 26794165 DOI: 10.2105/ajph.2015.302989] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Rapid advances in human microbiome research point to an increasing range of health outcomes related to the composition of an individual's microbiome. To date, much research has focused on individual health, with a paucity of attention to public health implications. This is a critical oversight owing to the potentially shared nature of the human microbiome across communities and vertical and horizontal mechanisms for transferring microbiomes among humans. We explored some key ethical and social implications of human microbiome research for public health. We focused on (1) insights from microbiome research about damage to individual and shared microbiomes from prevalent societal practices, and (2) ethical and social implications of novel technologies developed on the basis of emerging microbiome science.
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Affiliation(s)
- Kieran C O'Doherty
- Kieran C. O'Doherty is with the Department of Psychology, University of Guelph, Guelph, ON, Canada. Alice Virani is with the Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada. Elizabeth S. Wilcox is with the School of Population and Public Health, University of British Columbia
| | - Alice Virani
- Kieran C. O'Doherty is with the Department of Psychology, University of Guelph, Guelph, ON, Canada. Alice Virani is with the Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada. Elizabeth S. Wilcox is with the School of Population and Public Health, University of British Columbia
| | - Elizabeth S Wilcox
- Kieran C. O'Doherty is with the Department of Psychology, University of Guelph, Guelph, ON, Canada. Alice Virani is with the Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada. Elizabeth S. Wilcox is with the School of Population and Public Health, University of British Columbia
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34
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Ling Z, Liu X, Cheng Y, Li L. Potential roles of disordered airway microbiota in patients with severe asthma. J Allergy Clin Immunol 2015; 137:648. [PMID: 26684289 DOI: 10.1016/j.jaci.2015.09.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 09/24/2015] [Indexed: 12/31/2022]
Affiliation(s)
- Zongxin Ling
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xia Liu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yiwen Cheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lanjuan Li
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
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35
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Saeedi P, Salimian J, Ahmadi A, Imani Fooladi AA. The transient but not resident (TBNR) microbiome: a Yin Yang model for lung immune system. Inhal Toxicol 2015; 27:451-61. [PMID: 26307905 DOI: 10.3109/08958378.2015.1070220] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The concept of microbial content of the lung is still controversial. What make this more complicated are controversial results obtaining from different methodologies about lung microbiome and the definition of "lung sterility". Lungs may have very low bacteria but are not completely germ-free. Bacteria are constantly entering from the upper respiratory tract, but are then quickly being cleared. We can find bacterial DNA in the lungs, but it is much harder to ask about living bacteria. Here, we propose that if there is any trafficking of the microorganisms in the lung, it should be a "Transient But Not Resident (TBNR)" model. So, we speculate a "Yin Yang model" for the lung immune system and TBNR. Despite beneficial roles of microbiome on the development of lung immune system, any disruption and alteration in the microbiota composition of upper and lower airways may trigger or lead to several diseases such as asthma, chronic obstructive pulmonary disease and mustard lung disease.
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Affiliation(s)
| | - Jafar Salimian
- b Chemical Injuries Research Center, Baqiyatallah University of Medical Sciences , Tehran , Iran
| | - Ali Ahmadi
- a Applied Microbiology Research Center and
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36
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Mansour NM, Heine H, Abdou SM, Shenana ME, Zakaria MK, El-Diwany A. Isolation of Enterococcus faecium NM113, Enterococcus faecium NM213 and Lactobacillus casei NM512 as novel probiotics with immunomodulatory properties. Microbiol Immunol 2015; 58:559-69. [PMID: 25130071 DOI: 10.1111/1348-0421.12187] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 07/18/2014] [Accepted: 07/23/2014] [Indexed: 01/07/2023]
Abstract
Probiotics, defined as living bacteria that are beneficial for human health, mainly function through their immunomodulatory abilities. Hence, these microorganisms have proven successful for treating diseases resulting from immune deregulation. The aim of this study was to find novel candidates to improve on and complement current probiotic treatment strategies. Of 60 lactic acid bacterial strains that were isolated from fecal samples of healthy, full-term, breast-fed infants, three were chosen because of their ability to activate human immune cells. These candidates were then tested with regard to immunomodulatory properties, antimicrobial effects on pathogens, required pharmacological properties and their safety profiles. To identify the immunomodulatory structures of the selected isolates, activation of specific innate immune receptors was studied. The three candidates for probiotic treatment were assigned Enterococcus faecium NM113, Enterococcus faecium NM213 and Lactobacillus casei NM512. Compared with the established allergy-protective strain Lactococcus lactis G121, these isolates induced release of similar amounts of IL-12, a potent inducer of T helper 1 cells. In addition, all three neonatal isolates had antimicrobial activity against pathogens. Analysis of pharmacological suitability showed high tolerance of low pH, bile salts and pancreatic enzymes. In terms of safe application in humans, the isolates were sensitive to three antibiotics (chloramphenicol, tetracycline and erythromycin). In addition, the Enterococcus isolates were free from the four major virulence genes (cylA, agg, efaAfs and ccf). Moreover, the isolates strongly activated Toll-like receptor 2, which suggests lipopeptides as their active immunomodulatory structure. Thus, three novel bacterial strains with great potential as probiotic candidates and promising immunomodulatory properties have here been identified and characterized.
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Affiliation(s)
- Nahla M Mansour
- Gut Microbiology and Immunology Group, Center of Excellence for Advanced Sciences (CEAS), National Research Centre; Department of Chemistry of Natural and Microbial Products, Division of Pharmaceutical Industries, National Research Centre, El Buhouth St., Dokki, Giza, 12311, Egypt
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Alterations of the Murine Gut Microbiome with Age and Allergic Airway Disease. J Immunol Res 2015; 2015:892568. [PMID: 26090504 PMCID: PMC4451525 DOI: 10.1155/2015/892568] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/16/2015] [Indexed: 12/13/2022] Open
Abstract
The gut microbiota plays an important role in the development of asthma. With advanced age the microbiome and the immune system are changing and, currently, little is known about how these two factors contribute to the development of allergic asthma in the elderly. In this study we investigated the associations between the intestinal microbiome and allergic airway disease in young and old mice that were sensitized and challenged with house dust mite (HDM). After challenge, the animals were sacrificed, blood serum was collected for cytokine analysis, and the lungs were processed for histopathology. Fecal pellets were excised from the colon and subjected to 16S rRNA analysis. The microbial community structure changed with age and allergy development, where alterations in fecal communities from young to old mice resembled those after HDM challenge. Allergic mice had induced serum levels of IL-17A and old mice developed a greater allergic airway response compared to young mice. This study demonstrates that the intestinal bacterial community structure differs with age, possibly contributing to the exaggerated pulmonary inflammatory response in old mice. Furthermore, our results show that the composition of the gut microbiota changes with pulmonary allergy, indicating bidirectional gut-lung communications.
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38
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Rödiger S, Kramer T, Frömmel U, Weinreich J, Roggenbuck D, Guenther S, Schaufler K, Schröder C, Schierack P. Intestinal Escherichia coli colonization in a mallard duck population over four consecutive winter seasons. Environ Microbiol 2015; 17:3352-61. [PMID: 25684458 DOI: 10.1111/1462-2920.12807] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 01/31/2015] [Accepted: 02/01/2015] [Indexed: 01/04/2023]
Abstract
We report the population structure and dynamics of one Escherichia coli population of wild mallard ducks in their natural environment over four winter seasons, following the characterization of 100 isolates each consecutive season. Macro-restriction analysis was used to define isolates variously as multi- or 1-year pulsed-field gel electrophoresis (PFGE) types. Isolates were characterized genotypically based on virulence-associated genes (VAGs), phylogenetic markers, and phenotypically based on haemolytic activity, antimicrobial resistance, adhesion to epithelial cells, microcin production, motility and carbohydrate metabolism. Only 12 out of 220 PFGE types were detectable over more than one winter, and classified as multi-year PFGE types. There was a dramatic change of PFGE types within two winter seasons. Nevertheless, the genetic pool (VAGs) and antimicrobial resistance pattern remained remarkably stable. The high diversity and dynamics of this E. coli population were also demonstrated by the occurrence of PFGE subtypes and differences between isolates of one PFGE type (based on VAGs, antimicrobial resistance and adhesion rates). Multi- and 1-year PFGE types differed in antimicrobial resistance, VAGs and adhesion. Other parameters were not prominent colonization factors. In conclusion, the high diversity, dynamics and stable genetic pool of an E. coli population seem to enable their successful colonization of host animal population over time.
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Affiliation(s)
- Stefan Rödiger
- Fakultät für Naturwissenschaften, Brandenburgische Technische Universität Cottbus - Senftenberg, Großenhainer Str. 57, 01968, Senftenberg, Germany
| | - Toni Kramer
- Fakultät für Naturwissenschaften, Brandenburgische Technische Universität Cottbus - Senftenberg, Großenhainer Str. 57, 01968, Senftenberg, Germany
| | - Ulrike Frömmel
- Fakultät für Naturwissenschaften, Brandenburgische Technische Universität Cottbus - Senftenberg, Großenhainer Str. 57, 01968, Senftenberg, Germany
| | - Jörg Weinreich
- Fakultät für Naturwissenschaften, Brandenburgische Technische Universität Cottbus - Senftenberg, Großenhainer Str. 57, 01968, Senftenberg, Germany
| | - Dirk Roggenbuck
- Fakultät für Naturwissenschaften, Brandenburgische Technische Universität Cottbus - Senftenberg, Großenhainer Str. 57, 01968, Senftenberg, Germany.,GA Generic Assays GmbH, Ludwig-Erhard-Ring 3, 15827, Dahlewitz, Germany
| | - Sebastian Guenther
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163, Berlin, Germany
| | - Katharina Schaufler
- Institute of Microbiology and Epizootics, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163, Berlin, Germany
| | - Christian Schröder
- Fakultät für Naturwissenschaften, Brandenburgische Technische Universität Cottbus - Senftenberg, Großenhainer Str. 57, 01968, Senftenberg, Germany
| | - Peter Schierack
- Fakultät für Naturwissenschaften, Brandenburgische Technische Universität Cottbus - Senftenberg, Großenhainer Str. 57, 01968, Senftenberg, Germany
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Jardi F, Aguilera M, Vergara P, Martinez V. Lipopolysaccharides facilitate colonic motor alterations associated to the sensitization to a luminal antigen in rats. J Neurogastroenterol Motil 2015; 21:222-35. [PMID: 25843075 PMCID: PMC4398237 DOI: 10.5056/jnm14136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 12/05/2014] [Accepted: 12/09/2014] [Indexed: 11/20/2022] Open
Abstract
Background/Aims Enteric dysbiosis is a risk factor for dietary proteins-associated intestinal alterations, contributing to the development of food allergies and the symptomatology of functional gastrointestinal disorders, mainly irritable bowel syndrome (IBS). We explored if a dysbiotic-like state, simulated by intraperitoneal administration of bacterial lipopolysaccharides (LPS), facilitates the sensitization to a luminal antigen, ovalbumin (OVA), in rats. Methods Rats were exposed to oral OVA for 1 week, alone or with LPS. Thereafter, colonic histology, goblet cell density, mucosal eosinophils and mucosal mast cell (MMC) and connective tissue mast cell (CTMC) were evaluated. Colonic expression (real-time quantitative polymerase chain reaction) of interleukins, IFN-α1 and integrins was assessed to determine local immune responses. Luminal and wall adhered microbiota were characterized by fluorescence in situ hybridization. Colonic contractility (in vitro) served to assess functional changes associated to OVA and/or LPS. Results Neither OVA nor LPS, alone or combined, lead to structural alterations, except for a reduced goblet cell density in OVA-LPS-treated rats. MMC density was unaffected, while CTMC counts increased within the submucosa of OVA-LPS-treated animals. Marginal immune activation (IFN-α1 up-regulation) was observed in OVA-LPS-treated rats. LPS induced a dysbiotic-like state characterized by decreased luminal bacterial counts, with a specific loss of clostridia. LPS facilitated Clostridium spp. wall adherence, an effect prevented by OVA. Colonic contractility was altered in OVA-LPS-treated animals, showing increased basal activity and enhanced motor responses to OVA. Conclusions Changes in gut microbiota and/or direct effects of LPS might enhance/facilitate local neuroimmune responses to food antigens leading to motor alterations similar to those observed in IBS.
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Affiliation(s)
- Ferran Jardi
- Department of Cell Biology, Physiology and Immunology, Universitat Autonoma de Barcelona, Spain
| | - Monica Aguilera
- Department of Cell Biology, Physiology and Immunology, Universitat Autonoma de Barcelona, Spain.,Instituto de Neurociencias, Universitat Autonoma de Barcelona, Spain
| | - Patri Vergara
- Department of Cell Biology, Physiology and Immunology, Universitat Autonoma de Barcelona, Spain.,Instituto de Neurociencias, Universitat Autonoma de Barcelona, Spain.,Centro de Investigacion Biomedica en Red de Enfermedades Hepaticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Vicente Martinez
- Department of Cell Biology, Physiology and Immunology, Universitat Autonoma de Barcelona, Spain.,Instituto de Neurociencias, Universitat Autonoma de Barcelona, Spain.,Centro de Investigacion Biomedica en Red de Enfermedades Hepaticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
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Abstract
Neonates face unique challenges in the period following birth. The postnatal immune system is in the early stages of development and has a range of functional capabilities that are distinct from the mature adult immune system. Bidirectional immune-microbial interactions regulate the development of mucosal immunity and alter the composition of the microbiota, which contributes to overall host well-being. In the past few years, nutrition has been highlighted as a third element in this interaction that governs host health by modulating microbial composition and the function of the immune system. Dietary changes and imbalances can disturb the immune-microbiota homeostasis, which might alter susceptibility to several autoimmune and metabolic diseases. Major changes in cultural traditions, socioeconomic status and agriculture are affecting the nutritional status of humans worldwide, which is altering core intestinal microbial communities. This phenomenon is especially relevant to the neonatal and paediatric populations, in which the microbiota and immune system are extremely sensitive to dietary influences. In this Review, we discuss the current state of knowledge regarding early-life nutrition, its effects on the microbiota and the consequences of diet-induced perturbation of the structure of the microbial community on mucosal immunity and disease susceptibility.
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Galley JD, Yu Z, Kumar P, Dowd SE, Lyte M, Bailey MT. The structures of the colonic mucosa-associated and luminal microbial communities are distinct and differentially affected by a prolonged murine stressor. Gut Microbes 2014; 5:748-60. [PMID: 25536463 PMCID: PMC4615309 DOI: 10.4161/19490976.2014.972241] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The commensal microbiota of the human gastrointestinal tract live in a largely stable community structure, assisting in host physiological and immunological functions. Changes to this structure can be injurious to the health of the host, a concept termed dysbiosis. Psychological stress is a factor that has been implicated in causing dysbiosis, and studies performed by our lab have shown that restraint stress can indeed shift the cecal microbiota structure as well as increase the severity of a colonic infection caused by Citrobacter rodentium. However, this study, like many others, have focused on fecal contents when examining the effect of dysbiosis-causing stimuli (e.g. psychological stress) upon the microbiota. Since the mucosa-associated microbiota have unique properties and functions that can act upon the host, it is important to understand how stressor exposure might affect this niche of bacteria. To begin to understand whether chronic restraint stress changes the mucosa-associated and/or luminal microbiota mice underwent 7 16-hour cycles of restraint stress, and the microbiota of both colonic tissue and fecal contents were analyzed by sequencing using next-gen bacterial tag-encoded FLX amplicon technology (bTEFAP) pyrosequencing. Both control and stress groups had significantly different mucosa-associated and luminal microbiota communities, highlighting the importance of focusing gastrointestinal community structure analysis by microbial niche. Furthermore, restraint stress was able to disrupt both the mucosa-associated and luminally-associated colonic microbiota by shifting the relative abundances of multiple groups of bacteria. Among these changes, there was a significant reduction in the immunomodulatory commensal genus Lactobacillus associated with colonic mucosa. The relative abundance of Lactobacillus spp. was not affected in the lumen. These results indicate that stressor-exposure can have distinct effects upon the colonic microbiota situated at the mucosal epithelium in comparison to the luminal-associated microbiota.
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Affiliation(s)
- Jeffrey D Galley
- Division of Oral Biolog; College of Dentistry; The Ohio State University; Columbus, OH USA
| | - Zhongtang Yu
- Department of Animal Sciences; College of Food; Agricultural and Environmental Sciences; The Ohio State University, Columbus, OH USA
| | - Purnima Kumar
- Division of Periodontology; College of Dentistry; The Ohio State University; Columbus, OH USA
| | - Scot E Dowd
- Research and Testing Laboratory; Lubbock, TX USA
| | - Mark Lyte
- Department of Immunotherapeutics and Biotechnology; School of Pharmacy; Texas Tech University Health Sciences Center; Abilene, TX USA
| | - Michael T Bailey
- Division of Oral Biolog; College of Dentistry; The Ohio State University; Columbus, OH USA,Institute for Behavioral Medicine Research; College of Medicine; The Ohio State University; Columbus, OH USA,Department of Pediatrics; Wexner Medical Center; The Ohio State University; Columbus, OH USA,Correspondence to: Michael T Bailey;
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43
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Gratacap RL, Bergeron AC, Wheeler RT. Modeling mucosal candidiasis in larval zebrafish by swimbladder injection. J Vis Exp 2014:e52182. [PMID: 25490695 DOI: 10.3791/52182] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Early defense against mucosal pathogens consists of both an epithelial barrier and innate immune cells. The immunocompetency of both, and their intercommunication, are paramount for the protection against infections. The interactions of epithelial and innate immune cells with a pathogen are best investigated in vivo, where complex behavior unfolds over time and space. However, existing models do not allow for easy spatio-temporal imaging of the battle with pathogens at the mucosal level. The model developed here creates a mucosal infection by direct injection of the fungal pathogen, Candida albicans, into the swimbladder of juvenile zebrafish. The resulting infection enables high-resolution imaging of epithelial and innate immune cell behavior throughout the development of mucosal disease. The versatility of this method allows for interrogation of the host to probe the detailed sequence of immune events leading to phagocyte recruitment and to examine the roles of particular cell types and molecular pathways in protection. In addition, the behavior of the pathogen as a function of immune attack can be imaged simultaneously by using fluorescent protein-expressing C. albicans. Increased spatial resolution of the host-pathogen interaction is also possible using the described rapid swimbladder dissection technique. The mucosal infection model described here is straightforward and highly reproducible, making it a valuable tool for the study of mucosal candidiasis. This system may also be broadly translatable to other mucosal pathogens such as mycobacterial, bacterial or viral microbes that normally infect through epithelial surfaces.
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Affiliation(s)
- Remi L Gratacap
- Department of Molecular and Biomedical Sciences, University of Maine
| | - Audrey C Bergeron
- Department of Molecular and Biomedical Sciences, University of Maine
| | - Robert T Wheeler
- Department of Molecular and Biomedical Sciences, University of Maine; Graduate School of Biomedical Sciences and Engineering, University of Maine;
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Karta MR, Gavala ML, Curran CS, Wickert LE, Keely PJ, Gern JE, Bertics PJ. LPS modulates rhinovirus-induced chemokine secretion in monocytes and macrophages. Am J Respir Cell Mol Biol 2014; 51:125-34. [PMID: 24498897 PMCID: PMC4091859 DOI: 10.1165/rcmb.2013-0404oc] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 01/30/2014] [Indexed: 01/01/2023] Open
Abstract
Recent studies suggest that both bacteria and rhinoviruses (RVs) contribute to asthma exacerbations. We hypothesized that bacteria might alter antiviral responses early in the course of infection by modifying monocyte-lineage chemokine responses to RV infection. To test this hypothesis, human blood monocytes or bronchoalveolar lavage (BAL) macrophages were treated with RV types A016, B014, A001, and/or A002 in the presence or absence of LPS, and secretion of chemokines (CXCL10, CXCL11, CCL2, and CCL8) and IFN-α was measured by ELISA. Treatment with RV alone induced blood monocytes and BAL macrophages to secrete CXCL10, CXCL11, CCL2, and CCL8. Pretreatment with LPS significantly attenuated RV-induced CXCL10, CXCL11, and CCL8 secretion by 68-99.9% on average (P < 0.0001, P < 0.004, and P < 0.002, respectively), but did not inhibit RV-induced CCL2 from blood monocytes. Similarly, LPS inhibited RV-induced CXCL10 and CXCL11 secretion by over 88% on average from BAL macrophages (P < 0.002 and P < 0.0001, respectively). Furthermore, LPS inhibited RV-induced signal transducer and activator of transcription 1 phosphorylation (P < 0.05), as determined by immunoblotting, yet augmented RV-induced IFN-α secretion (P < 0.05), and did not diminish expression of RV target receptors, as measured by flow cytometry. In summary, major and minor group RVs strongly induce chemokine expression and IFN-α from monocytic cells. The bacterial product, LPS, specifically inhibits monocyte and macrophage secretion of RV-induced CXCL10 and CXCL11, but not other highly induced chemokines or IFN-α. These effects suggest that airway bacteria could modulate the pattern of virus-induced cell recruitment and inflammation in the airways.
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Affiliation(s)
- Maya R. Karta
- Molecular and Cellular Pharmacology Graduate Program, and
- Departments of Biomolecular Chemistry
| | | | | | | | - Patricia J. Keely
- Molecular and Cellular Pharmacology Graduate Program, and
- Cellular and Regenerative Biology, and
| | - James E. Gern
- Pediatrics and Medicine, University of Wisconsin-Madison, Madison, Wisconsin
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Barzegari A, Saeedi N, Saei AA. Shrinkage of the human core microbiome and a proposal for launching microbiome biobanks. Future Microbiol 2014; 9:639-56. [DOI: 10.2217/fmb.14.22] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
ABSTRACT: The Human Microbiome Project (HMP) revealed the significance of the gut microbiome in promoting health. Disruptions in microbiome composition are associated with the pathogenesis of numerous diseases. The indigenous microflora has co-evolved with humans for millions of years and humans have preserved the inherited microbiomes through consumption of fermented foods and interactions with environmental microbes. Through modernization, traditional foods were abandoned, native food starters were substituted with industrial products, vaccines and antibiotics were used, extreme hygiene measures were taken, the rate of cesarean section increased, and breast feeding changed into formula. These factors have reduced human exposure to microbial symbionts and led to shrinkage of the core microbiome. Reduction in microbiome biodiversity can compromise the human immune system and predispose individuals to several modern diseases. This article suggests launching microbiome biobanks for archiving native microbiomes, supervising antibiotic use, probiotic design and native starter production, as well as advertising a revisit to native lifestyles.
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Affiliation(s)
- Abolfazl Barzegari
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
- Nutrition Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- The School of Advanced Biomedical Sciences (SABS), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nazli Saeedi
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Ata Saei
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
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Galley JD, Bailey MT. Impact of stressor exposure on the interplay between commensal microbiota and host inflammation. Gut Microbes 2014; 5:390-6. [PMID: 24690880 PMCID: PMC4153778 DOI: 10.4161/gmic.28683] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Exposure to stressful stimuli results in the activation of multiple physiological processes aimed at maintaining homeostasis within the body. These physiological processes also have the capacity to influence the composition of microbial communities, and research now indicates that exposure to stressful stimuli leads to gut microbiota dysbiosis. While the relative abundance of many different bacterial types can be altered during stressor exposure, findings in nonhuman primates and laboratory rodents, as well as humans, indicate that bacteria in the genus Lactobacillus are consistently reduced in the gut during stress. The gut microbiota, including the lactobacilli, have many functions that enhance the health of the host. This review presents studies involving germfree and antibiotic treated mice, as well as mice given Lactobacillus spp. to prevent stressor-induced reductions in lactobacilli, to provide evidence that the microbiota contribute to stressor-induced immunomodulation, both in gut mucosa as well as in systemic compartments. This review will also discuss the evidence that commensal gut microbes have bidirectional effects on gastrointestinal physiology during stressor exposure.
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Affiliation(s)
- Jeffrey D Galley
- Division of Oral Biology; College of Dentistry; The Ohio State University; Columbus, OH USA
| | - Michael T Bailey
- Division of Oral Biology; College of Dentistry; The Ohio State University; Columbus, OH USA,Institute for Behavioral Medicine Research; Wexner Medical Center; The Ohio State University; Columbus, OH USA,Correspondence to: Michael T Bailey,
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Chow J, Panasevich MR, Alexander D, Vester Boler BM, Rossoni Serao MC, Faber TA, Bauer LL, Fahey GC. Fecal Metabolomics of Healthy Breast-Fed versus Formula-Fed Infants before and during In Vitro Batch Culture Fermentation. J Proteome Res 2014; 13:2534-42. [DOI: 10.1021/pr500011w] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- JoMay Chow
- Abbott Nutrition, Columbus, Ohio 43219, United States
| | - Matthew R. Panasevich
- Department
of Animal Sciences, University of Illinois, Urbana, Illinois 61801, United States
| | - Danny Alexander
- Metabolon,
Inc., Durham, North Carolina 27713, United States
| | | | | | - Trevor A. Faber
- Department
of Animal Sciences, University of Illinois, Urbana, Illinois 61801, United States
| | - Laura L. Bauer
- Department
of Animal Sciences, University of Illinois, Urbana, Illinois 61801, United States
| | - George C. Fahey
- Department
of Animal Sciences, University of Illinois, Urbana, Illinois 61801, United States
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Abstract
The mammalian intestine must manage to contain 100 trillion intestinal bacteria without inducing inappropriate immune responses to these microorganisms. The effects of the immune system on intestinal microorganisms are numerous and well-characterized, and recent research has determined that the microbiota influences the intestinal immune system as well. In this review, we first discuss the intestinal immune system and its role in containing and maintaining tolerance to commensal organisms. We next introduce a category of immune cells, the innate lymphoid cells, and describe their classification and function in intestinal immunology. Finally, we discuss the effects of the intestinal microbiota on innate lymphoid cells.
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Influence of stressor-induced nervous system activation on the intestinal microbiota and the importance for immunomodulation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 817:255-76. [PMID: 24997038 DOI: 10.1007/978-1-4939-0897-4_12] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The body is colonized by a vast population of genetically diverse microbes, the majority of which reside within the intestines to comprise the intestinal microbiota. During periods of homeostasis, these microbes reside within stable climax communities, but exposure to physical, physiological, as well as psychological stressors can significantly impact the structure of the intestinal microbiota. This has been demonstrated in humans and laboratory animals, with the most consistent finding being a reduction in the abundance of bacteria in the genus Lactobacillus. Whether stressor exposure also changes the function of the microbiota, has not been as highly studied. The studies presented in this review suggest that stressor-induced disruption of the intestinal microbiota leads to increased susceptibility to enteric infection and overproduction of inflammatory mediators that can induce behavioral abnormalities, such as anxiety-like behavior. Studies involving germfree mice also demonstrate that the microbiota are necessary for stressor-induced increases in innate immunity to occur. Exposing mice to a social stressor enhances splenic macrophage microbicidal activity, but this effect fails to occur in germfree mice. These studies suggest a paradigm in which stressor exposure alters homeostatic interactions between the intestinal microbiota and mucosal immune system and leads to the translocation of pathogenic, and/or commensal, microbes from the lumen of the intestines to the interior of the body where they trigger systemic inflammatory responses and anxiety-like behavior. Restoring homeostasis in the intestines, either by removing the microbiota or by administering probiotic microorganisms, can ameliorate the stressor effects.
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Ahmer BMM. In this issue of Gut Microbes. Gut Microbes 2014; 5:83-5. [PMID: 24468723 PMCID: PMC4049943 DOI: 10.4161/gmic.28007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
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