601
|
Interactions between Host PPARs and Gut Microbiota in Health and Disease. Int J Mol Sci 2019; 20:ijms20020387. [PMID: 30658440 PMCID: PMC6359605 DOI: 10.3390/ijms20020387] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 12/28/2018] [Accepted: 01/05/2019] [Indexed: 12/12/2022] Open
Abstract
The human gastrointestinal tract is inhabited by many types of microbiota, including bacteria, viruses, and fungi. Dysregulations of their microenvironment are associated with various health problems, not only limited to gastrointestinal disorders, such as inflammatory bowel disease, but to impacts beyond the intestine. For example, intestinal microbiota can affect the liver in non-alcoholic fatty liver disease, visceral adipose tissue during adipogenesis, and the heart in atherosclerosis. The factors contributing to these pathogeneses involve the gut microbiota and the effector organs of the host, and everything in between. The nuclear receptor peroxisome proliferator-activated receptors (PPARs) are pivotal for the modulation of many of the pathogeneses mentioned above. It is, therefore, conceivable that, in the process of host-microbiota interactions, PPARs play important roles. In this review, we focus on the interactions between host PPARs in different organs and gut microbiota and their impacts on maintaining health and various diseases.
Collapse
|
602
|
Healthy infants harbor intestinal bacteria that protect against food allergy. Nat Med 2019; 25:448-453. [PMID: 30643289 PMCID: PMC6408964 DOI: 10.1038/s41591-018-0324-z] [Citation(s) in RCA: 270] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 12/05/2018] [Indexed: 12/30/2022]
Abstract
There has been a striking generational increase in life-threatening food allergies in Westernized societies1,2 One hypothesis to explain this rising prevalence is that 21st century lifestyle practices, including misuse of antibiotics, dietary changes, and higher rates of Caesarean birth and formula feeding have altered intestinal bacterial communities; early life alterations may be particularly detrimental.3,4 To better understand how commensal bacteria regulate food allergy in humans we colonized germ free (GF) mice with feces from healthy or cow’s milk allergic (CMA) infants 5. We show here that GF mice colonized with bacteria from healthy, but not CMA, infants were protected against anaphylactic responses to a cow’s milk allergen. Differences in bacterial composition separated the healthy and CMA populations in both the human donors and the colonized mice. Healthy and CMA colonized mice also exhibited unique transciptome signatures in the ileal epithelium. Correlation of ileal bacteria with genes upregulated in the ileum of healthy or CMA colonized mice identified a Clostridial species, Anaerostipes caccae, that protected against an allergic response to food. Our findings demonstrate that intestinal bacteria are critical for regulating allergic responses to dietary antigens and suggest that interventions that modulate bacterial communities may be therapeutically relevant for food allergy.
Collapse
|
603
|
Arredondo-Hernandez R, Orduña-Estrada P, Lopez-Vidal Y, Ponce de Leon-Rosales S. Clostridium Difficile Infection: An Immunological Conundrum. Arch Med Res 2019; 49:359-364. [PMID: 30617004 DOI: 10.1016/j.arcmed.2018.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 11/12/2018] [Indexed: 02/06/2023]
Abstract
The lack of comprehensive understanding of the way immunity backfires on incidence and complications has made Clostridium difficile infection (CDI), the infectious disease of our times, as evidenced by in the parallel course it follows along epidemic of chronic degenerative diseases. Within these ailments, if as suspected the main effect of Clostridium difficile A and B toxins depends on inflammation, then aberrant immune function due to antibiotics would explain IBD triggering after treatment but also, the higher incidence and mortality surrounding disorders that are inflammatory and/or that show abatement of neutrophils. This review will discuss severity of the disease in terms of challenges to immunity during the progression of acute illness. We will identify the common signals in the communication between microbiota and inflammatory cells, as well as the sequestration of the regulatory network by Clostridium difficile, which leads to tissue damage and prevents its elimination from intestinal lumen.
Collapse
Affiliation(s)
- Rene Arredondo-Hernandez
- División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Patricia Orduña-Estrada
- División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Yolanda Lopez-Vidal
- Departamento de Microbiologia y Parasitologia, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | |
Collapse
|
604
|
Niemarkt HJ, De Meij TG, van Ganzewinkel CJ, de Boer NKH, Andriessen P, Hütten MC, Kramer BW. Necrotizing Enterocolitis, Gut Microbiota, and Brain Development: Role of the Brain-Gut Axis. Neonatology 2019; 115:423-431. [PMID: 30974443 PMCID: PMC6604259 DOI: 10.1159/000497420] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 01/21/2019] [Indexed: 12/17/2022]
Abstract
Necrotizing enterocolitis (NEC) is a relatively common disease in very-low-birth-weight infants and is associated with high mortality and morbidity. In survivors, neurodevelopmental impairment is frequently seen. The exact etiology remains largely to be elucidated, but microbiota are considered to play a major role in the development of NEC. Furthermore, emerging evidence exists that the microbiota is also of importance in brain function and development. Therefore, microbiota characterization has not only potential as a diagnostic or even preventive tool to predict NEC, but may also serve as a biomarker to monitor and possibly even as a target to manipulate brain development. Analysis of fecal volatile organic compounds, which shape the volatile metabolome and reflect microbiota function and host interaction, has been shown to be of interest in the diagnosis of NEC and late-onset sepsis. In this review, we discuss evidence of the role of the complex interplay between microbiota, NEC, and brain development, including the brain-gut axis in preterm infants.
Collapse
Affiliation(s)
- Hendrik J Niemarkt
- Department of Neonatology, Máxima Medical Centre, Veldhoven, The Netherlands
| | - Tim G De Meij
- Department of Pediatric Gastroenterology, Amsterdam University Medical Centre, Amsterdam, The Netherlands
| | | | - Nanne K H de Boer
- Department of Gastroenterology and Hepatology, AG&M Research Institute, Amsterdam University Medical Centre, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Peter Andriessen
- Department of Neonatology, Máxima Medical Centre, Veldhoven, The Netherlands
| | - Matthias C Hütten
- Department of Pediatrics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Boris W Kramer
- Department of Pediatrics, Maastricht University Medical Centre, Maastricht, The Netherlands,
| |
Collapse
|
605
|
Acquistapace S, Patel L, Patin A, Forbes-Blom E, Cuenoud B, Wooster TJ. Effects of interesterified lipid design on the short/medium chain fatty acid hydrolysis rate and extent (in vitro). Food Funct 2019; 10:4166-4176. [DOI: 10.1039/c9fo00671k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Short/medium chain fatty acids have well known health effects such as gut immune regulation and ketogenesis.
Collapse
Affiliation(s)
| | | | - Amaury Patin
- Institute of Food Safety and Analytical Sciences
- Nestlé Research
- Lausanne
- Switzerland
| | | | - Bernard Cuenoud
- Translation Research
- Nestlé Health Science
- Epalinges
- Switzerland
| | - Tim J. Wooster
- Nestlé Institute of Material Sciences
- Nestlé Research
- Lausanne
- Switzerland
| |
Collapse
|
606
|
Fu A, Mo Q, Wu Y, Wang B, Liu R, Tang L, Zeng Z, Zhang X, Li W. Protective effect of Bacillus amyloliquefaciens against Salmonella via polarizing macrophages to M1 phenotype directly and to M2 depended on microbiota. Food Funct 2019; 10:7653-7666. [DOI: 10.1039/c9fo01651a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bacillus amyloliquefaciens SC06 (BaSC06), a potential probiotic, plays a positive role in animal growth performance and immune function.
Collapse
Affiliation(s)
- Aikun Fu
- Key Laboratory of Animal Molecular Nutrition of Education of Ministry
- College of Animal Sciences
- Zhejiang University
- Hangzhou
- China
| | - Qiufen Mo
- Key Laboratory of Animal Molecular Nutrition of Education of Ministry
- College of Animal Sciences
- Zhejiang University
- Hangzhou
- China
| | - Yanping Wu
- Key Laboratory of Animal Molecular Nutrition of Education of Ministry
- College of Animal Sciences
- Zhejiang University
- Hangzhou
- China
| | - Baikui Wang
- Key Laboratory of Animal Molecular Nutrition of Education of Ministry
- College of Animal Sciences
- Zhejiang University
- Hangzhou
- China
| | - Rongrong Liu
- Key Laboratory of Animal Molecular Nutrition of Education of Ministry
- College of Animal Sciences
- Zhejiang University
- Hangzhou
- China
| | - Li Tang
- Key Laboratory of Animal Molecular Nutrition of Education of Ministry
- College of Animal Sciences
- Zhejiang University
- Hangzhou
- China
| | - Zhonghua Zeng
- Key Laboratory of Animal Molecular Nutrition of Education of Ministry
- College of Animal Sciences
- Zhejiang University
- Hangzhou
- China
| | - Xiaoping Zhang
- China National Bamboo Research Center
- Key Laboratory of Resources and Utilization of Bamboo of State Forestry Administration
- Hangzhou
- China
| | - Weifen Li
- Key Laboratory of Animal Molecular Nutrition of Education of Ministry
- College of Animal Sciences
- Zhejiang University
- Hangzhou
- China
| |
Collapse
|
607
|
Renouf MJ, Cho YH, McPhee JB. Emergent Behavior of IBD-Associated Escherichia coli During Disease. Inflamm Bowel Dis 2019; 25:33-44. [PMID: 30321333 DOI: 10.1093/ibd/izy312] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Indexed: 12/12/2022]
Abstract
Inflammatory bowel diseases are becoming increasingly common throughout the world, both in developed countries and increasingly in rapidly developing countries. Multiple lines of evidence point to a role for the microbial composition of the gastrointestinal tract in the etiology of IBD, but to date, attempts to define a specific microbial cause for IBD have proved unsuccessful. Microbial 16S rRNA profiling shows that IBD patients have elevated levels of Enterobacteriaceae, in particular Escherichia coli, and reduced levels of Faecalibacterium prausnitzii. The observed E. coli have been assigned to a specific pathovar, adherent-invasive E. coli (AIEC). Adherent-invasive E. coli are a genomically heterogenous group, and whereas many groups have attempted to identify specific genetic markers that differentiate AIEC from non-AIEC strains, very few concrete genetic associations have been uncovered. Here, we highlight the advantages of applying a phenotyping approach to the study of these organisms, rather than solely depending on a sequencing or genomic-based screening strategy because virulence-associated phenotypes exhibit behaviors of emergent systems. In this respect, attempts at genetic reductionism are prone to failure because there are numerous metabolic, regulatory or genetic paths that can underlie these virulence-associated behaviors. Here, we review these IBD-associated phenotypes in E. coli and make recommendations for experimental approaches to advance our understanding of IBD-associated bacteria more generally. With advances in high-throughput screening and nongenetically based metabolomic characterization of IBD-associated bacteria, we anticipate a fuller understanding of how altered microbial communities contribute to the development of IBD.
Collapse
Affiliation(s)
| | - Youn Hee Cho
- Department of Chemistry and Biology, Ryerson University, Toronto ON, Canada
| | - Joseph B McPhee
- Department of Chemistry and Biology, Ryerson University, Toronto ON, Canada
| |
Collapse
|
608
|
Cani PD, Van Hul M, Lefort C, Depommier C, Rastelli M, Everard A. Microbial regulation of organismal energy homeostasis. Nat Metab 2019; 1:34-46. [PMID: 32694818 DOI: 10.1038/s42255-018-0017-4] [Citation(s) in RCA: 300] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/15/2018] [Indexed: 12/13/2022]
Abstract
The gut microbiome has emerged as a key regulator of host metabolism. Here we review the various mechanisms through which the gut microbiome influences the energy metabolism of its host, highlighting the complex interactions between gut microbes, their metabolites and host cells. Among the most important bacterial metabolites are short-chain fatty acids, which serve as a direct energy source for host cells, stimulate the production of gut hormones and act in the brain to regulate food intake. Other microbial metabolites affect systemic energy expenditure by influencing thermogenesis and adipose tissue browning. Both direct and indirect mechanisms of action are known for specific metabolites, such as bile acids, branched chain amino acids, indole propionic acid and endocannabinoids. We also discuss the roles of specific bacteria in the production of specific metabolites and explore how external factors, such as antibiotics and exercise, affect the microbiome and thereby energy homeostasis. Collectively, we present a large body of evidence supporting the concept that gut microbiota-based therapies can be used to modulate host metabolism, and we expect to see such approaches moving from bench to bedside in the near future.
Collapse
Affiliation(s)
- Patrice D Cani
- Metabolism and Nutrition Research Group, WELBIO-Walloon Excellence in Life Sciences and BIOtechnology, Louvain Drug Research Institute, UCLouvain, Université catholique de Louvain, Brussels, Belgium.
| | - Matthias Van Hul
- Metabolism and Nutrition Research Group, WELBIO-Walloon Excellence in Life Sciences and BIOtechnology, Louvain Drug Research Institute, UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Charlotte Lefort
- Metabolism and Nutrition Research Group, WELBIO-Walloon Excellence in Life Sciences and BIOtechnology, Louvain Drug Research Institute, UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Clara Depommier
- Metabolism and Nutrition Research Group, WELBIO-Walloon Excellence in Life Sciences and BIOtechnology, Louvain Drug Research Institute, UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Marialetizia Rastelli
- Metabolism and Nutrition Research Group, WELBIO-Walloon Excellence in Life Sciences and BIOtechnology, Louvain Drug Research Institute, UCLouvain, Université catholique de Louvain, Brussels, Belgium
| | - Amandine Everard
- Metabolism and Nutrition Research Group, WELBIO-Walloon Excellence in Life Sciences and BIOtechnology, Louvain Drug Research Institute, UCLouvain, Université catholique de Louvain, Brussels, Belgium
| |
Collapse
|
609
|
Abstract
Since the renaissance of microbiome research in the past decade, much insight has accumulated in comprehending forces shaping the architecture and functionality of resident microorganisms in the human gut. Of the multiple host-endogenous and host-exogenous factors involved, diet emerges as a pivotal determinant of gut microbiota community structure and function. By introducing dietary signals into the nexus between the host and its microbiota, nutrition sustains homeostasis or contributes to disease susceptibility. Herein, we summarize major concepts related to the effect of dietary constituents on the gut microbiota, highlighting chief principles in the diet-microbiota crosstalk. We then discuss the health benefits and detrimental consequences that the interactions between dietary and microbial factors elicit in the host. Finally, we present the promises and challenges that arise when seeking to incorporate microbiome data in dietary planning and portray the anticipated revolution that the field of nutrition is facing upon adopting these novel concepts.
Collapse
Affiliation(s)
- Niv Zmora
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel.,Gastroenterology Unit, Tel Aviv Sourasky Medical Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jotham Suez
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Elinav
- Immunology Department, Weizmann Institute of Science, Rehovot, Israel.
| |
Collapse
|
610
|
Whang A, Nagpal R, Yadav H. Bi-directional drug-microbiome interactions of anti-diabetics. EBioMedicine 2019; 39:591-602. [PMID: 30553752 PMCID: PMC6354569 DOI: 10.1016/j.ebiom.2018.11.046] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 11/13/2018] [Accepted: 11/21/2018] [Indexed: 12/18/2022] Open
Abstract
Type 2 diabetes (T2D) has become a global epidemic. Although several drugs are available to manage T2D, problems associated with person-to-person variability in drug efficacy and potential side-effects remain unresolved. Owing to the emerging role of the gut microbiome in obesity and T2D, the interaction between gut microbes and anti-diabetic drugs and its influence on drugs' functions remains of immediate research interest. On one hand, drugs can manipulate gut microbiome composition and metabolic capacity. Conversely, the metabolic activities of the microbiome and its metabolites can also influence drug metabolism and effects. Hence, understanding this bi-directional drug-microbiome interaction and how it influences the clinical outcomes of antidiabetic drugs can pave the way to develop next-generation strategies to ameliorate diabetes. This review presents evidences demonstrating the putative interactions between anti-diabetic drugs and the gut microbiome, and discusses the potential of microbiome modulators to manipulate drug-microbiome interactions and the drug metabolism.
Collapse
Affiliation(s)
- Andrew Whang
- Department of Internal Medicine- Molecular Medicine, Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Ravinder Nagpal
- Department of Internal Medicine- Molecular Medicine, Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Hariom Yadav
- Department of Internal Medicine- Molecular Medicine, Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, NC, USA.
| |
Collapse
|
611
|
Li Q, Chen H, Zhang M, Wu T, Liu R. Altered short chain fatty acid profiles induced by dietary fiber intervention regulate AMPK levels and intestinal homeostasis. Food Funct 2019; 10:7174-7187. [DOI: 10.1039/c9fo01465a] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Butanoate-mediated maintenance of intestinal integrity and homeostasis and the AMPK-dependent co-regulated pathway.
Collapse
Affiliation(s)
- Qian Li
- State Key Laboratory of Nutrition and Safety
- Tianjin University of Science & Technology
- Tianjin 300457
- China
| | - Haixia Chen
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency
- School of Pharmaceutical Science and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Min Zhang
- State Key Laboratory of Nutrition and Safety
- Tianjin University of Science & Technology
- Tianjin 300457
- China
- Tianjin University of Science and Technology
| | - Tao Wu
- State Key Laboratory of Nutrition and Safety
- Tianjin University of Science & Technology
- Tianjin 300457
- China
- Tianjin University of Science and Technology
| | - Rui Liu
- State Key Laboratory of Nutrition and Safety
- Tianjin University of Science & Technology
- Tianjin 300457
- China
| |
Collapse
|
612
|
Zhang Y, Zhang B, Dong L, Chang P. Potential of Omega-3 Polyunsaturated Fatty Acids in Managing Chemotherapy- or Radiotherapy-Related Intestinal Microbial Dysbiosis. Adv Nutr 2019; 10:133-147. [PMID: 30566596 PMCID: PMC6370266 DOI: 10.1093/advances/nmy076] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 09/10/2018] [Indexed: 02/06/2023] Open
Abstract
Chemotherapy- or radiotherapy-related intestinal microbial dysbiosis is one of the main causes of intestinal mucositis. Cases of bacterial translocation into peripheral blood and subsequent sepsis occur as a result of dysfunction in the intestinal barrier. Evidence from recent studies depicts the characteristics of chemotherapy- or radiotherapy-related intestinal microbial dysbiosis, which creates an imbalance between beneficial and harmful bacteria in the gut. Decreases in beneficial bacteria can lead to a weakening of the resistance of the gut to harmful bacteria, resulting in robust activation of proinflammatory signaling pathways. For example, lipopolysaccharide (LPS)-producing bacteria activate the nuclear transcription factor-κB signaling pathway through binding with Toll-like receptor 4 on stressed epithelial cells, subsequently leading to secretion of proinflammatory cytokines. Nevertheless, various studies have found that the omega-3 (n-3) polyunsaturated fatty acids (PUFAs) such as docosahexaenoic acid and eicosapentaenoic acid can reverse intestinal microbial dysbiosis by increasing beneficial bacteria species, including Lactobacillus, Bifidobacterium, and butyrate-producing bacteria, such as Roseburia and Coprococcus. In addition, the n-3 PUFAs decrease the proportions of LPS-producing and mucolytic bacteria in the gut, and they can reduce inflammation as well as oxidative stress. Importantly, the n-3 PUFAs also exert anticancer effects in colorectal cancers. In this review, we summarize the characteristics of chemotherapy- or radiotherapy-related intestinal microbial dysbiosis and introduce the contributions of dysbiosis to the pathogenesis of intestinal mucositis. Next, we discuss how n-3 PUFAs could alleviate chemotherapy- or radiotherapy-related intestinal microbial dysbiosis. This review provides new insights into the clinical administration of n-3 PUFAs for the management of chemotherapy- or radiotherapy-related intestinal microbial dysbiosis.
Collapse
Affiliation(s)
- Yue Zhang
- Department of Radiation Oncology, First Bethune Hospital of Jilin University, ChangChun, China
| | - Boyan Zhang
- Orthopedic Medical Center, The Second Hospital of Jilin University, ChangChun, China
| | - Lihua Dong
- Department of Radiation Oncology, First Bethune Hospital of Jilin University, ChangChun, China,Address correspondence to LD (e-mail: )
| | - Pengyu Chang
- Department of Radiation Oncology, First Bethune Hospital of Jilin University, ChangChun, China,Address correspondence to PC (e-mail: )
| |
Collapse
|
613
|
Sorbara MT, Pamer EG. Interbacterial mechanisms of colonization resistance and the strategies pathogens use to overcome them. Mucosal Immunol 2019; 12:1-9. [PMID: 29988120 PMCID: PMC6312114 DOI: 10.1038/s41385-018-0053-0] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/15/2018] [Accepted: 05/27/2018] [Indexed: 02/08/2023]
Abstract
The communities of bacteria that reside in the intestinal tract are in constant competition within this dynamic and densely colonized environment. At homeostasis, the equilibrium that exists between these species and strains is shaped by their metabolism and also by pathways of active antagonism, which drive competition with related and unrelated strains. Importantly, these normal activities contribute to colonization resistance by the healthy microbiota, which includes the ability to prevent the expansion of potential pathogens. Disruption of the microbiota, resulting from, for example, inflammation or antibiotic use, can reduce colonization resistance. Pathogens that engraft following disruption of the microbiota are often adapted to expand into newly created niches and compete in an altered gut environment. In this review, we examine both the interbacterial mechanisms of colonization resistance and the strategies of pathogenic strains to exploit gaps in colonization resistance.
Collapse
Affiliation(s)
- Matthew T. Sorbara
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Eric G. Pamer
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
- Center for Microbes, Inflammation and Cancer, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| |
Collapse
|
614
|
Natural polysaccharides exhibit anti-tumor activity by targeting gut microbiota. Int J Biol Macromol 2019; 121:743-751. [DOI: 10.1016/j.ijbiomac.2018.10.083] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/29/2018] [Accepted: 10/14/2018] [Indexed: 12/30/2022]
|
615
|
Singer-Englar T, Barlow G, Mathur R. Obesity, diabetes, and the gut microbiome: an updated review. Expert Rev Gastroenterol Hepatol 2019; 13:3-15. [PMID: 30791839 DOI: 10.1080/17474124.2019.1543023] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Obesity and diabetes are two of the most prevalent health problems and leading causes of death globally. As research on the intestinal microbiome increases, so does our understanding of its intricate relationship to these diseases, although this has yet to be fully elucidated. Areas covered: This review evaluates the role of the gut microbiome in obesity and diabetes, including the influences of internal and environmental factors. Literature searches were performed using the keywords 'diabetes,' 'insulin resistance,' 'gut microbiome,' 'gut microbes,' 'obesity,' and 'weight gain.' Expert commentary: Highlights of recent research include new findings regarding the effects of caloric restriction, which expound the importance of diet in shaping the gut microbiome, and studies reinforcing the lasting implications of antibiotic use for diabetes and obesity, particularly repeated doses in early childhood. Mechanistically, interactions between the microbiome and the host innate immune system, mediated by TLR4-LPS signaling, have been shown to meditate the metabolic benefits of caloric restriction. Further, gut microbes haven now been shown to regulate oxygen availability via butyrate production, thus protecting against the proliferation of pathogens such as E. coli and Salmonella. However, many microbial metabolites remain unidentified and their roles in obesity and diabetes remain to be determined.
Collapse
Affiliation(s)
- Tahli Singer-Englar
- a Medically Associated Science and Technology (MAST) Program , Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Gillian Barlow
- a Medically Associated Science and Technology (MAST) Program , Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Ruchi Mathur
- a Medically Associated Science and Technology (MAST) Program , Cedars-Sinai Medical Center , Los Angeles , CA , USA
| |
Collapse
|
616
|
Wang XQ, Zhang AH, Miao JH, Sun H, Yan GL, Wu FF, Wang XJ. Gut microbiota as important modulator of metabolism in health and disease. RSC Adv 2018; 8:42380-42389. [PMID: 35558413 PMCID: PMC9092240 DOI: 10.1039/c8ra08094a] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 12/02/2018] [Indexed: 12/12/2022] Open
Abstract
The human gastrointestinal tract colonizes a large number of microbial microflora, forms a host-microbiota co-metabolism structure with the host to participate in various metabolic processes in the human body, and plays a major role in the host immune response. In addition, the dysbiosis of intestinal microbial homeostasis is closely related to many diseases. Thus, an in-depth understanding of the relationship between them is of importance for disease pathogenesis, prevention and treatment. The combined use of metagenomics, transcriptomics, proteomics and metabolomics techniques for the analysis of gut microbiota can reveal the relationship between microbiota and the host in many ways, which has become a hot topic of analysis in recent years. This review describes the mechanism of co-metabolites in host health, including short-chain fatty acids (SCFA) and bile acid metabolism. The metabolic role of gut microbiota in obesity, liver diseases, gastrointestinal diseases and other diseases is also summarized, and the research methods for multi-omics combined application on gut microbiota are summarized. According to the studies of the interaction mechanism between gut microbiota and the host, we have a better understanding of the use of intestinal microflora in the treatment of related diseases. It is hoped that the gut microbiota can be utilized to maintain human health, providing a reference for future research.
Collapse
Affiliation(s)
- Xiang-Qian Wang
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plant Nanning Guangxi China +86-451-82110818 +86-451-82110818
- National Chinmedomics Research Center, Sino-America Chinmedomics Technology Collaboration Center, National TCM Key Laboratory of Serum Pharmacochemistry, Chinmedomics Research Center of State Administration of TCM, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine Heping Road 24 Harbin China
| | - Ai-Hua Zhang
- National Chinmedomics Research Center, Sino-America Chinmedomics Technology Collaboration Center, National TCM Key Laboratory of Serum Pharmacochemistry, Chinmedomics Research Center of State Administration of TCM, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine Heping Road 24 Harbin China
| | - Jian-Hua Miao
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plant Nanning Guangxi China +86-451-82110818 +86-451-82110818
| | - Hui Sun
- National Chinmedomics Research Center, Sino-America Chinmedomics Technology Collaboration Center, National TCM Key Laboratory of Serum Pharmacochemistry, Chinmedomics Research Center of State Administration of TCM, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine Heping Road 24 Harbin China
| | - Guang-Li Yan
- National Chinmedomics Research Center, Sino-America Chinmedomics Technology Collaboration Center, National TCM Key Laboratory of Serum Pharmacochemistry, Chinmedomics Research Center of State Administration of TCM, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine Heping Road 24 Harbin China
| | - Fang-Fang Wu
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plant Nanning Guangxi China +86-451-82110818 +86-451-82110818
| | - Xi-Jun Wang
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plant Nanning Guangxi China +86-451-82110818 +86-451-82110818
- National Chinmedomics Research Center, Sino-America Chinmedomics Technology Collaboration Center, National TCM Key Laboratory of Serum Pharmacochemistry, Chinmedomics Research Center of State Administration of TCM, Laboratory of Metabolomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine Heping Road 24 Harbin China
| |
Collapse
|
617
|
Sorbara MT, Dubin K, Littmann ER, Moody TU, Fontana E, Seok R, Leiner IM, Taur Y, Peled JU, van den Brink MRM, Litvak Y, Bäumler AJ, Chaubard JL, Pickard AJ, Cross JR, Pamer EG. Inhibiting antibiotic-resistant Enterobacteriaceae by microbiota-mediated intracellular acidification. J Exp Med 2018; 216:84-98. [PMID: 30563917 PMCID: PMC6314524 DOI: 10.1084/jem.20181639] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/26/2018] [Accepted: 12/07/2018] [Indexed: 12/17/2022] Open
Abstract
Klebsiella pneumoniae, Escherichia coli, and other members of the Enterobacteriaceae family are common human pathogens that have acquired broad antibiotic resistance, rendering infection by some strains virtually untreatable. Enterobacteriaceae are intestinal residents, but generally represent <1% of the adult colonic microbiota. Antibiotic-mediated destruction of the microbiota enables Enterobacteriaceae to expand to high densities in the colon, markedly increasing the risk of bloodstream invasion, sepsis, and death. Here, we demonstrate that an antibiotic-naive microbiota suppresses growth of antibiotic-resistant clinical isolates of Klebsiella pneumoniae, Escherichia coli, and Proteus mirabilis by acidifying the proximal colon and triggering short chain fatty acid (SCFA)-mediated intracellular acidification. High concentrations of SCFAs and the acidic environment counter the competitive edge that O2 and NO3 respiration confer upon Enterobacteriaceae during expansion. Reestablishment of a microbiota that produces SCFAs enhances clearance of Klebsiella pneumoniae, Escherichia coli, and Proteus mirabilis from the intestinal lumen and represents a potential therapeutic approach to enhance clearance of antibiotic-resistant pathogens.
Collapse
Affiliation(s)
- Matthew T Sorbara
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY .,Center for Microbes, Inflammation and Cancer, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Krista Dubin
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Eric R Littmann
- Center for Microbes, Inflammation and Cancer, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Thomas U Moody
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY.,Center for Microbes, Inflammation and Cancer, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Emily Fontana
- Center for Microbes, Inflammation and Cancer, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ruth Seok
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY.,Center for Microbes, Inflammation and Cancer, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ingrid M Leiner
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY.,Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Center for Microbes, Inflammation and Cancer, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ying Taur
- Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Jonathan U Peled
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Marcel R M van den Brink
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Yael Litvak
- Department of Medical Microbiology and Immunology, University of California, Davis School of Medicine, Davis, CA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, University of California, Davis School of Medicine, Davis, CA
| | - Jean-Luc Chaubard
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Amanda J Pickard
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Justin R Cross
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Eric G Pamer
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY .,Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY.,Center for Microbes, Inflammation and Cancer, Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| |
Collapse
|
618
|
Vonaesch P, Anderson M, Sansonetti PJ. Pathogens, microbiome and the host: emergence of the ecological Koch's postulates. FEMS Microbiol Rev 2018; 42:273-292. [PMID: 29325027 DOI: 10.1093/femsre/fuy003] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Indexed: 02/07/2023] Open
Abstract
Even though tremendous progress has been made in the last decades to elucidate the mechanisms of intestinal homeostasis, dysbiosis and disease, we are only at the beginning of understanding the complexity of the gut ecosystem and the underlying interaction networks. We are also only starting to unravel the mechanisms that pathogens have evolved to overcome the barriers imposed by the microbiota and host to exploit the system to their own benefit. Recent work in these domains clearly indicates that the 'traditional Koch's postulates', which state that a given pathogen leads to a distinct disease, are not valid for all 'infectious' diseases, but that a more complete and complex interpretation of Koch's postulates is needed in order to understand and explain them. This review summarises the current understanding of what defines a healthy gut ecosystem and highlights recent progress in uncovering the interplay between the host, its microbiota and invading intestinal pathogens. Based on these recent findings, we propose a new interpretation of Koch's postulates that we term 'ecological Koch's postulates'.
Collapse
Affiliation(s)
- Pascale Vonaesch
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 28 Rue du Dr. Roux, Paris 75015, France
| | - Mark Anderson
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 28 Rue du Dr. Roux, Paris 75015, France
| | - Philippe J Sansonetti
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 28 Rue du Dr. Roux, Paris 75015, France
| |
Collapse
|
619
|
Gut Microbiome Dysbiosis and Immunometabolism: New Frontiers for Treatment of Metabolic Diseases. Mediators Inflamm 2018; 2018:2037838. [PMID: 30622429 PMCID: PMC6304917 DOI: 10.1155/2018/2037838] [Citation(s) in RCA: 160] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 10/23/2018] [Indexed: 02/06/2023] Open
Abstract
Maintenance of healthy human metabolism depends on a symbiotic consortium among bacteria, archaea, viruses, fungi, and host eukaryotic cells throughout the human gastrointestinal tract. Microbial communities provide the enzymatic machinery and the metabolic pathways that contribute to food digestion, xenobiotic metabolism, and production of a variety of bioactive molecules. These include vitamins, amino acids, short-chain fatty acids (SCFAs), and metabolites, which are essential for the interconnected pathways of glycolysis, the tricarboxylic acid/Krebs cycle, oxidative phosphorylation (OXPHOS), and amino acid and fatty acid metabolism. Recent studies have been elucidating how nutrients that fuel the metabolic processes impact on the ways immune cells, in particular, macrophages, respond to different stimuli under physiological and pathological conditions and become activated and acquire a specialized function. The two major inflammatory phenotypes of macrophages are controlled through differential consumption of glucose, glutamine, and oxygen. M1 phenotype is triggered by polarization signal from bacterial lipopolysaccharide (LPS) and Th1 proinflammatory cytokines such as interferon-γ, TNF-α, and IL-1β, or both, whereas M2 phenotype is triggered by Th2 cytokines such as interleukin-4 and interleukin-13 as well as anti-inflammatory cytokines, IL-10 and TGFβ, or glucocorticoids. Glucose utilization and production of chemical mediators including ATP, reactive oxygen species (ROS), nitric oxide (NO), and NADPH support effector activities of M1 macrophages. Dysbiosis is an imbalance of commensal and pathogenic bacteria and the production of microbial antigens and metabolites. It is now known that the gut microbiota-derived products induce low-grade inflammatory activation of tissue-resident macrophages and contribute to metabolic and degenerative diseases, including diabetes, obesity, metabolic syndrome, and cancer. Here, we update the potential interplay of host gut microbiome dysbiosis and metabolic diseases. We also summarize on advances on fecal therapy, probiotics, prebiotics, symbiotics, and nutrients and small molecule inhibitors of metabolic pathway enzymes as prophylactic and therapeutic agents for metabolic diseases.
Collapse
|
620
|
Abstract
An imbalance in the colonic microbiota might underlie many human diseases, but the mechanisms that maintain homeostasis remain elusive. Recent insights suggest that colonocyte metabolism functions as a control switch, mediating a shift between homeostatic and dysbiotic communities. During homeostasis, colonocyte metabolism is directed toward oxidative phosphorylation, resulting in high epithelial oxygen consumption. The consequent epithelial hypoxia helps to maintain a microbial community dominated by obligate anaerobic bacteria, which provide benefit by converting fiber into fermentation products absorbed by the host. Conditions that alter the metabolism of the colonic epithelium increase epithelial oxygenation, thereby driving an expansion of facultative anaerobic bacteria, a hallmark of dysbiosis in the colon. Enteric pathogens subvert colonocyte metabolism to escape niche protection conferred by the gut microbiota. The reverse strategy, a metabolic reprogramming to restore colonocyte hypoxia, represents a promising new therapeutic approach for rebalancing the colonic microbiota in a broad spectrum of human diseases.
Collapse
Affiliation(s)
- Yael Litvak
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA
| | - Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA
| | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616, USA.
| |
Collapse
|
621
|
Sekiguchi K, Kurohane K, Tsutsumi M, Mochizuki N, Orii A, Nose M, Imai Y. Enhancement of mouse contact hypersensitivity appears with a short chain triacylglycerol but not with a long chain one. Toxicology 2018; 412:48-54. [PMID: 30503584 DOI: 10.1016/j.tox.2018.11.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/23/2018] [Accepted: 11/28/2018] [Indexed: 10/27/2022]
Abstract
The prevalence of skin allergies could be partly due to the increased exposure to chemicals from consumer products. Chemicals that can enhance hypersensitivity caused by other chemicals are the focus of this study. We have demonstrated that phthalate esters with short chain alcohols enhance fluorescein isothiocyanate (FITC)-induced contact hypersensitivity (CHS) in a mouse model. We have also found that tributyrin, a triacylglycerol (TAG) with three butyric acids, enhances sensitization to FITC. To elucidate such an enhanced skin sensitization might be based on a general feature of TAG, we compared tributyrin and triolein, a natural TAG, as to an adjuvant effect on FITC-CHS. Triolein is the dominant TAG in olive oil and contains long chain mono-unsaturated fatty acids. Unlike tributyrin and dibutyl phthalate (DBP), triolein did not exhibit an adjuvant effect. With triolein, enhancement of FITC-presenting CD11c+ dendritic cell trafficking to draining lymph nodes was weak, and the activation status of DC, as revealed as CD86 expression, was low. We found a difference in the pattern of skin cytokine production, i.e., that thymic stromal lymphopoietin was produced with DBP and interleukin-1β with tributyrin. Triolein did not induce either of these cytokines. This illustrates that the adjuvant effect of tributyrin on FITC-CHS is not a general phenomenon for TAGs. Although beneficial effects may be expected through oral administration of tributyrin, the effect on skin immune systems should be considered.
Collapse
Affiliation(s)
- Kota Sekiguchi
- Laboratory of Microbiology and Immunology, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka City, Shizuoka, 422-8526, Japan
| | - Kohta Kurohane
- Laboratory of Microbiology and Immunology, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka City, Shizuoka, 422-8526, Japan
| | - Masato Tsutsumi
- Laboratory of Microbiology and Immunology, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka City, Shizuoka, 422-8526, Japan
| | - Narumi Mochizuki
- Laboratory of Microbiology and Immunology, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka City, Shizuoka, 422-8526, Japan
| | - Akimasa Orii
- Laboratory of Microbiology and Immunology, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka City, Shizuoka, 422-8526, Japan
| | - Mutsumi Nose
- Laboratory of Microbiology and Immunology, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka City, Shizuoka, 422-8526, Japan
| | - Yasuyuki Imai
- Laboratory of Microbiology and Immunology, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka City, Shizuoka, 422-8526, Japan.
| |
Collapse
|
622
|
Suzuki TA, Martins FM, Nachman MW. Altitudinal variation of the gut microbiota in wild house mice. Mol Ecol 2018; 28:2378-2390. [PMID: 30346069 DOI: 10.1111/mec.14905] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/25/2018] [Accepted: 10/06/2018] [Indexed: 12/11/2022]
Abstract
The maintenance of oxygen homeostasis in the gut is critical for the maintenance of a healthy gut microbiota. However, few studies have explored how the concentration of atmospheric oxygen affects the gut microbiota in natural populations. High-altitude environments provide an opportunity to study the potential effects of atmospheric oxygen on the composition and function of the gut microbiota. Here, we characterized the caecal microbial communities of wild house mice (Mus musculus domesticus) in two independent altitudinal transects, one in Ecuador and one in Bolivia, from sea level to nearly 4,000 m. First, we found that differences in altitude were associated with differences in the gut microbial community after controlling for the effects of body mass, diet, reproductive status and population of origin. Second, obligate anaerobes tended to show a positive correlation with altitude, while all other microbes tended to show a negative correlation with altitude. These patterns were seen independently in both transects, consistent with the expected effects of atmospheric oxygen on gut microbes. Prevotella was the most-enriched genus at high elevations in both transects, consistent with observations in high-altitude populations of pikas, ruminants and humans, and also consistent with observations of laboratory mice exposed to hypoxic conditions. Lastly, the renin-angiotensin system, a recently proposed microbiota-mediated pathway of blood pressure regulation, was the top predicted metagenomic pathway enriched in high altitudes in both transects. These results suggest that high-altitude environments affect the composition and function of the gut microbiota in wild mammals.
Collapse
Affiliation(s)
- Taichi A Suzuki
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California
| | - Felipe M Martins
- Department of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australian Capital Territory, Australia
| | - Michael W Nachman
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California
| |
Collapse
|
623
|
Guo J, Han X, Zhan J, You Y, Huang W. Vanillin Alleviates High Fat Diet-Induced Obesity and Improves the Gut Microbiota Composition. Front Microbiol 2018; 9:2733. [PMID: 30483238 PMCID: PMC6243071 DOI: 10.3389/fmicb.2018.02733] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 10/25/2018] [Indexed: 12/17/2022] Open
Abstract
Vanillin, a simple phenolic compound, exists marginally in some plants and can be produced by microbes. This study uses high-fat-diet (HFD) induced obese mice to study the effect of vanillin on obesity and obtain positive results. First, both body and adipose tissue weight are reduced. Second, the blood properties signaling certain disorders such as ALT, LDH, glucose, cholesterol, LDL-C, TG and HDL-C are ameliorated and both insulin sensitivity, and glucose tolerance are improved. Third, vanillin reduced elevated levels of inflammatory factors including LPS, IL-6, and TNF-α in plasma and liver tissue resulting from obesity. Finally, the production of short chain fatty acids (SCFAs) is enhanced. Additionally, study results demonstrate that vanillin significantly alleviates obesity-related gut microbiota (GM) disorders including the decrease of alpha- and beta-diversity. Furthermore, vanillin reduces the abundance of Firmicutes phylum, increases the richness of Bacteroidetes and Verrucomicrobiota phyla, and inhibits the expansion of the lipopolysaccharide (LPS)-producing bacteria Bilophila genus and the H2S-producing bacteria Desulfovibrio genus.
Collapse
Affiliation(s)
- Jielong Guo
- College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Viticulture and Enology, China Agricultural University, Beijing, China
| | - Xue Han
- College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Viticulture and Enology, China Agricultural University, Beijing, China
| | - Jicheng Zhan
- College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Viticulture and Enology, China Agricultural University, Beijing, China
| | - Yilin You
- College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Viticulture and Enology, China Agricultural University, Beijing, China
| | - Weidong Huang
- College of Food Science and Nutritional Engineering, Beijing Key Laboratory of Viticulture and Enology, China Agricultural University, Beijing, China
| |
Collapse
|
624
|
Cani PD, Jordan BF. Gut microbiota-mediated inflammation in obesity: a link with gastrointestinal cancer. Nat Rev Gastroenterol Hepatol 2018; 15:671-682. [PMID: 29844585 DOI: 10.1038/s41575-018-0025-6] [Citation(s) in RCA: 224] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Overweight and obesity are associated with increased risk of developing metabolic disorders such as diabetes and cardiovascular diseases. However, besides these metabolic diseases, excess body weight is also associated with different cancers, including gastrointestinal cancers, such as liver, pancreatic and colon cancers. Inflammation is a common feature of both obesity and cancer; however, the origin of this inflammation has been largely debated. Over the past decade, growing evidence has shown that the composition of the gut microbiota and its activity might be associated not only with the onset of inflammation but also with metabolic disorders and cancer. Here, we review the links between the gut microbiota, gut barrier function and the onset of low-grade inflammation in the development of gastrointestinal cancer. We also describe the mechanisms by which specific microorganism-associated molecular patterns crosstalk with the immune system and how the metabolic activity of bacteria induces specific signalling pathways beyond the gut that eventually trigger carcinogenesis.
Collapse
Affiliation(s)
- Patrice D Cani
- Université catholique de Louvain, Louvain Drug Research Institute, WELBIO (Walloon Excellence in Life sciences and BIOtechnology), Metabolism and Nutrition Research Group, Brussels, Belgium.
| | - Benedicte F Jordan
- Université catholique de Louvain, Louvain Drug Research Institute, Biomedical Magnetic Resonance Research Group, Brussels, Belgium
| |
Collapse
|
625
|
Piccolo BD, Graham JL, Stanhope KL, Nookaew I, Mercer KE, Chintapalli SV, Wankhade UD, Shankar K, Havel PJ, Adams SH. Diabetes-associated alterations in the cecal microbiome and metabolome are independent of diet or environment in the UC Davis Type 2 Diabetes Mellitus Rat model. Am J Physiol Endocrinol Metab 2018; 315:E961-E972. [PMID: 30016149 PMCID: PMC6293161 DOI: 10.1152/ajpendo.00203.2018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/02/2018] [Accepted: 07/12/2018] [Indexed: 01/04/2023]
Abstract
The composition of the gut microbiome is altered in obesity and type 2 diabetes; however, it is not known whether these alterations are mediated by dietary factors or related to declines in metabolic health. To address this, cecal contents were collected from age-matched, chow-fed male University of California, Davis Type 2 Diabetes Mellitus (UCD-T2DM) rats before the onset of diabetes (prediabetic PD; n = 15), 2 wk recently diabetic (RD; n = 10), 3 mo (D3M; n = 11), and 6 mo (D6M; n = 8) postonset of diabetes. Bacterial species and functional gene counts were assessed by shotgun metagenomic sequencing of bacterial DNA in cecal contents, while metabolites were identified by gas chromatography-quadrupole time-off-flight-mass spectrometry. Metagenomic analysis showed a shift from Firmicutes species in early stages of diabetes (PD + RD) toward an enrichment of Bacteroidetes species in later stages of diabetes (D3M + D6M). In total, 45 bacterial species discriminated early and late stages of diabetes with 25 of these belonging to either Bacteroides or Prevotella genera. Furthermore, 61 bacterial gene clusters discriminated early and later stages of diabetes with elevations of enzymes related to stress response (e.g., glutathione and glutaredoxin) and amino acid, carbohydrate, and bacterial cell wall metabolism. Twenty-five cecal metabolites discriminated early vs. late stages of diabetes, with the largest differences observed in abundances of dehydroabietic acid and phosphate. Alterations in the gut microbiota and cecal metabolome track diabetes progression in UCD-T2DM rats when controlling for diet, age, and housing environment. Results suggest that diabetes-specific host signals impact the ecology and end product metabolites of the gut microbiome when diet is held constant.
Collapse
Affiliation(s)
- Brian D Piccolo
- Arkansas Children's Nutrition Center , Little Rock, Arkansas
- Department of Pediatrics, University of Arkansas for Medical Science , Little Rock, Arkansas
| | - James L Graham
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California , Davis, California
- Department of Nutrition, University of California , Davis, California
| | - Kimber L Stanhope
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California , Davis, California
- Department of Nutrition, University of California , Davis, California
| | - Intawat Nookaew
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences , Little Rock, Arkansas
| | - Kelly E Mercer
- Arkansas Children's Nutrition Center , Little Rock, Arkansas
- Department of Pediatrics, University of Arkansas for Medical Science , Little Rock, Arkansas
| | - Sree V Chintapalli
- Arkansas Children's Nutrition Center , Little Rock, Arkansas
- Department of Pediatrics, University of Arkansas for Medical Science , Little Rock, Arkansas
| | - Umesh D Wankhade
- Arkansas Children's Nutrition Center , Little Rock, Arkansas
- Department of Pediatrics, University of Arkansas for Medical Science , Little Rock, Arkansas
| | - Kartik Shankar
- Arkansas Children's Nutrition Center , Little Rock, Arkansas
- Department of Pediatrics, University of Arkansas for Medical Science , Little Rock, Arkansas
| | - Peter J Havel
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California , Davis, California
- Department of Nutrition, University of California , Davis, California
| | - Sean H Adams
- Arkansas Children's Nutrition Center , Little Rock, Arkansas
- Department of Pediatrics, University of Arkansas for Medical Science , Little Rock, Arkansas
| |
Collapse
|
626
|
Tsaousis AD, Hamblin KA, Elliott CR, Young L, Rosell-Hidalgo A, Gourlay CW, Moore AL, van der Giezen M. The Human Gut Colonizer Blastocystis Respires Using Complex II and Alternative Oxidase to Buffer Transient Oxygen Fluctuations in the Gut. Front Cell Infect Microbiol 2018; 8:371. [PMID: 30406045 PMCID: PMC6204527 DOI: 10.3389/fcimb.2018.00371] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/03/2018] [Indexed: 12/12/2022] Open
Abstract
Blastocystis is the most common eukaryotic microbe in the human gut. It is linked to irritable bowel syndrome (IBS), but its role in disease has been contested considering its widespread nature. This organism is well-adapted to its anoxic niche and lacks typical eukaryotic features, such as a cytochrome-driven mitochondrial electron transport. Although generally considered a strict or obligate anaerobe, its genome encodes an alternative oxidase. Alternative oxidases are energetically wasteful enzymes as they are non-protonmotive and energy is liberated in heat, but they are considered to be involved in oxidative stress protective mechanisms. Our results demonstrate that the Blastocystis cells themselves respire oxygen via this alternative oxidase thereby casting doubt on its strict anaerobic nature. Inhibition experiments using alternative oxidase and Complex II specific inhibitors clearly demonstrate their role in cellular respiration. We postulate that the alternative oxidase in Blastocystis is used to buffer transient oxygen fluctuations in the gut and that it likely is a common colonizer of the human gut and not causally involved in IBS. Additionally the alternative oxidase could act as a protective mechanism in a dysbiotic gut and thereby explain the absence of Blastocystis in established IBS environments.
Collapse
Affiliation(s)
- Anastasios D. Tsaousis
- RAPID Group, Laboratory of Molecular & Evolutionary Parasitology, School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Karleigh A. Hamblin
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
- Biosciences, University of Exeter, Exeter, United Kingdom
| | - Catherine R. Elliott
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Luke Young
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Alicia Rosell-Hidalgo
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Campbell W. Gourlay
- Kent Fungal Group, School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Anthony L. Moore
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | | |
Collapse
|
627
|
Keith JW, Pamer EG. Enlisting commensal microbes to resist antibiotic-resistant pathogens. J Exp Med 2018; 216:10-19. [PMID: 30309968 PMCID: PMC6314519 DOI: 10.1084/jem.20180399] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/31/2018] [Accepted: 09/11/2018] [Indexed: 12/13/2022] Open
Abstract
Keith and Pamer discuss how the bacterial species constituting the intestinal microbiota reduce the host’s susceptibility to enteric infections and describe experimental studies and clinical trials that elucidate new approaches to reducing the risk of infection and transmission of antibiotic-resistant bacteria. The emergence of antibiotic-resistant bacterial pathogens is an all-too-common consequence of antibiotic use. Although antibiotic resistance among virulent bacterial pathogens is a growing concern, the highest levels of antibiotic resistance occur among less pathogenic but more common bacteria that are prevalent in healthcare settings. Patient-to-patient transmission of these antibiotic-resistant bacteria is a perpetual concern in hospitals. Many of these resistant microbes, such as vancomycin-resistant Enterococcus faecium and carbapenem-resistant Klebsiella pneumoniae, emerge from the intestinal lumen and invade the bloodstream of vulnerable patients, causing disseminated infection. These infections are associated with preceding antibiotic administration, which changes the intestinal microbiota and compromises resistance to colonization by antibiotic-resistant bacteria. Recent and ongoing studies are increasingly defining commensal bacterial species and the inhibitory mechanisms they use to prevent infection. The use of next-generation probiotics derived from the intestinal microbiota represents an alternative approach to prevention of infection by enriching colonization with protective commensal species, thereby reducing the density of antibiotic-resistant bacteria and also reducing patient-to-patient transmission of infection in healthcare settings.
Collapse
Affiliation(s)
- James W Keith
- Immunology Program, Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, New York, NY
| | - Eric G Pamer
- Immunology Program, Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, New York, NY .,Sloan Kettering Institute, New York, NY.,Infectious Diseases Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| |
Collapse
|
628
|
Neuroimmunomodulation in Major Depressive Disorder: Focus on Caspase 1, Inducible Nitric Oxide Synthase, and Interferon-Gamma. Mol Neurobiol 2018; 56:4288-4305. [PMID: 30306457 PMCID: PMC6505498 DOI: 10.1007/s12035-018-1359-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Accepted: 09/19/2018] [Indexed: 12/13/2022]
Abstract
Major depressive disorder (MDD) is one of the leading causes of disability worldwide, and its incidence is expected to increase. Despite tremendous efforts to understand its underlying biological mechanisms, MDD pathophysiology remains elusive and pharmacotherapy outcomes are still far from ideal. Low-grade chronic inflammation seems to play a key role in mediating the interface between psychological stress, depressive symptomatology, altered intestinal microbiology, and MDD onset. We review the available pre-clinical and clinical evidence of an involvement of pro-inflammatory pathways in the pathogenesis, treatment, and remission of MDD. We focus on caspase 1, inducible nitric oxide synthase, and interferon gamma, three inflammatory systems dysregulated in MDD. Treatment strategies aiming at targeting such pathways alone or in combination with classical therapies could prove valuable in MDD. Further studies are needed to assess the safety and efficacy of immune modulation in MDD and other psychiatric disorders with neuroinflammatory components.
Collapse
|
629
|
Mullaney JA, Stephens JE, Geeling BE, Hamilton-Williams EE. Early-life exposure to gut microbiota from disease-protected mice does not impact disease outcome in type 1 diabetes susceptible NOD mice. Immunol Cell Biol 2018; 97:97-103. [DOI: 10.1111/imcb.12201] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/04/2018] [Accepted: 09/05/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Jane A Mullaney
- The University of Queensland Diamantina Institute; University of Queensland; Translational Research Institute; Brisbane QLD Australia
| | - Juliette E Stephens
- The University of Queensland Diamantina Institute; University of Queensland; Translational Research Institute; Brisbane QLD Australia
| | - Brooke E Geeling
- The University of Queensland Diamantina Institute; University of Queensland; Translational Research Institute; Brisbane QLD Australia
| | - Emma E Hamilton-Williams
- The University of Queensland Diamantina Institute; University of Queensland; Translational Research Institute; Brisbane QLD Australia
| |
Collapse
|
630
|
Schnupf P, Gaboriau-Routhiau V, Cerf-Bensussan N. Modulation of the gut microbiota to improve innate resistance. Curr Opin Immunol 2018; 54:137-144. [PMID: 30205357 DOI: 10.1016/j.coi.2018.08.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 08/17/2018] [Indexed: 02/07/2023]
Abstract
One major benefit from the association of hosts with the complex microbial communities that establish at body surfaces is the resistance to pathogen infection. This protective role of symbiotic microbes is becoming ever more relevant, given the alarming rise of multidrug-resistant pathogens and severe infections in patients following extensive antibiotic treatment. Herein, we highlight some recent mechanistic studies that have provided insights into how the highly dynamic dialogue amongst intestinal bacteria and between intestinal bacteria and their host can contribute to protect the host against pathogens in and outside the gut. We then discuss how delineating the rules of this dialogue can help design strategies to modulate the microbiota and improve host resistance to infections.
Collapse
Affiliation(s)
- Pamela Schnupf
- INSERM UMR 1163, Institut Imagine, Laboratory of Intestinal Immunity, Paris, France; Université Paris Descartes-Sorbonne Paris Cité, 75006 Paris, France
| | - Valérie Gaboriau-Routhiau
- INSERM UMR 1163, Institut Imagine, Laboratory of Intestinal Immunity, Paris, France; Université Paris Descartes-Sorbonne Paris Cité, 75006 Paris, France; INRA Micalis Institut, UMR1319, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Nadine Cerf-Bensussan
- INSERM UMR 1163, Institut Imagine, Laboratory of Intestinal Immunity, Paris, France; Université Paris Descartes-Sorbonne Paris Cité, 75006 Paris, France.
| |
Collapse
|
631
|
Gîlcă-Blanariu GE, Diaconescu S, Ciocoiu M, Ștefănescu G. New Insights into the Role of Trace Elements in IBD. BIOMED RESEARCH INTERNATIONAL 2018; 2018:1813047. [PMID: 30258848 PMCID: PMC6146599 DOI: 10.1155/2018/1813047] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 06/11/2018] [Accepted: 08/11/2018] [Indexed: 02/07/2023]
Abstract
Micronutrient deficiencies are common in inflammatory bowel disease and have clinical impact, being both a sign of complicated disease and a cause of morbidity. The involved systemic inflammatory response is responsible for altering the concentration of a wide range of trace elements in the serum, including zinc and selenium. This review summarizes recent advances and evidence-based knowledge regarding the impact of selenium and zinc on oxidative stress and microbiota changes in IBD patients. Getting new insight into the impact of malnutrition, particularly on the micronutrients' impact on the development, composition, and metabolism of microbiota, as well as the influence of oxidative stress and the mucosal immune response, could help in implementing new management strategies for IBD patients, with focus on a more integrated approach.
Collapse
Affiliation(s)
| | - Smaranda Diaconescu
- Department of Pediatrics, Titu Maiorescu University, Faculty of Medicine, Bucharest, Romania
| | - Manuela Ciocoiu
- Department of Pathophysiology, Grigore T Popa University of Medicine and Pharmacy, Iași, Romania
| | - Gabriela Ștefănescu
- Department of Gastroenterology, Grigore T Popa University of Medicine and Pharmacy, Iași, Romania
| |
Collapse
|
632
|
Disentangling Host-Microbiota Regulation of Lipid Secretion by Enterocytes: Insights from Commensals Lactobacillus paracasei and Escherichia coli. mBio 2018; 9:mBio.01493-18. [PMID: 30181250 PMCID: PMC6123438 DOI: 10.1128/mbio.01493-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The gut microbiota contributes to nutrients absorption and metabolism by enterocytes, but the molecular mechanisms involved remain poorly understood, and most conclusions are inferred from studies comparing germfree and conventional animals colonized with diverse bacterial species. We selected two model commensal microorganisms, Escherichia coli and Lactobacillus paracasei, to assess the role of the small-intestinal microbiota in modulating lipid absorption and metabolism by the epithelium. Using an integrated approach encompassing cellular and murine models and combining metabolic parameters measurement, lipid droplet imaging, and gene expression analysis, we demonstrated that under homeostatic conditions, L. paracasei promotes fat storage in enterocytes, whereas E. coli enhances lipid catabolism and reduces chylomicron circulating levels. The Akt/mammalian target of sirolimus (mTOR) pathway is inhibited by both bacterial species in vitro, indicating that several regulatory pathways are involved in the distinct intracellular lipid outcomes associated with each bacterial species. Moreover, soluble bacterial factors partially reproduce the effects observed with live microorganisms. However, reduction of chylomicron circulating levels in E. coli-colonized animals is lost under high-fat-diet conditions, whereas it is potentiated by L. paracasei colonization accompanied by resistance to hypercholesterolemia and excess body weight gain.IMPORTANCE The specific contribution of each bacterial species within a complex microbiota to the regulation of host lipid metabolism remains largely unknown. Using two model commensal microorganisms, L. paracasei and E. coli, we demonstrated that both bacterial species impacted host lipid metabolism in a diet-dependent manner and, notably, that L. paracasei-colonized mice but not E. coli-colonized mice resisted high-fat-diet-induced body weight gain. In addition, we set up cellular models of fatty acid absorption and secretion by enterocytes cocultured with bacteria and showed that, in vitro, both L. paracasei and E. coli inhibited lipid secretion, through increased intracellular fat storage and enhanced lipid catabolism, respectively.
Collapse
|
633
|
Byndloss MX, Pernitzsch SR, Bäumler AJ. Healthy hosts rule within: ecological forces shaping the gut microbiota. Mucosal Immunol 2018; 11:1299-1305. [PMID: 29743614 DOI: 10.1038/s41385-018-0010-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/05/2018] [Indexed: 02/04/2023]
Abstract
A balanced gut microbiota is important for human health, but the mechanisms that maintain homeostasis are incompletely understood. Recent insights suggest the host plays a key role in shaping its gut microbiota to be beneficial. While host control in the small intestine curbs bacterial numbers to avoid competition for simple sugars and amino acids, the host limits oxygen availability in the large intestine to obtain microbial fermentation products from fiber. Epithelial cells are major players in imposing ecological control mechanisms, which involves the release of antimicrobial peptides by small-intestinal Paneth cells and maintenance of luminal anaerobiosis by epithelial hypoxia in the colon. Harnessing these epithelial control mechanisms for therapeutic means could provide a novel lynchpin for strategies to remediate dysbiosis.
Collapse
Affiliation(s)
- Mariana X Byndloss
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, 95616, USA
| | | | - Andreas J Bäumler
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, 95616, USA.
| |
Collapse
|
634
|
The Intestinal Epithelium: Central Coordinator of Mucosal Immunity. Trends Immunol 2018; 39:677-696. [DOI: 10.1016/j.it.2018.04.002] [Citation(s) in RCA: 276] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/23/2018] [Accepted: 04/03/2018] [Indexed: 12/15/2022]
|
635
|
Abstract
The microbiome has received increasing attention over the last 15 years. Although gut microbes have been explored for several decades, investigations of the role of microorganisms that reside in the human gut has attracted much attention beyond classical infectious diseases. For example, numerous studies have reported changes in the gut microbiota during not only obesity, diabetes, and liver diseases but also cancer and even neurodegenerative diseases. The human gut microbiota is viewed as a potential source of novel therapeutics. Between 2013 and 2017, the number of publications focusing on the gut microbiota was, remarkably, 12 900, which represents four-fifths of the total number of publications over the last 40 years that investigated this topic. This review discusses recent evidence of the impact of the gut microbiota on metabolic disorders and focus on selected key mechanisms. This review also aims to provide a critical analysis of the current knowledge in this field, identify putative key issues or problems and discuss misinterpretations. The abundance of metagenomic data generated on comparing diseased and healthy subjects can lead to the erroneous claim that a bacterium is causally linked with the protection or the onset of a disease. In fact, environmental factors such as dietary habits, drug treatments, intestinal motility and stool frequency and consistency are all factors that influence the composition of the microbiota and should be considered. The cases of the bacteria Prevotella copri and Akkermansia muciniphila will be discussed as key examples.
Collapse
Affiliation(s)
- Patrice D Cani
- Metabolism and Nutrition Research Group, Université catholique de Louvain, WELBIO-Walloon Excellence in Life Sciences and BIOtechnology, Louvain Drug Research Institute, Brussels, Belgium
| |
Collapse
|
636
|
Pötgens SA, Brossel H, Sboarina M, Catry E, Cani PD, Neyrinck AM, Delzenne NM, Bindels LB. Klebsiella oxytoca expands in cancer cachexia and acts as a gut pathobiont contributing to intestinal dysfunction. Sci Rep 2018; 8:12321. [PMID: 30120320 PMCID: PMC6098145 DOI: 10.1038/s41598-018-30569-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/01/2018] [Indexed: 02/07/2023] Open
Abstract
Cancer cachexia is a complex multi-organ syndrome characterized by body weight loss, weakness, muscle atrophy and fat depletion. With a prevalence of 1 million people in Europe and only limited therapeutic options, there is a high medical need for new approaches to treat cachexia. Our latest results highlighted microbial dysbiosis, characterized by a bloom in Enterobacteriaceae and altered gut barrier function in preclinical models of cancer cachexia. They also demonstrated the potential of targeting the gut microbial dysbiosis in this pathology. However, the exact mechanisms underlying the gut microbiota-host crosstalk in cancer cachexia remain elusive. In this set of studies, we identified Klebsiella oxytoca as one of the main Enterobacteriaceae species increased in cancer cachexia and we demonstrated that this bacteria acts as a gut pathobiont by altering gut barrier function in cachectic mice. Moreover, we propose a conceptual framework for the lower colonization resistance to K. oxytoca in cancer cachexia that involves altered host gut epithelial metabolism and host-derived nitrate boosting the growth of the gut pathobiont. This set of studies constitutes a strong progression in the field of gut microbiota in cancer cachexia, by dissecting the mechanism of emergence of one bacterium, K. oxytoca, and establishing its role as a gut pathobiont in this severe disease.
Collapse
Affiliation(s)
- Sarah A Pötgens
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Hélène Brossel
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Martina Sboarina
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Emilie Catry
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Patrice D Cani
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium.,Walloon Excellence in Life Sciences and BIOtechnology (WELBIO), Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Audrey M Neyrinck
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Nathalie M Delzenne
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium
| | - Laure B Bindels
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute, Université catholique de Louvain, Brussels, Belgium.
| |
Collapse
|
637
|
Li Z, Yu E, Wang G, Yu D, Zhang K, Gong W, Xie J. Broad Bean ( Vicia faba L.) Induces Intestinal Inflammation in Grass Carp ( Ctenopharyngodon idellus C. et V) by Increasing Relative Abundances of Intestinal Gram-Negative and Flagellated Bacteria. Front Microbiol 2018; 9:1913. [PMID: 30174665 PMCID: PMC6107684 DOI: 10.3389/fmicb.2018.01913] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/30/2018] [Indexed: 01/06/2023] Open
Abstract
Constant consumption of broad bean (Vicia faba L.) induces intestinal inflammation and reduces growth rate in grass carp (Ctenopharyngodon idellus C. et V). However, the mechanisms underlying these effects are unclear. In mammalian models of inflammatory bowel disease (IBD), endotoxin and flagellin cause intestinal inflammation through upregulation of tumor necrosis factor (TNF)-α expression. We therefore speculated that broad bean consumption alters intestinal microbiota composition, thereby increasing the relative abundance of endotoxin-producing Gram-negative and flagellated bacteria and resulting in upregulation of TNF-α and intestinal inflammation in grass carp. We tested this hypothesis by comparing intestinal microbiota compositions of grass carp fed broad bean (GCBB), hybrid giant napier (Pennisetum sinese Roxb, GCHG), or formula feed (GCFF) by 16S rRNA gene sequencing. We also performed a histological analysis of the intestinal inner wall by scanning electron microscopy and measured intestinal wall and serum concentrations of TNF-α. Our results revealed epithelial cell damage including microvillus effacement and synechia along with increased TNF-α levels in the intestinal wall in the GCBB group as compared to the GCHG and GCFF groups. The relative abundances of Gram-negative and flagellated bacteria were also higher in the GCBB group than in the GCHG and GCFF groups; this was accompanied by upregulation of genes expressing endotoxin and flagellin in intestinal microbiota. Thus, broad bean-induced intestinal inflammation in grass carp shares features with IBD. Our findings demonstrate that the microbiome in fish is directly influenced by diet and provide a reference for deconstructing host–intestinal microbiota interactions.
Collapse
Affiliation(s)
- Zhifei Li
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, China
| | - Ermeng Yu
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, China
| | - Guangjun Wang
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, China
| | - Deguang Yu
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, China
| | - Kai Zhang
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, China
| | - Wangbao Gong
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, China
| | - Jun Xie
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Ecological Remediation of Aquaculture Pollution Research Center, Guangzhou, China
| |
Collapse
|
638
|
Davison JM, Wischmeyer PE. Probiotic and synbiotic therapy in the critically ill: State of the art. Nutrition 2018; 59:29-36. [PMID: 30415160 DOI: 10.1016/j.nut.2018.07.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 12/27/2022]
Abstract
Recent medical history has largely viewed our bacterial symbionts as pathogens to be eradicated rather than as essential partners in optimal health. However, one of the most exciting scientific advances in recent years has been the realization that commensal microorganisms (our microbiome) play vital roles in human physiology in nutrition, vitamin synthesis, drug metabolism, protection against infection, and recovery from illness. Recent data show that loss of "health-promoting" microbes and overgrowth of pathogenic bacteria (dysbiosis) in patients in the intensive care unit (ICU) appears to contribute to nosocomial infections, sepsis, and poor outcomes. Dysbiosis results from many factors, including ubiquitous antibiotic use and altered nutrition delivery in illness. Despite modern antibiotic therapy, infections and mortality from often multidrug-resistant organisms are increasing. This raises the question of whether restoration of a healthy microbiome via probiotics or synbiotics (probiotic and prebiotic combinations) to intervene on ubiquitous ICU dysbiosis would be an optimal intervention in critical illness to prevent infection and to improve recovery. This review will discuss recent innovative experimental data illuminating mechanistic pathways by which probiotics and synbiotics may provide clinical benefit. Furthermore, a review of recent clinical data demonstrating that probiotics and synbiotics can reduce complications in ICU and other populations will be undertaken. Overall, growing data for probiotic and symbiotic therapy reveal a need for definitive clinical trials of these therapies, as recently performed in healthy neonates. Future studies should target administration of probiotics and synbiotics with known mechanistic benefits to improve patient outcomes. Optimally, future probiotic and symbiotic studies will be conducted using microbiome signatures to characterize actual ICU dysbiosis and determine, and perhaps even personalize, ideal probiotic and symbiotic therapies.
Collapse
Affiliation(s)
- James M Davison
- Department of Anesthesiology and Duke Clinical Research Institute, Duke University, Durham, North Carolina, USA
| | - Paul E Wischmeyer
- Department of Anesthesiology and Duke Clinical Research Institute, Duke University, Durham, North Carolina, USA.
| |
Collapse
|
639
|
Fu L, Qiu Y, Shen L, Cui C, Wang S, Wang S, Xie Y, Zhao X, Gao X, Ning G, Nie A, Gu Y. The delayed effects of antibiotics in type 2 diabetes, friend or foe? J Endocrinol 2018; 238:137-149. [PMID: 29929986 DOI: 10.1530/joe-17-0709] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 05/31/2018] [Indexed: 12/26/2022]
Abstract
An increasing amount of evidence suggests that the delayed effect of antibiotics (abx) on gut microbiota after its cessation is not as favorable as its immediate effect on host metabolism. However, it is not known how the diverse abx-dependent metabolic effects influence diabetic subjects and how gut microbiota is involved. Here, we treated db/db mice with abx cocktail for 12 days and discontinued for 24 days. We found that db/db mice showed decreased body weight and blood glucose after abx treatment, which rapidly caught up after abx cessation. Twenty-four days after abx withdrawal, db/db mice exhibit increased plasma, hepatic total cholesterol (TC) levels and liver weight. The gut microbiota composition at that time showed decreased relative abundances (RAs) of Desulfovibrionaceae and Rikenellaceae, increased RA of Erysipelotrichaceae and Mogibacteriaceae, which were correlating with the reduced short-chain fatty acids (SCFAs) in gut content, such as propionic acid and valeric acid and with the elevated fecal taurine-conjugated bile acids (BAs) levels. The molecular biology studies showed inhibited hepatic BA synthesis from cholesterol, impeded intracellular transportation and biliary excretion of cholesterol that all conferred to liver TC accumulation. The associations among alterations of gut microbiota composition, microbial metabolite profiles and host phenotypes suggested the existence of gut microbiota-linked mechanisms that mediate the unfavorable delayed effects of abx on db/db mice cholesterol metabolism. Thus, we call upon the caution of applying abx in diabetic animal models for studying microbiota-host interaction and in type 2 diabetes subjects for preventing chronic cardiovascular consequences.
Collapse
Affiliation(s)
- Lihong Fu
- Shanghai National Research Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yixuan Qiu
- Shanghai National Research Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Linyan Shen
- Shanghai National Research Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Endocrinology, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Canqi Cui
- Shanghai National Research Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Shujie Wang
- Shanghai National Research Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yun Xie
- Department of Cardiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinjie Zhao
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Xianfu Gao
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guang Ning
- Shanghai National Research Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Aifang Nie
- Shanghai National Research Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanyun Gu
- Shanghai National Research Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
640
|
Livanos AE, Snider EJ, Whittier S, Chong DH, Wang TC, Abrams JA, Freedberg DE. Rapid gastrointestinal loss of Clostridial Clusters IV and XIVa in the ICU associates with an expansion of gut pathogens. PLoS One 2018; 13:e0200322. [PMID: 30067768 PMCID: PMC6070193 DOI: 10.1371/journal.pone.0200322] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/23/2018] [Indexed: 12/15/2022] Open
Abstract
Commensal gastrointestinal bacteria resist the expansion of pathogens and are lost during critical illness, facilitating pathogen colonization and infection. We performed a prospective, ICU-based study to determine risk factors for loss of gut colonization resistance during the initial period of critical illness. Rectal swabs were taken from adult ICU patients within 4 hours of admission and 72 hours later, and analyzed using 16S rRNA gene sequencing and selective culture for vancomycin-resistant Enterococcus (VRE). Microbiome data was visualized using principal coordinate analyses (PCoA) and assessed using a linear discriminant analysis algorithm and logistic regression modeling. 93 ICU patients were analyzed. At 72 hours following ICU admission, there was a significant decrease in the proportion of Clostridial Clusters IV/XIVa, taxa that produce short chain fatty acids (SCFAs). At the same time, there was a significant expansion in Enterococcus. Decreases in Cluster IV/XIVa Clostridia were associated with loss of gut microbiome colonization resistance (reduced diversity and community stability over time). In multivariable analysis, both decreased Cluster IV/XIVa Clostridia and increased Enterococcus after 72 hours were associated with receipt of antibiotics. Cluster IV/XIVa Clostridia, although a small fraction of the overall gastrointestinal microbiome, drove distinct clustering on PCoA. During initial treatment for critical illness, there was a loss of Cluster IV/XIVa Clostridia within the distal gut microbiome which associated with an expansion of VRE and with a loss of gut microbiome colonization resistance. Receipt of broad-spectrum antibiotics was associated with these changes.
Collapse
Affiliation(s)
- Alexandra E. Livanos
- Division of General Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Erik J. Snider
- Division of General Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Susan Whittier
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States of America
| | - David H. Chong
- Division of Allergy, Pulmonary, and Critical Care Medicine, Columbia University Medical Center, New York, NY, United States of America
| | - Timothy C. Wang
- Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, NY, United States of America
| | - Julian A. Abrams
- Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, NY, United States of America
| | - Daniel E. Freedberg
- Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, NY, United States of America
- * E-mail:
| |
Collapse
|
641
|
Klassen JL. Defining microbiome function. Nat Microbiol 2018; 3:864-869. [PMID: 30046174 DOI: 10.1038/s41564-018-0189-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 06/05/2018] [Indexed: 02/07/2023]
Abstract
Why does a microorganism associate with a host? What function does it perform? Such questions are difficult to unequivocally address and remain hotly debated. This is partially because scientists often use different philosophical definitions of 'function' ambiguously and interchangeably, as exemplified by the controversy surrounding the Encyclopedia of DNA Elements (ENCODE) project. Here, I argue that research studying host-associated microbial communities and their genomes (that is, microbiomes) faces similar pitfalls and that unclear or misapplied conceptions of function underpin many controversies in this field. In particular, experiments that support phenomenological models of function can inappropriately be used to support functional models that instead require specific measurements of evolutionary selection. Microbiome research also requires uniquely clear definitions of 'who the function is for', in contrast to most single-organism systems where this is implicit. I illustrate how obscuring either of these issues can lead to substantial confusion and misinterpretation of microbiome function, using the varied conceptions of the holobiont as a current and cogent example. Using clear functional definitions and appropriate types of evidence are essential to effectively communicate microbiome research and foster host health.
Collapse
Affiliation(s)
- Jonathan L Klassen
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
| |
Collapse
|
642
|
Cysteine Desulfurase IscS2 Plays a Role in Oxygen Resistance in Clostridium difficile. Infect Immun 2018; 86:IAI.00326-18. [PMID: 29866903 DOI: 10.1128/iai.00326-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 05/25/2018] [Indexed: 11/20/2022] Open
Abstract
Clostridium difficile is an anaerobic, spore-forming bacterium capable of colonizing the gastrointestinal tract of humans following disruption of the normal microbiota, typically from antibiotic therapy for an unrelated infection. With approximately 500,000 confirmed infections leading to 29,000 deaths per year in the United States, C. difficile infection (CDI) is an urgent public health threat. We previously determined that C. difficile survives in up to 3% oxygen. Low levels of oxygen are present in the intestinal tract, with the higher concentrations being associated with the epithelial cell surface. Additionally, antibiotic treatment, the greatest risk factor for CDI, increases the intestinal oxygen concentration. Therefore, we hypothesized that the C. difficile genome encodes mechanisms for survival during oxidative stress. Previous data have shown that cysteine desulfurases involved in iron-sulfur cluster assembly are involved in protecting bacteria from oxidative stress. In this study, deletion of a putative cysteine desulfurase (Cd630_12790/IscS2) involved in the iron-sulfur cluster (Isc) system caused a severe growth defect in the presence of 2% oxygen. Additionally, this mutant delayed colonization in a conventional mouse model of CDI and failed to colonize in a germfree model, which has higher intestinal oxygen levels. These data imply an undefined role for this cysteine desulfurase in protecting C. difficile from low levels of oxygen in the gut.
Collapse
|
643
|
Axelrad JE, Lebwohl B, Cuaresma E, Cadwell K, Green PHR, Freedberg DE. Gut colonization with vancomycin-resistant Enterococcus and risk for subsequent enteric infection. Gut Pathog 2018; 10:28. [PMID: 30002733 PMCID: PMC6038175 DOI: 10.1186/s13099-018-0259-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 07/03/2018] [Indexed: 02/08/2023] Open
Abstract
Background Gut colonization with vancomycin-resistant Enterococcus (VRE) is associated with poor outcomes. This study evaluated the impact of VRE colonization on subsequent acquisition of enteric pathogens. Methods We performed a retrospective cohort study of adults admitted to an ICU from 2012 to 2017 who were screened for VRE colonization and subsequently underwent stool testing with a gastrointestinal pathogen PCR panel (GI PCR) with or without PCR testing for Clostridium difficile. Our primary outcome was the presence of any enteric pathogen. Cox proportional hazards modeling was used to adjust for factors associated with enteric infection. Results Of 761 patients who underwent VRE screening and subsequent GI PCR, 131 (17%) were colonized with VRE. Patients with VRE colonization were less likely to test positive on GI PCR compared to patients without VRE (9.2% vs 18%, p = 0.01); specifically for E. coli species (p = 0.03) and viral (p = 0.04) enteric infections. In 716 patients who underwent C. difficile testing, there was a trend towards more C. difficile infections in patients colonized with VRE (15% vs 10%, p = 0.11). On multivariable analysis, patients with VRE had a decreased risk of a positive GI PCR (aHR 0.47, 95% CI 0.25-0.88, p = 0.02) but not C. difficile infection, effects which persisted during 5 years of follow-up. Among positive tests, there was a greater proportion of C. difficile with VRE (57% vs 28%, p < 0.01). Conclusions VRE colonization was associated with a decreased risk of subsequent non-C. difficile enteric infection. VRE domination of the gut microbiome may protect against acquisition of common enteric pathogens.
Collapse
Affiliation(s)
- Jordan E Axelrad
- 1Division of Gastroenterology, Department of Medicine, Inflammatory Bowel Disease Center, NYU Langone Health, 240 East 38th Street, 23rd Floor, New York, NY USA.,2Division of Digestive and Liver Disease, Department of Medicine, Columbia University Medical Center, New York, NY USA
| | - Benjamin Lebwohl
- 2Division of Digestive and Liver Disease, Department of Medicine, Columbia University Medical Center, New York, NY USA
| | - Edward Cuaresma
- 2Division of Digestive and Liver Disease, Department of Medicine, Columbia University Medical Center, New York, NY USA
| | - Ken Cadwell
- 3Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY USA.,4Department of Microbiology, New York University School of Medicine, New York, NY USA
| | - Peter H R Green
- 2Division of Digestive and Liver Disease, Department of Medicine, Columbia University Medical Center, New York, NY USA
| | - Daniel E Freedberg
- 2Division of Digestive and Liver Disease, Department of Medicine, Columbia University Medical Center, New York, NY USA
| |
Collapse
|
644
|
Zeng Y, Zeng D, Zhou Y, Niu L, Deng J, Li Y, Pu Y, Lin Y, Xu S, Liu Q, Xiong L, Zhou M, Pan K, Jing B, Ni X. Microbial Biogeography Along the Gastrointestinal Tract of a Red Panda. Front Microbiol 2018; 9:1411. [PMID: 30026734 PMCID: PMC6042058 DOI: 10.3389/fmicb.2018.01411] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 06/08/2018] [Indexed: 11/13/2022] Open
Abstract
The red panda (Ailurus fulgens) is a herbivorous carnivore that is protected worldwide. The gastrointestinal tract (GIT) microbial community has widely acknowledged its vital role in host health, especially in diet digestion; However, no study to date has revealed the GIT microbiota in the red panda. Here, we characterized the microbial biogeographical characteristics in the GIT of a red panda using high-throughput sequencing technology. Significant differences were observed among GIT segments by beta diversity of microbiota, which were divided into four distinct groups: the stomach, small intestine, large intestine, and feces. The stomach and duodenum showed less bacterial diversity, but contained higher bacterial abundance and the most unclassified tags. The number of species in the stomach and small intestine samples was higher than that of the large intestine and fecal samples. A total of 133 core operational taxonomic units were obtained from the GIT samples with 97% sequence identity. Proteobacteria (52.16%), Firmicutes (10.09%), and Bacteroidetes (7.90%) were the predominant phyla in the GIT of the red panda. Interestingly, Escherichia-Shigella were largely abundant in the stomach, small intestine, and feces whereas the abundance of Bacteroides in the large intestine was high. Overall, our study provides a deeper understanding of the gut biogeography of the red panda microbial population. Future research will be important to investigate the microbial culture, metagenomics and metabolism of red panda GIT, especially in Escherichia-Shigella.
Collapse
Affiliation(s)
- Yan Zeng
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
| | - Dong Zeng
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
| | - Yi Zhou
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
| | - Lili Niu
- Chengdu Wildlife Institute, Chengdu Zoo, Chengdu, China
| | - Jiabo Deng
- Chengdu Wildlife Institute, Chengdu Zoo, Chengdu, China
| | - Yang Li
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
| | - Yang Pu
- Chengdu Wildlife Institute, Chengdu Zoo, Chengdu, China
| | - Yicen Lin
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
| | - Shuai Xu
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
| | - Qian Liu
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
| | - Lvchen Xiong
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
| | - Mengjia Zhou
- Sichuan Animal Science Research Institute, Chengdu, China
| | - Kangcheng Pan
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
| | - Bo Jing
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
| | - Xueqin Ni
- Animal Microecology Institute, College of Veterinary, Sichuan Agricultural University, Ya'an, China
| |
Collapse
|
645
|
Fan ST, Nie SP, Huang XJ, Wang S, Hu JL, Xie JH, Nie QX, Xie MY. Protective properties of combined fungal polysaccharides from Cordyceps sinensis and Ganoderma atrum on colon immune dysfunction. Int J Biol Macromol 2018; 114:1049-1055. [DOI: 10.1016/j.ijbiomac.2018.04.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/18/2018] [Accepted: 04/03/2018] [Indexed: 12/15/2022]
|
646
|
Freedberg DE, Zhou MJ, Cohen ME, Annavajhala MK, Khan S, Moscoso DI, Brooks C, Whittier S, Chong DH, Uhlemann AC, Abrams JA. Pathogen colonization of the gastrointestinal microbiome at intensive care unit admission and risk for subsequent death or infection. Intensive Care Med 2018; 44:1203-1211. [PMID: 29936583 DOI: 10.1007/s00134-018-5268-8] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/05/2018] [Indexed: 02/07/2023]
Abstract
PURPOSE Loss of colonization resistance within the gastrointestinal microbiome facilitates the expansion of pathogens and has been associated with death and infection in select populations. We tested whether gut microbiome features at the time of intensive care unit (ICU) admission predict death or infection. METHODS This was a prospective cohort study of medical ICU adults. Rectal surveillance swabs were performed at admission, selectively cultured for vancomycin-resistant Enterococcus (VRE), and assessed using 16S rRNA gene sequencing. Patients were followed for 30 days for death or culture-proven bacterial infection. RESULTS Of 301 patients, 123 (41%) developed culture-proven infections and 76 (25%) died. Fecal biodiversity (Shannon index) did not differ based on death or infection (p = 0.49). The presence of specific pathogens at ICU admission was associated with subsequent infection with the same organism for Escherichia coli, Pseudomonas spp., Klebsiella spp., and Clostridium difficile, and VRE at admission was associated with subsequent Enterococcus infection. In a multivariable model adjusting for severity of illness, VRE colonization and Enterococcus domination (≥ 30% 16S reads) were both associated with death or all-cause infection (aHR 1.46, 95% CI 1.06-2.00 and aHR 1.47, 95% CI 1.00-2.19, respectively); among patients without VRE colonization, Enterococcus domination was associated with excess risk of death or infection (aHR 2.13, 95% CI 1.06-4.29). CONCLUSIONS Enterococcus status at ICU admission was associated with risk for death or all-cause infection, and rectal carriage of common ICU pathogens predicted specific infections. The gastrointestinal microbiome may have a role in risk stratification and early diagnosis of ICU infections.
Collapse
Affiliation(s)
- Daniel E Freedberg
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University Medical Center, 630 West 168th Street, New York, NY, 10032, USA.
| | - Margaret J Zhou
- Department of Medicine, Columbia University Medical Center, New York, USA
| | - Margot E Cohen
- Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, USA
| | - Medini K Annavajhala
- Microbiome and Pathogen Genomics Core, Department of Medicine, Columbia University Medical Center, New York, USA
| | - Sabrina Khan
- Microbiome and Pathogen Genomics Core, Department of Medicine, Columbia University Medical Center, New York, USA
| | - Dagmara I Moscoso
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University Medical Center, 630 West 168th Street, New York, NY, 10032, USA
| | - Christian Brooks
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University Medical Center, 630 West 168th Street, New York, NY, 10032, USA
| | - Susan Whittier
- Division of Laboratory Medicine, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, USA
| | - David H Chong
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Columbia University Medical Center, New York, USA
| | - Anne-Catrin Uhlemann
- Microbiome and Pathogen Genomics Core, Department of Medicine, Columbia University Medical Center, New York, USA.,Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, USA
| | - Julian A Abrams
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University Medical Center, 630 West 168th Street, New York, NY, 10032, USA.,Mailman School of Public Health, New York, USA
| |
Collapse
|
647
|
Cellular Stress Responses and Gut Microbiota in Inflammatory Bowel Disease. Gastroenterol Res Pract 2018; 2018:7192646. [PMID: 30026758 PMCID: PMC6031203 DOI: 10.1155/2018/7192646] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/08/2018] [Indexed: 12/11/2022] Open
Abstract
Progresses in the past two decades have greatly expanded our understanding of inflammatory bowel disease (IBD), an incurable disease with multifaceted and challenging clinical manifestations. The pathogenesis of IBD involves multiple processes on the cellular level, which include the stress response signaling such as endoplasmic reticulum (ER) stress, oxidative stress, and hypoxia. Under physiological conditions, the stress responses play key roles in cell survival, mucosal barrier integrity, and immunomodulation. However, they can also cause energy depletion, trigger cell death and tissue injury, promote inflammatory response, and drive the progression of clinical disease. In recent years, gut microflora has emerged as an essential pathogenic factor and therapeutic target for IBD. Altered compositional and metabolic profiles of gut microbiota, termed dysbiosis, are associated with IBD. Recent studies, although limited, have shed light on how ER stress, oxidative stress, and hypoxic stress interact with gut microorganisms, a potential source of stress in the microenvironment of gastrointestinal tract. Our knowledge of cellular stress responses in intestinal homeostasis as well as their cross-talks with gut microbiome will further our understanding of the pathogenesis of inflammatory bowel disease and probably open avenues for new therapies.
Collapse
|
648
|
Reese AT, Cho EH, Klitzman B, Nichols SP, Wisniewski NA, Villa MM, Durand HK, Jiang S, Midani FS, Nimmagadda SN, O'Connell TM, Wright JP, Deshusses MA, David LA. Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut. eLife 2018; 7:35987. [PMID: 29916366 PMCID: PMC6008055 DOI: 10.7554/elife.35987] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/26/2018] [Indexed: 12/18/2022] Open
Abstract
How host and microbial factors combine to structure gut microbial communities remains incompletely understood. Redox potential is an important environmental feature affected by both host and microbial actions. We assessed how antibiotics, which can impact host and microbial function, change redox state and how this contributes to post-antibiotic succession. We showed gut redox potential increased within hours of an antibiotic dose in mice. Host and microbial functioning changed under treatment, but shifts in redox potentials could be attributed specifically to bacterial suppression in a host-free ex vivo human gut microbiota model. Redox dynamics were linked to blooms of the bacterial family Enterobacteriaceae. Ecological succession to pre-treatment composition was associated with recovery of gut redox, but also required dispersal from unaffected gut communities. As bacterial competition for electron acceptors can be a key ecological factor structuring gut communities, these results support the potential for manipulating gut microbiota through managing bacterial respiration. The gut is home to a large and diverse community of bacteria and other microbes, known as the gut microbiota. The makeup of this community is important for the health of both the host and its residents. For instance, many gut bacteria help to digest food or keep disease-causing bacteria in check. In return, the host provides them with nutrients. When this balance is disturbed, the host is exposed to risks such as infections. In particular, treatments with antibiotics that kill gut bacteria can lead to side effects like diarrhea, because the gut becomes recolonized with harmful bacteria including Clostridium difficile and Salmonella. Reese et al. have now investigated what happens to the gut environment after antibiotic treatment and how the gut microbiota recovers. Mice treated with broad-spectrum antibiotics showed an increase in the “redox potential” of their gut environment. Redox potential captures a number of measures of the chemical makeup of an environment, and provides an estimate for how efficiently some bacteria in that environment can grow. Some of the change in redox potential came from the host’s own immune system releasing chemicals as it reacted to the effects of the treatment. However, Reese et al. found that treating gut bacteria in an artificial gut – which has no immune system – also increased the redox potential. This experiment suggests that bacteria actively shape their chemical environment in the gut. After the treatment, bacteria that thrive under high redox potentials, which include some disease-causing species, recovered first and fastest. This, in turn, helped to bring redox potential back to how it was before the treatment. Although the gut’s chemical environment recovered, some bacterial species were wiped out by the antibiotic treatment. The microbiota only returned to its previous state when the treated mice were housed together with non-treated mice. This was expected because mice that live together commonly exchange microbes, for instance by eating each other’s feces, and the treated mice received new species to replenish their microbiota. These findings are important because they show that the chemical environment shapes and is shaped by the bacterial communities in the gut. Future research may investigate if altering redox potential in the gut could help to keep the microbiota healthier in infections and diseases of the digestive tract.
Collapse
Affiliation(s)
- Aspen T Reese
- Department of Biology, Duke University, Durham, United States.,Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Eugenia H Cho
- Department of Bioengineering, University of Pennsylvania, Philadelphia, United States
| | - Bruce Klitzman
- Department of Surgery, Duke University Medical Center, Durham, United States
| | | | | | - Max M Villa
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Heather K Durand
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Sharon Jiang
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States
| | - Firas S Midani
- Program in Computational Biology and Bioinformatics, Duke University, Durham, United States
| | - Sai N Nimmagadda
- Department of Biomedical Engineering, Duke University, Durham, United States
| | - Thomas M O'Connell
- Department of Otolaryngology-Head and Neck Surgery, Indiana University School of Medicine, Indianapolis, United States
| | - Justin P Wright
- Department of Biology, Duke University, Durham, United States
| | - Marc A Deshusses
- Department of Civil and Environmental Engineering, Duke University, Durham, United States
| | - Lawrence A David
- Department of Molecular Genetics and Microbiology, Duke University, Durham, United States.,Program in Computational Biology and Bioinformatics, Duke University, Durham, United States.,Department of Biomedical Engineering, Duke University, Durham, United States.,Center for Genomic and Computational Biology, Duke University, Durham, United States
| |
Collapse
|
649
|
Martens EC, Neumann M, Desai MS. Interactions of commensal and pathogenic microorganisms with the intestinal mucosal barrier. Nat Rev Microbiol 2018; 16:457-470. [DOI: 10.1038/s41579-018-0036-x] [Citation(s) in RCA: 284] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
650
|
Xu J, Chen N, Wu Z, Song Y, Zhang Y, Wu N, Zhang F, Ren X, Liu Y. 5-Aminosalicylic Acid Alters the Gut Bacterial Microbiota in Patients With Ulcerative Colitis. Front Microbiol 2018; 9:1274. [PMID: 29951050 PMCID: PMC6008376 DOI: 10.3389/fmicb.2018.01274] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/24/2018] [Indexed: 12/15/2022] Open
Abstract
Background: The aim of this study was to clarify the effect of 5-aminosalicylic acid (5-ASA) treatment on gut bacterial microbiota in patients with ulcerative colitis (UC). Methods: A total of 57 UC patients, including 20 untreated and 37 5-ASA-treated, were recruited into an exploration cohort. We endoscopically collected both non-inflamed and inflamed mucosal samples from all patients, and compared the gut bacterial profiles using 16S rDNA sequencing. Ten untreated UC patients were then treated with 5-ASA and subsequently recruited for an independent validation study to confirm the acquired data. Results: In untreated UC patients, compared with those in non-inflamed mucosae, Firmicutes (such as Enterococcus) were decreased and Proteobacteria (e.g., Escherichia–Shigella) were increased in the inflamed mucosae. Compared with the inflamed mucosae of untreated UC patients, there was a higher abundance of Firmicutes (e.g., Enterococcus) and lower Proteobacteria (Escherichia–Shigella) in the inflamed mucosae of 5-ASA treated UC patients. In the validation cohort, after administration of 5-ASA, bacterial alteration was consistent with these data. Furthermore, there was a skewed negative correlation between Escherichia–Shigella and bacterial genera of Firmicutes in the inflamed mucosae. 5-ASA treatment decreased the strength of bacterial correlation and weakened the skewed negative correlation pattern. Conclusion: The microbial dysbiosis (mainly characterized by an increased abundance in the Escherichia–Shigella genus) and the skewed negative correlation between Escherichia–Shigella and bacterial genera of Firmicutes are two characteristics of the inflamed mucosae of UC patients. 5-ASA treatment decreases Escherichia–Shigella and weakens the skewed correlations, which may be related to its treatment efficiency.
Collapse
Affiliation(s)
- Jun Xu
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Ning Chen
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Zhe Wu
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Yang Song
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Yifan Zhang
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Na Wu
- Institute of Clinical Molecular Biology and Central Laboratory, Peking University People's Hospital, Beijing, China
| | - Feng Zhang
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Xinhua Ren
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| | - Yulan Liu
- Department of Gastroenterology, Peking University People's Hospital, Beijing, China.,Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing, China
| |
Collapse
|